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2. The Space Omics and Medical Atlas (SOMA) and international astronaut biobank

Author

Overbey, Eliah G., Kim, JangKeun, Tierney, Braden T., Park, Jiwoon, Houerbi, Nadia, Lucaci, Alexander G., Garcia Medina, Sebastian, Damle, Namita, Najjar, Deena, Grigorev, Kirill, Afshin, Evan E., Ryon, Krista A., Sienkiewicz, Karolina, Patras, Laura, Klotz, Remi, Ortiz, Veronica, MacKay, Matthew, Schweickart, Annalise, Chin, Christopher R., Sierra, Maria A., Valenzuela, Matias F., Dantas, Ezequiel, Nelson, Theodore M., Cekanaviciute, Egle, Deards, Gabriel, Foox, Jonathan, Narayanan, S. Anand, Schmidt, Caleb M., Schmidt, Michael A., Schmidt, Julian C., Mullane, Sean, Tigchelaar, Seth Stravers, Levitte, Steven, Westover, Craig, Bhattacharya, Chandrima, Lucotti, Serena, Wain Hirschberg, Jeremy, Proszynski, Jacqueline, Burke, Marissa, Kleinman, Ashley S., Butler, Daniel J., Loy, Conor, Mzava, Omary, Lenz, Joan, Paul, Doru, Mozsary, Christopher, Sanders, Lauren M., Taylor, Lynn E., Patel, Chintan O., Khan, Sharib A., Suhail Mohamad, Mir, Byhaqui, Syed Gufran Ahmad, Aslam, Burhan, Gajadhar, Aaron S., Williamson, Lucy, Tandel, Purvi, Yang, Qiu, Chu, Jessica, Benz, Ryan W., Siddiqui, Asim, Hornburg, Daniel, Blease, Kelly, Moreno, Juan, Boddicker, Andrew, Zhao, Junhua, Lajoie, Bryan, Scott, Ryan T., Gilbert, Rachel R., Lai Polo, San-huei, Altomare, Andrew, Kruglyak, Semyon, Levy, Shawn, Ariyapala, Ishara, Beer, Joanne, Zhang, Bingqing, Hudson, Briana M., Rininger, Aric, Church, Sarah E., Beheshti, Afshin, Church, George M., Smith, Scott M., Crucian, Brian E., Zwart, Sara R., Matei, Irina, Lyden, David C., Garrett-Bakelman, Francine, Krumsiek, Jan, Chen, Qiuying, Miller, Dawson, Shuga, Joe, Williams, Stephen, Nemec, Corey, Trudel, Guy, Pelchat, Martin, Laneuville, Odette, De Vlaminck, Iwijn, Gross, Steven, Bolton, Kelly L., Bailey, Susan M., Granstein, Richard, Furman, David, Melnick, Ari M., Costes, Sylvain V., Shirah, Bader, Yu, Min, Menon, Anil S., Mateus, Jaime, Meydan, Cem, and Mason, Christopher E.

Published
2024
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3. Longitudinal multi-omics analysis of host microbiome architecture and immune responses during short-term spaceflight

Author

Tierney, Braden T., Kim, JangKeun, Overbey, Eliah G., Ryon, Krista A., Foox, Jonathan, Sierra, Maria A., Bhattacharya, Chandrima, Damle, Namita, Najjar, Deena, Park, Jiwoon, Garcia Medina, J. Sebastian, Houerbi, Nadia, Meydan, Cem, Wain Hirschberg, Jeremy, Qiu, Jake, Kleinman, Ashley S., Al-Ghalith, Gabriel A., MacKay, Matthew, Afshin, Evan E., Dhir, Raja, Borg, Joseph, Gatt, Christine, Brereton, Nicholas, Readhead, Benjamin P., Beyaz, Semir, Venkateswaran, Kasthuri J., Wiseman, Kelly, Moreno, Juan, Boddicker, Andrew M., Zhao, Junhua, Lajoie, Bryan R., Scott, Ryan T., Altomare, Andrew, Kruglyak, Semyon, Levy, Shawn, Church, George M., and Mason, Christopher E.

Published
2024
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4. Sequencing by avidity enables high accuracy with low reagent consumption

Author

Arslan, Sinan, Garcia, Francisco J., Guo, Minghao, Kellinger, Matthew W., Kruglyak, Semyon, LeVieux, Jake A., Mah, Adeline H., Wang, Haosen, Zhao, Junhua, Zhou, Chunhong, Altomare, Andrew, Bailey, John, Byrne, Matthew B., Chang, Chiting, Chen, Steve X., Cho, Byungrae, Dennler, Claudia N., Dien, Vivian T., Fuller, Derek, Kelley, Ryan, Khandan, Omid, Klein, Michael G., Kim, Michael, Lajoie, Bryan R., Lin, Bill, Liu, Yu, Lopez, Tyler, Mains, Peter T., Price, Andrew D., Robertson, Samantha R., Taylor-Weiner, Hermes, Tippana, Ramreddy, Tomaney, Austin B., Zhang, Su, Abtahi, Minna, Ambroso, Mark R., Bajari, Rosita, Bellizzi, Ava M., Benitez, Chris B., Berard, Daniel R., Berti, Lorenzo, Blease, Kelly N., Blum, Angela P., Boddicker, Andrew M., Bondar, Leo, Brown, Chris, Bui, Chris A., Calleja-Aguirre, Juan, Cappa, Kevin, Chan, Joshua, Chang, Victor W., Charov, Katherine, Chen, Xiyi, Constandse, Rodger M., Damron, Weston, Dawood, Mariam, DeBuono, Nicole, Dimalanta, John D., Edoli, Laure, Elango, Keerthana, Faustino, Nikka, Feng, Chao, Ferrari, Matthew, Frankie, Keith, Fries, Adam, Galloway, Anne, Gavrila, Vlad, Gemmen, Gregory J., Ghadiali, James, Ghorbani, Arash, Goddard, Logan A., Guetter, Adriana Roginski, Hendricks, Garren L., Hentschel, Jendrik, Honigfort, Daniel J., Hsieh, Yun-Ting, Hwang Fu, Yu-Hsien, Im, Scott K., Jin, Chaoyi, Kabu, Shradha, Kincade, Daniel E., Levy, Shawn, Li, Yu, Liang, Vincent K., Light, William H., Lipsher, Jonathan B., Liu, Tsung-li, Long, Grace, Ma, Rui, Mailloux, John M., Mandla, Kyle A., Martinez, Anyssa R., Mass, Max, McKean, Daniel T., Meron, Michael, Miller, Edmund A., Moh, Celyne S., Moore, Rachel K., Moreno, Juan, Neysmith, Jordan M., Niman, Cassandra S., Nunez, Jesus M., Ojeda, Micah T., Ortiz, Sara Espinosa, Owens, Jenna, Piland, Geoffrey, Proctor, Daniel J., Purba, Josua B., Ray, Michael, Rong, Daisong, Saade, Virginia M., Saha, Sanchari, Tomas, Gustav Santo, Scheidler, Nicholas, Sirajudeen, Luqmanal H., Snow, Samantha, Stengel, Gudrun, Stinson, Ryan, Stone, Michael J., Sundseth, Keoni J., Thai, Eileen, Thompson, Connor J., Tjioe, Marco, Trejo, Christy L., Trieger, Greg, Truong, Diane Ni, Tse, Ben, Voiles, Benjamin, Vuong, Henry, Wong, Jennifer C., Wu, Chiung-Ting, Yu, Hua, Yu, Yingxian, Yu, Ming, Zhang, Xi, Zhao, Da, Zheng, Genhua, He, Molly, and Previte, Michael

Published
2024
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6. Viral activation and ecological restructuring characterize a microbiome axis of spaceflight-associated immune activation

Author

Mason, Christopher, primary, Tierney, Braden, additional, Kim, JangKeun, additional, Overbey, Eliah, additional, Ryon, Krista, additional, Foox, Jonathan, additional, Sierra, Maria, additional, Bhattacharya, Chandrima, additional, Damle, Namita, additional, Najjar, Deena, additional, Park, Jiwoon, additional, Medina, J. Sebastian Garcia, additional, Houerbi, Nadia, additional, Meydan, Cem, additional, Hirschberg, Jeremy, additional, Qiu, Jake, additional, Kleinman, Ashley, additional, Al-Ghalith, Gabriel, additional, MacKay, Matthew, additional, Afshin, Evan, additional, Dhir, Raja, additional, Borg, Joseph, additional, Gatt, Christine, additional, Brereton, Nicholas, additional, Readhead, Ben, additional, Beyaz, Semir, additional, Venkateswaran, Kasthuri, additional, Blease, Kelly, additional, Moreno, Juan, additional, Boddicker, Andrew, additional, Zhao, Junhua, additional, Lajoie, Bryan, additional, Scott, Ryan, additional, Altomare, Andrew, additional, Kruglyak, Semyon, additional, Levy, Shawn, additional, and Church, George, additional

Published
2023
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8. Sequencing by avidity enables high accuracy with low reagent consumption

Author

Arslan, Sinan, primary, Garcia, Francisco J., additional, Guo, Minghao, additional, Kellinger, Matthew W., additional, Kruglyak, Semyon, additional, LeVieux, Jake A., additional, Mah, Adeline H., additional, Wang, Haosen, additional, Zhao, Junhua, additional, Zhou, Chunhong, additional, Altomare, Andrew, additional, Bailey, John, additional, Byrne, Matthew B., additional, Chang, Chiting, additional, Chen, Steve X., additional, Cho, Byungrae, additional, Dennler, Claudia N., additional, Dien, Vivian T., additional, Fuller, Derek, additional, Kelley, Ryan, additional, Khandan, Omid, additional, Klein, Michael G., additional, Kim, Michael, additional, Lajoie, Bryan R., additional, Lin, Bill, additional, Liu, Yu, additional, Lopez, Tyler, additional, Mains, Peter T., additional, Price, Andrew D., additional, Robertson, Samantha R., additional, Taylor-Weiner, Hermes, additional, Tippana, Ramreddy, additional, Tomaney, Austin B., additional, Zhang, Su, additional, Abtahi, Minna, additional, Ambroso, Mark R., additional, Bajari, Rosita, additional, Bellizzi, Ava M., additional, Benitez, Chris B., additional, Berard, Daniel R., additional, Berti, Lorenzo, additional, Blease, Kelly N., additional, Blum, Angela P., additional, Boddicker, Andrew M., additional, Bondar, Leo, additional, Brown, Chris, additional, Bui, Chris A., additional, Calleja-Aguirre, Juan, additional, Cappa, Kevin, additional, Chan, Joshua, additional, Chang, Victor W., additional, Charov, Katherine, additional, Chen, Xiyi, additional, Constandse, Rodger M., additional, Damron, Weston, additional, Dawood, Mariam, additional, DeBuono, Nicole, additional, Dimalanta, John D., additional, Edoli, Laure, additional, Elango, Keerthana, additional, Faustino, Nikka, additional, Feng, Chao, additional, Ferrari, Matthew, additional, Frankie, Keith, additional, Fries, Adam, additional, Galloway, Anne, additional, Gavrila, Vlad, additional, Gemmen, Gregory J., additional, Ghadiali, James, additional, Ghorbani, Arash, additional, Goddard, Logan A., additional, Guetter, Adriana Roginski, additional, Hendricks, Garren L., additional, Hentschel, Jendrik, additional, Honigfort, Daniel J., additional, Hsieh, Yun-Ting, additional, Hwang Fu, Yu-Hsien, additional, Im, Scott K., additional, Jin, Chaoyi, additional, Kabu, Shradha, additional, Kincade, Daniel E., additional, Levy, Shawn, additional, Li, Yu, additional, Liang, Vincent K., additional, Light, William H., additional, Lipsher, Jonathan B., additional, Liu, Tsung-li, additional, Long, Grace, additional, Ma, Rui, additional, Mailloux, John M., additional, Mandla, Kyle A., additional, Martinez, Anyssa R., additional, Mass, Max, additional, McKean, Daniel T., additional, Meron, Michael, additional, Miller, Edmund A., additional, Moh, Celyne S., additional, Moore, Rachel K., additional, Moreno, Juan, additional, Neysmith, Jordan M., additional, Niman, Cassandra S., additional, Nunez, Jesus M., additional, Ojeda, Micah T., additional, Ortiz, Sara Espinosa, additional, Owens, Jenna, additional, Piland, Geoffrey, additional, Proctor, Daniel J., additional, Purba, Josua B., additional, Ray, Michael, additional, Rong, Daisong, additional, Saade, Virginia M., additional, Saha, Sanchari, additional, Tomas, Gustav Santo, additional, Scheidler, Nicholas, additional, Sirajudeen, Luqmanal H., additional, Snow, Samantha, additional, Stengel, Gudrun, additional, Stinson, Ryan, additional, Stone, Michael J., additional, Sundseth, Keoni J., additional, Thai, Eileen, additional, Thompson, Connor J., additional, Tjioe, Marco, additional, Trejo, Christy L., additional, Trieger, Greg, additional, Truong, Diane Ni, additional, Tse, Ben, additional, Voiles, Benjamin, additional, Vuong, Henry, additional, Wong, Jennifer C., additional, Wu, Chiung-Ting, additional, Yu, Hua, additional, Yu, Yingxian, additional, Yu, Ming, additional, Zhang, Xi, additional, Zhao, Da, additional, Zheng, Genhua, additional, He, Molly, additional, and Previte, Michael, additional

Published
2023
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9. Sequencing by Avidity Enables High Accuracy With Low Reagent Consumption

Author

Arslan, Sinan, primary, Kellinger, Matthew, additional, Kruglyak, Semyon, additional, LeVieux, Jake, additional, Mah, Adeline, additional, Wang, Haosen, additional, Zhao, Junhua, additional, Zhou, Chunhong, additional, Bailey, John, additional, Byrne, Matthew, additional, Chang, Chiting, additional, Chen, Steve, additional, Dennler, Claudia, additional, Dennler, Samantha, additional, Dien, Vivian, additional, Fuller, Derek, additional, Garcia, Francisco, additional, Guo, Minghao, additional, Kelley, Ryan, additional, Khandan, Omid, additional, Klein, Michael, additional, Kim, Michael, additional, Lin, Bill, additional, Liu, Yu, additional, Lopez, Tyler, additional, Mains, Peter, additional, Price, Andrew, additional, Taylor, Hermes, additional, Tippana, Ramreddy, additional, Tomaney, Austin, additional, Zhang, Richard, additional, Abtahi, Minna, additional, Ambroso, Mark, additional, Bajari, Rosi, additional, Bellizi, Ava, additional, Benitez, Chris, additional, Berard, Daniel, additional, Berti, Lorenzo, additional, Blease, Kelly, additional, Blum, Angela, additional, Boddicker, Andrew, additional, Bondar, Leo, additional, Bui, Chris, additional, Cappa, Kevin, additional, Chan, Joshua, additional, Chang, Victor, additional, Charov, Katia, additional, Chen, Xiyi, additional, Constandse, Rodger, additional, Damron, Weston, additional, Dawood, Mariam, additional, Debruno, Nicole, additional, Dmalanta, John, additional, Edoli, Laure, additional, Elango, Keerthi, additional, Faustino, Nikka, additional, Feng, Chao, additional, Ferrari, Matthew, additional, Frankie, Kieth, additional, Fries, Adam, additional, Galloway, Anne, additional, Gavrila, Vlad, additional, Gemmen, Gregory, additional, Ghadiali, James, additional, Goddard, Logan, additional, Roginski, Adriana, additional, Hendricks, Garren, additional, Hentschel, Jendrick, additional, Hseih, Doris, additional, Hwang-fu, Yu-Hsein, additional, Im, Scott, additional, Jin, Chaoyi, additional, Kincade, Daniel, additional, Lajooie, Bryan, additional, Levy, Shawn, additional, Li, Yu, additional, Liang, Vincent, additional, Light, William, additional, Lipsher, Jonathan, additional, Liu, Tsungli, additional, Long, Guixia, additional, Ma, Rui, additional, Mailloux, Jack, additional, Mandla, Kyle, additional, Martinez, Anyssa, additional, Mass, Max, additional, Meron, Michael, additional, Moh, Celyne, additional, Moore, Rachel, additional, Moreno, Juan, additional, Neysmith, Jordan, additional, Niman, Cassandra, additional, Nunez, Jesus, additional, Ojeda, Micah, additional, Owens, Jenna, additional, Ortiz, Sara Espinosa, additional, Piland, Geoffrey, additional, Proctor, Dan, additional, Purba, Josua, additional, Ray, Michael, additional, Rong, Daisong, additional, Saade, Virginia, additional, Saha, Sanchari, additional, Sirajudeen, Luqmanal, additional, Stengel, Gudrun, additional, Stinson, Ryan, additional, Stone, Michael, additional, Sundseth, Keoni, additional, Thai, Eileen, additional, Thompson, Connor, additional, Tomas, Gustav Santo, additional, Trejo, Christy, additional, Trieger, Greg, additional, Truong, Diane, additional, Tse, Ben, additional, Voiles, Benjamin, additional, Vuong, Henry, additional, Wong, Jennifer, additional, Wu, Chiung-Ting, additional, Yu, Hua, additional, Yu, Ming, additional, Zhang, Cindy, additional, Zhao, Da, additional, Zheng, Frank, additional, He, Molly, additional, and Previte, Michael, additional

Published
2022
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15. Genome and clonal hematopoiesis stability contrasts with immune, cfDNA, mitochondrial, and telomere length changes during short duration spaceflight

Author

Garcia-Medina, J Sebastian, Sienkiewicz, Karolina, Narayanan, S Anand, Overbey, Eliah G, Grigorev, Kirill, Ryon, Krista A, Burke, Marissa, Proszynski, Jacqueline, Tierney, Braden, Schmidt, Caleb M, Mencia-Trinchant, Nuria, Klotz, Remi, Ortiz, Veronica, Foox, Jonathan, Chin, Christopher, Najjar, Deena, Matei, Irina, Chan, Irenaeus, Cruchaga, Carlos, Kleinman, Ashley, Kim, JangKeun, Lucaci, Alexander, Loy, Conor, Mzava, Omary, De Vlaminck, Iwijn, Singaraju, Anvita, Taylor, Lynn E, Schmidt, Julian C, Schmidt, Michael A, Blease, Kelly, Moreno, Juan, Boddicker, Andrew, Zhao, Junhua, Lajoie, Bryan, Altomare, Andrew, Kruglyak, Semyon, Levy, Shawn, Yu, Min, Hassane, Duane C, Bailey, Susan M, Bolton, Kelly, Mateus, Jaime, and Mason, Christopher E

Published
2024
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16. Genomic profiling of four cultivated CandidatusNitrotoga spp. predicts broad metabolic potential and environmental distribution

Author

Boddicker, Andrew and Mosier, Annika

Abstract

Nitrite-oxidizing bacteria (NOB) play a critical role in the mitigation of nitrogen pollution by metabolizing nitrite to nitrate, which is removed via assimilation, denitrification, or anammox. Recent studies showed that NOB are phylogenetically and metabolically diverse, yet most of our knowledge of NOB comes from only a few cultured representatives. Using cultivation and genomic sequencing, we identified four putative CandidatusNitrotoga NOB species from freshwater sediments and water column samples in Colorado, USA. Genome analyses indicated highly conserved 16S rRNA gene sequences, but broad metabolic potential including genes for nitrogen, sulfur, hydrogen, and organic carbon metabolism. Genomic predictions suggested that Ca. Nitrotoga can metabolize in low oxygen or anoxic conditions, which may support an expanded environmental niche for Ca. Nitrotoga similar to other NOB. An array of antibiotic and metal resistance genes likely allows Ca. Nitrotoga to withstand environmental pressures in impacted systems. Phylogenetic analyses highlighted a deeply divergent nitrite oxidoreductase alpha subunit (NxrA), suggesting a novel evolutionary trajectory for Ca. Nitrotoga separate from any other NOB and further revealing the complex evolutionary history of nitrite oxidation in the bacterial domain. Ca. Nitrotoga-like 16S rRNA gene sequences were prevalent in globally distributed environments over a range of reported temperatures. This work considerably expands our knowledge of the Ca. Nitrotoga genus and suggests that their contribution to nitrogen cycling should be considered alongside other NOB in wide variety of habitats.

Published
2018
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17. Efficient small fragment sequencing of human, cow, and bison miRNA, small RNA or csRNA-seq libraries using AVITI.

Author

McDonald AL, Boddicker AM, Savenkova MI, Brabb IM, Qi X, Moré DD, Cunha CW, Zhao J, and Duttke SH

Abstract

Next-Generation Sequencing (NGS) catalyzed breakthroughs across various scientific domains. Illumina's sequencing by synthesis method has long been essential for NGS but emerging technologies like Element Biosciences' sequencing by avidity (AVITI) represent a novel approach. It has been reported that AVITI offers improved signal-to-noise ratios and cost reductions. However, the method relies on rolling circle amplification which can be impacted by polymer size, raising questions about its efficacy sequencing small RNAs (sRNA) molecules including microRNAs (miRNAs), piwi-interacting RNAs (piRNAs), and others that are crucial regulators of gene expression and involved in various biological processes. In addition, capturing capped small RNAs (csRNA-seq) has emerged as a powerful method to map active or "nascent" RNA polymerase II transcription initiation in tissues and clinical samples. Here, we report a new protocol for seamlessly sequencing short DNA fragments on the AVITI and demonstrate that AVITI and Illumina sequencing technologies equivalently capture human, cattle ( Bos taurus ) and the bison ( Bison bison ) sRNA or csRNA sequencing libraries, augmenting the confidence in both approaches. Additionally, analysis of generated nascent transcription start sites (TSSs) data for cattle and bison revealed inaccuracies in their current genome annotations and highlighted the possibility and need to translate small RNA sequencing methodologies to livestock. Our accelerated and optimized protocol therefore bridges the advantages of AVITI sequencing and critical methods that rely on sequencing short DNA fragments., Competing Interests: COMPETING INTERESTS A.M.B, X.Q., and J.Z are employees of Element Biosciences. S.H.D. is leading nascent Transcriptomic Services (nTSS) at Washington State University.

Published
2024
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18. Viral activation and ecological restructuring characterize a microbiome axis of spaceflight-associated immune activation.

Author

Tierney BT, Kim J, Overbey EG, Ryon KA, Foox J, Sierra M, Bhattacharya C, Damle N, Najjar D, Park J, Garcia Medina S, Houerbi N, Meydan C, Wain Hershberg J, Qiu J, Kleinman A, Al Ghalith G, MacKay M, Afshin EE, Dhir R, Borg J, Gatt C, Brereton N, Readhead B, Beyaz S, Venkateswaran KJ, Blease K, Moreno J, Boddicker A, Zhao J, Lajoie B, Scott RT, Altomare A, Kruglyak S, Levy S, Church G, and Mason CE

Abstract

Maintenance of astronaut health during spaceflight will require monitoring and potentially modulating their microbiomes, which play a role in some space-derived health disorders. However, documenting the response of microbiota to spaceflight has been difficult thus far due to mission constraints that lead to limited sampling. Here, we executed a six-month longitudinal study centered on a three-day flight to quantify the high-resolution microbiome response to spaceflight. Via paired metagenomics and metatranscriptomics alongside single immune profiling, we resolved a microbiome "architecture" of spaceflight characterized by time-dependent and taxonomically divergent microbiome alterations across 750 samples and ten body sites. We observed pan-phyletic viral activation and signs of persistent changes that, in the oral microbiome, yielded plaque-associated pathobionts with strong associations to immune cell gene expression. Further, we found enrichments of microbial genes associated with antibiotic production, toxin-antitoxin systems, and stress response enriched universally across the body sites. We also used strain-level tracking to measure the potential propagation of microbial species from the crew members to each other and the environment, identifying microbes that were prone to seed the capsule surface and move between the crew. Finally, we identified associations between microbiome and host immune cell shifts, proposing both a microbiome axis of immune changes during flight as well as the sources of some of those changes. In summary, these datasets and methods reveal connections between crew immunology, the microbiome, and their likely drivers and lay the groundwork for future microbiome studies of spaceflight., Competing Interests: BTT is compensated for consulting with Seed Health and Enzymetrics Biosciences on microbiome study design and holds an ownership stake in the former. RD and GA are employees of Seed Health and additionally hold ownership stakes. CEM is a co-Founder of Onegevity, Twin Orbit, and Cosmica Biosciences. EEA is a consultant for Thorne HealthTech. GC has conflicts. JF and MM are employees of Tempus Labs. KB, JM, AB, JZ, BL, AA, SK, and SL are employees of Element Biosciences, which sequenced a subset of samples used in this study. Unless otherwise mentioned, none of the companies listed had a role in conceiving, executing, or funding the work described here.

Published
2023
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