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1. Diversity and scale: Genetic architecture of 2068 traits in the VA Million Veteran Program

Author

Verma, Anurag, Huffman, Jennifer E, Rodriguez, Alex, Conery, Mitchell, Liu, Molei, Ho, Yuk-Lam, Kim, Youngdae, Heise, David A, Guare, Lindsay, Panickan, Vidul Ayakulangara, Garcon, Helene, Linares, Franciel, Costa, Lauren, Goethert, Ian, Tipton, Ryan, Honerlaw, Jacqueline, Davies, Laura, Whitbourne, Stacey, Cohen, Jeremy, Posner, Daniel C, Sangar, Rahul, Murray, Michael, Wang, Xuan, Dochtermann, Daniel R, Devineni, Poornima, Shi, Yunling, Nandi, Tarak Nath, Assimes, Themistocles L, Brunette, Charles A, Carroll, Robert J, Clifford, Royce, Duvall, Scott, Gelernter, Joel, Hung, Adriana, Iyengar, Sudha K, Joseph, Jacob, Kember, Rachel, Kranzler, Henry, Kripke, Colleen M, Levey, Daniel, Luoh, Shiuh-Wen, Merritt, Victoria C, Overstreet, Cassie, Deak, Joseph D, Grant, Struan FA, Polimanti, Renato, Roussos, Panos, Shakt, Gabrielle, Sun, Yan V, Tsao, Noah, Venkatesh, Sanan, Voloudakis, Georgios, Justice, Amy, Begoli, Edmon, Ramoni, Rachel, Tourassi, Georgia, Pyarajan, Saiju, Tsao, Philip, O'Donnell, Christopher J, Muralidhar, Sumitra, Moser, Jennifer, Casas, Juan P, Bick, Alexander G, Zhou, Wei, Cai, Tianxi, Voight, Benjamin F, Cho, Kelly, Gaziano, J Michael, Madduri, Ravi K, Damrauer, Scott, and Liao, Katherine P

Subjects
Epidemiology, Biological Sciences, Health Sciences, Genetics, Human Genome, 2.1 Biological and endogenous factors, Mental health, Humans, Male, Genetic Predisposition to Disease, Genetic Variation, Genome-Wide Association Study, Longitudinal Studies, Polymorphism, Single Nucleotide, Quantitative Trait Loci, United States, United States Department of Veterans Affairs, Veterans, Female, General Science & Technology
Abstract

One of the justifiable criticisms of human genetic studies is the underrepresentation of participants from diverse populations. Lack of inclusion must be addressed at-scale to identify causal disease factors and understand the genetic causes of health disparities. We present genome-wide associations for 2068 traits from 635,969 participants in the Department of Veterans Affairs Million Veteran Program, a longitudinal study of diverse United States Veterans. Systematic analysis revealed 13,672 genomic risk loci; 1608 were only significant after including non-European populations. Fine-mapping identified causal variants at 6318 signals across 613 traits. One-third (n = 2069) were identified in participants from non-European populations. This reveals a broadly similar genetic architecture across populations, highlights genetic insights gained from underrepresented groups, and presents an extensive atlas of genetic associations.

Published
2024

2. Variation in human water turnover associated with environmental and lifestyle factors

Author

Yamada, Yosuke, Zhang, Xueying, Henderson, Mary ET, Sagayama, Hiroyuki, Pontzer, Herman, Watanabe, Daiki, Yoshida, Tsukasa, Kimura, Misaka, Ainslie, Philip N, Andersen, Lene F, Anderson, Liam J, Arab, Lenore, Baddou, Issad, Bedu-Addo, Kweku, Blaak, Ellen E, Blanc, Stephane, Bonomi, Alberto G, Bouten, Carlijn VC, Bovet, Pascal, Buchowski, Maciej S, Butte, Nancy F, Camps, Stefan G, Close, Graeme L, Cooper, Jamie A, Cooper, Richard, Das, Sai Krupa, Dugas, Lara R, Eaton, Simon, Ekelund, Ulf, Entringer, Sonja, Forrester, Terrence, Fudge, Barry W, Goris, Annelies H, Gurven, Michael, Halsey, Lewis G, Hambly, Catherine, Hamdouchi, Asmaa El, Hoos, Marije B, Hu, Sumei, Joonas, Noorjehan, Joosen, Annemiek M, Katzmarzyk, Peter, Kempen, Kitty P, Kraus, William E, Kriengsinyos, Wantanee, Kushner, Robert F, Lambert, Estelle V, Leonard, William R, Lessan, Nader, Martin, Corby K, Medin, Anine C, Meijer, Erwin P, Morehen, James C, Morton, James P, Neuhouser, Marian L, Nicklas, Theresa A, Ojiambo, Robert M, Pietiläinen, Kirsi H, Pitsiladis, Yannis P, Plange-Rhule, Jacob, Plasqui, Guy, Prentice, Ross L, Rabinovich, Roberto A, Racette, Susan B, Raichlen, David A, Ravussin, Eric, Redman, Leanne M, Reilly, John J, Reynolds, Rebecca M, Roberts, Susan B, Schuit, Albertine J, Sardinha, Luis B, Silva, Analiza M, Sjödin, Anders M, Stice, Eric, Urlacher, Samuel S, Valenti, Giulio, Van Etten, Ludo M, Van Mil, Edgar A, Wells, Jonathan CK, Wilson, George, Wood, Brian M, Yanovski, Jack A, Murphy-Alford, Alexia J, Loechl, Cornelia U, Luke, Amy H, Rood, Jennifer, Westerterp, Klaas R, Wong, William W, Miyachi, Motohiko, Schoeller, Dale A, Speakman, John R, and Consortium§, International Atomic Energy Agency Doubly Labeled Water Database

Subjects
Prevention, Clean Water and Sanitation, Female, Humans, Pregnancy, Exercise, Humidity, Life Style, Social Class, Water, Infant, Newborn, Infant, Child, Preschool, Child, Adolescent, Young Adult, Adult, Middle Aged, Aged, Aged, 80 and over, Drinking, International Atomic Energy Agency (IAEA) Doubly Labeled Water (DLW) Database Consortium§, General Science & Technology
Abstract

Water is essential for survival, but one in three individuals worldwide (2.2 billion people) lacks access to safe drinking water. Water intake requirements largely reflect water turnover (WT), the water used by the body each day. We investigated the determinants of human WT in 5604 people from the ages of 8 days to 96 years from 23 countries using isotope-tracking (2H) methods. Age, body size, and composition were significantly associated with WT, as were physical activity, athletic status, pregnancy, socioeconomic status, and environmental characteristics (latitude, altitude, air temperature, and humidity). People who lived in countries with a low human development index (HDI) had higher WT than people in high-HDI countries. On the basis of this extensive dataset, we provide equations to predict human WT in relation to anthropometric, economic, and environmental factors.

Published
2022

3. The complete sequence of a human genome

Author

Nurk, Sergey, Koren, Sergey, Rhie, Arang, Rautiainen, Mikko, Bzikadze, Andrey V, Mikheenko, Alla, Vollger, Mitchell R, Altemose, Nicolas, Uralsky, Lev, Gershman, Ariel, Aganezov, Sergey, Hoyt, Savannah J, Diekhans, Mark, Logsdon, Glennis A, Alonge, Michael, Antonarakis, Stylianos E, Borchers, Matthew, Bouffard, Gerard G, Brooks, Shelise Y, Caldas, Gina V, Chen, Nae-Chyun, Cheng, Haoyu, Chin, Chen-Shan, Chow, William, de Lima, Leonardo G, Dishuck, Philip C, Durbin, Richard, Dvorkina, Tatiana, Fiddes, Ian T, Formenti, Giulio, Fulton, Robert S, Fungtammasan, Arkarachai, Garrison, Erik, Grady, Patrick GS, Graves-Lindsay, Tina A, Hall, Ira M, Hansen, Nancy F, Hartley, Gabrielle A, Haukness, Marina, Howe, Kerstin, Hunkapiller, Michael W, Jain, Chirag, Jain, Miten, Jarvis, Erich D, Kerpedjiev, Peter, Kirsche, Melanie, Kolmogorov, Mikhail, Korlach, Jonas, Kremitzki, Milinn, Li, Heng, Maduro, Valerie V, Marschall, Tobias, McCartney, Ann M, McDaniel, Jennifer, Miller, Danny E, Mullikin, James C, Myers, Eugene W, Olson, Nathan D, Paten, Benedict, Peluso, Paul, Pevzner, Pavel A, Porubsky, David, Potapova, Tamara, Rogaev, Evgeny I, Rosenfeld, Jeffrey A, Salzberg, Steven L, Schneider, Valerie A, Sedlazeck, Fritz J, Shafin, Kishwar, Shew, Colin J, Shumate, Alaina, Sims, Ying, Smit, Arian FA, Soto, Daniela C, Sović, Ivan, Storer, Jessica M, Streets, Aaron, Sullivan, Beth A, Thibaud-Nissen, Françoise, Torrance, James, Wagner, Justin, Walenz, Brian P, Wenger, Aaron, Wood, Jonathan MD, Xiao, Chunlin, Yan, Stephanie M, Young, Alice C, Zarate, Samantha, Surti, Urvashi, McCoy, Rajiv C, Dennis, Megan Y, Alexandrov, Ivan A, Gerton, Jennifer L, O’Neill, Rachel J, Timp, Winston, Zook, Justin M, Schatz, Michael C, Eichler, Evan E, Miga, Karen H, and Phillippy, Adam M

Subjects
Biological Sciences, Bioinformatics and Computational Biology, Genetics, Human Genome, 1.1 Normal biological development and functioning, Generic health relevance, Cell Line, Chromosomes, Artificial, Bacterial, Chromosomes, Human, Genome, Human, Human Genome Project, Humans, Reference Values, Sequence Analysis, DNA, General Science & Technology
Abstract

Since its initial release in 2000, the human reference genome has covered only the euchromatic fraction of the genome, leaving important heterochromatic regions unfinished. Addressing the remaining 8% of the genome, the Telomere-to-Telomere (T2T) Consortium presents a complete 3.055 billion-base pair sequence of a human genome, T2T-CHM13, that includes gapless assemblies for all chromosomes except Y, corrects errors in the prior references, and introduces nearly 200 million base pairs of sequence containing 1956 gene predictions, 99 of which are predicted to be protein coding. The completed regions include all centromeric satellite arrays, recent segmental duplications, and the short arms of all five acrocentric chromosomes, unlocking these complex regions of the genome to variational and functional studies.

Published
2022

4. A plant lipocalin promotes retinal-mediated oscillatory lateral root initiation

Author

Dickinson, Alexandra J, Zhang, Jingyuan, Luciano, Michael, Wachsman, Guy, Sandoval, Evan, Schnermann, Martin, Dinneny, José R, and Benfey, Philip N

Subjects
Biomedical and Clinical Sciences, Ophthalmology and Optometry, Eye Disease and Disorders of Vision, Arabidopsis, Arabidopsis Proteins, Fluorescence, Lipocalins, Meristem, Mutation, Organogenesis, Plant, Plant Roots, Protein Binding, Pyrimidinones, Retinaldehyde, Signal Transduction, General Science & Technology
Abstract

In Arabidopsis, de novo organogenesis of lateral roots is patterned by an oscillatory mechanism called the root clock, which is dependent on unidentified metabolites. To determine whether retinoids regulate the root clock, we used a chemical reporter for retinaldehyde (retinal)–binding proteins. We found that retinal binding precedes the root clock and predicts sites of lateral root organogenesis. Application of retinal increased root clock oscillations and promoted lateral root formation. Expression of an Arabidopsis protein with homology to vertebrate retinoid-binding proteins, TEMPERATURE INDUCED LIPOCALIN (TIL), oscillates in the region of retinal binding to the reporter, confers retinal-binding activity in a heterologous system, and, when mutated, decreases retinal sensitivity. These results demonstrate a role for retinal and its binding partner in lateral root organogenesis.

Published
2021

5. Response to Comments on “Aberrant type 1 immunity drives susceptibility to mucosal fungal infections”

Author

Break, Timothy J, Oikonomou, Vasileios, Dutzan, Nicolas, Desai, Jigar V, Swidergall, Marc, Freiwald, Tilo, Chauss, Daniel, Harrison, Oliver J, Alejo, Julie, Williams, Drake W, Pittaluga, Stefania, Lee, Chyi-Chia R, Bouladoux, Nicolas, Swamydas, Muthulekha, Hoffman, Kevin W, Greenwell-Wild, Teresa, Bruno, Vincent M, Rosen, Lindsey B, Lwin, Wint, Renteria, Andy, Pontejo, Sergio M, Shannon, John P, Myles, Ian A, Olbrich, Peter, Ferré, Elise MN, Schmitt, Monica, Martin, Daniel, Core16, Genomics and Computational Biology, Barber, Daniel L, Solis, Norma V, Notarangelo, Luigi D, Serreze, David V, Matsumoto, Mitsuru, Hickman, Heather D, Murphy, Philip M, Anderson, Mark S, Lim, Jean K, Holland, Steven M, Filler, Scott G, Afzali, Behdad, Belkaid, Yasmine, Moutsopoulos, Niki M, and Lionakis, Michail S

Subjects
Autoimmune Disease, Clinical Research, Infectious Diseases, Rare Diseases, 2.1 Biological and endogenous factors, Aetiology, Humans, Immunity, Mucosal, Mucous Membrane, Mycoses, Genomics and Computational Biology Core16, General Science & Technology
Abstract

Puel and Casanova and Kisand et al. challenge our conclusions that interferonopathy and not IL-17/IL-22 autoantibodies promote candidiasis in autoimmune polyendocrinopathy–candidiasis–ectodermal dystrophy. We acknowledge that conclusive evidence for causation is difficult to obtain in complex human diseases. However, our studies clearly document interferonopathy driving mucosal candidiasis with intact IL-17/IL-22 responses in Aire-deficient mice, with strong corroborative evidence in patients.

Published
2021

6. Daily energy expenditure through the human life course

Author

Pontzer, Herman, Yamada, Yosuke, Sagayama, Hiroyuki, Ainslie, Philip N, Andersen, Lene F, Anderson, Liam J, Arab, Lenore, Baddou, Issaad, Bedu-Addo, Kweku, Blaak, Ellen E, Blanc, Stephane, Bonomi, Alberto G, Bouten, Carlijn VC, Bovet, Pascal, Buchowski, Maciej S, Butte, Nancy F, Camps, Stefan G, Close, Graeme L, Cooper, Jamie A, Cooper, Richard, Das, Sai Krupa, Dugas, Lara R, Ekelund, Ulf, Entringer, Sonja, Forrester, Terrence, Fudge, Barry W, Goris, Annelies H, Gurven, Michael, Hambly, Catherine, Hamdouchi, Asmaa El, Hoos, Marjije B, Hu, Sumei, Joonas, Noorjehan, Joosen, Annemiek M, Katzmarzyk, Peter, Kempen, Kitty P, Kimura, Misaka, Kraus, William E, Kushner, Robert F, Lambert, Estelle V, Leonard, William R, Lessan, Nader, Martin, Corby, Medin, Anine C, Meijer, Erwin P, Morehen, James C, Morton, James P, Neuhouser, Marian L, Nicklas, Teresa A, Ojiambo, Robert M, Pietiläinen, Kirsi H, Pitsiladis, Yannis P, Plange-Rhule, Jacob, Plasqui, Guy, Prentice, Ross L, Rabinovich, Roberto A, Racette, Susan B, Raichlen, David A, Ravussin, Eric, Reynolds, Rebecca M, Roberts, Susan B, Schuit, Albertine J, Sjödin, Anders M, Stice, Eric, Urlacher, Samuel S, Valenti, Giulio, Van Etten, Ludo M, Van Mil, Edgar A, Wells, Jonathan CK, Wilson, George, Wood, Brian M, Yanovski, Jack, Yoshida, Tsukasa, Zhang, Xueying, Murphy-Alford, Alexia J, Loechl, Cornelia, Luke, Amy H, Rood, Jennifer, Schoeller, Dale A, Westerterp, Klaas R, Wong, William W, Speakman, John R, and Consortium§, IAEA DLW Database

Subjects
Aging, Nutrition, Adolescent, Adult, Aged, Aged, 80 and over, Basal Metabolism, Body Composition, Body Weight, Child, Child, Preschool, Energy Metabolism, Exercise, Female, Humans, Infant, Infant, Newborn, Male, Middle Aged, Pregnancy, Young Adult, IAEA DLW Database Consortium, General Science & Technology
Abstract

Total daily energy expenditure ("total expenditure") reflects daily energy needs and is a critical variable in human health and physiology, but its trajectory over the life course is poorly studied. We analyzed a large, diverse database of total expenditure measured by the doubly labeled water method for males and females aged 8 days to 95 years. Total expenditure increased with fat-free mass in a power-law manner, with four distinct life stages. Fat-free mass-adjusted expenditure accelerates rapidly in neonates to ~50% above adult values at ~1 year; declines slowly to adult levels by ~20 years; remains stable in adulthood (20 to 60 years), even during pregnancy; then declines in older adults. These changes shed light on human development and aging and should help shape nutrition and health strategies across the life span.

Published
2021

7. Aberrant type 1 immunity drives susceptibility to mucosal fungal infections

Author

Break, Timothy J, Oikonomou, Vasileios, Dutzan, Nicolas, Desai, Jigar V, Swidergall, Marc, Freiwald, Tilo, Chauss, Daniel, Harrison, Oliver J, Alejo, Julie, Williams, Drake W, Pittaluga, Stefania, Lee, Chyi-Chia R, Bouladoux, Nicolas, Swamydas, Muthulekha, Hoffman, Kevin W, Greenwell-Wild, Teresa, Bruno, Vincent M, Rosen, Lindsey B, Lwin, Wint, Renteria, Andy, Pontejo, Sergio M, Shannon, John P, Myles, Ian A, Olbrich, Peter, Ferré, Elise MN, Schmitt, Monica, Martin, Daniel, Core16, Genomics and Computational Biology, Barber, Daniel L, Solis, Norma V, Notarangelo, Luigi D, Serreze, David V, Matsumoto, Mitsuru, Hickman, Heather D, Murphy, Philip M, Anderson, Mark S, Lim, Jean K, Holland, Steven M, Filler, Scott G, Afzali, Behdad, Belkaid, Yasmine, Moutsopoulos, Niki M, and Lionakis, Michail S

Subjects
Autoimmune Disease, Emerging Infectious Diseases, Infectious Diseases, 2.1 Biological and endogenous factors, Aetiology, Infection, Inflammatory and immune system, Adolescent, Adult, Aged, Animals, Candida albicans, Candidiasis, Chronic Mucocutaneous, Disease Models, Animal, Female, Humans, Immunity, Mucosal, Immunologic Surveillance, Interferon-gamma, Interleukins, Janus Kinases, Male, Mice, Mice, Inbred BALB C, Middle Aged, Mouth Mucosa, Polyendocrinopathies, Autoimmune, Receptors, Interleukin-17, STAT1 Transcription Factor, T-Lymphocytes, Young Adult, Genomics and Computational Biology Core, General Science & Technology
Abstract

Human monogenic disorders have revealed the critical contribution of type 17 responses in mucosal fungal surveillance. We unexpectedly found that in certain settings, enhanced type 1 immunity rather than defective type 17 responses can promote mucosal fungal infection susceptibility. Notably, in mice and humans with AIRE deficiency, an autoimmune disease characterized by selective susceptibility to mucosal but not systemic fungal infection, mucosal type 17 responses are intact while type 1 responses are exacerbated. These responses promote aberrant interferon-γ (IFN-γ)- and signal transducer and activator of transcription 1 (STAT1)-dependent epithelial barrier defects as well as mucosal fungal infection susceptibility. Concordantly, genetic and pharmacologic inhibition of IFN-γ or Janus kinase (JAK)-STAT signaling ameliorates mucosal fungal disease. Thus, we identify aberrant T cell-dependent, type 1 mucosal inflammation as a critical tissue-specific pathogenic mechanism that promotes mucosal fungal infection susceptibility in mice and humans.

Published
2021

8. Sequence diversity analyses of an improved rhesus macaque genome enhance its biomedical utility

Author

Warren, Wesley C, Harris, R Alan, Haukness, Marina, Fiddes, Ian T, Murali, Shwetha C, Fernandes, Jason, Dishuck, Philip C, Storer, Jessica M, Raveendran, Muthuswamy, Hillier, LaDeana W, Porubsky, David, Mao, Yafei, Gordon, David, Vollger, Mitchell R, Lewis, Alexandra P, Munson, Katherine M, DeVogelaere, Elizabeth, Armstrong, Joel, Diekhans, Mark, Walker, Jerilyn A, Tomlinson, Chad, Graves-Lindsay, Tina A, Kremitzki, Milinn, Salama, Sofie R, Audano, Peter A, Escalona, Merly, Maurer, Nicholas W, Antonacci, Francesca, Mercuri, Ludovica, Maggiolini, Flavia AM, Catacchio, Claudia Rita, Underwood, Jason G, O'Connor, David H, Sanders, Ashley D, Korbel, Jan O, Ferguson, Betsy, Kubisch, H Michael, Picker, Louis, Kalin, Ned H, Rosene, Douglas, Levine, Jon, Abbott, David H, Gray, Stanton B, Sanchez, Mar M, Kovacs-Balint, Zsofia A, Kemnitz, Joseph W, Thomasy, Sara M, Roberts, Jeffrey A, Kinnally, Erin L, Capitanio, John P, Skene, JH Pate, Platt, Michael, Cole, Shelley A, Green, Richard E, Ventura, Mario, Wiseman, Roger W, Paten, Benedict, Batzer, Mark A, Rogers, Jeffrey, and Eichler, Evan E

Subjects
Biological Sciences, Bioinformatics and Computational Biology, Genetics, Human Genome, Biotechnology, Animals, Genetic Predisposition to Disease, Genetic Variation, Genome, Humans, Macaca mulatta, Molecular Sequence Annotation, Polymorphism, Single Nucleotide, Whole Genome Sequencing, General Science & Technology
Abstract

The rhesus macaque (Macaca mulatta) is the most widely studied nonhuman primate (NHP) in biomedical research. We present an updated reference genome assembly (Mmul_10, contig N50 = 46 Mbp) that increases the sequence contiguity 120-fold and annotate it using 6.5 million full-length transcripts, thus improving our understanding of gene content, isoform diversity, and repeat organization. With the improved assembly of segmental duplications, we discovered new lineage-specific genes and expanded gene families that are potentially informative in studies of evolution and disease susceptibility. Whole-genome sequencing (WGS) data from 853 rhesus macaques identified 85.7 million single-nucleotide variants (SNVs) and 10.5 million indel variants, including potentially damaging variants in genes associated with human autism and developmental delay, providing a framework for developing noninvasive NHP models of human disease.

Published
2020

9. Cryptic transmission of SARS-CoV-2 in Washington state

Author

Bedford, Trevor, Greninger, Alexander L, Roychoudhury, Pavitra, Starita, Lea M, Famulare, Michael, Huang, Meei-Li, Nalla, Arun, Pepper, Gregory, Reinhardt, Adam, Xie, Hong, Shrestha, Lasata, Nguyen, Truong N, Adler, Amanda, Brandstetter, Elisabeth, Cho, Shari, Giroux, Danielle, Han, Peter D, Fay, Kairsten, Frazar, Chris D, Ilcisin, Misja, Lacombe, Kirsten, Lee, Jover, Kiavand, Anahita, Richardson, Matthew, Sibley, Thomas R, Truong, Melissa, Wolf, Caitlin R, Nickerson, Deborah A, Rieder, Mark J, Englund, Janet A, Hadfield, James, Hodcroft, Emma B, Huddleston, John, Moncla, Louise H, Müller, Nicola F, Neher, Richard A, Deng, Xianding, Gu, Wei, Federman, Scot, Chiu, Charles, Duchin, Jeffrey S, Gautom, Romesh, Melly, Geoff, Hiatt, Brian, Dykema, Philip, Lindquist, Scott, Queen, Krista, Tao, Ying, Uehara, Anna, Tong, Suxiang, MacCannell, Duncan, Armstrong, Gregory L, Baird, Geoffrey S, Chu, Helen Y, Shendure, Jay, Jerome, Keith R, Boeckh, Michael, Lutz, Barry R, Thompson, Matthew, Huang, Shichu, Jackson, Michael L, Kimball, Louise E, Logue, Jennifer, Lyon, Victoria, Newman, Kira L, and Suchsland, Monica L Zigman

Subjects
Infectious Diseases, Pneumonia & Influenza, Lung, Prevention, Emerging Infectious Diseases, Biodefense, Vaccine Related, Pneumonia, Infection, Good Health and Well Being, Bayes Theorem, Betacoronavirus, COVID-19, Coronavirus Infections, Genome, Viral, Humans, Likelihood Functions, Pandemics, Phylogeny, Pneumonia, Viral, SARS-CoV-2, Washington, Seattle Flu Study Investigators, General Science & Technology
Abstract

After its emergence in Wuhan, China, in late November or early December 2019, the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) virus rapidly spread globally. Genome sequencing of SARS-CoV-2 allows the reconstruction of its transmission history, although this is contingent on sampling. We analyzed 453 SARS-CoV-2 genomes collected between 20 February and 15 March 2020 from infected patients in Washington state in the United States. We find that most SARS-CoV-2 infections sampled during this time derive from a single introduction in late January or early February 2020, which subsequently spread locally before active community surveillance was implemented.

Published
2020

10. On impact and volcanism across the Cretaceous-Paleogene boundary

Author

Hull, Pincelli M, Bornemann, André, Penman, Donald E, Henehan, Michael J, Norris, Richard D, Wilson, Paul A, Blum, Peter, Alegret, Laia, Batenburg, Sietske J, Bown, Paul R, Bralower, Timothy J, Cournede, Cecile, Deutsch, Alexander, Donner, Barbara, Friedrich, Oliver, Jehle, Sofie, Kim, Hojung, Kroon, Dick, Lippert, Peter C, Loroch, Dominik, Moebius, Iris, Moriya, Kazuyoshi, Peppe, Daniel J, Ravizza, Gregory E, Röhl, Ursula, Schueth, Jonathan D, Sepúlveda, Julio, Sexton, Philip F, Sibert, Elizabeth C, Śliwińska, Kasia K, Summons, Roger E, Thomas, Ellen, Westerhold, Thomas, Whiteside, Jessica H, Yamaguchi, Tatsuhiko, and Zachos, James C

Subjects
Carbon Cycle, Carbon Dioxide, Extinction, Biological, Global Warming, Mexico, Models, Theoretical, Volcanic Eruptions, General Science & Technology
Abstract

The cause of the end-Cretaceous mass extinction is vigorously debated, owing to the occurrence of a very large bolide impact and flood basalt volcanism near the boundary. Disentangling their relative importance is complicated by uncertainty regarding kill mechanisms and the relative timing of volcanogenic outgassing, impact, and extinction. We used carbon cycle modeling and paleotemperature records to constrain the timing of volcanogenic outgassing. We found support for major outgassing beginning and ending distinctly before the impact, with only the impact coinciding with mass extinction and biologically amplified carbon cycle change. Our models show that these extinction-related carbon cycle changes would have allowed the ocean to absorb massive amounts of carbon dioxide, thus limiting the global warming otherwise expected from postextinction volcanism.

Published
2020

11. Oligogenic inheritance of a human heart disease involving a genetic modifier

Author

Gifford, Casey A, Ranade, Sanjeev S, Samarakoon, Ryan, Salunga, Hazel T, de Soysa, T Yvanka, Huang, Yu, Zhou, Ping, Elfenbein, Aryé, Wyman, Stacia K, Bui, Yen Kim, Cordes Metzler, Kimberly R, Ursell, Philip, Ivey, Kathryn N, and Srivastava, Deepak

Subjects
Biological Sciences, Biomedical and Clinical Sciences, Genetics, Rare Diseases, Cardiovascular, Pediatric, Stem Cell Research - Induced Pluripotent Stem Cell - Human, Stem Cell Research, Heart Disease, Human Genome, Stem Cell Research - Induced Pluripotent Stem Cell, Aetiology, 2.1 Biological and endogenous factors, Animals, CRISPR-Associated Protein 9, Cardiac Myosins, Cardiomyopathies, Clustered Regularly Interspaced Short Palindromic Repeats, Exome, Gene Frequency, Heterozygote, Homeobox Protein Nkx-2.5, Humans, Induced Pluripotent Stem Cells, Mice, Mice, Mutant Strains, Multifactorial Inheritance, Mutation, Missense, Myocytes, Cardiac, Myosin Heavy Chains, Paternal Inheritance, Thyroid Nuclear Factor 1, Transcription Factors, General Science & Technology
Abstract

Complex genetic mechanisms are thought to underlie many human diseases, yet experimental proof of this model has been elusive. Here, we show that a human cardiac anomaly can be caused by a combination of rare, inherited heterozygous mutations. Whole-exome sequencing of a nuclear family revealed that three offspring with childhood-onset cardiomyopathy had inherited three missense single-nucleotide variants in the MKL2, MYH7, and NKX2-5 genes. The MYH7 and MKL2 variants were inherited from the affected, asymptomatic father and the rare NKX2-5 variant (minor allele frequency, 0.0012) from the unaffected mother. We used CRISPR-Cas9 to generate mice encoding the orthologous variants and found that compound heterozygosity for all three variants recapitulated the human disease phenotype. Analysis of murine hearts and human induced pluripotent stem cell-derived cardiomyocytes provided histologic and molecular evidence for the NKX2-5 variant's contribution as a genetic modifier.

Published
2019

13. Strengthened scientific support for the Endangerment Finding for atmospheric greenhouse gases

Author

Duffy, Philip B, Field, Christopher B, Diffenbaugh, Noah S, Doney, Scott C, Dutton, Zoe, Goodman, Sherri, Heinzerling, Lisa, Hsiang, Solomon, Lobell, David B, Mickley, Loretta J, Myers, Samuel, Natali, Susan M, Parmesan, Camille, Tierney, Susan, and Williams, A Park

Subjects
Climate Action, Agriculture, Air Pollution, Climate Change, Disasters, Greenhouse Gases, Humans, Public Health, Risk Assessment, United States, United States Environmental Protection Agency, Weather, General Science & Technology
Abstract

We assess scientific evidence that has emerged since the U.S. Environmental Protection Agency's 2009 Endangerment Finding for six well-mixed greenhouse gases and find that this new evidence lends increased support to the conclusion that these gases pose a danger to public health and welfare. Newly available evidence about a wide range of observed and projected impacts strengthens the association between the risk of some of these impacts and anthropogenic climate change, indicates that some impacts or combinations of impacts have the potential to be more severe than previously understood, and identifies substantial risk of additional impacts through processes and pathways not considered in the Endangerment Finding.

Published
2019

14. Toward unrestricted use of public genomic data

Author

Amann, Rudolf I, Baichoo, Shakuntala, Blencowe, Benjamin J, Bork, Peer, Borodovsky, Mark, Brooksbank, Cath, Chain, Patrick SG, Colwell, Rita R, Daffonchio, Daniele G, Danchin, Antoine, de Lorenzo, Victor, Dorrestein, Pieter C, Finn, Robert D, Fraser, Claire M, Gilbert, Jack A, Hallam, Steven J, Hugenholtz, Philip, Ioannidis, John PA, Jansson, Janet K, Kim, Jihyun F, Klenk, Hans-Peter, Klotz, Martin G, Knight, Rob, Konstantinidis, Konstantinos T, Kyrpides, Nikos C, Mason, Christopher E, McHardy, Alice C, Meyer, Folker, Ouzounis, Christos A, Patrinos, Aristides AN, Podar, Mircea, Pollard, Katherine S, Ravel, Jacques, Muñoz, Alejandro Reyes, Roberts, Richard J, Rosselló-Móra, Ramon, Sansone, Susanna-Assunta, Schloss, Patrick D, Schriml, Lynn M, Setubal, João C, Sorek, Rotem, Stevens, Rick L, Tiedje, James M, Turjanski, Adrian, Tyson, Gene W, Ussery, David W, Weinstock, George M, White, Owen, Whitman, William B, and Xenarios, Ioannis

Subjects
Information and Computing Sciences, Law and Legal Studies, Library and Information Studies, Access to Information, Databases, Genetic, Genome, Human, Genomics, Humans, Information Dissemination, General Science & Technology
Abstract

Publication interests should not limit access to public data

Published
2019

15. Analysis of shared heritability in common disorders of the brain

Author

Consortium, The Brainstorm, Anttila, Verneri, Bulik-Sullivan, Brendan, Finucane, Hilary K, Walters, Raymond K, Bras, Jose, Duncan, Laramie, Escott-Price, Valentina, Falcone, Guido J, Gormley, Padhraig, Malik, Rainer, Patsopoulos, Nikolaos A, Ripke, Stephan, Wei, Zhi, Yu, Dongmei, Lee, Phil H, Turley, Patrick, Grenier-Boley, Benjamin, Chouraki, Vincent, Kamatani, Yoichiro, Berr, Claudine, Letenneur, Luc, Hannequin, Didier, Amouyel, Philippe, Boland, Anne, Deleuze, Jean-François, Duron, Emmanuelle, Vardarajan, Badri N, Reitz, Christiane, Goate, Alison M, Huentelman, Matthew J, Kamboh, M Ilyas, Larson, Eric B, Rogaeva, Ekaterina, St George-Hyslop, Peter, Hakonarson, Hakon, Kukull, Walter A, Farrer, Lindsay A, Barnes, Lisa L, Beach, Thomas G, Demirci, F Yesim, Head, Elizabeth, Hulette, Christine M, Jicha, Gregory A, Kauwe, John SK, Kaye, Jeffrey A, Leverenz, James B, Levey, Allan I, Lieberman, Andrew P, Pankratz, Vernon S, Poon, Wayne W, Quinn, Joseph F, Saykin, Andrew J, Schneider, Lon S, Smith, Amanda G, Sonnen, Joshua A, Stern, Robert A, Van Deerlin, Vivianna M, Van Eldik, Linda J, Harold, Denise, Russo, Giancarlo, Rubinsztein, David C, Bayer, Anthony, Tsolaki, Magda, Proitsi, Petra, Fox, Nick C, Hampel, Harald, Owen, Michael J, Mead, Simon, Passmore, Peter, Morgan, Kevin, Nöthen, Markus M, Schott, Jonathan M, Rossor, Martin, Lupton, Michelle K, Hoffmann, Per, Kornhuber, Johannes, Lawlor, Brian, McQuillin, Andrew, Al-Chalabi, Ammar, Bis, Joshua C, Ruiz, Agustin, Boada, Mercè, Seshadri, Sudha, Beiser, Alexa, Rice, Kenneth, van der Lee, Sven J, De Jager, Philip L, Geschwind, Daniel H, Riemenschneider, Matthias, Riedel-Heller, Steffi, Rotter, Jerome I, Ransmayr, Gerhard, Hyman, Bradley T, Cruchaga, Carlos, Alegret, Montserrat, Winsvold, Bendik, Palta, Priit, Farh, Kai-How, and Cuenca-Leon, Ester

Subjects
Biological Sciences, Genetics, Biological Psychology, Health Sciences, Psychology, Neurosciences, Clinical Research, Mental Health, Human Genome, Brain Disorders, Mental Illness, 2.1 Biological and endogenous factors, Neurological, Mental health, Brain Diseases, Genetic Variation, Genome-Wide Association Study, Humans, Mental Disorders, Phenotype, Quantitative Trait, Heritable, Risk Factors, Brainstorm Consortium, General Science & Technology
Abstract

Disorders of the brain can exhibit considerable epidemiological comorbidity and often share symptoms, provoking debate about their etiologic overlap. We quantified the genetic sharing of 25 brain disorders from genome-wide association studies of 265,218 patients and 784,643 control participants and assessed their relationship to 17 phenotypes from 1,191,588 individuals. Psychiatric disorders share common variant risk, whereas neurological disorders appear more distinct from one another and from the psychiatric disorders. We also identified significant sharing between disorders and a number of brain phenotypes, including cognitive measures. Further, we conducted simulations to explore how statistical power, diagnostic misclassification, and phenotypic heterogeneity affect genetic correlations. These results highlight the importance of common genetic variation as a risk factor for brain disorders and the value of heritability-based methods in understanding their etiology.

Published
2018

17. Elevated HLA-A expression impairs HIV control through inhibition of NKG2A-expressing cells

Author

Ramsuran, Veron, Naranbhai, Vivek, Horowitz, Amir, Qi, Ying, Martin, Maureen P, Yuki, Yuko, Gao, Xiaojiang, Walker-Sperling, Victoria, Del Prete, Gregory Q, Schneider, Douglas K, Lifson, Jeffrey D, Fellay, Jacques, Deeks, Steven G, Martin, Jeffrey N, Goedert, James J, Wolinsky, Steven M, Michael, Nelson L, Kirk, Gregory D, Buchbinder, Susan, Haas, David, Ndung’u, Thumbi, Goulder, Philip, Parham, Peter, Walker, Bruce D, Carlson, Jonathan M, and Carrington, Mary

Subjects
Medical Microbiology, Biomedical and Clinical Sciences, Immunology, Infectious Diseases, Sexually Transmitted Infections, Women's Health, HIV/AIDS, 2.1 Biological and endogenous factors, Inflammatory and immune system, Infection, Alleles, CD4 Lymphocyte Count, Cohort Studies, HIV, HIV Infections, HLA Antigens, Humans, Killer Cells, Natural, Ligands, NK Cell Lectin-Like Receptor Subfamily C, Protein Sorting Signals, Viremia, General Science & Technology
Abstract

The highly polymorphic human leukocyte antigen (HLA) locus encodes cell surface proteins that are critical for immunity. HLA-A expression levels vary in an allele-dependent manner, diversifying allele-specific effects beyond peptide-binding preference. Analysis of 9763 HIV-infected individuals from 21 cohorts shows that higher HLA-A levels confer poorer control of HIV. Elevated HLA-A expression provides enhanced levels of an HLA-A-derived signal peptide that specifically binds and determines expression levels of HLA-E, the ligand for the inhibitory NKG2A natural killer (NK) cell receptor. HLA-B haplotypes that favor NKG2A-mediated NK cell licensing (i.e., education) exacerbate the deleterious effect of high HLA-A on HIV control, consistent with NKG2A-mediated inhibition impairing NK cell clearance of HIV-infected targets. Therapeutic blockade of HLA-E:NKG2A interaction may yield benefit in HIV disease.

Published
2018

18. Ancient genomes show social and reproductive behavior of early Upper Paleolithic foragers

Author

Sikora, Martin, Seguin-Orlando, Andaine, Sousa, Vitor C, Albrechtsen, Anders, Korneliussen, Thorfinn, Ko, Amy, Rasmussen, Simon, Dupanloup, Isabelle, Nigst, Philip R, Bosch, Marjolein D, Renaud, Gabriel, Allentoft, Morten E, Margaryan, Ashot, Vasilyev, Sergey V, Veselovskaya, Elizaveta V, Borutskaya, Svetlana B, Deviese, Thibaut, Comeskey, Dan, Higham, Tom, Manica, Andrea, Foley, Robert, Meltzer, David J, Nielsen, Rasmus, Excoffier, Laurent, Mirazon Lahr, Marta, Orlando, Ludovic, and Willerslev, Eske

Subjects
Biological Sciences, Anthropology, Genetics, Human Society, DNA, Ancient, Genome, Human, History, Ancient, Humans, Population Density, Reproductive Behavior, Russia, Social Behavior, General Science & Technology
Abstract

Present-day hunter-gatherers (HGs) live in multilevel social groups essential to sustain a population structure characterized by limited levels of within-band relatedness and inbreeding. When these wider social networks evolved among HGs is unknown. To investigate whether the contemporary HG strategy was already present in the Upper Paleolithic, we used complete genome sequences from Sunghir, a site dated to ~34,000 years before the present, containing multiple anatomically modern human individuals. We show that individuals at Sunghir derive from a population of small effective size, with limited kinship and levels of inbreeding similar to HG populations. Our findings suggest that Upper Paleolithic social organization was similar to that of living HGs, with limited relatedness within residential groups embedded in a larger mating network.

Published
2017

19. Single-cell RNA-seq reveals new types of human blood dendritic cells, monocytes, and progenitors.

Author

Fletcher, James, Griesbeck, Morgane, Butler, Andrew, Zheng, Shiwei, Lazo, Suzan, Jardine, Laura, Dixon, David, Stephenson, Emily, Nilsson, Emil, Grundberg, Ida, McDonald, David, Filby, Andrew, Li, Weibo, De Jager, Philip, Rozenblatt-Rosen, Orit, Lane, Andrew, Haniffa, Muzlifah, Regev, Aviv, Hacohen, Nir, Villani, Alexandra-Chloé, Satija, Rahul, Reynolds, Gary, Sarkizova, Siranush, and Shekhar, Karthik

Subjects
Adult, Antigen Presentation, Classification, Dendritic Cells, Female, Gene Expression Profiling, Humans, Lymphocyte Activation, Male, Monitoring, Immunologic, Monocytes, Neoplasms, Sequence Analysis, RNA, Single-Cell Analysis, T-Lymphocytes, Transcriptome, Young Adult
Abstract

Dendritic cells (DCs) and monocytes play a central role in pathogen sensing, phagocytosis, and antigen presentation and consist of multiple specialized subtypes. However, their identities and interrelationships are not fully understood. Using unbiased single-cell RNA sequencing (RNA-seq) of ~2400 cells, we identified six human DCs and four monocyte subtypes in human blood. Our study reveals a new DC subset that shares properties with plasmacytoid DCs (pDCs) but potently activates T cells, thus redefining pDCs; a new subdivision within the CD1C+ subset of DCs; the relationship between blastic plasmacytoid DC neoplasia cells and healthy DCs; and circulating progenitor of conventional DCs (cDCs). Our revised taxonomy will enable more accurate functional and developmental analyses as well as immune monitoring in health and disease.

Published
2017

20. Single-cell RNA-seq reveals new types of human blood dendritic cells, monocytes, and progenitors

Author

Villani, Alexandra-Chloé, Satija, Rahul, Reynolds, Gary, Sarkizova, Siranush, Shekhar, Karthik, Fletcher, James, Griesbeck, Morgane, Butler, Andrew, Zheng, Shiwei, Lazo, Suzan, Jardine, Laura, Dixon, David, Stephenson, Emily, Nilsson, Emil, Grundberg, Ida, McDonald, David, Filby, Andrew, Li, Weibo, De Jager, Philip L, Rozenblatt-Rosen, Orit, Lane, Andrew A, Haniffa, Muzlifah, Regev, Aviv, and Hacohen, Nir

Subjects
Neurosciences, Stem Cell Research, Prevention, Vaccine Related, Clinical Research, Genetics, 1.1 Normal biological development and functioning, Underpinning research, Inflammatory and immune system, Good Health and Well Being, Adult, Antigen Presentation, Classification, Dendritic Cells, Female, Gene Expression Profiling, Humans, Lymphocyte Activation, Male, Monitoring, Immunologic, Monocytes, Neoplasms, Sequence Analysis, RNA, Single-Cell Analysis, T-Lymphocytes, Transcriptome, Young Adult, General Science & Technology
Abstract

Dendritic cells (DCs) and monocytes play a central role in pathogen sensing, phagocytosis, and antigen presentation and consist of multiple specialized subtypes. However, their identities and interrelationships are not fully understood. Using unbiased single-cell RNA sequencing (RNA-seq) of ~2400 cells, we identified six human DCs and four monocyte subtypes in human blood. Our study reveals a new DC subset that shares properties with plasmacytoid DCs (pDCs) but potently activates T cells, thus redefining pDCs; a new subdivision within the CD1C+ subset of DCs; the relationship between blastic plasmacytoid DC neoplasia cells and healthy DCs; and circulating progenitor of conventional DCs (cDCs). Our revised taxonomy will enable more accurate functional and developmental analyses as well as immune monitoring in health and disease.

Published
2017

22. Peru’s zoning amendment endangers forests

Author

Martel, Carlos, primary, Mendieta-Leiva, Glenda, additional, Alvarez-Loayza, Patricia C., additional, Cano, Asunción, additional, Cosio, Eric G., additional, Decock, Cony, additional, Farfan-Rios, William, additional, Feeley, Kenneth, additional, Honorio Coronado, Eurídice, additional, Huamantupa, Isau, additional, Ibañez, Alfredo J., additional, Koepcke de Diller, Juliane, additional, León, Blanca, additional, Linares-Palomino, Reynaldo, additional, Marcelo Peña, José L., additional, Millán, Betty, additional, Moat, Justin F., additional, Pennington, R. Toby, additional, Pitman, Nigel, additional, Salinas, Norma, additional, Rojas-VeraPinto, Roxana, additional, Stevenson, Philip C., additional, Tovar, Carolina, additional, Whaley, Oliver Q., additional, and Young, Kenneth R., additional

Published
2024
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23. MoS2 transistors with 1-nanometer gate lengths

Author

Desai, Sujay B, Madhvapathy, Surabhi R, Sachid, Angada B, Llinas, Juan Pablo, Wang, Qingxiao, Ahn, Geun Ho, Pitner, Gregory, Kim, Moon J, Bokor, Jeffrey, Hu, Chenming, Wong, H-S Philip, and Javey, Ali

Subjects
Physical Sciences, Engineering, Nanotechnology, Condensed Matter Physics, Bioengineering, MSD-General, MSD-EMAT, General Science & Technology
Abstract

Scaling of silicon (Si) transistors is predicted to fail below 5-nanometer (nm) gate lengths because of severe short channel effects. As an alternative to Si, certain layered semiconductors are attractive for their atomically uniform thickness down to a monolayer, lower dielectric constants, larger band gaps, and heavier carrier effective mass. Here, we demonstrate molybdenum disulfide (MoS2) transistors with a 1-nm physical gate length using a single-walled carbon nanotube as the gate electrode. These ultrashort devices exhibit excellent switching characteristics with near ideal subthreshold swing of ~65 millivolts per decade and an On/Off current ratio of ~106 Simulations show an effective channel length of ~3.9 nm in the Off state and ~1 nm in the On state.

Published
2016

24. Preprints for the life sciences

Author

Berg, Jeremy M, Bhalla, Needhi, Bourne, Philip E, Chalfie, Martin, Drubin, David G, Fraser, James S, Greider, Carol W, Hendricks, Michael, Jones, Chonnettia, Kiley, Robert, King, Susan, Kirschner, Marc W, Krumholz, Harlan M, Lehmann, Ruth, Leptin, Maria, Pulverer, Bernd, Rosenzweig, Brooke, Spiro, John E, Stebbins, Michael, Strasser, Carly, Swaminathan, Sowmya, Turner, Paul, Vale, Ronald D, VijayRaghavan, K, and Wolberger, Cynthia

Subjects
Philosophy and Religious Studies, History and Philosophy Of Specific Fields, Biological Science Disciplines, Information Dissemination, Publishing, General Science & Technology
Abstract

The time is right for biologists to post their research findings onto preprint servers

Published
2016

31. Spatial control of heavy-fermion superconductivity in CeIrIn₅

Author

Bachmann, Maja D., Ferguson, G. M., Theuss, Florian, Meng, Tobias, Putzke, Carsten, Helm, Toni, Shirer, K. R., Li, You-Sheng, Modic, K. A., Nicklas, Michael, König, Markus, Low, D., Ghosh, Sayak, Mackenzie, Andrew P., Arnold, Frank, Hassinger, Elena, McDonald, Ross D., Winter, Laurel E., Bauer, Eric D., Ronning, Filip, Ramshaw, B. J., Nowack, Katja C., and Moll, Philip J. W.

Published
2019

34. IRE1α–XBP1 signaling in leukocytes controls prostaglandin biosynthesis and pain

Author

Chopra, Sahil, Giovanelli, Paolo, Alvarado-Vazquez, Perla Abigail, Alonso, Sara, Song, Minkyung, Sandoval, Tito A., Chae, Chang-Suk, Tan, Chen, Fonseca, Miriam M., Gutierrez, Silvia, Jimenez, Leandro, Subbaramaiah, Kotha, Iwawaki, Takao, Kingsley, Philip J., Marnett, Lawrence J., Kossenkov, Andrew V., Crespo, Mariano Sanchez, Dannenberg, Andrew J., Glimcher, Laurie H., Romero-Sandoval, E. Alfonso, and Cubillos-Ruiz, Juan R.

Published
2019

36. Close-range remote sensing of Saturn’s rings during Cassini’s ring-grazing orbits and Grand Finale

Author

Tiscareno, Matthew S., Nicholson, Philip D., Cuzzi, Jeffrey N., Spilker, Linda J., Murray, Carl D., Hedman, Matthew M., Colwell, Joshua E., Burns, Joseph A., Brooks, Shawn M., Clark, Roger N., Cooper, Nicholas J., Deau, Estelle, Ferrari, Cecile, Filacchione, Gianrico, Jerousek, Richard G., Le Mouélic, Stéphane, Morishima, Ryuji, Pilorz, Stu, Rodriguez, Sébastien, Showalter, Mark R., Badman, Sarah V., Baker, Emily J., Buratti, Bonnie J., Baines, Kevin H., and Sotin, Christophe

Published
2019

37. RNA sequence analysis reveals macroscopic somatic clonal expansion across normal tissues

Author

Yizhak, Keren, Aguet, François, Kim, Jaegil, Hess, Julian M., Kübler, Kirsten, Grimsby, Jonna, Frazer, Ruslana, Zhang, Hailei, Haradhvala, Nicholas J., Rosebrock, Daniel, Livitz, Dimitri, Li, Xiao, Arich-Landkof, Eila, Shoresh, Noam, Stewart, Chip, Segrè, Ayellet V., Branton, Philip A., Polak, Paz, Ardlie, Kristin G., and Getz, Gad

Published
2019

38. Response

Author

Amann, Rudolf I., Baichoo, Shakuntala, Blencowe, Benjamin J., Bork, Peer, Borodovsky, Mark, Brooksbank, Cath, Chain, Patrick S. G., Colwell, Rita R., Daffonchio, Daniele G., Danchin, Antoine, de Lorenzo, Victor, Dorrestein, Pieter C., Finn, Robert D., Fraser, Claire M., Gilbert, Jack A., Hallam, Steven J., Hugenholtz, Philip, Ioannidis, John P. A., K. Jansson, Janet, Kim, Jihyun F., Klenk, Hans-Peter, Klotz, Martin G., Knight, Rob, Konstantinidis, Konstantinos T., Kyrpides, Nikos C., Mason, Christopher E., C. McHardy, Alice, Meyer, Folker, Ouzounis, Christos A., Patrinos, Aristides A. N., Podar, Mircea, Pollard, Katherine S., Ravel, Jacques, Muñoz, Alejandro Reyes, Roberts, Richard J., Rosselló-Móra, Ramon, Sansone, Susanna-Assunta, Schloss, Patrick D., Schriml, Lynn M., Setubal, João C., Sorek, Rotem, Stevens, Rick L., Tiedje, James M., Turjanski, Adrian, Tyson, Gene W., Ussery, David W., Weinstock, George M., White, Owen, Whitman, William B., and Xenarios, Ioannis

Published
2019

41. Epithelial endoplasmic reticulum stress orchestrates a protective IgA response

Author

Grootjans, Joep, Krupka, Niklas, Hosomi, Shuhei, Matute, Juan D., Hanley, Thomas, Saveljeva, Svetlana, Gensollen, Thomas, Heijmans, Jarom, Li, Hai, Limenitakis, Julien P., Ganal-Vonarburg, Stephanie C., Suo, Shengbao, Luoma, Adrienne M., Shimodaira, Yosuke, Duan, Jinzhi, Shih, David Q., Conner, Margaret E., Glickman, Jonathan N., Fuhler, Gwenny M., Palm, Noah W., de Zoete, Marcel R., van der Woude, C. Janneke, Yuan, Guo-Cheng, Wucherpfennig, Kai W., Targan, Stephan R., Rosenstiel, Philip, Flavell, Richard A., McCoy, Kathy D., Macpherson, Andrew J., Kaser, Arthur, and Blumberg, Richard S.

Published
2019

42. Atmospheric Waves and Global Seismoacoustic Observations of the January 2022 Hunga Eruption, Tonga

Author

Robin S Matoza, David Fee, Jelle D Assink, Alexandra M Iezzi, David N Green, Keehoon Kim, Liam Toney, Thomas Lecocq, Siddharth Krishnamoorthy, Jean-Marie Lalande, Kiwamu Nishida, Kent L Gee, Matthew M Haney, Hugo D Ortiz, Quentin Brissaud, Leo Martire, Lucie Rolland, Panagiotis Vergados, Alexandra Nippress, Junghyun Park, Shahar Shani-Kadmiel, Alex Witsil, Stephen Arrowsmith, Corentin Caudron, Shingo Watada, Anna B Perttu, Benoit Taisne, Pierrick Mialle, Alexis Le Pichon, Julien Vergoz, Patrick Hupe, Philip S Blom, Roger Waxler, Attila Komjathy, and Kathleen F McKee

Subjects
Acoustics, Meteorology and Climatology
Abstract

The 15 January 2022 climactic eruption of Hunga volcano, Tonga, produced an explosion in the atmosphere of a size that has not been documented in the modern geophysical record. The event generated a broad range of atmospheric waves observed globally by various ground-based and spaceborne instrumentation networks. Most prominent was the surface-guided Lamb wave (≲0.01 hertz), which we observed propagating for four (plus three antipodal) passages around Earth over 6 days. As measured by the Lamb wave amplitudes, the climactic Hunga explosion was comparable in size to that of the 1883 Krakatau eruption. The Hunga eruption produced remarkable globally detected infrasound (0.01 to 20 hertz), long-range (~10,000 kilometers) audible sound, and ionospheric perturbations. Seismometers worldwide recorded pure seismic and air-to-ground coupled waves. Air-to-sea coupling likely contributed to fast-arriving tsunamis. Here, we highlight exceptional observations of the atmospheric waves.

Published
2022
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43. Oxygen rise in the tropical upper ocean during the Paleocene-Eocene Thermal Maximum

Author

Moretti, Simone, primary, Auderset, Alexandra, additional, Deutsch, Curtis, additional, Schmitz, Ronja, additional, Gerber, Lukas, additional, Thomas, Ellen, additional, Luciani, Valeria, additional, Petrizzo, Maria Rose, additional, Schiebel, Ralf, additional, Tripati, Aradhna, additional, Sexton, Philip, additional, Norris, Richard, additional, D’Onofrio, Roberta, additional, Zachos, James, additional, Sigman, Daniel M., additional, Haug, Gerald H., additional, and Martínez-García, Alfredo, additional

Published
2024
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45. Genomic structure in Europeans dating back at least 36,200 years

Author

Seguin-Orlando, Andaine, Korneliussen, Thorfinn S, Sikora, Martin, Malaspinas, Anna-Sapfo, Manica, Andrea, Moltke, Ida, Albrechtsen, Anders, Ko, Amy, Margaryan, Ashot, Moiseyev, Vyacheslav, Goebel, Ted, Westaway, Michael, Lambert, David, Khartanovich, Valeri, Wall, Jeffrey D, Nigst, Philip R, Foley, Robert A, Lahr, Marta Mirazon, Nielsen, Rasmus, Orlando, Ludovic, and Willerslev, Eske

Subjects
Genetics, Human Genome, DNA, Europe, Fossils, Genome, Human, Genomics, History, Ancient, Humans, Male, Siberia, Whites, White People, General Science & Technology
Abstract

The origin of contemporary Europeans remains contentious. We obtained a genome sequence from Kostenki 14 in European Russia dating from 38,700 to 36,200 years ago, one of the oldest fossils of anatomically modern humans from Europe. We find that Kostenki 14 shares a close ancestry with the 24,000-year-old Mal'ta boy from central Siberia, European Mesolithic hunter-gatherers, some contemporary western Siberians, and many Europeans, but not eastern Asians. Additionally, the Kostenki 14 genome shows evidence of shared ancestry with a population basal to all Eurasians that also relates to later European Neolithic farmers. We find that Kostenki 14 contains more Neandertal DNA that is contained in longer tracts than present Europeans. Our findings reveal the timing of divergence of western Eurasians and East Asians to be more than 36,200 years ago and that European genomic structure today dates back to the Upper Paleolithic and derives from a metapopulation that at times stretched from Europe to central Asia.

Published
2014

46. Intersection of population variation and autoimmunity genetics in human T cell activation

Author

Ye, Chun Jimmie, Feng, Ting, Kwon, Ho-Keun, Raj, Towfique, Wilson, Michael T, Asinovski, Natasha, McCabe, Cristin, Lee, Michelle H, Frohlich, Irene, Paik, Hyun-il, Zaitlen, Noah, Hacohen, Nir, Stranger, Barbara, De Jager, Philip, Mathis, Diane, Regev, Aviv, and Benoist, Christophe

Subjects
Human Genome, Genetics, Clinical Research, Biotechnology, Autoimmune Disease, 2.1 Biological and endogenous factors, Aetiology, Inflammatory and immune system, Asians, Autoimmunity, Blacks, CD4-Positive T-Lymphocytes, Cytokines, Gene Expression Regulation, Genetic Variation, Genome-Wide Association Study, Humans, Lymphocyte Activation, Multigene Family, Quantitative Trait Loci, Th17 Cells, Whites, Asian People, White People, Black People, General Science & Technology
Abstract

T lymphocyte activation by antigen conditions adaptive immune responses and immunopathologies, but we know little about its variation in humans and its genetic or environmental roots. We analyzed gene expression in CD4(+) T cells during unbiased activation or in T helper 17 (T(H)17) conditions from 348 healthy participants representing European, Asian, and African ancestries. We observed interindividual variability, most marked for cytokine transcripts, with clear biases on the basis of ancestry, and following patterns more complex than simple T(H)1/2/17 partitions. We identified 39 genetic loci specifically associated in cis with activated gene expression. We further fine-mapped and validated a single-base variant that modulates YY1 binding and the activity of an enhancer element controlling the autoimmune-associated IL2RA gene, affecting its activity in activated but not regulatory T cells. Thus, interindividual variability affects the fundamental immunologic process of T helper activation, with important connections to autoimmune disease.

Published
2014

47. Polarization of the Effects of Autoimmune and Neurodegenerative Risk Alleles in Leukocytes

Author

Raj, Towfique, Rothamel, Katie, Mostafavi, Sara, Ye, Chun, Lee, Mark N, Replogle, Joseph M, Feng, Ting, Lee, Michelle, Asinovski, Natasha, Frohlich, Irene, Imboywa, Selina, Von Korff, Alina, Okada, Yukinori, Patsopoulos, Nikolaos A, Davis, Scott, McCabe, Cristin, Paik, Hyun-il, Srivastava, Gyan P, Raychaudhuri, Soumya, Hafler, David A, Koller, Daphne, Regev, Aviv, Hacohen, Nir, Mathis, Diane, Benoist, Christophe, Stranger, Barbara E, and De Jager, Philip L

Subjects
Aging, Neurodegenerative, Genetics, Dementia, Acquired Cognitive Impairment, Clinical Research, Brain Disorders, Human Genome, Prevention, Neurosciences, 2.1 Biological and endogenous factors, Aetiology, Inflammatory and immune system, Adaptive Immunity, Alleles, Alzheimer Disease, Autoimmune Diseases, Autoimmunity, CD4-Positive T-Lymphocytes, Ethnicity, Genetic Predisposition to Disease, Genome-Wide Association Study, Humans, Immunity, Innate, Monocytes, Multiple Sclerosis, Neurodegenerative Diseases, Parkinson Disease, Polymorphism, Single Nucleotide, Quantitative Trait Loci, Rheumatic Fever, Transcriptome, General Science & Technology
Abstract

To extend our understanding of the genetic basis of human immune function and dysfunction, we performed an expression quantitative trait locus (eQTL) study of purified CD4(+) T cells and monocytes, representing adaptive and innate immunity, in a multi-ethnic cohort of 461 healthy individuals. Context-specific cis- and trans-eQTLs were identified, and cross-population mapping allowed, in some cases, putative functional assignment of candidate causal regulatory variants for disease-associated loci. We note an over-representation of T cell-specific eQTLs among susceptibility alleles for autoimmune diseases and of monocyte-specific eQTLs among Alzheimer's and Parkinson's disease variants. This polarization implicates specific immune cell types in these diseases and points to the need to identify the cell-autonomous effects of disease susceptibility variants.

Published
2014

48. Common Genetic Variants Modulate Pathogen-Sensing Responses in Human Dendritic Cells

Author

Lee, Mark N, Ye, Chun, Villani, Alexandra-Chloé, Raj, Towfique, Li, Weibo, Eisenhaure, Thomas M, Imboywa, Selina H, Chipendo, Portia I, Ran, F Ann, Slowikowski, Kamil, Ward, Lucas D, Raddassi, Khadir, McCabe, Cristin, Lee, Michelle H, Frohlich, Irene Y, Hafler, David A, Kellis, Manolis, Raychaudhuri, Soumya, Zhang, Feng, Stranger, Barbara E, Benoist, Christophe O, De Jager, Philip L, Regev, Aviv, and Hacohen, Nir

Subjects
Infectious Diseases, Influenza, Genetics, Biodefense, Emerging Infectious Diseases, Vaccine Related, Prevention, Pneumonia & Influenza, Aetiology, 2.1 Biological and endogenous factors, Infection, Inflammatory and immune system, Adult, Autoimmune Diseases, Communicable Diseases, Dendritic Cells, Escherichia coli, Female, Gene-Environment Interaction, Genetic Loci, Genome-Wide Association Study, HEK293 Cells, Host-Pathogen Interactions, Humans, Influenza A virus, Interferon Regulatory Factor-7, Interferon-beta, Lipopolysaccharides, Male, Middle Aged, Polymorphism, Single Nucleotide, Quantitative Trait Loci, STAT Transcription Factors, Transcriptome, Young Adult, General Science & Technology
Abstract

Little is known about how human genetic variation affects the responses to environmental stimuli in the context of complex diseases. Experimental and computational approaches were applied to determine the effects of genetic variation on the induction of pathogen-responsive genes in human dendritic cells. We identified 121 common genetic variants associated in cis with variation in expression responses to Escherichia coli lipopolysaccharide, influenza, or interferon-β (IFN-β). We localized and validated causal variants to binding sites of pathogen-activated STAT (signal transducer and activator of transcription) and IRF (IFN-regulatory factor) transcription factors. We also identified a common variant in IRF7 that is associated in trans with type I IFN induction in response to influenza infection. Our results reveal common alleles that explain interindividual variation in pathogen sensing and provide functional annotation for genetic variants that alter susceptibility to inflammatory diseases.

Published
2014

50. Time-reversal symmetry breaking superconductivity between twisted cuprate superconductors

Author

Zhao, S. Y. Frank, primary, Cui, Xiaomeng, additional, Volkov, Pavel A., additional, Yoo, Hyobin, additional, Lee, Sangmin, additional, Gardener, Jules A., additional, Akey, Austin J., additional, Engelke, Rebecca, additional, Ronen, Yuval, additional, Zhong, Ruidan, additional, Gu, Genda, additional, Plugge, Stephan, additional, Tummuru, Tarun, additional, Kim, Miyoung, additional, Franz, Marcel, additional, Pixley, Jedediah H., additional, Poccia, Nicola, additional, and Kim, Philip, additional

Published
2023
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