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1. Autoantibodies against type I IFNs in humans with alternative NF-κB pathway deficiency.

Author: Yu, David, Miller, Corey, Feng, Yi, Guichard, Audrey, Béziat, Vivien, Bustamante, Jacinta, Pan-Hammarström, Qiang, Zhang, Yu, Rosen, Lindsey, Holland, Steve, Bosticardo, Marita, Kenney, Heather, Castagnoli, Riccardo, Slade, Charlotte, Boztuğ, Kaan, Mahlaoui, Nizar, Latour, Sylvain, Abraham, Roshini, Lougaris, Vassilios, Hauck, Fabian, Sediva, Anna, Atschekzei, Faranaz, Sogkas, Georgios, Poli, M, Slatter, Mary, Palterer, Boaz, Keller, Michael, Pinzon-Charry, Alberto, Sullivan, Anna, Droney, Luke, Suan, Daniel, Wong, Melanie, Kane, Alisa, Hu, Hannah, Ma, Cindy, Grombiříková, Hana, Ciznar, Peter, Dalal, Ilan, Aladjidi, Nathalie, Hie, Miguel, Lazaro, Estibaliz, Franco, Jose, Keles, Sevgi, Malphettes, Marion, Pasquet, Marlene, Maccari, Maria, Meinhardt, Andrea, Ikinciogullari, Aydan, Shahrooei, Mohammad, Celmeli, Fatih, Frosk, Patrick, Goodnow, Christopher, Gray, Paul, Belot, Alexandre, Kuehn, Hye, Rosenzweig, Sergio, Miyara, Makoto, Licciardi, Francesco, Servettaz, Amélie, Barlogis, Vincent, Le Guenno, Guillaume, Herrmann, Vera-Maria, Kuijpers, Taco, Ducoux, Grégoire, Sarrot-Reynauld, Françoise, Schuetz, Catharina, Cunningham-Rundles, Charlotte, Rieux-Laucat, Frédéric, Tangye, Stuart, Sobacchi, Cristina, Doffinger, Rainer, Warnatz, Klaus, Grimbacher, Bodo, Fieschi, Claire, Berteloot, Laureline, Bryant, Vanessa, Trouillet Assant, Sophie, Su, Helen, Neven, Benedicte, Abel, Laurent, Zhang, Qian, Boisson, Bertrand, Cobat, Aurélie, Jouanguy, Emmanuelle, Kampe, Olle, Bastard, Paul, Roifman, Chaim, Landegren, Nils, Notarangelo, Luigi, Le Voyer, Tom, Parent, Audrey, Liu, Xian, Cederholm, Axel, Gervais, Adrian, Rosain, Jérémie, Nguyen, Tina, Perez Lorenzo, Malena, Rackaityte, Elze, Rinchai, Darawan, and Zhang, Peng
Subjects: Humans, Autoantibodies, COVID-19, Gain of Function Mutation, Genetic Predisposition to Disease, Heterozygote, I-kappa B Proteins, Interferon Type I, Loss of Function Mutation, NF-kappa B, NF-kappa B p52 Subunit, Pneumonia, Viral, Thymus Gland, Thyroid Epithelial Cells
Abstract: Patients with autoimmune polyendocrinopathy syndrome type 1 (APS-1) caused by autosomal recessive AIRE deficiency produce autoantibodies that neutralize type I interferons (IFNs)1,2, conferring a predisposition to life-threatening COVID-19 pneumonia3. Here we report that patients with autosomal recessive NIK or RELB deficiency, or a specific type of autosomal-dominant NF-κB2 deficiency, also have neutralizing autoantibodies against type I IFNs and are at higher risk of getting life-threatening COVID-19 pneumonia. In patients with autosomal-dominant NF-κB2 deficiency, these autoantibodies are found only in individuals who are heterozygous for variants associated with both transcription (p52 activity) loss of function (LOF) due to impaired p100 processing to generate p52, and regulatory (IκBδ activity) gain of function (GOF) due to the accumulation of unprocessed p100, therefore increasing the inhibitory activity of IκBδ (hereafter, p52LOF/IκBδGOF). By contrast, neutralizing autoantibodies against type I IFNs are not found in individuals who are heterozygous for NFKB2 variants causing haploinsufficiency of p100 and p52 (hereafter, p52LOF/IκBδLOF) or gain-of-function of p52 (hereafter, p52GOF/IκBδLOF). In contrast to patients with APS-1, patients with disorders of NIK, RELB or NF-κB2 have very few tissue-specific autoantibodies. However, their thymuses have an abnormal structure, with few AIRE-expressing medullary thymic epithelial cells. Human inborn errors of the alternative NF-κB pathway impair the development of AIRE-expressing medullary thymic epithelial cells, thereby underlying the production of autoantibodies against type I IFNs and predisposition to viral diseases.
Published: 2023

2. Non-viral precision T cell receptor replacement for personalized cell therapy

Author: Foy, Susan P, Jacoby, Kyle, Bota, Daniela A, Hunter, Theresa, Pan, Zheng, Stawiski, Eric, Ma, Yan, Lu, William, Peng, Songming, Wang, Clifford L, Yuen, Benjamin, Dalmas, Olivier, Heeringa, Katharine, Sennino, Barbara, Conroy, Andy, Bethune, Michael T, Mende, Ines, White, William, Kukreja, Monica, Gunturu, Swetha, Humphrey, Emily, Hussaini, Adeel, An, Duo, Litterman, Adam J, Quach, Boi Bryant, Ng, Alphonsus HC, Lu, Yue, Smith, Chad, Campbell, Katie M, Anaya, Daniel, Skrdlant, Lindsey, Huang, Eva Yi-Hsuan, Mendoza, Ventura, Mathur, Jyoti, Dengler, Luke, Purandare, Bhamini, Moot, Robert, Yi, Michael C, Funke, Roel, Sibley, Alison, Stallings-Schmitt, Todd, Oh, David Y, Chmielowski, Bartosz, Abedi, Mehrdad, Yuan, Yuan, Sosman, Jeffrey A, Lee, Sylvia M, Schoenfeld, Adam J, Baltimore, David, Heath, James R, Franzusoff, Alex, Ribas, Antoni, Rao, Arati V, and Mandl, Stefanie J
Subjects: Biomedical and Clinical Sciences, Oncology and Carcinogenesis, Immunology, Gene Therapy, Genetics, Cancer Genomics, Clinical Research, Human Genome, Clinical Trials and Supportive Activities, Immunotherapy, Cancer, Health Disparities, Precision Medicine, Biotechnology, Minority Health, Gene Therapy Clinical Trials, Rare Diseases, 5.2 Cellular and gene therapies, 2.1 Biological and endogenous factors, Inflammatory and immune system, Good Health and Well Being, Humans, Antigens, Neoplasm, Biopsy, Cell- and Tissue-Based Therapy, Cytokine Release Syndrome, Disease Progression, Encephalitis, Gene Editing, Gene Knock-In Techniques, Gene Knockout Techniques, Genes, T-Cell Receptor alpha, Genes, T-Cell Receptor beta, Mutation, Neoplasms, Patient Safety, Receptors, Antigen, T-Cell, T-Lymphocytes, Transgenes, HLA Antigens, CRISPR-Cas Systems, General Science & Technology
Abstract: T cell receptors (TCRs) enable T cells to specifically recognize mutations in cancer cells1-3. Here we developed a clinical-grade approach based on CRISPR-Cas9 non-viral precision genome-editing to simultaneously knockout the two endogenous TCR genes TRAC (which encodes TCRα) and TRBC (which encodes TCRβ). We also inserted into the TRAC locus two chains of a neoantigen-specific TCR (neoTCR) isolated from circulating T cells of patients. The neoTCRs were isolated using a personalized library of soluble predicted neoantigen-HLA capture reagents. Sixteen patients with different refractory solid cancers received up to three distinct neoTCR transgenic cell products. Each product expressed a patient-specific neoTCR and was administered in a cell-dose-escalation, first-in-human phase I clinical trial ( NCT03970382 ). One patient had grade 1 cytokine release syndrome and one patient had grade 3 encephalitis. All participants had the expected side effects from the lymphodepleting chemotherapy. Five patients had stable disease and the other eleven had disease progression as the best response on the therapy. neoTCR transgenic T cells were detected in tumour biopsy samples after infusion at frequencies higher than the native TCRs before infusion. This study demonstrates the feasibility of isolating and cloning multiple TCRs that recognize mutational neoantigens. Moreover, simultaneous knockout of the endogenous TCR and knock-in of neoTCRs using single-step, non-viral precision genome-editing are achieved. The manufacture of neoTCR engineered T cells at clinical grade, the safety of infusing up to three gene-edited neoTCR T cell products and the ability of the transgenic T cells to traffic to the tumours of patients are also demonstrated.
Published: 2023

3. Early Release Science of the exoplanet WASP-39b with JWST NIRCam.

Author: Ahrer, Eva-Maria, Stevenson, Kevin, Mansfield, Megan, Moran, Sarah, Brande, Jonathan, Morello, Giuseppe, Murray, Catriona, Nikolov, Nikolay, Petit Dit de la Roche, Dominique, Schlawin, Everett, Wheatley, Peter, Zieba, Sebastian, Batalha, Natasha, Damiano, Mario, Goyal, Jayesh, Lendl, Monika, Lothringer, Joshua, Mukherjee, Sagnick, Ohno, Kazumasa, Batalha, Natalie, Battley, Matthew, Bean, Jacob, Beatty, Thomas, Benneke, Björn, Berta-Thompson, Zachory, Carter, Aarynn, Cubillos, Patricio, Daylan, Tansu, Espinoza, Néstor, Gao, Peter, Gibson, Neale, Gill, Samuel, Harrington, Joseph, Hu, Renyu, Kreidberg, Laura, Lewis, Nikole, Line, Michael, López-Morales, Mercedes, Parmentier, Vivien, Powell, Diana, Sing, David, Wakeford, Hannah, Welbanks, Luis, Alam, Munazza, Alderson, Lili, Allen, Natalie, Anderson, David, Barstow, Joanna, Bayliss, Daniel, Bell, Taylor, Blecic, Jasmina, Bryant, Edward, Burleigh, Matthew, Carone, Ludmila, Casewell, S, Changeat, Quentin, Chubb, Katy, Crossfield, Ian, Crouzet, Nicolas, Decin, Leen, Désert, Jean-Michel, Feinstein, Adina, Flagg, Laura, Fortney, Jonathan, Gizis, John, Heng, Kevin, Iro, Nicolas, Kempton, Eliza, Kendrew, Sarah, Kirk, James, Knutson, Heather, Komacek, Thaddeus, Lagage, Pierre-Olivier, Leconte, Jérémy, Lustig-Yaeger, Jacob, MacDonald, Ryan, Mancini, Luigi, May, E, Mayne, N, Miguel, Yamila, Mikal-Evans, Thomas, Molaverdikhani, Karan, Palle, Enric, Piaulet, Caroline, Rackham, Benjamin, Redfield, Seth, Rogers, Laura, Roy, Pierre-Alexis, Rustamkulov, Zafar, Shkolnik, Evgenya, Sotzen, Kristin, Taylor, Jake, Tremblin, P, Tucker, Gregory, Turner, Jake, de Val-Borro, Miguel, Venot, Olivia, Zhang, Xi, and Tsai, Shang-Min
Abstract: Measuring the metallicity and carbon-to-oxygen (C/O) ratio in exoplanet atmospheres is a fundamental step towards constraining the dominant chemical processes at work and, if in equilibrium, revealing planet formation histories. Transmission spectroscopy (for example, refs. 1,2) provides the necessary means by constraining the abundances of oxygen- and carbon-bearing species; however, this requires broad wavelength coverage, moderate spectral resolution and high precision, which, together, are not achievable with previous observatories. Now that JWST has commenced science operations, we are able to observe exoplanets at previously uncharted wavelengths and spectral resolutions. Here we report time-series observations of the transiting exoplanet WASP-39b using JWSTs Near InfraRed Camera (NIRCam). The long-wavelength spectroscopic and short-wavelength photometric light curves span 2.0-4.0 micrometres, exhibit minimal systematics and reveal well defined molecular absorption features in the planets spectrum. Specifically, we detect gaseous water in the atmosphere and place an upper limit on the abundance of methane. The otherwise prominent carbon dioxide feature at 2.8 micrometres is largely masked by water. The best-fit chemical equilibrium models favour an atmospheric metallicity of 1-100-times solar (that is, an enrichment of elements heavier than helium relative to the Sun) and a substellar C/O ratio. The inferred high metallicity and low C/O ratio may indicate significant accretion of solid materials during planet formation (for example, refs. 3,4,) or disequilibrium processes in the upper atmosphere (for example, refs. 5,6).
Published: 2023

4. K2P2.1 (TREK-1)–activator complexes reveal a cryptic selectivity filter binding site

Author: Lolicato, Marco, Arrigoni, Cristina, Mori, Takahiro, Sekioka, Yoko, Bryant, Clifford, Clark, Kimberly A, and Minor, Daniel L
Subjects: Inorganic Chemistry, Chemical Sciences, Generic health relevance, Animals, Arachidonic Acid, Benzamides, Binding Sites, HEK293 Cells, Humans, Ion Channel Gating, Lipids, Mice, Models, Molecular, Pichia, Potassium Channels, Tandem Pore Domain, Protein Conformation, Sulfonamides, Thiophenes, Xenopus laevis, General Science & Technology
Abstract: Polymodal thermo- and mechanosensitive two-pore domain potassium (K2P) channels of the TREK subfamily generate 'leak' currents that regulate neuronal excitability, respond to lipids, temperature and mechanical stretch, and influence pain, temperature perception and anaesthetic responses. These dimeric voltage-gated ion channel (VGIC) superfamily members have a unique topology comprising two pore-forming regions per subunit. In contrast to other potassium channels, K2P channels use a selectivity filter 'C-type' gate as the principal gating site. Despite recent advances, poor pharmacological profiles of K2P channels limit mechanistic and biological studies. Here we describe a class of small-molecule TREK activators that directly stimulate the C-type gate by acting as molecular wedges that restrict interdomain interface movement behind the selectivity filter. Structures of K2P2.1 (also known as TREK-1) alone and with two selective K2P2.1 (TREK-1) and K2P10.1 (TREK-2) activators-an N-aryl-sulfonamide, ML335, and a thiophene-carboxamide, ML402-define a cryptic binding pocket unlike other ion channel small-molecule binding sites and, together with functional studies, identify a cation-π interaction that controls selectivity. Together, our data reveal a druggable K2P site that stabilizes the C-type gate 'leak mode' and provide direct evidence for K2P selectivity filter gating.
Published: 2017

5. Harnessing landrace diversity empowers wheat breeding.

Author: Cheng, Shifeng, Feng, Cong, Wingen, Luzie U., Cheng, Hong, Riche, Andrew B., Jiang, Mei, Leverington-Waite, Michelle, Huang, Zejian, Collier, Sarah, Orford, Simon, Wang, Xiaoming, Awal, Rajani, Barker, Gary, O’Hara, Tom, Lister, Clare, Siluveru, Ajay, Quiroz-Chávez, Jesús, Ramírez-González, Ricardo H., Bryant, Ruth, and Berry, Simon
Abstract: Harnessing genetic diversity in major staple crops through the development of new breeding capabilities is essential to ensure food security1. Here we examined the genetic and phenotypic diversity of the A. E. Watkins landrace collection2 of bread wheat (Triticum aestivum), a major global cereal, by whole-genome re-sequencing of 827 Watkins landraces and 208 modern cultivars and in-depth field evaluation spanning a decade. We found that modern cultivars are derived from two of the seven ancestral groups of wheat and maintain very long-range haplotype integrity. The remaining five groups represent untapped genetic sources, providing access to landrace-specific alleles and haplotypes for breeding. Linkage disequilibrium-based haplotypes and association genetics analyses link Watkins genomes to the thousands of identified high-resolution quantitative trait loci and significant marker–trait associations. Using these structured germplasm, genotyping and informatics resources, we revealed many Watkins-unique beneficial haplotypes that can confer superior traits in modern wheat. Furthermore, we assessed the phenotypic effects of 44,338 Watkins-unique haplotypes, introgressed from 143 prioritized quantitative trait loci in the context of modern cultivars, bridging the gap between landrace diversity and current breeding. This study establishes a framework for systematically utilizing genetic diversity in crop improvement to achieve sustainable food security.Genomic and phenomic screens of 827 wheat landraces from the A. E. Watkins collection provide insight into the wheat population genetic background, unlocking many agronomic traits and revealing haplotypes that could potentially be used to improve modern wheat cultivars. [ABSTRACT FROM AUTHOR]
Published: 2024
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6. Identification of plant transcriptional activation domains.

Author: Morffy, Nicholas, Van den Broeck, Lisa, Miller, Caelan, Emenecker, Ryan J., Bryant Jr., John A., Lee, Tyler M., Sageman-Furnas, Katelyn, Wilkinson, Edward G., Pathak, Sunita, Kotha, Sanjana R., Lam, Angelica, Mahatma, Saloni, Pande, Vikram, Waoo, Aman, Wright, R. Clay, Holehouse, Alex S., Staller, Max V., Sozzani, Rosangela, and Strader, Lucia C.
Abstract: Gene expression in Arabidopsis is regulated by more than 1,900 transcription factors (TFs), which have been identified genome-wide by the presence of well-conserved DNA-binding domains. Activator TFs contain activation domains (ADs) that recruit coactivator complexes; however, for nearly all Arabidopsis TFs, we lack knowledge about the presence, location and transcriptional strength of their ADs1. To address this gap, here we use a yeast library approach to experimentally identify Arabidopsis ADs on a proteome-wide scale, and find that more than half of the Arabidopsis TFs contain an AD. We annotate 1,553 ADs, the vast majority of which are, to our knowledge, previously unknown. Using the dataset generated, we develop a neural network to accurately predict ADs and to identify sequence features that are necessary to recruit coactivator complexes. We uncover six distinct combinations of sequence features that result in activation activity, providing a framework to interrogate the subfunctionalization of ADs. Furthermore, we identify ADs in the ancient AUXIN RESPONSE FACTOR family of TFs, revealing that AD positioning is conserved in distinct clades. Our findings provide a deep resource for understanding transcriptional activation, a framework for examining function in intrinsically disordered regions and a predictive model of ADs.A high-throughput yeast-based assay is used to identify more than 1,500 activation domains (ADs) in Arabidopsis transcription factors, and a deep learning approach applied to this dataset can predict AD activity on the basis of sequence features. [ABSTRACT FROM AUTHOR]
Published: 2024
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7. Structures, functions and adaptations of the human LINE-1 ORF2 protein

Author: Baldwin, Eric T., primary, van Eeuwen, Trevor, additional, Hoyos, David, additional, Zalevsky, Arthur, additional, Tchesnokov, Egor P., additional, Sánchez, Roberto, additional, Miller, Bryant D., additional, Di Stefano, Luciano H., additional, Ruiz, Francesc Xavier, additional, Hancock, Matthew, additional, Işik, Esin, additional, Mendez-Dorantes, Carlos, additional, Walpole, Thomas, additional, Nichols, Charles, additional, Wan, Paul, additional, Riento, Kirsi, additional, Halls-Kass, Rowan, additional, Augustin, Martin, additional, Lammens, Alfred, additional, Jestel, Anja, additional, Upla, Paula, additional, Xibinaku, Kera, additional, Congreve, Samantha, additional, Hennink, Maximiliaan, additional, Rogala, Kacper B., additional, Schneider, Anna M., additional, Fairman, Jennifer E., additional, Christensen, Shawn M., additional, Desrosiers, Brian, additional, Bisacchi, Gregory S., additional, Saunders, Oliver L., additional, Hafeez, Nafeeza, additional, Miao, Wenyan, additional, Kapeller, Rosana, additional, Zaller, Dennis M., additional, Sali, Andrej, additional, Weichenrieder, Oliver, additional, Burns, Kathleen H., additional, Götte, Matthias, additional, Rout, Michael P., additional, Arnold, Eddy, additional, Greenbaum, Benjamin D., additional, Romero, Donna L., additional, LaCava, John, additional, and Taylor, Martin S., additional
Published: 2023
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8. A resonant sextuplet of sub-Neptunes transiting the bright star HD 110067

Author: Luque, R., primary, Osborn, H. P., additional, Leleu, A., additional, Pallé, E., additional, Bonfanti, A., additional, Barragán, O., additional, Wilson, T. G., additional, Broeg, C., additional, Cameron, A. Collier, additional, Lendl, M., additional, Maxted, P. F. L., additional, Alibert, Y., additional, Gandolfi, D., additional, Delisle, J.-B., additional, Hooton, M. J., additional, Egger, J. A., additional, Nowak, G., additional, Lafarga, M., additional, Rapetti, D., additional, Twicken, J. D., additional, Morales, J. C., additional, Carleo, I., additional, Orell-Miquel, J., additional, Adibekyan, V., additional, Alonso, R., additional, Alqasim, A., additional, Amado, P. J., additional, Anderson, D. R., additional, Anglada-Escudé, G., additional, Bandy, T., additional, Bárczy, T., additional, Barrado Navascues, D., additional, Barros, S. C. C., additional, Baumjohann, W., additional, Bayliss, D., additional, Bean, J. L., additional, Beck, M., additional, Beck, T., additional, Benz, W., additional, Billot, N., additional, Bonfils, X., additional, Borsato, L., additional, Boyle, A. W., additional, Brandeker, A., additional, Bryant, E. M., additional, Cabrera, J., additional, Carrazco-Gaxiola, S., additional, Charbonneau, D., additional, Charnoz, S., additional, Ciardi, D. R., additional, Cochran, W. D., additional, Collins, K. A., additional, Crossfield, I. J. M., additional, Csizmadia, Sz., additional, Cubillos, P. E., additional, Dai, F., additional, Davies, M. B., additional, Deeg, H. J., additional, Deleuil, M., additional, Deline, A., additional, Delrez, L., additional, Demangeon, O. D. S., additional, Demory, B.-O., additional, Ehrenreich, D., additional, Erikson, A., additional, Esparza-Borges, E., additional, Falk, B., additional, Fortier, A., additional, Fossati, L., additional, Fridlund, M., additional, Fukui, A., additional, Garcia-Mejia, J., additional, Gill, S., additional, Gillon, M., additional, Goffo, E., additional, Gómez Maqueo Chew, Y., additional, Güdel, M., additional, Guenther, E. W., additional, Günther, M. N., additional, Hatzes, A. P., additional, Helling, Ch., additional, Hesse, K. M., additional, Howell, S. B., additional, Hoyer, S., additional, Ikuta, K., additional, Isaak, K. G., additional, Jenkins, J. M., additional, Kagetani, T., additional, Kiss, L. L., additional, Kodama, T., additional, Korth, J., additional, Lam, K. W. F., additional, Laskar, J., additional, Latham, D. W., additional, Lecavelier des Etangs, A., additional, Leon, J. P. D., additional, Livingston, J. H., additional, Magrin, D., additional, Matson, R. A., additional, Matthews, E. C., additional, Mordasini, C., additional, Mori, M., additional, Moyano, M., additional, Munari, M., additional, Murgas, F., additional, Narita, N., additional, Nascimbeni, V., additional, Olofsson, G., additional, Osborne, H. L. M., additional, Ottensamer, R., additional, Pagano, I., additional, Parviainen, H., additional, Peter, G., additional, Piotto, G., additional, Pollacco, D., additional, Queloz, D., additional, Quinn, S. N., additional, Quirrenbach, A., additional, Ragazzoni, R., additional, Rando, N., additional, Ratti, F., additional, Rauer, H., additional, Redfield, S., additional, Ribas, I., additional, Ricker, G. R., additional, Rudat, A., additional, Sabin, L., additional, Salmon, S., additional, Santos, N. C., additional, Scandariato, G., additional, Schanche, N., additional, Schlieder, J. E., additional, Seager, S., additional, Ségransan, D., additional, Shporer, A., additional, Simon, A. E., additional, Smith, A. M. S., additional, Sousa, S. G., additional, Stalport, M., additional, Szabó, Gy. M., additional, Thomas, N., additional, Tuson, A., additional, Udry, S., additional, Vanderburg, A. M., additional, Van Eylen, V., additional, Van Grootel, V., additional, Venturini, J., additional, Walter, I., additional, Walton, N. A., additional, Watanabe, N., additional, Winn, J. N., additional, and Zingales, T., additional
Published: 2023
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9. Structural basis for alternating access of a eukaryotic calcium/proton exchanger

Author: Waight, Andrew B, Pedersen, Bjørn Panyella, Schlessinger, Avner, Bonomi, Massimiliano, Chau, Bryant H, Roe-Zurz, Zygy, Risenmay, Aaron J, Sali, Andrej, and Stroud, Robert M
Subjects: Biochemistry and Cell Biology, Biological Sciences, Underpinning research, 1.1 Normal biological development and functioning, Generic health relevance, Amino Acid Sequence, Antiporters, Binding Sites, Calcium, Crystallography, X-Ray, Cytosol, Ion Transport, Methanococcus, Models, Molecular, Molecular Sequence Data, Protein Conformation, Protein Folding, Protons, Saccharomyces cerevisiae, Saccharomyces cerevisiae Proteins, Structure-Activity Relationship, General Science & Technology
Abstract: Eukaryotic Ca(2+) regulation involves sequestration into intracellular organelles, and expeditious Ca(2+) release into the cytosol is a hallmark of key signalling transduction pathways. Bulk removal of Ca(2+) after such signalling events is accomplished by members of the Ca(2+):cation (CaCA) superfamily. The CaCA superfamily includes the Na(+)/Ca(2+) (NCX) and Ca(2+)/H(+) (CAX) antiporters, and in mammals the NCX and related proteins constitute families SLC8 and SLC24, and are responsible for the re-establishment of Ca(2+) resting potential in muscle cells, neuronal signalling and Ca(2+) reabsorption in the kidney. The CAX family members maintain cytosolic Ca(2+) homeostasis in plants and fungi during steep rises in intracellular Ca(2+) due to environmental changes, or following signal transduction caused by events such as hyperosmotic shock, hormone response and response to mating pheromones. The cytosol-facing conformations within the CaCA superfamily are unknown, and the transport mechanism remains speculative. Here we determine a crystal structure of the Saccharomyces cerevisiae vacuolar Ca(2+)/H(+) exchanger (Vcx1) at 2.3 Å resolution in a cytosol-facing, substrate-bound conformation. Vcx1 is the first structure, to our knowledge, within the CAX family, and it describes the key cytosol-facing conformation of the CaCA superfamily, providing the structural basis for a novel alternating access mechanism by which the CaCA superfamily performs high-throughput Ca(2+) transport across membranes.
Published: 2013

10. Crystal structure of a eukaryotic phosphate transporter

Author: Pedersen, Bjørn P, Kumar, Hemant, Waight, Andrew B, Risenmay, Aaron J, Roe-Zurz, Zygy, Chau, Bryant H, Schlessinger, Avner, Bonomi, Massimiliano, Harries, William, Sali, Andrej, Johri, Atul K, and Stroud, Robert M
Subjects: Biochemistry and Cell Biology, Biological Sciences, Generic health relevance, Basidiomycota, Binding Sites, Crystallography, X-Ray, Eukaryotic Cells, Humans, Models, Biological, Models, Molecular, Phosphate Transport Proteins, Phosphates, Protein Conformation, Protons, Structure-Activity Relationship, General Science & Technology
Abstract: Phosphate is crucial for structural and metabolic needs, including nucleotide and lipid synthesis, signalling and chemical energy storage. Proton-coupled transporters of the major facilitator superfamily (MFS) are essential for phosphate uptake in plants and fungi, and also have a function in sensing external phosphate levels as transceptors. Here we report the 2.9 Å structure of a fungal (Piriformospora indica) high-affinity phosphate transporter, PiPT, in an inward-facing occluded state, with bound phosphate visible in the membrane-buried binding site. The structure indicates both proton and phosphate exit pathways and suggests a modified asymmetrical 'rocker-switch' mechanism of phosphate transport. PiPT is related to several human transporter families, most notably the organic cation and anion transporters of the solute carrier family (SLC22), which are implicated in cancer-drug resistance. We modelled representative cation and anion SLC22 transporters based on the PiPT structure to surmise the structural basis for substrate binding and charge selectivity in this important family. The PiPT structure demonstrates and expands on principles of substrate transport by the MFS transporters and illuminates principles of phosphate uptake in particular.
Published: 2013

11. A first update on mapping the human genetic architecture of COVID-19

Author: COVID-19 Host Genetics Initiative, Pathak, GA, Karjalainen, J, Stevens, C, Neale, BM, Daly, M, Ganna, A, Andrews, SJ, Kanai, M, Cordioli, M, Polimanti, R, Harerimana, N, Pirinen, M, Liao, RG, Chwialkowska, K, Trankiem, A, Balaconis, MK, Nguyen, H, Solomonson, M, Veerapen, K, Wolford, B, Roberts, G, Park, D, Ball, CA, Coignet, M, McCurdy, S, Knight, S, Partha, R, Rhead, B, Zhang, M, Berkowitz, N, Gaddis, M, Noto, K, Ruiz, L, Pavlovic, M, Hong, EL, Rand, K, Girshick, A, Guturu, H, Baltzell, AH, Niemi, MEK, Rahmouni, S, Guntz, J, Beguin, Y, Pigazzini, S, Nkambule, L, Georges, M, Moutschen, M, Misset, B, Darcis, G, Guiot, J, Azarzar, S, Gofflot, S, Claassen, S, Malaise, O, Huynen, P, Meuris, C, Thys, M, Jacques, J, Leonard, P, Frippiat, F, Giot, J-B, Sauvage, A-S, Frenckell, CV, Belhaj, Y, Lambermont, B, Nakanishi, T, Morrison, DR, Mooser, V, Richards, JB, Butler-Laporte, G, Forgetta, V, Li, R, Ghosh, B, Laurent, L, Belisle, A, Henry, D, Abdullah, T, Adeleye, O, Mamlouk, N, Kimchi, N, Afrasiabi, Z, Rezk, N, Vulesevic, B, Bouab, M, Guzman, C, Petitjean, L, Tselios, C, Xue, X, Afilalo, J, Afilalo, M, Oliveira, M, Brenner, B, Brassard, N, Durand, M, Schurr, E, Lepage, P, Ragoussis, J, Auld, D, Chassé, M, Kaufmann, DE, Lathrop, GM, Adra, D, Hayward, C, Glessner, JT, Shaw, DM, Campbell, A, Morris, M, Hakonarson, H, Porteous, DJ, Below, J, Richmond, A, Chang, X, Polikowski, H, Lauren, PE, Chen, H-H, Wanying, Z, Fawns-Ritchie, C, North, K, McCormick, JB, Glessner, JR, Gignoux, CR, Wicks, SJ, Crooks, K, Barnes, KC, Daya, M, Shortt, J, Rafaels, N, Chavan, S, Timmers, PRHJ, Wilson, JF, Tenesa, A, Kerr, SM, D’Mellow, K, Shahin, D, El-Sherbiny, YM, von Hohenstaufen, KA, Sobh, A, Eltoukhy, MM, Nkambul, L, Elhadidy, TA, Abd Elghafar, MS, El-Jawhari, JJ, Mohamed, AAS, Elnagdy, MH, Samir, A, Abdel-Aziz, M, Khafaga, WT, El-Lawaty, WM, Torky, MS, El-shanshory, MR, Yassen, AM, Hegazy, MAF, Okasha, K, Eid, MA, Moahmed, HS, Medina-Gomez, C, Ikram, MA, Uitterlinden, AG, Mägi, R, Milani, L, Metspalu, A, Laisk, T, Läll, K, Lepamets, M, Esko, T, Reimann, E, Naaber, P, Laane, E, Pesukova, J, Peterson, P, Kisand, K, Tabri, J, Allos, R, Hensen, K, Starkopf, J, Ringmets, I, Tamm, A, Kallaste, A, Alavere, H, Metsalu, K, Puusepp, M, Batini, C, Tobin, MD, Venn, LD, Lee, PH, Shrine, N, Williams, AT, Guyatt, AL, John, C, Packer, RJ, Ali, A, Free, RC, Wang, X, Wain, LV, Hollox, EJ, Bee, CE, Adams, EL, Palotie, A, Ripatti, S, Ruotsalainen, S, Kristiansson, K, Koskelainen, S, Perola, M, Donner, K, Kivinen, K, Kaunisto, M, Rivolta, C, Bochud, P-Y, Bibert, S, Boillat, N, Nussle, SG, Albrich, W, Quinodoz, M, Kamdar, D, Suh, N, Neofytos, D, Erard, V, Voide, C, Friolet, R, Vollenweider, P, Pagani, JL, Oddo, M, zu Bentrup, FM, Conen, A, Clerc, O, Marchetti, O, Guillet, A, Guyat-Jacques, C, Foucras, S, Rime, M, Chassot, J, Jaquet, M, Viollet, RM, Lannepoudenx, Y, Portopena, L, Bochud, PY, Desgranges, F, Filippidis, P, Guéry, B, Haefliger, D, Kampouri, EE, Manuel, O, Munting, A, Papadimitriou-Olivgeris, M, Regina, J, Rochat-Stettler, L, Suttels, V, Tadini, E, Tschopp, J, Van Singer, M, Viala, B, Boillat-Blanco, N, Brahier, T, Hügli, O, Meuwly, JY, Pantet, O, Gonseth Nussle, S, Bochud, M, D’Acremont, V, Estoppey Younes, S, Albrich, WC, Cerny, A, O’Mahony, L, von Mering, C, Frischknecht, M, Kleger, G-R., Filipovic, M, Kahlert, CR, Wozniak, H, Negro, TR, Pugin, J, Bouras, K, Knapp, C, Egger, T, Perret, A, Montillier, P, di Bartolomeo, C, Barda, B, de Cid, R, Carreras, A, Moreno, V, Kogevinas, M, Galván-Femenía, I, Blay, N, Farré, X, Sumoy, L, Cortés, B, Mercader, JM, Guindo-Martinez, M, Torrents, D, Garcia-Aymerich, J, Castaño-Vinyals, G, Dobaño, C, Gori, M, Renieri, A, Mari, F, Mondelli, MU, Castelli, F, Vaghi, M, Rusconi, S, Montagnani, F, Bargagli, E, Franchi, F, Mazzei, MA, Cantarini, L, Tacconi, D, Feri, M, Scala, R, Spargi, G, Nencioni, C, Bandini, M, Caldarelli, GP, Canaccini, A, Ognibene, A, D’Arminio Monforte, A, Girardis, M, Antinori, A, Francisci, D, Schiaroli, E, Scotton, PG, Panese, S, Scaggiante, R, Monica, MD, Capasso, M, Fiorentino, G, Castori, M, Aucella, F, Biagio, AD, Masucci, L, Valente, S, Mandalà, M, Zucchi, P, Giannattasio, F, Coviello, DA, Mussini, C, Tavecchia, L, Crotti, L, Rizzi, M, Rovere, MTL, Sarzi-Braga, S, Bussotti, M, Ravaglia, S, Artuso, R, Perrella, A, Romani, D, Bergomi, P, Catena, E, Vincenti, A, Ferri, C, Grassi, D, Pessina, G, Tumbarello, M, Pietro, MD, Sabrina, R, Luchi, S, Furini, S, Dei, S, Benetti, E, Picchiotti, N, Sanarico, M, Ceri, S, Pinoli, P, Raimondi, F, Biscarini, F, Stella, A, Zguro, K, Capitani, K, Tanfoni, M, Fallerini, C, Daga, S, Baldassarri, M, Fava, F, Frullanti, E, Valentino, F, Doddato, G, Giliberti, A, Tita, R, Amitrano, S, Bruttini, M, Croci, S, Meloni, I, Mencarelli, MA, Rizzo, CL, Pinto, AM, Beligni, G, Tommasi, A, Sarno, LD, Palmieri, M, Carriero, ML, Alaverdian, D, Busani, S, Bruno, R, Vecchia, M, Belli, MA, Mantovani, S, Ludovisi, S, Quiros-Roldan, E, Antoni, MD, Zanella, I, Siano, M, Emiliozzi, A, Fabbiani, M, Rossetti, B, Bergantini, L, D’Alessandro, M, Cameli, P, Bennett, D, Anedda, F, Marcantonio, S, Scolletta, S, Guerrini, S, Conticini, E, Frediani, B, Spertilli, C, Donati, A, Guidelli, L, Corridi, M, Croci, L, Piacentini, P, Desanctis, E, Cappelli, S, Verzuri, A, Anemoli, V, Pancrazzi, A, Lorubbio, M, Miraglia, FG, Venturelli, S, Cossarizza, A, Vergori, A, Gabrieli, A, Riva, A, Paciosi, F, Andretta, F, Gatti, F, Parisi, SG, Baratti, S, Piscopo, C, Russo, R, Andolfo, I, Iolascon, A, Carella, M, Merla, G, Squeo, GM, Raggi, P, Marciano, C, Perna, R, Bassetti, M, Sanguinetti, M, Giorli, A, Salerni, L, Parravicini, P, Menatti, E, Trotta, T, Coiro, G, Lena, F, Martinelli, E, Mancarella, S, Gabbi, C, Maggiolo, F, Ripamonti, D, Bachetti, T, Suardi, C, Parati, G, Bottà, G, Domenico, PD, Rancan, I, Bianchi, F, Colombo, R, Barbieri, C, Acquilini, D, Andreucci, E, Segala, FV, Tiseo, G, Falcone, M, Lista, M, Poscente, M, Vivo, OD, Petrocelli, P, Guarnaccia, A, 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Rader, D, Li, B, Verma, SS, Lucas, A, Bradford, Y, Abedalthagafi, M, Alaamery, M, Alshareef, A, Sawaji, M, Massadeh, S, AlMalik, A, Alqahtani, S, Baraka, D, Harthi, FA, Alsolm, E, Safieh, LA, Alowayn, AM, Alqubaishi, F, Mutairi, AA, Mangul, S, Almutairi, M, Aljawini, N, Albesher, N, Arabi, YM, Mahmoud, ES, Khattab, AK, Halawani, RT, Alahmadey, ZZ, Albakri, JK, Felemban, WA, Suliman, BA, Hasanato, R, Al-Awdah, L, Alghamdi, J, AlZahrani, D, AlJohani, S, Al-Afghani, H, AlDhawi, N, AlBardis, H, Alkwai, S, Alswailm, M, Almalki, F, Albeladi, M, Almohammed, I, Barhoush, E, Albader, A, Alotaibi, S, Alghamdi, B, Jung, J, fawzy, MS, Alrashed, M, Zeberg, H, Frithiof, R, Hultström, M, Lipcsey, M, Tardif, N, Rooyackers, O, Grip, J, Maricic, T, Helgeland, Ø, Magnus, P, Trogstad, L-IS, Lee, Y, Harris, JR, Mangino, M, Spector, TD, Emma, D, Moutsianas, L, Caulfield, MJ, Scott, RH, Kousathanas, A, Pasko, D, Walker, S, Stuckey, A, Odhams, CA, Rhodes, D, Fowler, T, Rendon, A, Chan, G, Arumugam, P, Karczewski, KJ, Martin, AR, Wilson, DJ, Spencer, CCA, Crook, DW, Wyllie, DH, O’Connell, AM, Atkinson, EG, Tsuo, K, Baya, N, Turley, P, Gupta, R, Walters, RK, Palmer, DS, Sarma, G, Cheng, N, Lu, W, Churchhouse, C, Goldstein, JI, King, D, Seed, C, Daly, MJ, Finucane, H, Bryant, S, Satterstrom, FK, Band, G, Earle, SG, Lin, S-K, Arning, N, Koelling, N, Armstrong, J, Rudkin, JK, Callier, S, Cusick, C, Soranzo, N, Zhao, JH, Danesh, J, Angelantonio, ED, Butterworth, AS, Sun, YV, Huffman, JE, Cho, K, O’Donnell, CJ, Tsao, P, Gaziano, JM, Peloso, G, Ho, Y-L, Smieszek, SP, Polymeropoulos, C, Polymeropoulos, V, Polymeropoulos, MH, Przychodzen, BP, Fernandez-Cadenas, I, Planas, AM, Perez-Tur, J, Llucià-Carol, L, Cullell, N, Muiño, E, Cárcel-Márquez, J, DeDiego, ML, Iglesias, LL, Soriano, A, Rico, V, Agüero, D, Bedini, JL, Lozano, F, Domingo, C, Robles, V, Ruiz-Jaén, F, Márquez, L, Gomez, J, Coto, E, Albaiceta, GM, García-Clemente, M, Dalmau, D, Arranz, MJ, Dietl, B, Serra-Llovich, A, Soler, P, Colobrán, R, Martín-Nalda, A, Martínez, AP, Bernardo, D, Rojo, S, Fiz-López, A, Arribas, E, de la Cal-Sabater, P, Segura, T, González-Villa, E, Serrano-Heras, G, Martí-Fàbregas, J, Jiménez-Xarrié, E, de Felipe Mimbrera, A, Masjuan, J, García-Madrona, S, Domínguez-Mayoral, A, Villalonga, JM, Menéndez-Valladares, P, Chasman, DI, Sesso, HD, Manson, JE, Buring, JE, Ridker, PM, Franco, G, Davis, L, Lee, S, Priest, J, Sankaran, VG, van Heel, D, Biesecker, L, Kerchberger, VE, Baillie, JK, Pathak, Gita A., Karjalainen, Juha, Stevens, Christine, Neale, Benjamin M., Daly, Mark, Ganna, Andrea, Andrews, Shea J., Kanai, Masahiro, Cordioli, Mattia, Polimanti, Renato, Harerimana, Nadia, Pirinen, Matti, Liao, Rachel G., Chwialkowska, Karolina, Trankiem, Amy, Balaconis, Mary K., Nguyen, Huy, Solomonson, Matthew, Veerapen, Kumar, Wolford, Brooke, Roberts, Genevieve, Park, Danny, Ball, Catherine A., Coignet, Marie, McCurdy, Shannon, Knight, Spencer, Partha, Raghavendran, Rhead, Brooke, Zhang, Miao, Berkowitz, Nathan, Gaddis, Michael, Noto, Keith, Ruiz, Luong, Pavlovic, Milo, Hong, Eurie L., Rand, Kristin, Girshick, Ahna, Guturu, Harendra, Baltzell, Asher Haug, Niemi, Mari E. K., Rahmouni, Souad, Guntz, Julien, Beguin, Yve, Pigazzini, Sara, Nkambule, Lindokuhle, Georges, Michel, Moutschen, Michel, Misset, Benoit, Darcis, Gille, Guiot, Julien, Azarzar, Samira, Gofflot, Stéphanie, Claassen, Sabine, Malaise, Olivier, Huynen, Pascale, Meuris, Christelle, Thys, Marie, Jacques, Jessica, Léonard, Philippe, Frippiat, Frederic, Giot, Jean-Baptiste, Sauvage, Anne-Sophie, Frenckell, Christian Von, Belhaj, Yasmine, Lambermont, Bernard, Nakanishi, Tomoko, Morrison, David R., Mooser, Vincent, Richards, J. Brent, Butler-Laporte, Guillaume, Forgetta, Vincenzo, Li, Rui, Ghosh, Biswarup, Laurent, Laetitia, Belisle, Alexandre, Henry, Danielle, Abdullah, Tala, Adeleye, Olumide, Mamlouk, Noor, Kimchi, Nofar, Afrasiabi, Zaman, Rezk, Nardin, Vulesevic, Branka, Bouab, Meriem, Guzman, Charlotte, Petitjean, Loui, Tselios, Chri, Xue, Xiaoqing, Afilalo, Jonathan, Afilalo, Marc, Oliveira, Maureen, Brenner, Bluma, Brassard, Nathalie, Durand, Madeleine, Schurr, Erwin, Lepage, Pierre, Ragoussis, Jianni, Auld, Daniel, Chassé, Michaël, Kaufmann, Daniel E., Lathrop, G. Mark, Adra, Darin, Hayward, Caroline, Glessner, Joseph T., Shaw, Douglas M., Campbell, Archie, Morris, Marcela, Hakonarson, Hakon, Porteous, David J., Below, Jennifer, Richmond, Anne, Chang, Xiao, Polikowski, Hannah, Lauren, Petty E., Chen, Hung-Hsin, Wanying, Zhu, Fawns-Ritchie, Chloe, North, Kari, McCormick, Joseph B., Glessner, Joseph R., Gignoux, Christopher R., Wicks, Stephen J., Crooks, Kristy, Barnes, Kathleen C., Daya, Michelle, Shortt, Jonathan, Rafaels, Nichola, Chavan, Sameer, Timmers, Paul R. H. J., Wilson, James F., Tenesa, Albert, Kerr, Shona M., D’Mellow, Kenton, Shahin, Doaa, El-Sherbiny, Yasser M., von Hohenstaufen, Kathrin Aprile, Sobh, Ali, Eltoukhy, Madonna M., Nkambul, Lindokuhle, Elhadidy, Tamer A., Abd Elghafar, Mohamed S., El-Jawhari, Jehan J., Mohamed, Attia A. S., Elnagdy, Marwa H., Samir, Amr, Abdel-Aziz, Mahmoud, Khafaga, Walid T., El-Lawaty, Walaa M., Torky, Mohamed S., El-shanshory, Mohamed R., Yassen, Amr M., Hegazy, Mohamed A. F., Okasha, Kamal, Eid, Mohammed A., Moahmed, Hanteera S., Medina-Gomez, Carolina, Ikram, M. Arfan, Uitterlinden, Andre G., Mägi, Reedik, Milani, Lili, Metspalu, Andre, Laisk, Triin, Läll, Kristi, Lepamets, Maarja, Esko, Tõnu, Reimann, Ene, Naaber, Paul, Laane, Edward, Pesukova, Jaana, Peterson, Pärt, Kisand, Kai, Tabri, Jekaterina, Allos, Raili, Hensen, Kati, Starkopf, Joel, Ringmets, Inge, Tamm, Anu, Kallaste, Anne, Alavere, Helene, Metsalu, Kristjan, Puusepp, Mairo, Batini, Chiara, Tobin, Martin D., Venn, Laura D., Lee, Paul H., Shrine, Nick, Williams, Alexander T., Guyatt, Anna L., John, Catherine, Packer, Richard J., Ali, Altaf, Free, Robert C., Wang, Xueyang, Wain, Louise V., Hollox, Edward J., Bee, Catherine E., Adams, Emma L., Palotie, Aarno, Ripatti, Samuli, Ruotsalainen, Sanni, Kristiansson, Kati, Koskelainen, Sami, Perola, Marku, Donner, Kati, Kivinen, Katja, Kaunisto, Mari, Rivolta, Carlo, Bochud, Pierre-Yve, Bibert, Stéphanie, Boillat, Noémie, Nussle, Semira Gonseth, Albrich, Werner, Quinodoz, Mathieu, Kamdar, Dhryata, Suh, Noémie, Neofytos, Dionysio, Erard, Véronique, Voide, Cathy, Friolet, R., Vollenweider, P., Pagani, J. L., Oddo, M., zu Bentrup, F. Meyer, Conen, A., Clerc, O., Marchetti, O., Guillet, A., Guyat-Jacques, C., Foucras, S., Rime, M., Chassot, J., Jaquet, M., Viollet, R. Merlet, Lannepoudenx, Y., Portopena, L., Bochud, P. Y., Desgranges, F., Filippidis, P., Guéry, B., Haefliger, D., Kampouri, E. E., Manuel, O., Munting, A., Papadimitriou-Olivgeris, M., Regina, J., Rochat-Stettler, L., Suttels, V., Tadini, E., Tschopp, J., Van Singer, M., Viala, B., Boillat-Blanco, N., Brahier, T., Hügli, O., Meuwly, J. Y., Pantet, O., Gonseth Nussle, S., Bochud, M., D’Acremont, V., Estoppey Younes, S., Albrich, W. C., Suh, N., Cerny, A., O’Mahony, L., von Mering, C., Frischknecht, M., Kleger, G-R., Filipovic, M., Kahlert, C. R., Wozniak, H., Negro, T. Rochat, Pugin, J., Bouras, K., Knapp, C., Egger, T., Perret, A., Montillier, P., di Bartolomeo, C., Barda, B., de Cid, Rafael, Carreras, Anna, Moreno, Victor, Kogevinas, Manoli, Galván-Femenía, Iván, Blay, Natalia, Farré, Xavier, Sumoy, Lauro, Cortés, Beatriz, Mercader, Josep Maria, Guindo-Martinez, Marta, Torrents, David, Garcia-Aymerich, Judith, Castaño-Vinyals, Gemma, Dobaño, Carlota, Gori, Marco, Renieri, Alessandra, Mari, Francesca, Mondelli, Mario Umberto, Castelli, Francesco, Vaghi, Massimo, Rusconi, Stefano, Montagnani, Francesca, Bargagli, Elena, Franchi, Federico, Mazzei, Maria Antonietta, Cantarini, Luca, Tacconi, Danilo, Feri, Marco, Scala, Raffaele, Spargi, Genni, Nencioni, Cesira, Bandini, Maria, Caldarelli, Gian Piero, Canaccini, Anna, Ognibene, Agostino, D’Arminio Monforte, Antonella, Girardis, Massimo, Antinori, Andrea, Francisci, Daniela, Schiaroli, Elisabetta, Scotton, Pier Giorgio, Panese, Sandro, Scaggiante, Renzo, Monica, Matteo Della, Capasso, Mario, Fiorentino, Giuseppe, Castori, Marco, Aucella, Filippo, Biagio, Antonio Di, Masucci, Luca, Valente, Serafina, Mandalà, Marco, Zucchi, Patrizia, Giannattasio, Ferdinando, Coviello, Domenico A., Mussini, Cristina, Tavecchia, Luisa, Crotti, Lia, Rizzi, Marco, Rovere, Maria Teresa La, Sarzi-Braga, Simona, Bussotti, Maurizio, Ravaglia, Sabrina, Artuso, Rosangela, Perrella, Antonio, Romani, Davide, Bergomi, Paola, Catena, Emanuele, Vincenti, Antonella, Ferri, Claudio, Grassi, Davide, Pessina, Gloria, Tumbarello, Mario, Pietro, Massimo Di, Sabrina, Ravaglia, Luchi, Sauro, Furini, Simone, Dei, Simona, Benetti, Elisa, Picchiotti, Nicola, Sanarico, Maurizio, Ceri, Stefano, Pinoli, Pietro, Raimondi, Francesco, Biscarini, Filippo, Stella, Alessandra, Zguro, Kristina, Capitani, Katia, Tanfoni, Marco, Fallerini, Chiara, Daga, Sergio, Baldassarri, Margherita, Fava, Francesca, Frullanti, Elisa, Valentino, Floriana, Doddato, Gabriella, Giliberti, Annarita, Tita, Rossella, Amitrano, Sara, Bruttini, Mirella, Croci, Susanna, Meloni, Ilaria, Mencarelli, Maria Antonietta, Rizzo, Caterina Lo, Pinto, Anna Maria, Beligni, Giada, Tommasi, Andrea, Sarno, Laura Di, Palmieri, Maria, Carriero, Miriam Lucia, Alaverdian, Diana, Busani, Stefano, Bruno, Raffaele, Vecchia, Marco, Belli, Mary Ann, Mantovani, Stefania, Ludovisi, Serena, Quiros-Roldan, Eugenia, Antoni, Melania Degli, Zanella, Isabella, Siano, Matteo, Emiliozzi, Arianna, Fabbiani, Massimiliano, Rossetti, Barbara, Bergantini, Laura, D’Alessandro, Miriana, Cameli, Paolo, Bennett, David, Anedda, Federico, Marcantonio, Simona, Scolletta, Sabino, Guerrini, Susanna, Conticini, Edoardo, Frediani, Bruno, Spertilli, Chiara, Donati, Alice, Guidelli, Luca, Corridi, Marta, Croci, Leonardo, Piacentini, Paolo, Desanctis, Elena, Cappelli, Silvia, Verzuri, Agnese, Anemoli, Valentina, Pancrazzi, Alessandro, Lorubbio, Maria, Miraglia, Federica Gaia, Venturelli, Sophie, Cossarizza, Andrea, Vergori, Alessandra, Gabrieli, Arianna, Riva, Agostino, Paciosi, Francesco, Andretta, Francesca, Gatti, Francesca, Parisi, Saverio Giuseppe, Baratti, Stefano, Piscopo, Carmelo, Russo, Roberta, Andolfo, Immacolata, Iolascon, Achille, Carella, Massimo, Merla, Giuseppe, Squeo, Gabriella Maria, Raggi, Pamela, Marciano, Carmen, Perna, Rita, Bassetti, Matteo, Sanguinetti, Maurizio, Giorli, Alessia, Salerni, Lorenzo, Parravicini, Pierpaolo, Menatti, Elisabetta, Trotta, Tullio, Coiro, Gabriella, Lena, Fabio, Martinelli, Enrico, Mancarella, Sandro, Gabbi, Chiara, Maggiolo, Franco, Ripamonti, Diego, Bachetti, Tiziana, Suardi, Claudia, Parati, Gianfranco, Bottà, Giordano, Domenico, Paolo Di, Rancan, Ilaria, Bianchi, Francesco, Colombo, Riccardo, Barbieri, Chiara, Acquilini, Donatella, Andreucci, Elena, Segala, Francesco Vladimiro, Tiseo, Giusy, Falcone, Marco, Lista, Mirjam, Poscente, Monica, Vivo, Oreste De, Petrocelli, Paola, Guarnaccia, Alessandra, Baroni, Silvia, van Heel, David A., Hunt, Karen A., Trembath, Richard C., Huang, Qin Qin, Martin, Hilary C., Mason, Dan, Trivedi, Bhavi, Wright, John, Finer, Sarah, Akhtar, Shaheen, Anwar, Mohammad, Arciero, Elena, Ashraf, Samina, Breen, Gerome, Chung, Raymond, Curtis, Charles J., Chowdhury, Maharun, Colligan, Grainne, Deloukas, Pano, Durham, Ceri, Griffiths, Chri, Hurles, Matt, Hussain, Shapna, Islam, Kamrul, Khan, Ahsan, Khan, Amara, Lavery, Cath, Lee, Sang Hyuck, Lerner, Robin, MacArthur, Daniel, MacLaughlin, Bev, Martin, Hilary, Miah, Shefa, Newman, Bill, Safa, Nishat, Tahmasebi, Farah, Griffiths, Christopher J., Smith, Albert V., Boughton, Andrew P., Li, Kevin W., LeFaive, Jonathon, Annis, Aubrey, Niavarani, Ahmadreza, Aliannejad, Rasoul, Sharififard, Bahareh, Amirsavadkouhi, Ali, Naderpour, Zeinab, Tadi, Hengameh Ansari, Aleagha, Afshar Etemadi, Ahmadi, Saeideh, Moghaddam, Seyed Behrooz Mohseni, Adamsara, Alireza, Saeedi, Morteza, Abdollahi, Hamed, Hosseini, Abdolmajid, Chariyavilaskul, Pajaree, Jantarabenjakul, Watsamon, Hirankarn, Nattiya, Chamnanphon, Monpat, Suttichet, Thitima B., Shotelersuk, Vorasuk, Pongpanich, Monnat, Phokaew, Chureerat, Chetruengchai, Wanna, Putchareon, Opa, Torvorapanit, Pattama, Puthanakit, Thanyawee, Suchartlikitwong, Pintip, Nilaratanakul, Voraphoj, Sodsai, Pimpayao, Brumpton, Ben M., Hveem, Kristian, Willer, Cristen, Zhou, Wei, Rogne, Tormod, Solligard, Erik, Åsvold, Bjørn Olav, Franke, Lude, Boezen, Marike, Deelen, Patrick, Claringbould, Annique, Lopera, Esteban, Warmerdam, Robert, Vonk, Judith. M., van Blokland, Irene, Lanting, Pauline, Ori, Anil P. S., Feng, Yen-Chen Anne, Mercader, Josep, Weiss, Scott T., Karlson, Elizabeth W., Smoller, Jordan W., Murphy, Shawn N., Meigs, James B., Woolley, Ann E., Green, Robert C., Perez, Emma F., Zöllner, Sebastian, Wang, Jiongming, Beck, Andrew, Sloofman, Laura G., Ascolillo, Steven, Sebra, Robert P., Collins, Brett L., Levy, Te, Buxbaum, Joseph D., Sealfon, Stuart C., Jordan, Daniel M., Thompson, Ryan C., Gettler, Kyle, Chaudhary, Kumardeep, Belbin, Gillian M., Preuss, Michael, Hoggart, Clive, Choi, Sam, Underwood, Slayton J., Salib, Irene, Britvan, Bari, Keller, Katherine, Tang, Lara, Peruggia, Michael, Hiester, Liam L., Niblo, Kristi, Aksentijevich, Alexandra, Labkowsky, Alexander, Karp, Avromie, Zlatopolsky, Menachem, Zyndorf, Marissa, Charney, Alexander W., Beckmann, Noam D., Schadt, Eric E., Abul-Husn, Noura S., Cho, Judy H., Itan, Yuval, Kenny, Eimear E., Loos, Ruth J. F., Nadkarni, Girish N., Do, Ron, O’Reilly, Paul, Huckins, Laura M., Ferreira, Manuel A. R., Abecasis, Goncalo R., Leader, Joseph B., Cantor, Michael N., Justice, Anne E., Carey, Dave J., Chittoor, Geetha, Josyula, Navya Shilpa, Kosmicki, Jack A., Horowitz, Julie E., Baras, Ari, Gass, Matthew C., Yadav, Ashish, Mirshahi, Tooraj, Hottenga, Jouke Jan, Bartels, Meike, de geus, Eco E. J. C., Nivard, Michel M. G., Verma, Anurag, Ritchie, Marylyn D., Rader, Daniel, Li, Binglan, Verma, Shefali S., Lucas, Anastasia, Bradford, Yuki, Abedalthagafi, Malak, Alaamery, Manal, Alshareef, Abdulraheem, Sawaji, Mona, Massadeh, Salam, AlMalik, Abdulaziz, Alqahtani, Saleh, Baraka, Dona, Harthi, Fawz Al, Alsolm, Ebtehal, Safieh, Leen Abu, Alowayn, Albandary M., Alqubaishi, Fatimah, Mutairi, Amal Al, Mangul, Serghei, Almutairi, Mansour, Aljawini, Nora, Albesher, Nour, Arabi, Yaseen M., Mahmoud, Ebrahim S., Khattab, Amin K., Halawani, Roaa T., Alahmadey, Ziab Z., Albakri, Jehad K., Felemban, Walaa A., Suliman, Bandar A., Hasanato, Rana, Al-Awdah, Laila, Alghamdi, Jahad, AlZahrani, Deema, AlJohani, Sameera, Al-Afghani, Hani, AlDhawi, Nouf, AlBardis, Hadeel, Alkwai, Sarah, Alswailm, Moneera, Almalki, Faisal, Albeladi, Maha, Almohammed, Iman, Barhoush, Eman, Albader, Anoud, Alotaibi, Sara, Alghamdi, Bader, Jung, Junghyun, fawzy, Mohammad S., Alrashed, May, Zeberg, Hugo, Nkambul, Lindo, Frithiof, Robert, Hultström, Michael, Lipcsey, Miklo, Tardif, Nicola, Rooyackers, Olav, Grip, Jonathan, Maricic, Tomislav, Helgeland, Øyvind, Magnus, Per, Trogstad, Lill-Iren S., Lee, Yunsung, Harris, Jennifer R., Mangino, Massimo, Spector, Tim D., Emma, Duncan, Moutsianas, Louka, Caulfield, Mark J., Scott, Richard H., Kousathanas, Athanasio, Pasko, Dorota, Walker, Susan, Stuckey, Alex, Odhams, Christopher A., Rhodes, Daniel, Fowler, Tom, Rendon, Augusto, Chan, Georgia, Arumugam, Prabhu, Karczewski, Konrad J., Martin, Alicia R., Wilson, Daniel J., Spencer, Chris C. A., Crook, Derrick W., Wyllie, David H., O’Connell, Anne Marie, Atkinson, Elizabeth G., Tsuo, Kristin, Baya, Nikola, Turley, Patrick, Gupta, Rahul, Walters, Raymond K., Palmer, Duncan S., Sarma, Gopal, Cheng, Nathan, Lu, Wenhan, Churchhouse, Claire, Goldstein, Jacqueline I., King, Daniel, Seed, Cotton, Daly, Mark J., Finucane, Hilary, Bryant, Sam, Satterstrom, F. Kyle, Band, Gavin, Earle, Sarah G., Lin, Shang-Kuan, Arning, Nicola, Koelling, Nil, Armstrong, Jacob, Rudkin, Justine K., Callier, Shawneequa, Cusick, Caroline, Soranzo, Nicole, Zhao, Jing Hua, Danesh, John, Angelantonio, Emanuele Di, Butterworth, Adam S., Sun, Yan V., Huffman, Jennifer E., Cho, Kelly, O’Donnell, Christopher J., Tsao, Phil, Gaziano, J. Michael, Peloso, Gina, Ho, Yuk-Lam, Smieszek, Sandra P., Polymeropoulos, Christo, Polymeropoulos, Vasilio, Polymeropoulos, Mihael H., Przychodzen, Bartlomiej P., Fernandez-Cadenas, Israel, Planas, Anna M., Perez-Tur, Jordi, Llucià-Carol, Laia, Cullell, Natalia, Muiño, Elena, Cárcel-Márquez, Jara, DeDiego, Marta L., Iglesias, Lara Lloret, Soriano, Alex, Rico, Veronica, Agüero, Daiana, Bedini, Josep L., Lozano, Francisco, Domingo, Carlo, Robles, Veronica, Ruiz-Jaén, Francisca, Márquez, Leonardo, Gomez, Juan, Coto, Eliecer, Albaiceta, Guillermo M., García-Clemente, Marta, Dalmau, David, Arranz, Maria J., Dietl, Beatriz, Serra-Llovich, Alex, Soler, Pere, Colobrán, Roger, Martín-Nalda, Andrea, Martínez, Alba Parra, Bernardo, David, Rojo, Silvia, Fiz-López, Aida, Arribas, Elisa, de la Cal-Sabater, Paloma, Segura, Tomá, González-Villa, Esther, Serrano-Heras, Gemma, Martí-Fàbregas, Joan, Jiménez-Xarrié, Elena, de Felipe Mimbrera, Alicia, Masjuan, Jaime, García-Madrona, Sebastian, Domínguez-Mayoral, Anna, Villalonga, Joan Montaner, Menéndez-Valladares, Paloma, Chasman, Daniel I., Sesso, Howard D., Manson, JoAnn E., Buring, Julie E., Ridker, Paul M., Franco, Giulianini, Davis, Lea, Lee, Sulggi, Priest, Jame, Sankaran, Vijay G., van Heel, David, Biesecker, Le, Kerchberger, V. Eric, Baillie, J. Kenneth, APH - Personalized Medicine, APH - Health Behaviors & Chronic Diseases, Biological Psychology, APH - Mental Health, AMS - Sports, AMS - Ageing & Vitality, APH - Methodology, Mccurdy, Shannon, Mccormick, Joseph B., Macarthur, Daniel, Maclaughlin, Bev, Lefaive, Jonathon, Almalik, Abdulaziz, Alzahrani, Deema, Aljohani, Sameera, Aldhawi, Nouf, Albardis, Hadeel, Fawzy, Mohammad S., Dediego, Marta L., Stem Cell Aging Leukemia and Lymphoma (SALL), Groningen Institute for Gastro Intestinal Genetics and Immunology (3GI), Life Course Epidemiology (LCE), Groningen Research Institute for Asthma and COPD (GRIAC), University of Zurich, COVID-19 Host Genetics Initiative, Barcelona Supercomputing Center, COVID-19 Genetics Initiative, including authors, Institute for Molecular Medicine Finland, and Data Science Genetic Epidemiology Lab
Subjects: Informàtica::Aplicacions de la informàtica::Bioinformàtica [Àrees temàtiques de la UPC], Quantitative Trait Loci, MUC5B PROMOTER POLYMORPHISM, Genome-wide association studies, COVID-19 (Malaltia), UFSP13-7 Evolution in Action: From Genomes to Ecosystems, COVID-19 (Disease), Settore BIO/12 - BIOCHIMICA CLINICA E BIOLOGIA MOLECOLARE CLINICA, SDG 3 - Good Health and Well-being, Humans, genetics, Genetic variation, Genomes, Medicinsk genetik, 1000 Multidisciplinary, Multidisciplinary, Chromosome Mapping, COVID-19, Human Genetics, 10124 Institute of Molecular Life Sciences, covid-19, 3121 General medicine, internal medicine and other clinical medicine, 570 Life sciences, biology, Medical Genetics
Abstract: Matters arising from: Mapping the human genetic architecture of COVID-19 Original Article published on 08 July 2021 https://www.nature.com/articles/s41586-021-03767-x The COVID-19 pandemic continues to pose a major public health threat, especially in countries with low vaccination rates. To better understand the biological underpinnings of SARS-CoV-2 infection and COVID-19 severity, we formed the COVID-19 Host Genetics Initiative1. Here we present a genome-wide association study meta-analysis of up to 125,584 cases and over 2.5 million control individuals across 60 studies from 25 countries, adding 11 genome-wide significant loci compared with those previously identified2. Genes at new loci, including SFTPD, MUC5B and ACE2, reveal compelling insights regarding disease susceptibility and severity. Here we present meta-analyses bringing together 60 studies from 25 countries (Fig. 1 and Supplementary Table 1) for three COVID-19-related phenotypes: (1) individuals critically ill with COVID-19 on the basis of requiring respiratory support in hospital or who died as a consequence of the disease (9,376 cases, of which 3,197 are new in this data release, and 1,776,645 control individuals); (2) individuals with moderate or severe COVID-19 defined as those hospitalized due to symptoms associated with the infection (25,027 cases, 11,386 new and 2,836,272 control individuals); and (3) all cases with reported SARS-CoV-2 infection regardless of symptoms (125,584 cases, 76,022 new and 2,575,347 control individuals). Most studies have reported results before the roll out of the COVID-19 vaccination campaign. An overview of the study design is provided in Supplementary Fig. 1. We found a total of 23 genome-wide significant loci (P
Published: 2022

12. Genome sequencing and analysis of the model grass Brachypodium distachyon

Author: Vogel, John P, Garvin, David F, Mockler, Todd C, Schmutz, Jeremy, Rokhsar, Dan, Bevan, Michael W, Barry, Kerrie, Lucas, Susan, Harmon-Smith, Miranda, Lail, Kathleen, Tice, Hope, Schmutz (Leader), Jeremy, Grimwood, Jane, McKenzie, Neil, Huo, Naxin, Gu, Yong Q, Lazo, Gerard R, Anderson, Olin D, Vogel (Leader), John P, You, Frank M, Luo, Ming-Cheng, Dvorak, Jan, Wright, Jonathan, Febrer, Melanie, Idziak, Dominika, Hasterok, Robert, Lindquist, Erika, Wang, Mei, Fox, Samuel E, Priest, Henry D, Filichkin, Sergei A, Givan, Scott A, Bryant, Douglas W, Chang, Jeff H, Mockler (Leader), Todd C, Wu, Haiyan, Wu, Wei, Hsia, An-Ping, Schnable, Patrick S, Kalyanaraman, Anantharaman, Barbazuk, Brad, Michael, Todd P, Hazen, Samuel P, Bragg, Jennifer N, Laudencia-Chingcuanco, Debbie, Weng, Yiqun, Haberer, Georg, Spannagl, Manuel, Mayer (Leader), Klaus, Rattei, Thomas, Mitros, Therese, Lee, Sang-Jik, Rose, Jocelyn K. C, Mueller, Lukas A, York, Thomas L, Wicker (Leader), Thomas, Buchmann, Jan P, Tanskanen, Jaakko, Schulman (Leader), Alan H, Gundlach, Heidrun, Bevan, Michael, Costa de Oliveira, Antonio, da C. Maia, Luciano, Belknap, William, Jiang, Ning, Lai, Jinsheng, Zhu, Liucun, Ma, Jianxin, Sun, Cheng, Pritham, Ellen, Salse (Leader), Jerome, Murat, Florent, Abrouk, Michael, Mayer, Klaus, Bruggmann, Remy, Messing, Joachim, Fahlgren, Noah, Sullivan, Christopher M, Carrington, James C, Chapman, Elisabeth J, May, Greg D, Zhai, Jixian, and Ganssmann, Matthias
Published: 2010

13. Compositionally complex doping for zero-strain zero-cobalt layered cathodes

Author: Rui Zhang, Chunyang Wang, Peichao Zou, Ruoqian Lin, Lu Ma, Liang Yin, Tianyi Li, Wenqian Xu, Hao Jia, Qiuyan Li, Sami Sainio, Kim Kisslinger, Stephen E. Trask, Steven N. Ehrlich, Yang Yang, Andrew M. Kiss, Mingyuan Ge, Bryant J. Polzin, Sang Jun Lee, Wu Xu, Yang Ren, and Huolin L. Xin
Subjects: Multidisciplinary
Abstract: The high volatility of the price of cobalt and the geopolitical limitations of cobalt mining have made the elimination of Co a pressing need for the automotive industry
Published: 2022

14. Structures, functions and adaptations of the human LINE-1 ORF2 protein.

Author: Baldwin, Eric T., van Eeuwen, Trevor, Hoyos, David, Zalevsky, Arthur, Tchesnokov, Egor P., Sánchez, Roberto, Miller, Bryant D., Di Stefano, Luciano H., Ruiz, Francesc Xavier, Hancock, Matthew, Işik, Esin, Mendez-Dorantes, Carlos, Walpole, Thomas, Nichols, Charles, Wan, Paul, Riento, Kirsi, Halls-Kass, Rowan, Augustin, Martin, Lammens, Alfred, and Jestel, Anja
Abstract: The LINE-1 (L1) retrotransposon is an ancient genetic parasite that has written around one-third of the human genome through a 'copy and paste' mechanism catalysed by its multifunctional enzyme, open reading frame 2 protein (ORF2p)1. ORF2p reverse transcriptase (RT) and endonuclease activities have been implicated in the pathophysiology of cancer2,3, autoimmunity4,5 and ageing6,7, making ORF2p a potential therapeutic target. However, a lack of structural and mechanistic knowledge has hampered efforts to rationally exploit it. We report structures of the human ORF2p 'core' (residues 238–1061, including the RT domain) by X-ray crystallography and cryo-electron microscopy in several conformational states. Our analyses identified two previously undescribed folded domains, extensive contacts to RNA templates and associated adaptations that contribute to unique aspects of the L1 replication cycle. Computed integrative structural models of full-length ORF2p show a dynamic closed-ring conformation that appears to open during retrotransposition. We characterize ORF2p RT inhibition and reveal its underlying structural basis. Imaging and biochemistry show that non-canonical cytosolic ORF2p RT activity can produce RNA:DNA hybrids, activating innate immune signalling through cGAS/STING and resulting in interferon production6–8. In contrast to retroviral RTs, L1 RT is efficiently primed by short RNAs and hairpins, which probably explains cytosolic priming. Other biochemical activities including processivity, DNA-directed polymerization, non-templated base addition and template switching together allow us to propose a revised L1 insertion model. Finally, our evolutionary analysis demonstrates structural conservation between ORF2p and other RNA- and DNA-dependent polymerases. We therefore provide key mechanistic insights into L1 polymerization and insertion, shed light on the evolutionary history of L1 and enable rational drug development targeting L1. X-ray crystallography, cryo-electron microscopy, structural modelling, biochemistry, cell biology, and evolutionary analysis enable characterization of ORF2p, the reverse transcriptase of the ancient 'parasitic' LINE-1 retrotransposon that has written around one-third of the human genome. [ABSTRACT FROM AUTHOR]
Published: 2024
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15. A remnant planetary core in the hot-Neptune desert

Author: David J. Armstrong, Théo A. Lopez, Vardan Adibekyan, Richard A. Booth, Edward M. Bryant, Karen A. Collins, Magali Deleuil, Alexandre Emsenhuber, Chelsea X. Huang, George W. King, Jorge Lillo-Box, Jack J. Lissauer, Elisabeth Matthews, Olivier Mousis, Louise D. Nielsen, Hugh Osborn, Jon Otegi, Nuno C. Santos, Sérgio G. Sousa, Keivan G. Stassun, Dimitri Veras, Carl Ziegler, Jack S. Acton, Jose M. Almenara, David R. Anderson, David Barrado, Susana C. C. Barros, Daniel Bayliss, Claudia Belardi, Francois Bouchy, César Briceño, Matteo Brogi, David J. A. Brown, Matthew R. Burleigh, Sarah L. Casewell, Alexander Chaushev, Kevin I. Collins, Knicole D. Colón, Benjamin F. Cooke, Ian J. M. Crossfield, Rodrigo F. Díaz, Elisa Delgado Mena, Olivier D. S. Demangeon, Caroline Dorn, Xavier Dumusque, Philipp Eigmüller, Michael Fausnaugh, Pedro Figueira, Tianjun Gan, Siddharth Gandhi, Samuel Gill, Erica J. Gonzales, Michael R. Goad, Ravit Helled, Saeed Hojjatpanah, Steve B. Howell, James Jackman, James S. Jenkins, Jon M. Jenkins, Eric L. N. Jensen, Grant M. Kennedy, David W. Latham, Nicholas Law, Monika Lendl, Michael Lozovsky, Andrew W. Mann, Maximiliano Moyano, James McCormac, Farzana Meru, Christoph Mordasini, Ares Osborn, Don Pollacco, Didier Queloz, Liam Raynard, George R. Ricker, Pamela Rowden, Alexandre Santerne, Joshua E. Schlieder, Sara Seager, Lizhou Sha, Thiam-Guan Tan, Rosanna H. Tilbrook, Eric Ting, Stéphane Udry, Roland Vanderspek, Christopher A. Watson, Richard G. West, Paul A. Wilson, Joshua N. Winn, Peter Wheatley, Jesus Noel Villasenor, Jose I. Vines, and Zhuchang Zhan
Subjects: Exobiology, Lunar And Planetary Science And Exploration
Abstract: The interiors of giant planets remain poorly understood. Even for the planets in the Solar System, difficulties in observation lead to large uncertainties in the properties of planetary cores. Exoplanets that have undergone rare evolutionary processes provide a route to understanding planetary interiors. Planets found in and near the typically barren hot-Neptune ‘desert’ (a region in mass–radius space that contains few planets) have proved to be particularly valuable in this regard. These planets include HD149026b, which is thought to have an unusually massive core, and recent discoveries such as LTT9779b and NGTS-4b, on which photoevaporation has removed a substantial part of their outer atmospheres. Here we report observations of the planet TOI-849b, which has a radius smaller than Neptune’s but an anomalously large mass of 39.1(+2.7−2.6) Earth masses and a density of 5.2(+0.7−0.8) grams per cubic centimetre, similar to Earth’s. Interior-structure models suggest that any gaseous envelope of pure hydrogen and helium consists of no more than 3.9(+0.8−0.9) per cent of the total planetary mass. The planet could have been a gas giant before undergoing extreme mass loss via thermal self-disruption or giant planet collisions, or it could have avoided substantial gas accretion, perhaps through gap opening or late formation. Although photoevaporation rates cannot account for the mass loss required to reduce a Jupiter-like gas giant, they can remove a small (a few Earth masses) hydrogen and helium envelope on timescales of several billion years, implying that any remaining atmosphere on TOI-849b is likely to be enriched by water or other volatiles from the planetary interior. We conclude that TOI-849b is the remnant core of a giant planet.
Published: 2020
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16. Non-viral precision T cell receptor replacement for personalized cell therapy

Author: Foy, Susan P., primary, Jacoby, Kyle, additional, Bota, Daniela A., additional, Hunter, Theresa, additional, Pan, Zheng, additional, Stawiski, Eric, additional, Ma, Yan, additional, Lu, William, additional, Peng, Songming, additional, Wang, Clifford L., additional, Yuen, Benjamin, additional, Dalmas, Olivier, additional, Heeringa, Katharine, additional, Sennino, Barbara, additional, Conroy, Andy, additional, Bethune, Michael T., additional, Mende, Ines, additional, White, William, additional, Kukreja, Monica, additional, Gunturu, Swetha, additional, Humphrey, Emily, additional, Hussaini, Adeel, additional, An, Duo, additional, Litterman, Adam J., additional, Quach, Boi Bryant, additional, Ng, Alphonsus H. C., additional, Lu, Yue, additional, Smith, Chad, additional, Campbell, Katie M., additional, Anaya, Daniel, additional, Skrdlant, Lindsey, additional, Huang, Eva Yi-Hsuan, additional, Mendoza, Ventura, additional, Mathur, Jyoti, additional, Dengler, Luke, additional, Purandare, Bhamini, additional, Moot, Robert, additional, Yi, Michael C., additional, Funke, Roel, additional, Sibley, Alison, additional, Stallings-Schmitt, Todd, additional, Oh, David Y., additional, Chmielowski, Bartosz, additional, Abedi, Mehrdad, additional, Yuan, Yuan, additional, Sosman, Jeffrey A., additional, Lee, Sylvia M., additional, Schoenfeld, Adam J., additional, Baltimore, David, additional, Heath, James R., additional, Franzusoff, Alex, additional, Ribas, Antoni, additional, Rao, Arati V., additional, and Mandl, Stefanie J., additional
Published: 2022
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17. Compositionally complex doping for zero-strain zero-cobalt layered cathodes

Author: Zhang, Rui, primary, Wang, Chunyang, additional, Zou, Peichao, additional, Lin, Ruoqian, additional, Ma, Lu, additional, Yin, Liang, additional, Li, Tianyi, additional, Xu, Wenqian, additional, Jia, Hao, additional, Li, Qiuyan, additional, Sainio, Sami, additional, Kisslinger, Kim, additional, Trask, Stephen E., additional, Ehrlich, Steven N., additional, Yang, Yang, additional, Kiss, Andrew M., additional, Ge, Mingyuan, additional, Polzin, Bryant J., additional, Lee, Sang Jun, additional, Xu, Wu, additional, Ren, Yang, additional, and Xin, Huolin L., additional
Published: 2022
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18. Fire frequency drives decadal changes in soil carbon and nitrogen and ecosystem productivity

Author: Pellegrini, Adam F. A., Ahlström, Anders, Hobbie, Sarah E., Reich, Peter B., Nieradzik, Lars P., Staver, Carla A., Scharenbroch, Bryant C., Jumpponen, Ari, Anderegg, William R. L., Randerson, James T., and Jackson, Robert B.
Published: 2018
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19. Genetic mechanisms of critical illness in COVID-19

Author: Pairo-Castineira, Erola, Clohisey, Sara, Klaric, Lucija, Bretherick, Andrew D, Rawlik, Konrad, Pasko, Dorota, Walker, Susan, Parkinson, Nick, Fourman, Max Head, Russell, Clark D, Furniss, James, Richmond, Anne, Gountouna, Elvina, Wrobel, Nicola, Harrison, David, Wang, Bo, Yang, Wu, Meynert, Alison, Griffiths, Fiona, Oosthuyzen, Wilna, Kousathanas, Athanasios, Moutsianas, Loukas, Yang, Zhijian, Zhai, Ranran, Zheng, Chenqing, Grimes, Graeme, Beale, Rupert, Millar, Jonathan, Shih, Barbara, Keating, Sean, Zechner, Marie, Haley, Chris, Porteous, David J, Hayward, Caroline, Yang, Jian, Knight, Julian, Summers, Charlotte, Shankar-Hari, Manu, Klenerman, Paul, Turtle, Lance, Antonia, Ho, Moore, Shona C, Hinds, Charles, Horby, Peter, Nichol, Alistair, Maslove, David, Ling, Lowell, Mcauley, Danny, Montgomery, Hugh, Walsh, Timothy, Pereira, Alexandre C, Renieri, Johnny, Millar, Alistair, Nichol, Tim, Walsh, Manu, Shankar-Hari, Chris, Ponting, Jen, Meikle, Paul, Finernan, Ellie, Mcmaster, Andy, Law, J Kenneth Baillie, Trevor, Paterson, Tony, Wackett, Ruth, Armstrong, Richard, Clark, Audrey, Coutts, Lorna, Donnelly, Tammy, Gilchrist, Katarzyna, Hafezi, Louise, Macgillivray, Alan, Maclean, Sarah, Mccafferty, Kirstie, Morrice, Jane, Weaver, Ceilia, Boz, Ailsa, Golightly, Mari, Ward, Hanning, Mal, Helen, Szoor-McElhinney, Adam, Brown, Ross, Hendry, Andrew, Stenhouse, Louise, Cullum, Dawn, Law, Sarah, Law, Rachel, Law, Maaike, Swets, Nicky, Day, Filip, Taneski, Esther, Duncan, Nicholas, Parkinson, Collier, D, Wood, S, Zak, A, Borra, C, Matharu, M, May, P, Alldis, Z, Mitchelmore, O, Bowles, R, Easthope, A, Bibi, F, Lancoma-Malcolm, I, Gurasashvili, J, Pheby, J, Shiel, J, Bolton, M, Patel, M, Taylor, M, Zongo, O, Ebano, P, Harding, P, Astin-Chamberlain, R, Choudhury, Y, Cox, A, Kallon, D, Burton, M, Hall, R, Blowes, S, Prime, Z, Biddle, J, Prysyazhna, O, Newman, T, Tierney, C, Kassam, J, Shankar-Hari, M, Ostermann, M, Campos, S, Bociek, A, Lim, R, Grau, N, O Jones, T, Whitton, C, Marotti, M, Arbane, G, Bonner, S, Hugill, K, Reid, J, Welters, I, Waugh, V, Williams, K, Shaw, D, J Fernandez Roman, M Lopez Martinez, Johnson, E, Waite, A, Johnston, B, Hamilton, D, Mulla, S, Mcphail, M, Smith, J, K Baillie, J, Barclay, L, Hope, D, Mcculloch, C, Mcquillan, L, Clark, S, Singleton, J, Priestley, K, Rea, N, Callaghan, M, Campbell, R, Andrew, G, Marshall, L, Mckechnie, S, Hutton, P, Bashyal, A, Davidson, N, Summers, C, Polgarova, P, Stroud, K, Pathan, N, Elston, K, Agrawal, S, Battle, C, Newey, L, Rees, T, Harford, R, Brinkworth, E, Williams, M, Murphy, C, White, I, Croft, M, Bandla, N, Gellamucho, M, Tomlinson, J, Turner, H, Davies, M, Quinn, A, Hussain, I, Thompson, C, Parker, H, Bradley, R, Griffiths, R, Scriven, J, Nilsson, A, Bates, M, Dasgin, J, Gill, J, Puxty, A, Cathcart, S, Salutous, D, Turner, L, Duffy, K, Puxty, K, Joseph, A, Herdman-Grant, R, Simms, R, Swain, A, Naranjo, A, Crowe, R, Sollesta, K, Loveridge, A, Baptista, D, Morino, E, Davey, M, Golden, D, 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Wei Shen Lim, Alexander, J Mentzer, Laura, Merson, Alison, M Meynert, Mahdad, Noursadeghi, Shona, C Moore, Massimo, Palmarini, William, A Paxton, Georgios, Pollakis, Nicholas, Price, Andrew, Rambaut, David, L Robertson, Vanessa, Sancho-Shimizu, Janet, T Scott, Thushan de Silva, Louise, Sigfrid, Tom, Solomon, Shiranee, Sriskandan, David, Stuart, Richard, S Tedder, Emma, C Thomson, A Roger Thompson, A, Ryan, S Thwaites, Lance C, W Turtle, Maria, Zambon, Hayley, Hardwick, Chloe, Donohue, Ruth, Lyons, Lisa, Norman, Riinu, Pius, Thomas, M Drake, Cameron, J Fairfield, Stephen, R Knight, Kenneth, A Mclean, Derek, Murphy, Catherine, A Shaw, Dalton, Jo, Michelle, Girvan, Egle, Saviciute, Stephanie, Roberts, Janet, Harrison, Laura, Marsh, Marie, Connor, Sophie, Halpin, Clare, Jackson, Carrol, Gamble, Gary, Leeming, Murray, Wham, William, Greenhalf, Victoria, Shaw, Sara, Mcdonald, Seán, Keating, Andrea, Ganna, Patrick, Sulem, David, A van Heel, Mattia, Cordioli, Gardar, Sveinbjornsson, Mari E, K Niemi, Janie, F Shelton, Anjali, J Shastri, Chelsea, Ye, Catherine, H Weldon, Teresa, Filshtein-Sonmez, Daniella, Coker, Antony, Symons, Jorge, Esparza-Gordillo, Stella, Aslibekyan, Adam, Auton, Jose, E Krieger, Emmanuelle, Marques, Cinthia, E Jannes, Mari, Francesca, Daga, Sergio, Baldassarri, Margherita, Benetti, Elisa, Simone, Furini, Fallerini, Chiara, Fava, Francesca, Floriana, Valentino, Gabriella, Doddato, Annarita, Giliberti, Tita, Rossella, Amitrano, Sara, Bruttini, Mirella, Croci, Susanna, Meloni, Ilaria, Pinto, ANNA MARIA, Frullanti, Elisa, Mencarelli, MARIA ANTONIETTA, LO RIZZO, Caterina, Montagnani, Francesca, DI SARNO, Laura, Tommasi, Andrea, Palmieri, Maria, Emiliozzi, Arianna, Fabbiani, Massimiliano, Rossetti, Barbara, Zanelli, Giacomo, Bargagli, Elena, Bergantini, Laura, D'Alessandro, Miriana, Cameli, Paolo, David, Bennet, Anedda, Federico, Marcantonio, Simona, Scolletta, Sabino, Franchi, Federico, Mazzei, MARIA ANTONIETTA, Guerrini, Susanna, Conticini, Edoardo, 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Konrad [0000-0002-0010-370X], Walker, Susan [0000-0002-5016-6426], Fourman, Max Head [0000-0001-7381-2278], Russell, Clark D [0000-0002-9873-8243], Gountouna, Elvina [0000-0001-7870-2780], Wang, Bo [0000-0002-1580-797X], Wu, Yang [0000-0002-0128-7280], Kousathanas, Athanasios [0000-0001-6265-6521], Moutsianas, Loukas [0000-0001-5453-345X], Zhai, Ranran [0000-0002-5834-9120], Beale, Rupert [0000-0002-6705-8560], Keating, Sean [0000-0001-8552-5604], Haley, Chris [0000-0002-9811-0210], Porteous, David J [0000-0003-1249-6106], Hayward, Caroline [0000-0002-9405-9550], Yang, Jian [0000-0003-2001-2474], Knight, Julian [0000-0002-0377-5536], Summers, Charlotte [0000-0002-7269-2873], Shankar-Hari, Manu [0000-0002-5338-2538], Turtle, Lance [0000-0002-0778-1693], Moore, Shona C [0000-0001-8610-2806], Hinds, Charles [0000-0001-5094-8324], McAuley, Danny [0000-0002-3283-1947], Montgomery, Hugh [0000-0001-8797-5019], Renieri, Alessandra [0000-0002-0846-9220], Shen, Xia [0000-0003-4390-1979], 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T., Massey, E., Croston, G., Reschreiter, H., Camsooksai, J., Patch, S., Jenkins, S., Humphrey, C., Wadams, B., Msiska, M., Adanini, O., Attwood, B., Parsons, P., Tatham, K., Jhanji, S., Black, E., Dela Rosa, A., Howle, R., Thomas, B., Bemand, T., Raobaikady, R., Saha, R., Staines, N., Daniel, A., Finn, J., Hutter, J., Doble, P., Shovelton, C., Pawley, C., Kannan, T., Hill, M., Combes, E., Monnery, S., Joefield, T., Popescu, M., Thankachen, M., Oblak, M., Little, J., Mcivor, S., Brady, A., Whittle, H., Prady, H., Chan, R., Ahmed, A., Morris, A., Gibson, C., Gordon, E., Keenan, S., Quinn, H., Benyon, S., Marriott, S., Zitter, L., Park, L., Baines, K., Lyons, M., Holland, M., Keenan, N., Young, M., Garrioch, S., Dawson, J., Tolson, M., Scholefield, B., Bi, R., Richardson, N., Schumacher, N., Cosier, T., Millen, G., Higham, A., Turki, S., Allen, L., Crisp, N., Hazleton, T., Knight, A., Deery, J., Price, C., Turney, S., Tilbey, S., Beranova, E., Wright, D., George, L., Twiss, S., Wadd, S., Postlethwaite, K., Gondo, P., Masunda, B., Kayani, A., Hadebe, B., Whiteside, J., Clarke, N., Donnison, P., Trim, F., Leadbitter, I., Butcher, D., O'Sullivan, S., Purewal, B., Bell, S., Rivers, V., O'Leary, R., Birch, J., Collins, E., Anderson, S., Hammerton, K., Andrews, E., Burns, K., Edmond, I., Todd, A., Donnachie, J., Turner, P., Prentice, L., Symon, L., Runciman, N., Auld, F., Halkes, M., Mercer, P., Thornton, L., Debreceni, G., Wilkins, J., Crickmore, V., Subramanian, G., Marshall, R., Jennings, C., Latif, M., Bunni, L., Spivey, M., Bean, S., Burt, K., Linnett, V., Ritzema, J., Sanderson, A., Mccormick, W., Bokhari, M., Kapoor, R., Loader, D., Ayers, A., Harrison, W., North, J., Belagodu, Z., Paramsothy, R., Olufuwa, O., Gherman, A., Fuller, B., Stuart, C., Kelsall, O., Davis, C., Wild, L., Wood, H., Thrush, J., Durie, A., Austin, K., Archer, K., Anderson, P., Vigurs, C., Thorpe, C., Knights, E., Boyle, N., Price, A., Kubisz-Pudelko, A., Wood, D., Lewis, A., Board, S., Pippard, L., Perry, J., Beesley, K., Rattray, A., Lee, E., Lennon, L., Douglas, K., Bell, D., Boyle, R., Glass, L., Nauman Akhtar, M., Dent, K., Potoczna, D., Pearson, S., Horsley, E., Spencer, S., Mullan, D., Skinner, D., Gaylard, J., Barber, R., Hewitt, C., Hilldrith, A., Shepardson, S., Wills, M., Jackson-Lawrence, K., Gupta, A., Timlick, E., Gorman, C., Otahal, I., Gales, A., Coetzee, S., Sell, C., Raj, M., Peiu, M., Quaid, S., Watson, E., Elliott, K., Mallinson, J., Chandler, B., Turnbull, A., Finch, C., Holl, C., Cooper, J., Evans, A., Khaliq, W., Collins, A., Gude, E. T., Love, N., van Koutrik, L., Hunt, J., Kaye, D., Fisher, E., Brayne, A., Tuckey, V., Jackson, P., Parkin, J., Tariq, A., Houlden, H., Tucci, A., Hardy, J., Moncur, E., Highgate, J., Cowley, A., Mitra, A., Stead, R., Behan, T., Burnett, C., Newton, M., Heeney, E., Pollard, R., Hatton, J., Patel, A., Kasipandian, V., Allibone, S., Genetu, R. M., O'Brien, L., Omar, Z., Perkins, E., Davies, K., Tetla, D., Shelley, B., Irvine, V., Williams, S., Williams, P., Goodsell, J., Tutton, R., Bough, L., Winter-Goodwin, B., Kitson, R., Pinnell, J., Wilson, A., Nortcliffe, T., Wood, T., Home, M., Holdroyd, K., Robinson, M., Shaw, R., Greig, J., Brady, M., Haigh, A., Matupe, L., Usher, M., Mellor, S., Dale, S., Gledhill, L., Shaw, L., Turner, G., Kelly, D., Anwar, B., Riley, H., Sturgeon, H., Ali, A., Thomis, L., Melia, D., Dance, A., Humphreys, S., Frost, I., Gopal, V., Godden, J., Holden, A., Swann, S., Smith, T., Clapham, M., Poultney, U., Harper, R., Rice, P., Reece-Anthony, R., Gurung, B., Moultrie, S., Odam, M., Mayer, A., Bellini, A., Pickard, A., Bryant, J., Roe, N., Sowter, J., Lang, K., Taylor, J., Barry, P., Hobrok, M., Tench, H., Wolf-Roberts, R., Mcguinness, H., Loosley, R., Hawcutt, D., Rad, L., O'Malley, L., Saunderson, P., Seddon, G., Anderson, T., Rogers, N., Ruddy, J., Harkins, M., Beith, C., Mcalpine, A., Ferguson, L., Grant, P., Macfadyen, S., Mclaughlin, M., Baird, T., Rundell, S., Welsh, B., Hamill, R., Fisher, F., Gregory, J., Campbell, A., Smuts, S., Kenneth Baillie, J., Carson, G., Alex, B., Bach, B., Barclay, W. S., Bogaert, D., Chand, M., Cooke, G. S., Docherty, A. B., Dunning, J., da Silva Filipe, A., Fletcher, T., Green, C. A., Harrison, E. M., Hiscox, J. A., Ho, A. Y. W., Horby, P. W., Ijaz, S., Khoo, S., Lim, W. S., Mentzer, A. J., Merson, L., Meynert, A. M., Noursadeghi, M., Palmarini, M., Paxton, W. A., Pollakis, G., Price, N., Rambaut, A., Robertson, D. L., Sancho-Shimizu, V., Scott, J. T., de Silva, T., Sigfrid, L., Solomon, T., Sriskandan, S., Stuart, D., Tedder, R. S., Thomson, E. C., Thompson, A. A. R., Thwaites, R. S., Turtle, L. C. W., Zambon, M., Hardwick, H., Donohue, C., Lyons, R., Norman, L., Pius, R., Drake, T. M., Fairfield, C. J., Knight, S. R., Mclean, K. A., Murphy, D., Shaw, C. A., Dalton, J., Girvan, M., Saviciute, E., Roberts, S., Harrison, J., Marsh, L., Connor, M., Halpin, S., Gamble, C., Leeming, G., Wham, M., Greenhalf, W., Shaw, V., Mcdonald, S., Ganna, A., Sulem, P., van Heel, D. A., Cordioli, M., Sveinbjornsson, G., Niemi, M. E. K., Shelton, J. F., Shastri, A. J., Ye, C., Weldon, C. H., Filshtein-Sonmez, T., Coker, D., Symons, A., Esparza-Gordillo, J., Aslibekyan, S., Auton, A., Krieger, J. E., Marques, E., Jannes, C. E., Mari, F., Daga, S., Baldassarri, M., Benetti, E., Furini, S., Fallerini, C., Fava, F., Valentino, F., Doddato, G., Giliberti, A., Tita, R., Amitrano, S., Bruttini, M., Croci, S., Meloni, I., Pinto, A. M., Frullanti, E., Mencarelli, M. A., Rizzo, C. L., Montagnani, F., Di Sarno, L., Tommasi, A., Palmieri, M., Emiliozzi, A., Fabbiani, M., Rossetti, B., Zanelli, G., Bargagli, E., Bergantini, L., D'Alessandro, M., Cameli, P., Bennet, D., Anedda, F., Marcantonio, S., Scolletta, S., Franchi, F., Mazzei, M. A., Guerrini, S., Conticini, E., Cantarini, L., Frediani, B., Tacconi, D., Spertilli, C., Feri, M., Donati, A., Scala, R., Guidelli, L., Spargi, G., Corridi, M., Nencioni, C., Croci, L., Caldarelli, G. P., Spagnesi, M., Piacentini, P., Bandini, M., Desanctis, E., Cappelli, S., Canaccini, A., Verzuri, A., Anemoli, V., Ognibene, A., Vaghi, M., D'Arminio Monforte, A., Merlini, E., Mondelli, M. U., Mantovani, S., Ludovisi, S., Girardis, M., Venturelli, S., Sita, M., Cossarizza, A., Antinori, A., Vergori, A., Rusconi, S., Siano, M., Gabrieli, A., Riva, A., Francisci, D., Schiaroli, E., Scotton, P. G., Andretta, F., Panese, S., Scaggiante, R., Gatti, F., Parisi, S. G., Castelli, F., Quiros-Roldan, M. E., Magro, P., Zanella, I., Della Monica, M., Piscopo, C., Capasso, M., Russo, R., Andolfo, I., Iolascon, A., Fiorentino, G., Carella, M., Castori, M., Merla, G., Aucella, F., Raggi, P., Marciano, C., Perna, R., Bassetti, M., Di Biagio, A., Sanguinetti, M., Masucci, L., Valente, S., Mandala, M., Giorli, A., Salerni, L., Zucchi, P., Parravicini, P., Menatti, E., Baratti, S., Trotta, T., Giannattasio, F., Coiro, G., Lena, F., Coviello, D. A., Mussini, C., Bosio, G., Martinelli, E., Mancarella, S., Tavecchia, L., Crotti, L., Picchiotti, N., Gori, M., Gabbi, C., Sanarico, M., Ceri, S., Pinoli, P., Raimondi, F., Biscarini, F., Stella, A., Shen, X., Ponting, C. P., Fawkes, A., Tenesa, A., Caulfield, M., Scott, R., Rowan, K., Murphy, L., Openshaw, P. J. M., Semple, M. G., Vitart, V., and Wilson, J. F.
Subjects: 0301 basic medicine, Male, CCR2, Chromosomes, Human, Pair 21, Genome-wide association study, Receptor, Interferon alpha-beta, Disease, Bioinformatics, Genome-wide association studies, 23andMe Investigators, Interferon alpha-beta, 0302 clinical medicine, Receptors, 2',5'-Oligoadenylate Synthetase, Pair 12, genetics, Lung, BRACOVID Investigators, Multidisciplinary, GenOMICC Investigators, Tyrosine kinase 2, 030220 oncology & carcinogenesis, Multigene Family, Medical genetics, Female, Dipeptidyl-Peptidases and Tripeptidyl-Peptidase, 5'-Oligoadenylate Synthetase, Human, Receptor, medicine.medical_specialty, Critical Care, Receptors, CCR2, General Science & Technology, Critical Illness, Chromosomes, 03 medical and health sciences, Intensive care, Mendelian randomization, Immunogenetics, medicine, Humans, Dipeptidyl-Peptidases and Tripeptidyl-Peptidases, Gen-COVID Investigators, Inflammation, TYK2 Kinase, Chromosomes, Human, Pair 12, Pair 19, SARS-CoV-2, business.industry, Drug Repositioning, COVID-19, United Kingdom, COVID-19 Human Genetics Initiative, 030104 developmental biology, Viral infection, Chromosomes, Human, Pair 19, Genome-Wide Association Study, Pharmacogenomics, ISARICC Investigators, Pair 21, 2', business
Abstract: Host-mediated lung inflammation is present1, and drives mortality2, in the critical illness caused by coronavirus disease 2019 (COVID-19). Host genetic variants associated with critical illness may identify mechanistic targets for therapeutic development3. Here we report the results of the GenOMICC (Genetics Of Mortality In Critical Care) genome-wide association study in 2,244 critically ill patients with COVID-19 from 208 UK intensive care units. We have identified and replicated the following new genome-wide significant associations: on chromosome 12q24.13 (rs10735079,P=1.65×10−8) in a gene cluster that encodes antiviral restriction enzyme activators (OAS1,OAS2andOAS3); on chromosome 19p13.2 (rs74956615,P=2.3×10−8) near the gene that encodes tyrosine kinase 2 (TYK2); on chromosome 19p13.3 (rs2109069,P=3.98× 10−12) within the gene that encodes dipeptidyl peptidase 9 (DPP9); and on chromosome 21q22.1 (rs2236757,P=4.99×10−8) in the interferon receptor geneIFNAR2. We identified potential targets for repurposing of licensed medications: using Mendelian randomization, we found evidence that low expression ofIFNAR2, or high expression ofTYK2, are associated with life-threatening disease; and transcriptome-wide association in lung tissue revealed that high expression of the monocyte–macrophage chemotactic receptorCCR2is associated with severe COVID-19. Our results identify robust genetic signals relating to key host antiviral defence mechanisms and mediators of inflammatory organ damage in COVID-19. Both mechanisms may be amenable to targeted treatment with existing drugs. However, large-scale randomized clinical trials will be essential before any change to clinical practice.
Published: 2020
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20. Bring on the bodyNET

Author: Chu, Bryant, Burnett, William, Chung, Jong Won, and Bao, Zhenan
Published: 2017
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21. Single-molecule sequencing of the desiccation--tolerant grass Oropetium thomaeum

Author: VanBuren, Robert, Bryant, Doug, Edger, Patrick P., Tang, Haibao, Burgess, Diane, Challabathula, Dinakar, Spittle, Kristi, Hall, Richard, Gu, Jenny, Lyons, Eric, Freeling, Michael, Bartels, Dorothea, Hallers, Boudewijn Ten, Hastie, Alex, Michael, Todd P., and Mockler, Todd C.
Subjects: Nucleotide sequencing -- Research, Plant genetics -- Research, Genomics -- Research, DNA sequencing -- Research, Genomes -- Research, Environmental issues, Science and technology, Zoology and wildlife conservation
Abstract: Plant genomes, and eukaryotic genomes in general, are typically repetitive, polyploid and heterozygous, which complicates genome assembly (1). The short read lengths of early Sanger and current next-generation sequencing platforms [...]
Published: 2015

22. Endosymbiotic origin and differential loss of eukaryotic genes

Author: Ku, Chuan, Nelson-Sathi, Shijulal, Roettger, Mayo, Sousa, Filipa L., Lockhart, Peter J., Bryant, David, Hazkani-Covo, Einat, McInerney, James O., Landan, Giddy, and Martin, William F.
Subjects: Genetic research, Eukaryotes -- Genetic aspects, Genetic transformation -- Research, Environmental issues, Science and technology, Zoology and wildlife conservation
Abstract: Chloroplasts arose from cyanobacteria, mitochondria arose from proteobacteria. Both organelles have conserved their prokaryotic biochemistry, but their genomes are reduced, and most organelle proteins are encoded in the nucleus. Endosymbiotic theory posits that bacterial genes in eukaryotic genomes entered the eukaryotic lineage via organelle ancestors. It predicts episodic influx of prokaryotic genes into the eukaryotic lineage, with acquisition corresponding to endosymbiotic events. Eukaryotic genome sequences, however, increasingly implicate lateral gene transfer, both from prokaryotes to eukaryotes and among eukaryotes, as a source of gene content variation in eukaryotic genomes, which predicts continuous, lineage-specific acquisition of prokaryotic genes in divergent eukaryotic groups. Here we discriminate between these two alternatives by clustering and phylogenetic analysis of eukaryotic gene families having prokaryotic homologues. Our results indicate (1) that gene transfer from bacteria to eukaryotes is episodic, as revealed by gene distributions, and coincides with major evolutionary transitions at the origin of chloroplasts and mitochondria; (2) that gene inheritance in eukaryotes is vertical, as revealed by extensive topological comparison, sparse gene distributions stemming from differential loss; and (3) that continuous, lineage-specific lateral gene transfer, although it sometimes occurs, does not contribute to long-term gene content evolution in eukaryotic genomes., In prokaryotes, inheritance involves recombination superimposed upon clonal growth (1) and the mechanisms of recombination are the mechanisms of lateral gene transfer (LGT): transformation, conjugation, transduction, and gene transfer agents [...]
Published: 2015
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23. Erosion of organic carbon in the arctic as a geological carbon dioxide sink

Author: Hilton, Robert G., Galy, Valier, Gaillardet, Jerome, Dellinger, Mathieu, Bryant, Charlotte, O'Regan, Matt, Grocke, Darren R., Coxall, Helen, Bouchez, Julien, and Calmels, Damien
Subjects: Marine sediments, Soils -- Carbon content, Carbon dioxide -- Environmental aspects, Air pollution, Environmental issues, Science and technology, Zoology and wildlife conservation
Abstract: Soils of the northern high latitudes store carbon over millennial timescales (thousands of years) and contain approximately double the carbon stock of the atmosphere (1-3). Warming and associated permafrost thaw can expose soil organic carbon and result in mineralization and carbon dioxide (C[O.sub.2]) release (4-6). However, some of this soil organic carbon may be eroded and transferred to rivers (7-9). If it escapes degradation during river transport and is buried in marine sediments, then it can contribute to a longer-term (more than ten thousand years), geological C[O.sub.2] sink (8-10). Despite this recognition, the erosional flux and fate of particulate organic carbon (POC) in large rivers at high latitudes remains poorly constrained. Here, we quantify the source of POC in the Mackenzie River, the main sediment supplier to the Arctic Ocean (11, 12), and assess its flux and fate. We combine measurements of radiocarbon, stable carbon isotopes and element ratios to correct for rock-derived POC (10, 13, 14). Our samples reveal that the eroded biospheric POC has resided in the basin for millennia, with a mean radiocarbon age of 5,800 ± 800 years, much older than the POC in large tropical rivers (13, 14). From the measured biospheric POC content and variability in annual sediment yield (15), we calculate a biospheric POC flux of [2.2.sup.+1.3.sub.-0.9] teragrams of carbon per year from the Mackenzie River, which is three times the C[O.sub.2] draw down by silicate weathering in this basin (16). Offshore, we find evidence for efficient terrestrial organic carbon burial over the Holocene period, suggesting that erosion of organic carbon-rich, high-latitude soils may result in an important geological C[O.sub.2] sink., Photosynthesis and the production of organic carbon by the terrestrial biosphere (O[C.sub.biosphere]) is a major pathway of atmospheric C[O.sub.2] drawdown. Over millennial timescales, some O[C.sub.biosphere] escapes oxidation and contributes to [...]
Published: 2015

24. Origins of major archaeal clades correspond to gene acquisitions from bacteria

Author: Nelson-Sathi, Shijulal, Sousa, Filipa L., Roettger, Mayo, Lozada-Chavez, Nabor, Thiergart, Thorsten, Janssen, Arnold, Bryant, David, Landan, Giddy, Schonheit, Peter, Siebers, Bettina, McInerney, James O., and Martin, William F.
Subjects: Archaeabacteria -- Genetic aspects -- Origin, Environmental issues, Science and technology, Zoology and wildlife conservation
Abstract: The mechanisms that underlie the origin of major prokaryotic groups are poorly understood. In principle, the origin of both species and higher taxa among prokaryotes should entail similar mechanisms--ecological interactions with the environment paired with natural genetic variation involving lineage-specific gene innovations and lineage-specific gene acquisitions (1-4). To investigate the origin of higher taxa in archaea, we have determined gene distributions and gene phylogenies for the 267,568 protein-coding genes of 134 sequenced archaeal genomes in the context of their homologues from 1,847 reference bacterial genomes. Archaeal-specific gene families define 13 traditionally recognized archaeal higher taxa in our sample. Here we report that the origins of these 13 groups unexpectedly correspond to 2,264 group-specific gene acquisitions from bacteria. Interdomain gene transfer is highly asymmetric, transfers from bacteria to archaea are more than fivefold more frequent than vice versa. Gene transfers identified at major evolutionary transitions among prokaryotes specifically implicate gene acquisitions for metabolic functions from bacteria as key innovations in the origin of higher archaeal taxa., Genome evolution in prokaryotes entails both tree-like components generated by vertical descent and network-like components generated by lateral gene transfer (LGT) (5,6). Both processes operate in the formation of prokaryotic [...]
Published: 2015
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25. A mouse-adapted model of SARS-CoV-2 to test COVID-19 countermeasures

Author: Alexandra Schäfer, Boyd Yount, Ariane J. Brown, Caitlin E. Edwards, Stephanie A. Montgomery, Ande West, Ralph S. Baric, Kendra Gully, Yixuan J. Hou, David R. Martinez, Lily E. Adams, Jeffrey S. Glenn, Matthew D. Bryant, Emily Huang, Lisa E. Gralinski, Timothy P. Sheahan, Ingrid Choong, Sarah R. Leist, and Kenneth H. Dinnon
Subjects: Male, Models, Molecular, 0301 basic medicine, Genetically modified mouse, Aging, Virus genetics, COVID-19 Vaccines, Transgene, viruses, Pneumonia, Viral, Mice, Transgenic, Disease, Peptidyl-Dipeptidase A, Recombinant virus, Article, Betacoronavirus, Mice, 03 medical and health sciences, 0302 clinical medicine, Animals, Humans, skin and connective tissue diseases, Receptor, Pandemics, Mice, Inbred BALB C, Multidisciplinary, biology, SARS-CoV-2, Interleukins, fungi, COVID-19, Interferon-alpha, virus diseases, Forkhead Transcription Factors, Viral Vaccines, biology.organism_classification, Phenotype, Virology, respiratory tract diseases, Disease Models, Animal, 030104 developmental biology, Receptors, Virus, Female, Angiotensin-Converting Enzyme 2, Interferons, Coronavirus Infections, 030217 neurology & neurosurgery
Abstract: Coronaviruses are prone to transmission to new host species, as recently demonstrated by the spread to humans of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the causative agent of the coronavirus disease 2019 (COVID-19) pandemic1. Small animal models that recapitulate SARS-CoV-2 disease are needed urgently for rapid evaluation of medical countermeasures2,3. SARS-CoV-2 cannot infect wild-type laboratory mice owing to inefficient interactions between the viral spike protein and the mouse orthologue of the human receptor, angiotensin-converting enzyme 2 (ACE2)4. Here we used reverse genetics5 to remodel the interaction between SARS-CoV-2 spike protein and mouse ACE2 and designed mouse-adapted SARS-CoV-2 (SARS-CoV-2 MA), a recombinant virus that can use mouse ACE2 for entry into cells. SARS-CoV-2 MA was able to replicate in the upper and lower airways of both young adult and aged BALB/c mice. SARS-CoV-2 MA caused more severe disease in aged mice, and exhibited more clinically relevant phenotypes than those seen in Hfh4-ACE2 transgenic mice, which express human ACE2 under the control of the Hfh4 (also known as Foxj1) promoter. We demonstrate the utility of this model using vaccine-challenge studies in immune-competent mice with native expression of mouse ACE2. Finally, we show that the clinical candidate interferon-λ1a (IFN-λ1a) potently inhibits SARS-CoV-2 replication in primary human airway epithelial cells in vitro-both prophylactic and therapeutic administration of IFN-λ1a diminished SARS-CoV-2 replication in mice. In summary, the mouse-adapted SARS-CoV-2 MA model demonstrates age-related disease pathogenesis and supports the clinical use of pegylated IFN-λ1a as a treatment for human COVID-196.
Published: 2020

26. Pre-Columbian mycobacterial genomes reveal seals as a source of New World human tuberculosis

Author: Bos, Kirsten I., Harkins, Kelly M., Herbig, Alexander, Coscolla, Mireia, Weber, Nico, Comas, Inaki, Forrest, Stephen A., Bryant, Josephine M., Harris, Simon R., Schuenemann, Verena J., Campbell, Tessa J., Majander, Kerttu, Wilbur, Alicia K., Guichon, Ricardo A., Steadman, Dawnie L. Wolfe, Cook, Della Collins, Niemann, Stefan, Behr, Marcel A., Zumarraga, Martin, Bastida, Ricardo, Huson, Daniel, Nieselt, Kay, Young, Douglas, Parkhill, Julian, Buikstra, Jane E., Gagneux, Sebastien, Stone, Anne C., and Krause, Johannes
Subjects: Mycobacterium -- Genetic aspects -- Health aspects, Genetic research, Mycobacteria -- Genetic aspects -- Health aspects, Genomes -- Research, Tuberculosis -- Causes of -- Genetic aspects, Environmental issues, Science and technology, Zoology and wildlife conservation
Abstract: Modern strains of Mycobacterium tuberculosis from the Americas are closely related to those from Europe, supporting the assumption that human tuberculosis was introduced post-contact (1). This notion, however, is incompatible with archaeological evidence of pre-contact tuberculosis in the New World (2). Comparative genomics of modern isolates suggests that M. tuberculosisattained its worldwide distribution following human dispersals out of Africa during the Pleistocene epoch (3), although this has yet to be confirmed with ancient calibration points. Here we present three 1,000-year-old mycobacterial genomes from Peruvian human skeletons, revealing that a member of the M. tuberculosis complex caused human disease before contact. The ancient strains are distinct from known human-adapted forms and are most closely related to those adapted to seals and sea lions. Two independent dating approaches suggest a most recent common ancestor for the M. tuberculosis complex less than 6,000 years ago, which supports a Holocene dispersal of the disease. Our results implicate sea mammals as having played a role in transmitting the disease to humans across the ocean., Mycobacterium tuberculosis has had a long history with humans, although consensus has not been reached on when this interaction began (1, 3, 4). Previous models held that the human-adapted pathogen [...]
Published: 2014

27. Architecture and evolution of a minute plant genome

Author: Ibarra-Laclette, Enrique, Lyons, Eric, Hernandez-Guzman, Gustavo, Perez-Torres, Claudia Anahi, Carretero-Paulet, Lorenzo, Chang, Tien-Hao, Lan, Tianying, Welch, Andreanna J., Juarez, Maria Jazmin Abraham, Simpson, June, Fernandez-Cortes, Araceli, Arteaga-Vazquez, Mario, Gongora-Castillo, Elsa, Acevedo-Hernandez, Gustavo, Schuster, Stephan C., Himmelbauer, Heinz, Minoche, Andre E., Xu, Sen, Lynch, Michael, Oropeza-Aburto, Araceli, Cervantes-Perez, Sergio Alan, de Jesiis Ortega- Estrada, Maria, Cervantes-Luevano, Jacob Israel, Michael, Todd P., Mockler, Todd, Bryant, Douglas, Herrera-Estrella, Alfredo, Albert, Victor A., and Herrera-Estrella, Luis
Subjects: Plant genetics -- Research, Nucleotide sequencing -- Analysis, DNA sequencing -- Analysis, Evolutionary genetics -- Research, Environmental issues, Science and technology, Zoology and wildlife conservation
Abstract: It has been argued that the evolution of plant genome size is principally unidirectional and increasing owing to the varied action of whole-genome duplications (WGDs) and mobile element proliferation (1). [...]
Published: 2013

28. Impact of caloric restriction on health and survival in rhesus monkeys from the NIA study

Author: Mattison, Julie A., Roth, George S., Beasley, T. Mark, Tilmont, Edward M., Handy, April M., Herbert, Richard L., Longo, Dan L., Allison, David B., Young, Jennifer E., Bryant, Mark, Barnard, Dennis, Ward, Walter F., Qi, Wenbo, Ingram, Donald K., and de Cabo, Rafael
Subjects: United States. National Institute on Aging -- Reports, Rhesus monkey -- Health aspects -- Physiological aspects, Low-calorie diet -- Health aspects -- Physiological aspects, Environmental issues, Science and technology, Zoology and wildlife conservation
Abstract: Calorie restriction (CR), a reduction of 10-40% in intake of a nutritious diet, is often reported as the most robust non-genetic mechanism to extend lifespan and healthspan. CR is frequently [...]
Published: 2012

29. Comprehensive molecular profiling of lung adenocarcinoma

Author: Collisson, Eric A., Campbell, Joshua D., Brooks, Angela N., Berger, Alice H., Lee, William, Chmielecki, Juliann, Beer, David G., Cope, Leslie, Creighton, Chad J., Danilova, Ludmila, Ding, Li, Getz, Gad, Hammerman, Peter S., Neil Hayes, D., Hernandez, Bryan, Herman, James G., Heymach, John V., Jurisica, Igor, Kucherlapati, Raju, Kwiatkowski, David, Ladanyi, Marc, Robertson, Gordon, Schultz, Nikolaus, Shen, Ronglai, Sinha, Rileen, Sougnez, Carrie, Tsao, Ming-Sound, Travis, William D., Weinstein, John N., Wigle, Dennis A., Wilkerson, Matthew D., Chu, Andy, Cherniack, Andrew D., Hadjipanayis, Angela, Rosenberg, Mara, Weisenberger, Daniel J., Laird, Peter W., Radenbaugh, Amie, Ma, Singer, Stuart, Joshua M., Averett Byers, Lauren, Baylin, Stephen B., Govindan, Ramaswamy, Meyerson, Matthew, Rosenberg, Mara, Gabriel, Stacey B., Cibulskis, Kristian, Sougnez, Carrie, Kim, Jaegil, Stewart, Chip, Lichtenstein, Lee, Lander, Eric S., Lawrence, Michael S., Getz, Gad, Kandoth, Cyriac, Fulton, Robert, Fulton, Lucinda L., McLellan, Michael D., Wilson, Richard K., Ye, Kai, Fronick, Catrina C., Maher, Christopher A., Miller, Christopher A., Wendl, Michael C., Cabanski, Christopher, Ding, Li, Mardis, Elaine, Govindan, Ramaswamy, Creighton, Chad J., Wheeler, David, Balasundaram, Miruna, Butterfield, Yaron S. N., Carlsen, Rebecca, Chu, Andy, Chuah, Eric, Dhalla, Noreen, Guin, Ranabir, Hirst, Carrie, Lee, Darlene, Li, Haiyan I., Mayo, Michael, Moore, Richard A., Mungall, Andrew J., Schein, Jacqueline E., Sipahimalani, Payal, Tam, Angela, Varhol, Richard, Gordon Robertson, A., Wye, Natasja, Thiessen, Nina, Holt, Robert A., Jones, Steven J. M., Marra, Marco A., Campbell, Joshua D., Brooks, Angela N., Chmielecki, Juliann, Imielinski, Marcin, Onofrio, Robert C., Hodis, Eran, Zack, Travis, Sougnez, Carrie, Helman, Elena, Sekhar Pedamallu, Chandra, Mesirov, Jill, Cherniack, Andrew D., Saksena, Gordon, Schumacher, Steven E., Carter, Scott L., Hernandez, Bryan, Garraway, Levi, Beroukhim, Rameen, Gabriel, Stacey B., Getz, Gad, Meyerson, Matthew, Hadjipanayis, Angela, Lee, Semin, Mahadeshwar, Harshad S., Pantazi, Angeliki, Protopopov, Alexei, Ren, Xiaojia, Seth, Sahil, Song, Xingzhi, Tang, Jiabin, Yang, Lixing, Zhang, Jianhua, Chen, Peng-Chieh, Parfenov, Michael, Wei Xu, Andrew, Santoso, Netty, Chin, Lynda, Park, Peter J., Kucherlapati, Raju, Hoadley, Katherine A., Todd Auman, J., Meng, Shaowu, Shi, Yan, Buda, Elizabeth, Waring, Scot, Veluvolu, Umadevi, Tan, Donghui, Mieczkowski, Piotr A., Jones, Corbin D., Simons, Janae V., Soloway, Matthew G., Bodenheimer, Tom, Jefferys, Stuart R., Roach, Jeffrey, Hoyle, Alan P., Wu, Junyuan, Balu, Saianand, Singh, Darshan, Prins, Jan F., Marron, J. S., Parker, Joel S., Neil Hayes, D., Perou, Charles M., Liu, Jinze, Cope, Leslie, Danilova, Ludmila, Weisenberger, Daniel J., Maglinte, Dennis T., Lai, Philip H., Bootwalla, Moiz S., Van Den Berg, David J., Triche Jr, Timothy, Baylin, Stephen B., Laird, Peter W., Rosenberg, Mara, Chin, Lynda, Zhang, Jianhua, Cho, Juok, DiCara, Daniel, Heiman, David, Lin, Pei, Mallard, William, Voet, Douglas, Zhang, Hailei, Zou, Lihua, Noble, Michael S., Lawrence, Michael S., Saksena, Gordon, Gehlenborg, Nils, Thorvaldsdottir, Helga, Mesirov, Jill, Nazaire, Marc-Danie, Robinson, Jim, Getz, Gad, Lee, William, Arman Aksoy, B., Ciriello, Giovanni, Taylor, Barry S., Dresdner, Gideon, Gao, Jianjiong, Gross, Benjamin, Seshan, Venkatraman E., Ladanyi, Marc, Reva, Boris, Sinha, Rileen, Onur Sumer, S., Weinhold, Nils, Schultz, Nikolaus, Shen, Ronglai, Sander, Chris, Ng, Sam, Ma, Singer, Zhu, Jingchun, Radenbaugh, Amie, Stuart, Joshua M., Benz, Christopher C., Yau, Christina, Haussler, David, Spellman, Paul T., Wilkerson, Matthew D., Parker, Joel S., Hoadley, Katherine A., Kimes, Patrick K., Neil Hayes, D., Perou, Charles M., Broom, Bradley M., Wang, Jing, Lu, Yiling, Kwok Shing Ng, Patrick, Diao, Lixia, Averett Byers, Lauren, Liu, Wenbin, Heymach, John V., Amos, Christopher I., Weinstein, John N., Akbani, Rehan, Mills, Gordon B., Curley, Erin, Paulauskis, Joseph, Lau, Kevin, Morris, Scott, Shelton, Troy, Mallery, David, Gardner, Johanna, Penny, Robert, Saller, Charles, Tarvin, Katherine, Richards, William G., Cerfolio, Robert, Bryant, Ayesha, Raymond, Daniel P., Pennell, Nathan A., Farver, Carol, Czerwinski, Christine, Huelsenbeck-Dill, Lori, Iacocca, Mary, Petrelli, Nicholas, Rabeno, Brenda, Brown, Jennifer, Bauer, Thomas, Dolzhanskiy, Oleg, Potapova, Olga, Rotin, Daniil, Voronina, Olga, Nemirovich-Danchenko, Elena, Fedosenko, Konstantin V., Gal, Anthony, Behera, Madhusmita, Ramalingam, Suresh S., Sica, Gabriel, Flieder, Douglas, Boyd, Jeff, Weaver, JoEllen, Kohl, Bernard, Huy Quoc Thinh, Dang, Sandusky, George, Juhl, Hartmut, Duhig, Edwina, Illei, Peter, Gabrielson, Edward, Shin, James, Lee, Beverly, Rogers, Kristen, Trusty, Dante, Brock, Malcolm V., Williamson, Christina, Burks, Eric, Rieger-Christ, Kimberly, Holway, Antonia, Sullivan, Travis, Wigle, Dennis A., Asiedu, Michael K., Kosari, Farhad, Travis, William D., Rekhtman, Natasha, Zakowski, Maureen, Rusch, Valerie W., Zippile, Paul, Suh, James, Pass, Harvey, Goparaju, Chandra, Owusu-Sarpong, Yvonne, Bartlett, John M. S., Kodeeswaran, Sugy, Parfitt, Jeremy, Sekhon, Harmanjatinder, Albert, Monique, Eckman, John, Myers, Jerome B., Cheney, Richard, Morrison, Carl, Gaudioso, Carmelo, Borgia, Jeffrey A., Bonomi, Philip, Pool, Mark, Liptay, Michael J., Moiseenko, Fedor, Zaytseva, Irina, Dienemann, Hendrik, Meister, Michael, Schnabel, Philipp A., Muley, Thomas R., Peifer, Martin, Gomez-Fernandez, Carmen, Herbert, Lynn, Egea, Sophie, Huang, Mei, Thorne, Leigh B., Boice, Lori, Hill Salazar, Ashley, Funkhouser, William K., Kimryn Rathmell, W., Dhir, Rajiv, Yousem, Samuel A., Dacic, Sanja, Schneider, Frank, Siegfried, Jill M., Hajek, Richard, Watson, Mark A., McDonald, Sandra, Meyers, Bryan, Clarke, Belinda, Yang, Ian A., Fong, Kwun M., Hunter, Lindy, Windsor, Morgan, Bowman, Rayleen V., Peters, Solange, Letovanec, Igor, Khan, Khurram Z., Jensen, Mark A., Snyder, Eric E., Srinivasan, Deepak, Kahn, Ari B., Baboud, Julien, Pot, David A., Mills Shaw, Kenna R., Sheth, Margi, Davidsen, Tanja, Demchok, John A., Yang, Liming, Wang, Zhining, Tarnuzzer, Roy, Claude Zenklusen, Jean, Ozenberger, Bradley A., Sofia, Heidi J., Travis, William D., Cheney, Richard, Clarke, Belinda, Dacic, Sanja, Duhig, Edwina, Funkhouser, William K., Illei, Peter, Farver, Carol, Rekhtman, Natasha, Sica, Gabriel, Suh, James, and Tsao, Ming-Sound
Published: 2014
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30. Autoantibodies against type I IFNs in humans with alternative NF-κB pathway deficiency

Author: Le Voyer, Tom, Parent, Audrey V., Liu, Xian, Cederholm, Axel, Gervais, Adrian, Rosain, Jérémie, Nguyen, Tina, Perez Lorenzo, Malena, Rackaityte, Elze, Rinchai, Darawan, Zhang, Peng, Bizien, Lucy, Hancioglu, Gonca, Ghillani-Dalbin, Pascale, Charuel, Jean-Luc, Philippot, Quentin, Gueye, Mame Sokhna, Maglorius Renkilaraj, Majistor Raj Luxman, Ogishi, Masato, Soudée, Camille, Migaud, Mélanie, Rozenberg, Flore, Momenilandi, Mana, Riller, Quentin, Imberti, Luisa, Delmonte, Ottavia M., Müller, Gabriele, Keller, Baerbel, Orrego, Julio, Franco Gallego, William Alexander, Rubin, Tamar, Emiroglu, Melike, Parvaneh, Nima, Eriksson, Daniel, Aranda-Guillen, Maribel, Berrios, David I., Vong, Linda, Katelaris, Constance H., Mustillo, Peter, Raedler, Johannes, Bohlen, Jonathan, Bengi Celik, Jale, Astudillo, Camila, Winter, Sarah, McLean, Catriona, Guffroy, Aurélien, DeRisi, Joseph L., Yu, David, Miller, Corey, Feng, Yi, Guichard, Audrey, Béziat, Vivien, Bustamante, Jacinta, Pan-Hammarström, Qiang, Zhang, Yu, Rosen, Lindsey B., Holland, Steve M., Bosticardo, Marita, Kenney, Heather, Castagnoli, Riccardo, Slade, Charlotte A., Boztuğ, Kaan, Mahlaoui, Nizar, Latour, Sylvain, Abraham, Roshini S., Lougaris, Vassilios, Hauck, Fabian, Sediva, Anna, Atschekzei, Faranaz, Sogkas, Georgios, Poli, M. Cecilia, Slatter, Mary A., Palterer, Boaz, Keller, Michael D., Pinzon-Charry, Alberto, Sullivan, Anna, Droney, Luke, Suan, Daniel, Wong, Melanie, Kane, Alisa, Hu, Hannah, Ma, Cindy, Grombiříková, Hana, Ciznar, Peter, Dalal, Ilan, Aladjidi, Nathalie, Hie, Miguel, Lazaro, Estibaliz, Franco, Jose, Keles, Sevgi, Malphettes, Marion, Pasquet, Marlene, Maccari, Maria Elena, Meinhardt, Andrea, Ikinciogullari, Aydan, Shahrooei, Mohammad, Celmeli, Fatih, Frosk, Patrick, Goodnow, Christopher C., Gray, Paul E., Belot, Alexandre, Kuehn, Hye Sun, Rosenzweig, Sergio D., Miyara, Makoto, Licciardi, Francesco, Servettaz, Amélie, Barlogis, Vincent, Le Guenno, Guillaume, Herrmann, Vera-Maria, Kuijpers, Taco, Ducoux, Grégoire, Sarrot-Reynauld, Françoise, Schuetz, Catharina, Cunningham-Rundles, Charlotte, Rieux-Laucat, Frédéric, Tangye, Stuart G., Sobacchi, Cristina, Doffinger, Rainer, Warnatz, Klaus, Grimbacher, Bodo, Fieschi, Claire, Berteloot, Laureline, Bryant, Vanessa L., Trouillet Assant, Sophie, Su, Helen, Neven, Benedicte, Abel, Laurent, Zhang, Qian, Boisson, Bertrand, Cobat, Aurélie, Jouanguy, Emmanuelle, Kampe, Olle, Bastard, Paul, Roifman, Chaim M., Landegren, Nils, Notarangelo, Luigi D., Anderson, Mark S., Casanova, Jean-Laurent, and Puel, Anne
Abstract: Patients with autoimmune polyendocrinopathy syndrome type 1 (APS-1) caused by autosomal recessive AIRE deficiency produce autoantibodies that neutralize type I interferons (IFNs)1,2, conferring a predisposition to life-threatening COVID-19 pneumonia3. Here we report that patients with autosomal recessive NIK or RELB deficiency, or a specific type of autosomal-dominant NF-κB2 deficiency, also have neutralizing autoantibodies against type I IFNs and are at higher risk of getting life-threatening COVID-19 pneumonia. In patients with autosomal-dominant NF-κB2 deficiency, these autoantibodies are found only in individuals who are heterozygous for variants associated with both transcription (p52 activity) loss of function (LOF) due to impaired p100 processing to generate p52, and regulatory (IκBδ activity) gain of function (GOF) due to the accumulation of unprocessed p100, therefore increasing the inhibitory activity of IκBδ (hereafter, p52LOF/IκBδGOF). By contrast, neutralizing autoantibodies against type I IFNs are not found in individuals who are heterozygous for NFKB2variants causing haploinsufficiency of p100 and p52 (hereafter, p52LOF/IκBδLOF) or gain-of-function of p52 (hereafter, p52GOF/IκBδLOF). In contrast to patients with APS-1, patients with disorders of NIK, RELB or NF-κB2 have very few tissue-specific autoantibodies. However, their thymuses have an abnormal structure, with few AIRE-expressing medullary thymic epithelial cells. Human inborn errors of the alternative NF-κB pathway impair the development of AIRE-expressing medullary thymic epithelial cells, thereby underlying the production of autoantibodies against type I IFNs and predisposition to viral diseases.
Published: 2023
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31. Evidence of Xist RNA-independent initiation of mouse imprinted X-chromosome inactivation

Author: Kalantry, Sundeep, Purushothamant, Sonya, Bowen, Randall Bryant, Starmer, Joshua, and Magnuson, Terry
Subjects: Gene expression -- Research -- Physiological aspects -- Genetic aspects, X chromosome inactivation -- Physiological aspects -- Genetic aspects -- Research, RNA -- Physiological aspects -- Research -- Genetic aspects, X chromosome -- Physiological aspects -- Genetic aspects -- Research, Environmental issues, Science and technology, Zoology and wildlife conservation, Physiological aspects, Research, Genetic aspects
Abstract: XX female mammals undergo transcriptional silencing of most genes on one of their two X chromosomes to equalize X-linked gene dosage with XY males in a process referred to as [...]
Published: 2009

32. K2P2.1 (TREK-1)activator complexes reveal a cryptic selectivity filter binding site

Author: Lolicato, Marco, Arrigoni, Cristina, Mori, Takahiro, Sekioka, Yoko, Bryant, Clifford, Clark, Kimberly A., and Minor, Daniel L., Jr
Subjects: Binding sites (Biochemistry) -- Observations, Environmental issues, Science and technology, Zoology and wildlife conservation
Abstract: Author(s): Marco Lolicato [1]; Cristina Arrigoni [1]; Takahiro Mori [2]; Yoko Sekioka [2]; Clifford Bryant [3]; Kimberly A. Clark [1]; Daniel L. Minor, Jr (corresponding author) [1, 4, 5, 6, [...]
Published: 2017
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33. Evolution of genes and genomes on the Drosophila phylogeny

Author: Clark, Andrew G., Eisen, Michael B., Smith, Douglas R., Bergman, Casey M., Oliver, Brian, Markow, Therese A., Kaufman, Thomas C., Kellis, Manolis, Gelbart, William, Iyer, Venky N., Pollard, Daniel A., Sackton, Timothy B., Larracuente, Amanda M., Singh, Nadia D., Abad, Jose P., Abt, Dawn N., Adryan, Boris, Aguade, Montserrat, Akashi, Hiroshi, Anderson, Wyatt W., Aquadro, Charles F., Ardell, David H., Arguello, Roman, Artieri, Carlo G., Barbash, Daniel A., Barker, Daniel, Barsanti, Paolo, Batterham, Phil, Batzoglou, Serafim, Begun, Dave, Bhutkar, Arjun, Blanco, Enrico, Bosak, Stephanie A., Bradley, Robert K., Brand, Adrianne D., Brent, Michael R., Brooks, Angela N., Brown, Randall H., Butlin, Roger K., Caggese, Corrado, Calvi, Brian R., Bernardo de Carvalho, A., Caspi, Anat, Castrezana, Sergio, Celniker, Susan E., Chang, Jean L., Chapple, Charles, Chatterji, Sourav, Chinwalla, Asif, Civetta, Alberto, Clifton, Sandra W., Comeron, Josep M., Costello, James C., Coyne, Jerry A., Daub, Jennifer, David, Robert G., Delcher, Arthur L., Delehaunty, Kim, Do, Chuong B., Ebling, Heather, Edwards, Kevin, Eickbush, Thomas, Evans, Jay D., Filipski, Alan, Findeiß, Sven, Freyhult, Eva, Fulton, Lucinda, Fulton, Robert, Garcia, Ana C. L., Gardiner, Anastasia, Garfield, David A., Garvin, Barry E., Gibson, Greg, Gilbert, Don, Gnerre, Sante, Godfrey, Jennifer, Good, Robert, Gotea, Valer, Gravely, Brenton, Greenberg, Anthony J., Griffiths-Jones, Sam, Gross, Samuel, Guigo, Roderic, Gustafson, Erik A., Haerty, Wilfried, Hahn, Matthew W., Halligan, Daniel L., Halpern, Aaron L., Halter, Gillian M., Han, Mira V., Heger, Andreas, Hillier, LaDeana, Hinrichs, Angie S., Holmes, Ian, Hoskins, Roger A., Hubisz, Melissa J., Hultmark, Dan, Huntley, Melanie A., Jaffe, David B., Jagadeeshan, Santosh, Jeck, William R., Johnson, Justin, Jones, Corbin D., Jordan, William C., Karpen, Gary H., Kataoka, Eiko, Keightley, Peter D., Kheradpour, Pouya, Kirkness, Ewen F., Koerich, Leonardo B., Kristiansen, Karsten, Kudrna, Dave, Kulathinal, Rob J., Kumar, Sudhir, Kwok, Roberta, Lander, Eric, Langley, Charles H., Lapoint, Richard, Lazzaro, Brian P., Lee, So-Jeong, Levesque, Lisa, Li, Ruiqiang, Lin, Chiao-Feng, Lin, Michael F., Lindblad-Toh, Kerstin, Llopart, Ana, Long, Manyuan, Low, Lloyd, Lozovsky, Elena, Lu, Jian, Luo, Meizhong, Machado, Carlos A., Makalowski, Wojciech, Marzo, Mar, Matsuda, Muneo, Matzkin, Luciano, McAllister, Bryant, McBride, Carolyn S., McKernan, Brendan, McKernan, Kevin, Mendez-Lago, Maria, Minx, Patrick, Mollenhauer, Michael U., Montooth, Kristi, Mount, Stephen M., Mu, Xu, Myers, Eugene, Negre, Barbara, Newfeld, Stuart, Nielsen, Rasmus, Noor, Mohamed A. F., O'Grady, Patrick, Pachter, Lior, Papaceit, Montserrat, Parisi, Matthew J., Parisi, Michael, Parts, Leopold, Pedersen, Jakob S., Pesole, Graziano, Phillippy, Adam M., Ponting, Chris P., Pop, Mihai, Porcelli, Damiano, Powell, Jeffrey R., Prohaska, Sonja, Pruitt, Kim, Puig, Marta, Quesneville, Hadi, Ravi Ram, Kristipati, Rand, David, Rasmussen, Matthew D., Reed, Laura K., Reenan, Robert, Reily, Amy, Remington, Karin A., Rieger, Tania T., Ritchie, Michael G., Robin, Charles, Rogers, Yu-Hui, Rohde, Claudia, Rozas, Julio, Rubenfield, Marc J., Ruiz, Alfredo, Russo, Susan, Salzberg, Steven L., Sanchez-Gracia, Alejandro, Saranga, David J., Sato, Hajime, Schaeffer, Stephen W., Schatz, Michael C., Schlenke, Todd, Schwartz, Russell, Segarra, Carmen, Singh, Rama S., Sirot, Laura, Sirota, Marina, Sisneros, Nicholas B., Smith, Chris D., Smith, Temple F., Spieth, John, Stage, Deborah E., Stark, Alexander, Stephan, Wolfgang, Strausberg, Robert L., Strempel, Sebastian, Sturgill, David, Sutton, Granger, Sutton, Granger G., Tao, Wei, Teichmann, Sarah, Tobari, Yoshiko N., Tomimura, Yoshihiko, Tsolas, Jason M., Valente, Vera L. S., Venter, Eli, Craig Venter, J., Vicario, Saverio, Vieira, Filipe G., Vilella, Albert J., Villasante, Alfredo, Walenz, Brian, Wang, Jun, Wasserman, Marvin, Watts, Thomas, Wilson, Derek, Wilson, Richard K., Wing, Rod A., Wolfner, Mariana F., Wong, Alex, Ka-Shu Wong, Gane, Wu, Chung-I, Wu, Gabriel, Yamamoto, Daisuke, Yang, Hsiao-Pei, Yang, Shiaw-Pyng, Yorke, James A., Yoshida, Kiyohito, Zdobnov, Evgeny, Zhang, Peili, Zhang, Yu, Zimin, Aleksey V., Baldwin, Jennifer, Abdouelleil, Amr, Abdulkadir, Jamal, Abebe, Adal, Abera, Brikti, Abreu, Justin, Christophe Acer, St, Aftuck, Lynne, Alexander, Allen, An, Peter, Anderson, Erica, Anderson, Scott, Arachi, Harindra, Azer, Marc, Bachantsang, Pasang, Barry, Andrew, Bayul, Tashi, Berlin, Aaron, Bessette, Daniel, Bloom, Toby, Blye, Jason, Boguslavskiy, Leonid, Bonnet, Claude, Boukhgalter, Boris, Bourzgui, Imane, Brown, Adam, Cahill, Patrick, Channer, Sheridon, Cheshatsang, Yama, Chuda, Lisa, Citroen, Mieke, Collymore, Alville, Cooke, Patrick, Costello, Maura, D'Aco, Katie, Daza, Riza, De Haan, Georgius, DeGray, Stuart, DeMaso, Christina, Dhargay, Norbu, Dooley, Kimberly, Dooley, Erin, Doricent, Missole, Dorje, Passang, Dorjee, Kunsang, Dupes, Alan, Elong, Richard, Falk, Jill, Farina, Abderrahim, Faro, Susan, Ferguson, Diallo, Fisher, Sheila, Foley, Chelsea D., Franke, Alicia, Friedrich, Dennis, Gadbois, Loryn, Gearin, Gary, Gearin, Christina R., Giannoukos, Georgia, Goode, Tina, Graham, Joseph, Grandbois, Edward, Grewal, Sharleen, Gyaltsen, Kunsang, Hafez, Nabil, Hagos, Birhane, Hall, Jennifer, Henson, Charlotte, Hollinger, Andrew, Honan, Tracey, Huard, Monika D., Hughes, Leanne, Hurhula, Brian, Erii Husby, M, Kamat, Asha, Kanga, Ben, Kashin, Seva, Khazanovich, Dmitry, Kisner, Peter, Lance, Krista, Lara, Marcia, Lee, William, Lennon, Niall, Letendre, Frances, LeVine, Rosie, Lipovsky, Alex, Liu, Xiaohong, Liu, Jinlei, Liu, Shangtao, Lokyitsang, Tashi, Lokyitsang, Yeshi, Lubonja, Rakela, Lui, Annie, MacDonald, Pen, Magnisalis, Vasilia, Maru, Kebede, Matthews, Charles, McCusker, William, McDonough, Susan, Mehta, Teena, Meldrim, James, Meneus, Louis, Mihai, Oana, Mihalev, Atanas, Mihova, Tanya, Mittelman, Rachel, Mlenga, Valentine, Montmayeur, Anna, Mulrain, Leonidas, Navidi, Adam, Naylor, Jerome, Negash, Tamrat, Nguyen, Thu, Nguyen, Nga, Nicol, Robert, Norbu, Choe, Norbu, Nyima, Novod, Nathaniel, O'Neill, Barry, Osman, Sahal, Markiewicz, Eva, Oyono, Otero L., Patti, Christopher, Phunkhang, Pema, Pierre, Fritz, Priest, Margaret, Raghuraman, Sujaa, Rege, Filip, Reyes, Rebecca, Rise, Cecil, Rogov, Peter, Ross, Keenan, Ryan, Elizabeth, Settipalli, Sampath, Shea, Terry, Sherpa, Ngawang, Shi, Lu, Shih, Diana, Sparrow, Todd, Spaulding, Jessica, Stalker, John, Stange-Thomann, Nicole, Stavropoulos, Sharon, Stone, Catherine, Strader, Christopher, Tesfaye, Senait, Thomson, Talene, Thoulutsang, Yama, Thoulutsang, Dawa, Topham, Kerri, Topping, Ira, Tsamla, Tsamla, Vassiliev, Helen, Vo, Andy, Wangchuk, Tsering, Wangdi, Tsering, Weiand, Michael, Wilkinson, Jane, Wilson, Adam, Yadav, Shailendra, Young, Geneva, Yu, Qing, Zembek, Lisa, Zhong, Danni, Zimmer, Andrew, Zwirko, Zac, Alvarez, Pablo, Brockman, Will, Butler, Jonathan, Chin, CheeWhye, Grabherr, Manfred, Kleber, Michael, Mauceli, Evan, and MacCallum, Iain
Subjects: Environmental issues, Science and technology, Zoology and wildlife conservation
Abstract: Author(s): Drosophila 12 Genomes Consortium; Project Leaders; Andrew G. Clark (corresponding author) [1]; Michael B. Eisen (corresponding author) [2, 3]; Douglas R. Smith (corresponding author) [4]; Casey M. Bergman (corresponding [...]
Published: 2007
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34. Functional genomic landscape of acute myeloid leukaemia

Author: Robert H. Collins, Deirdre Devine, Beth Wilmot, Justin Ramsdill, Erik Segerdell, Bruno C. Medeiros, Brian J. Druker, Dylan Nelson, Micaela E. Martinez, Ryan C. Johnson, Robert Schuff, Robert P. Searles, Scott Weir, James Dibb, Elie Traer, Pierrette Lo, Haijiao Zhang, Rachel Henson, Tara A. Macey, Isabel English, Cody Coblentz, Christopher A. Eide, Ceilidh Nichols, Aurora Blucher, Ryan M. Winters, David L. Wiest, Corinne Visser, Michael W. Deininger, Stephen E. Kurtz, Daniel A. Pollyea, Justin M. Watts, Amy S. Carlos, Denise C. Connolly, Andy Kaempf, Angela Rofelty, Samuel B. Luty, Rachel J. Cook, Jill Peters, Kristen Werth, Shannon K. McWeeney, Joseph Carroll, Samantha L. Savage, Ronan T. Swords, Uma Borate, Aashis Thapa, Abdusebur Jemal, Joelle Wolf, Patricia Kropf, Rebecca Smith, Tyler Sweeney, Russell T. Burke, Rachel R. Pallapati, Anna Reister Schultz, Kim Hien T. Dao, Daniel Bottomly, Cristina E. Tognon, Alexey V. Danilov, Jason M. Glover, Jason D. MacManiman, Michie Degnin, Amy Yates, Libbey White, David K. Edwards, Anupriya Agarwal, Christopher R. Cogle, Kevin Watanabe-Smith, Leylah Drusbosky, Nicola Long, Motomi Mori, Christopher S. Hourigan, Tara L. Lin, Chenwei Lin, Jacqueline Martinez, Bill H. Chang, Richie Carpenter, Stephen E. Spurgeon, Brian Junio, Marc M. Loriaux, Craig T. Jordan, Hibery Ho, Selina Qiuying Liu, Melissa L. Abel, Amanda d’Almeida, Jake Wagner, Jade Bryant, Jeffrey W. Tyner, Jessica Leonard, and Kara Johnson
Subjects: Male, 0301 basic medicine, Myeloid, Gene regulatory network, Datasets as Topic, Genomics, Computational biology, Biology, Article, DNA Methyltransferase 3A, Transcriptome, 03 medical and health sciences, 0302 clinical medicine, Proto-Oncogene Proteins, hemic and lymphatic diseases, medicine, Humans, Exome, DNA (Cytosine-5-)-Methyltransferases, Molecular Targeted Therapy, Exome sequencing, Regulation of gene expression, Multidisciplinary, Serine-Arginine Splicing Factors, Genome, Human, Sequence Analysis, RNA, Nuclear Proteins, medicine.disease, Human genetics, 3. Good health, Gene Expression Regulation, Neoplastic, Repressor Proteins, Leukemia, Myeloid, Acute, Leukemia, 030104 developmental biology, medicine.anatomical_structure, 030220 oncology & carcinogenesis, Core Binding Factor Alpha 2 Subunit, Female, Nucleophosmin
Abstract: The implementation of targeted therapies for acute myeloid leukaemia (AML) has been challenging because of the complex mutational patterns within and across patients as well as a dearth of pharmacologic agents for most mutational events. Here we report initial findings from the Beat AML programme on a cohort of 672 tumour specimens collected from 562 patients. We assessed these specimens using whole-exome sequencing, RNA sequencing and analyses of ex vivo drug sensitivity. Our data reveal mutational events that have not previously been detected in AML. We show that the response to drugs is associated with mutational status, including instances of drug sensitivity that are specific to combinatorial mutational events. Integration with RNA sequencing also revealed gene expression signatures, which predict a role for specific gene networks in the drug response. Collectively, we have generated a dataset—accessible through the Beat AML data viewer (Vizome)—that can be leveraged to address clinical, genomic, transcriptomic and functional analyses of the biology of AML. Analyses of samples from patients with acute myeloid leukaemia reveal that drug response is associated with mutational status and gene expression; the generated dataset provides a basis for future clinical and functional studies of this disease.
Published: 2018

35. The finished DNA sequence of human chromosome 12

Author: Scherer, Steven E., Muzny, Donna M., Buhay, Christian J., Chen, Rui, Cree, Andrew, Ding, Yan, Dugan-Rocha, Shannon, Gill, Rachel, Gunaratne, Preethi, Harris, R. Alan, Hawes, Alicia C., Hernandez, Judith, Hodgson, Anne V., Hume, Jennifer, Jackson, Andrew, Khan, Ziad Mohid, Kovar-Smith, Christie, Lewis, Lora R., Lozado, Ryan J., Metzker, Michael L., Milosavljevic, Aleksandar, Miner, George R., Montgomery, Kate T., Morgan, Margaret B., Nazareth, Lynne V., Scott, Graham, Sodergren, Erica, Song, Xing-Zhi, Steffen, David, Lovering, Ruth C., Wheeler, David A., Worley, Kim C., Yuan, Yi, Zhang, Zhengdong, Adams, Charles Q., Ansari-Lari, M. Ali, Ayele, Mulu, Brown, Mary J., Chen, Guan, Chen, Zhijian, Clerc-Blankenburg, Kerstin P., Davis, Clay, Delgado, Oliver, Dinh, Huyen H., Draper, Heather, Gonzalez-Garay, Manuel L., Havlak, Paul, Jackson, Laronda R., Jacob, Leni S., Kelly, Susan H., Li, Li, Li, Zhangwan, Liu, Jing, Liu, Wen, Lu, Jing, Maheshwari, Manjula, Nguyen, Bao-Viet, Okwuonu, Geoffrey O., Pasternak, Shiran, Perez, Lesette M., Plopper, Farah J. H., Santibanez, Jireh, Shen, Hua, Tabor, Paul E., Verduzco, Daniel, Waldron, Lenee, Wang, Qiaoyan, Williams, Gabrielle A., Zhang, JingKun, Zhou, Jianling, Allen, Carlana C., Amin, Anita G., Anyalebechi, Vivian, Bailey, Michael, Barbaria, Joseph A., Bimage, Kesha E., Bryant, Nathaniel P., Burch, Paula E., Burkett, Carrie E., Burrell, Kevin L., Calderon, Eliana, Cardenas, Veronica, Carter, Kelvin, Casias, Kristal, Cavazos, Iracema, Cavazos, Sandra R., Ceasar, Heather, Chacko, Joseph, Chan, Sheryl N., Chavez, Dean, Christopoulos, Constantine, Chu, Joseph, Cockrell, Raynard, Cox, Caroline D., Dang, Michelle, Dathorne, Stephanie R., David, Robert, Davis, Candi Mon'Et, Davy-Carroll, Latarsha, Deshazo, Denise R., Donlin, Jeremy E., D'Souza, Lisa, Eaves, Kristy A., Egan, Amy, Emery-Cohen, Alexandra J., Escotto, Michael, Flagg, Nicole, Forbes, Lisa D., Gabisi, Abdul M., Garza, Melissa, Hamilton, Cerissa, Henderson, Nicholas, Hernandez, Omar, Hines, Sandra, Hogues, Marilyn E., Huang, Mei, Idlebird, DeVincent G., Johnson, Rudy, Jolivet, Angela, Jones, Sally, Kagan, Ryan, King, Laquisha M., Leal, Belita, Lebow, Heather, Lee, Sandra, LeVan, Jaclyn M., Lewis, Lakeshia C., London, Pamela, Lorensuhewa, Lorna M., Loulseged, Hermela, Lovett, Demetria A., Lucier, Alice, Lucier, Raymond L., Ma, Jie, Madu, Renita C., Mapua, Patricia, Martindale, Ashley D., Martinez, Evangelina, Massey, Elizabeth, Mawhiney, Samantha, Meador, Michael G., Mendez, Sylvia, Mercado, Christian, Mercado, Iracema C., Merritt, Christina E., Miner, Zachary L., Minja, Emmanuel, Mitchell, Teresa, Mohabbat, Farida, Mohabbat, Khatera, Montgomery, Baize, Moore, Niki, Morris, Sidney, Munidasa, Mala, Ngo, Robin N., Nguyen, Ngoc B., Nickerson, Elizabeth, Nwaokelemeh, Ogechi O., Nwokenkwo, Stanley, Obregon, Melissa, Oguh, Maryann, Oragunye, Njideka, Oviedo, Rodolfo J., Parish, Bridgette J., Parker, David N., Parrish, Julia, Parks, Kenya L., Paul, Heidie A., Payton, Brett A., Perez, Agapito, Perrin, William, Pickens, Adam, Primus, Eltrick L., Pu, Ling-Ling, Puazo, Maria, Quiles, Miyo M., Quiroz, Juana B., Rabata, Dina, Reeves, Kacy, Ruiz, San Juana, Shao, Hongmei, Sisson, Ida, Sonaike, Titilola, Sorelle, Richard P., Sutton, Angelica E., Svatek, Amanda F., Svetz, Leah Anne, Tamerisa, Kavitha S., Taylor, Tineace R., Teague, Brian, Thomas, Nicole, Thorn, Rachel D., Trejos, Zulma Y., Trevino, Brenda K., Ukegbu, Ogechi N., Urban, Jeremy B., Vasquez, Lydia I., Vera, Virginia A., Villasana, Donna M., Wang, Ling, Ward-Moore, Stephanie, Warren, James T., Wei, Xuehong, White, Flower, Williamson, Angela L., Wleczyk, Regina, Wooden, Hailey S., Wooden, Steven H., Yen, Jennifer, Yoon, Lillienne, Yoon, Vivienne, Zorrilla, Sara E., Nelson, David, Kucherlapati, Raju, Weinstock, George, and Gibbs, Richard A.
Subjects: Environmental issues, Science and technology, Zoology and wildlife conservation
Abstract: Author(s): Steven E. Scherer (corresponding author) [1]; Donna M. Muzny [1]; Christian J. Buhay [1]; Rui Chen [1]; Andrew Cree [1]; Yan Ding [1]; Shannon Dugan-Rocha [1]; Rachel Gill [1]; [...]
Published: 2006
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36. Mechanochemical analysis of DNA gyrase using rotor bead tracking

Author: Gore, Jeff, Bryant, Zev, Stone, Michael D., Nollmann, Marcelo, Cozzarelli, Nicholas R., and Bustamante, Carlos
Subjects: Environmental issues, Science and technology, Zoology and wildlife conservation
Abstract: Author(s): Jeff Gore [1, 6]; Zev Bryant [2, 3, 6, 5]; Michael D. Stone [2, 6, 5]; Marcelo NÃ¶llmann [2]; Nicholas R. Cozzarelli (corresponding author) [2]; Carlos Bustamante (corresponding author) [...]
Published: 2006
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37. Fire frequency drives decadal changes in soil carbon and nitrogen and ecosystem productivity

Author: Adam F. A. Pellegrini, Bryant C. Scharenbroch, Lars Nieradzik, Anders Ahlström, Peter B. Reich, Robert B. Jackson, James T. Randerson, A. Carla Staver, Sarah E. Hobbie, William R. L. Anderegg, and Ari Jumpponen
Subjects: 0106 biological sciences, Carbon Sequestration, Time Factors, 010504 meteorology & atmospheric sciences, Nitrogen, Geographic Mapping, Carbon sequestration, Atmospheric sciences, 010603 evolutionary biology, 01 natural sciences, Wildfires, Carbon cycle, Soil, Spatio-Temporal Analysis, Ecosystem, Nitrogen cycle, 0105 earth and related environmental sciences, Multidisciplinary, Fire regime, Carbon sink, Primary production, Phosphorus, Soil carbon, Grassland, Carbon, Potassium, Environmental science, Calcium
Abstract: Fire frequency is changing globally and is projected to affect the global carbon cycle and climate. However, uncertainty about how ecosystems respond to decadal changes in fire frequency makes it difficult to predict the effects of altered fire regimes on the carbon cycle; for instance, we do not fully understand the long-term effects of fire on soil carbon and nutrient storage, or whether fire-driven nutrient losses limit plant productivity. Here we analyse data from 48 sites in savanna grasslands, broadleaf forests and needleleaf forests spanning up to 65 years, during which time the frequency of fires was altered at each site. We find that frequently burned plots experienced a decline in surface soil carbon and nitrogen that was non-saturating through time, having 36 per cent (±13 per cent) less carbon and 38 per cent (±16 per cent) less nitrogen after 64 years than plots that were protected from fire. Fire-driven carbon and nitrogen losses were substantial in savanna grasslands and broadleaf forests, but not in temperate and boreal needleleaf forests. We also observe comparable soil carbon and nitrogen losses in an independent field dataset and in dynamic model simulations of global vegetation. The model study predicts that the long-term losses of soil nitrogen that result from more frequent burning may in turn decrease the carbon that is sequestered by net primary productivity by about 20 per cent of the total carbon that is emitted from burning biomass over the same period. Furthermore, we estimate that the effects of changes in fire frequency on ecosystem carbon storage may be 30 per cent too low if they do not include multidecadal changes in soil carbon, especially in drier savanna grasslands. Future changes in fire frequency may shift ecosystem carbon storage by changing soil carbon pools and nitrogen limitations on plant growth, altering the carbon sink capacity of frequently burning savanna grasslands and broadleaf forests.
Published: 2017

38. Publisher Correction: A mouse-adapted model of SARS-CoV-2 to test COVID-19 countermeasures

Author: Dinnon, Kenneth H., primary, Leist, Sarah R., additional, Schäfer, Alexandra, additional, Edwards, Caitlin E., additional, Martinez, David R., additional, Montgomery, Stephanie A., additional, West, Ande, additional, Yount, Boyd L., additional, Hou, Yixuan J., additional, Adams, Lily E., additional, Gully, Kendra L., additional, Brown, Ariane J., additional, Huang, Emily, additional, Bryant, Matthew D., additional, Choong, Ingrid C., additional, Glenn, Jeffrey S., additional, Gralinski, Lisa E., additional, Sheahan, Timothy P., additional, and Baric, Ralph S., additional
Published: 2021
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39. Specific killing of BRCA2-deficient tumours with inhibitors of poly(ADP-ribose) polymerase

Author: Bryant, Helen E., Schultz, Niklas, Thomas, Huw D., Parker, Kayan M., Flower, Dan, Lopez, Elena, Kyle, Suzanne, Meuth, Mark, Curtin, Nicola J., and Helleday, Thomas
Subjects: Environmental issues, Science and technology, Zoology and wildlife conservation
Abstract: Author(s): Helen E. Bryant [1]; Niklas Schultz [2]; Huw D. Thomas [3]; Kayan M. Parker [1]; Dan Flower [1]; Elena Lopez [1]; Suzanne Kyle [3]; Mark Meuth [1]; Nicola J. [...]
Published: 2005
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40. Effect of extrinsic mortality on the evolution of senescence in guppies

Author: Reznick, David N., Bryant, Michael J., Roff, Derek, Ghalambor, Cameron K., and Ghalambor, Dionna E.
Subjects: Environmental issues, Science and technology, Zoology and wildlife conservation
Abstract: Author(s): David N. Reznick (corresponding author) [1]; Michael J. Bryant [1, 2]; Derek Roff [1]; Cameron K. Ghalambor [3]; Dionna E. Ghalambor [3] Classical theories [1, 2] for the evolution [...]
Published: 2004
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41. Functional genomic hypothesis generation and experimentation by a robot scientist

Author: King, Ross D., Whelan, Kenneth E., Jones, Ffion M., Reiser, Philip G. K., Bryant, Christopher H., Muggleton, Stephen H., Kell, Douglas B., and Oliver, Stephen G.
Subjects: Environmental issues, Science and technology, Zoology and wildlife conservation
Abstract: Author(s): Ross D. King [1]; Kenneth E. Whelan [1]; Ffion M. Jones [1]; Philip G. K. Reiser [1]; Christopher H. Bryant [2]; Stephen H. Muggleton [3]; Douglas B. Kell [4]; [...]
Published: 2004
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42. Enhancements of energetic particles near the heliospheric termination shock

Author: McDonald, Frank B., Stone, Edward C., Cummings, Alan C., Heikkila, Bryant, Lal, Nand, and Webber, William R.
Subjects: Environmental issues, Science and technology, Zoology and wildlife conservation
Abstract: Author(s): Frank B. McDonald (corresponding author) [1]; Edward C. Stone [3]; Alan C. Cummings [3]; Bryant Heikkila [2]; Nand Lal [2]; William R. Webber [4] The spacecraft Voyager 1 is [...]
Published: 2003
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43. Structural transitions and elasticity from torque measurements on DNA

Author: Bryant, Zev, Stone, Michael D., Gore, Jeff, Smith, Steven B., Cozzarelli, Nicholas R., and Bustamante, Carlos
Subjects: Environmental issues, Science and technology, Zoology and wildlife conservation
Abstract: Author(s): Zev Bryant [1]; Michael D. Stone [1]; Jeff Gore [2]; Steven B. Smith [2, 3]; Nicholas R. Cozzarelli [1]; Carlos Bustamante (corresponding author) [1, 2, 3, 4] Knowledge of [...]
Published: 2003
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44. Ten years of tension: single-molecule DNA mechanics

Author: Bustamante, Carlos, Bryant, Zev, and Smith, Steven B.
Subjects: Environmental issues, Science and technology, Zoology and wildlife conservation
Abstract: Author(s): Carlos Bustamante (corresponding author) [1, 2]; Zev Bryant (corresponding author) [1]; Steven B. Smith (corresponding author) [2] The physical properties of the DNA double helix are unlike those of [...]
Published: 2003
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45. Distinct molecular mechanism for initiating TRAF6 signalling

Author: Ye, Hong, Arron, Joseph R., Lamothe, Betty, Cirilli, Maurizio, Kobayashi, Takashi, Shevde, Nirupama K., Segal, Deena, Dzivenu, Oki K., Vologodskaia, Masha, Yim, Mijung, Du, Khoi, Singh, Sujay, Pike, J. Wesley, Darnay, Bryant G., Choi, Yongwon, and Wu, Hao
Subjects: Environmental issues, Science and technology, Zoology and wildlife conservation
Abstract: Author(s): Hong Ye [1, 2]; Joseph R. Arron [2, 3, 4]; Betty Lamothe [5, 6]; Maurizio Cirilli [1, 7]; Takashi Kobayashi [4]; Nirupama K. Shevde [8]; Deena Segal [1]; Oki [...]
Published: 2002
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46. A mouse-adapted model of SARS-CoV-2 to test COVID-19 countermeasures

Author: Dinnon, Kenneth H., primary, Leist, Sarah R., additional, Schäfer, Alexandra, additional, Edwards, Caitlin E., additional, Martinez, David R., additional, Montgomery, Stephanie A., additional, West, Ande, additional, Yount, Boyd L., additional, Hou, Yixuan J., additional, Adams, Lily E., additional, Gully, Kendra L., additional, Brown, Ariane J., additional, Huang, Emily, additional, Bryant, Matthew D., additional, Choong, Ingrid C., additional, Glenn, Jeffrey S., additional, Gralinski, Lisa E., additional, Sheahan, Timothy P., additional, and Baric, Ralph S., additional
Published: 2020
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47. A remnant planetary core in the hot-Neptune desert

Author: Armstrong, David J., primary, Lopez, Théo A., additional, Adibekyan, Vardan, additional, Booth, Richard A., additional, Bryant, Edward M., additional, Collins, Karen A., additional, Deleuil, Magali, additional, Emsenhuber, Alexandre, additional, Huang, Chelsea X., additional, King, George W., additional, Lillo-Box, Jorge, additional, Lissauer, Jack J., additional, Matthews, Elisabeth, additional, Mousis, Olivier, additional, Nielsen, Louise D., additional, Osborn, Hugh, additional, Otegi, Jon, additional, Santos, Nuno C., additional, Sousa, Sérgio G., additional, Stassun, Keivan G., additional, Veras, Dimitri, additional, Ziegler, Carl, additional, Acton, Jack S., additional, Almenara, Jose M., additional, Anderson, David R., additional, Barrado, David, additional, Barros, Susana C. C., additional, Bayliss, Daniel, additional, Belardi, Claudia, additional, Bouchy, Francois, additional, Briceño, César, additional, Brogi, Matteo, additional, Brown, David J. A., additional, Burleigh, Matthew R., additional, Casewell, Sarah L., additional, Chaushev, Alexander, additional, Ciardi, David R., additional, Collins, Kevin I., additional, Colón, Knicole D., additional, Cooke, Benjamin F., additional, Crossfield, Ian J. M., additional, Díaz, Rodrigo F., additional, Mena, Elisa Delgado, additional, Demangeon, Olivier D. S., additional, Dorn, Caroline, additional, Dumusque, Xavier, additional, Eigmüller, Philipp, additional, Fausnaugh, Michael, additional, Figueira, Pedro, additional, Gan, Tianjun, additional, Gandhi, Siddharth, additional, Gill, Samuel, additional, Gonzales, Erica J., additional, Goad, Michael R., additional, Günther, Maximilian N., additional, Helled, Ravit, additional, Hojjatpanah, Saeed, additional, Howell, Steve B., additional, Jackman, James, additional, Jenkins, James S., additional, Jenkins, Jon M., additional, Jensen, Eric L. N., additional, Kennedy, Grant M., additional, Latham, David W., additional, Law, Nicholas, additional, Lendl, Monika, additional, Lozovsky, Michael, additional, Mann, Andrew W., additional, Moyano, Maximiliano, additional, McCormac, James, additional, Meru, Farzana, additional, Mordasini, Christoph, additional, Osborn, Ares, additional, Pollacco, Don, additional, Queloz, Didier, additional, Raynard, Liam, additional, Ricker, George R., additional, Rowden, Pamela, additional, Santerne, Alexandre, additional, Schlieder, Joshua E., additional, Seager, Sara, additional, Sha, Lizhou, additional, Tan, Thiam-Guan, additional, Tilbrook, Rosanna H., additional, Ting, Eric, additional, Udry, Stéphane, additional, Vanderspek, Roland, additional, Watson, Christopher A., additional, West, Richard G., additional, Wilson, Paul A., additional, Winn, Joshua N., additional, Wheatley, Peter, additional, Villasenor, Jesus Noel, additional, Vines, Jose I., additional, and Zhan, Zhuchang, additional
Published: 2020
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48. Accurate whole human genome sequencing using reversible terminator chemistry

Author: Bentley, David R., Balasubramanian, Shankar, Swerdlow, Harold P., Smith, Geoffrey P., Milton, John, Brown, Clive G., Hall, Kevin P., Evers, Dirk J., Barnes, Colin L., Bignell, Helen R., Boutell, Jonathan M., Bryant, Jason, Carter, Richard J., Cheetham, R. Keira, Cox, Anthony J., Ellis, Darren J., Flatbush, Michael R., Gormley, Niall A., Humphray, Sean J., Irving, Leslie J., Karbelashvili, Mirian S., Kirk, Scott M., Li, Heng, Liu, Xiaohai, Maisinger, Klaus S., Murray, Lisa J., Obradovic, Bojan, Ost, Tobias, Parkinson, Michael L., Pratt, Mark R., Rasolonjatovo, Isabelle M. J., Reed, Mark T., Rigatti, Roberto, Rodighiero, Chiara, Ross, Mark T., Sabot, Andrea, Sankar, Subramanian V., Scally, Aylwyn, Schroth, Gary P., Smith, Mark E., Smith, Vincent P., Spiridou, Anastassia, Torrance, Peta E., Tzonev, Svilen S., Vermaas, Eric H., Walter, Klaudia, Wu, Xiaolin, Zhang, Lu, Alam, Mohammed D., Anastasi, Carole, Aniebo, Ify C., Bailey, David M. D., Bancarz, Iain R., Banerjee, Saibal, Barbour, Selena G., Baybayan, Primo A., Benoit, Vincent A., Benson, Kevin F., Bevis, Claire, Black, Phillip J., Boodhun, Asha, Brennan, Joe S., Bridgham, John A., Brown, Rob C., Brown, Andrew A., Buermann, Dale H., Bundu, Abass A., Burrows, James C., Carter, Nigel P., Castillo, Nestor, Catenazzi, Maria Chiara E., Chang, Simon, Cooley, R. Neil, Crake, Natasha R., Dada, Olubunmi O., Diakoumakos, Konstantinos D., Dominguez-Fernandez, Belen, Earnshaw, David J., Egbujor, Ugonna C., Elmore, David W., Etchin, Sergey S, Ewan, Mark R., Fedurco, Milan, Fraser, Louise J., Fuentes Fajardo, Karin V., Furey, W. Scott, George, David, Gietzen, Kimberley J., Goddard, Colin P., Golda, George S., Granieri, Philip A., Green, David E., Gustafson, David L., Hansen, Nancy F., Harnish, Kevin, Haudenschild, Christian D., Heyer, Narinder I, Hims, Matthew M., Ho, Johnny T., Horgan, Adrian M., Hoschler, Katya, Hurwitz, Steve, Ivanov, Denis V., Johnson, Maria Q., James, Terena, Huw Jones, T. A., Kang, Gyoung-Dong, Kerelska, Tzvetana H., Kersey, Alan D., Khrebtukova, Irina, Kindwall, Alex P., Kingsbury, Zoya, Kokko-Gonzales, Paula I., Kumar, Anil, Laurent, Marc A., Lawley, Cynthia T., Lee, Sarah E., Lee, Xavier, Liao, Arnold K., Loch, Jennifer A., Lok, Mitch, Luo, Shujun, Mammen, Radhika M., Martin, John W., McCauley, Patrick G., McNitt, Paul, Mehta, Parul, Moon, Keith W., Mullens, Joe W., Newington, Taksina, Ning, Zemin, Ling Ng, Bee, Novo, Sonia M., O'Neill, Michael J., Osborne, Mark A., Osnowski, Andrew, Ostadan, Omead, Paraschos, Lambros L., Pickering, Lea, Pike, Andrew C., Pike, Alger C., Pinkard, D. Chris, Pliskin, Daniel P., Podhasky, Joe, Quijano, Victor J., Raczy, Come, Rae, Vicki H., Rawlings, Stephen R., Rodriguez, Ana Chiva, Roe, Phyllida M., Rogers, John, Rogert Bacigalupo, Maria C., Romanov, Nikolai, Romieu, Anthony, Roth, Rithy K., Rourke, Natalie J., Ruediger, Silke T., Rusman, Eli, Sanches-Kuiper, Raquel M., Schenker, Martin R., Seoane, Josefina M., Shaw, Richard J., Shiver, Mitch K., Short, Steven W., Sizto, Ning L., Sluis, Johannes P., Smith, Melanie A., Sohna Sohna, Jean Ernest, Spence, Eric J., Stevens, Kim, Sutton, Neil, Szajkowski, Lukasz, Tregidgo, Carolyn L., Turcatti, Gerardo, vandeVondele, Stephanie, Verhovsky, Yuli, Virk, Selene M., Wakelin, Suzanne, Walcott, Gregory C., Wang, Jingwen, Worsley, Graham J., Yan, Juying, Yau, Ling, Zuerlein, Mike, Rogers, Jane, Mullikin, James C., Hurles, Matthew E., McCooke, Nick J., West, John S., Oaks, Frank L., Lundberg, Peter L., Klenerman, David, Durbin, Richard, and Smith, Anthony J.
Published: 2008
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49. An asymmetric solar wind termination shock

Author: Stone, Edward C., Cummings, Alan C., McDonald, Frank B., Heikkila, Bryant C., Lal, Nand, and Webber, William R.
Published: 2008
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50. DEVELOPMENT: Inflationary pressures

Author: Bryant, David and Mostov, Keith
Published: 2007
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