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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. Population-based heteropolymer design to mimic protein mixtures

Author: Ruan, Zhiyuan, Li, Shuni, Grigoropoulos, Alexandra, Amiri, Hossein, Hilburg, Shayna L, Chen, Haotian, Jayapurna, Ivan, Jiang, Tao, Gu, Zhaoyi, Alexander-Katz, Alfredo, Bustamante, Carlos, Huang, Haiyan, and Xu, Ting
Subjects: Biochemistry and Cell Biology, Bioinformatics and Computational Biology, Biological Sciences, Generic health relevance, Amino Acid Sequence, Polymers, Protein Conformation, Protein Folding, Proteins, Biomimetic Materials, Body Fluids, Cytosol, Serum Albumin, Bovine, Biomimetics, Synthetic Biology, MSD-General, MSD-Nanocomposites, General Science & Technology
Abstract: Biological fluids, the most complex blends, have compositions that constantly vary and cannot be molecularly defined1. Despite these uncertainties, proteins fluctuate, fold, function and evolve as programmed2-4. We propose that in addition to the known monomeric sequence requirements, protein sequences encode multi-pair interactions at the segmental level to navigate random encounters5,6; synthetic heteropolymers capable of emulating such interactions can replicate how proteins behave in biological fluids individually and collectively. Here, we extracted the chemical characteristics and sequential arrangement along a protein chain at the segmental level from natural protein libraries and used the information to design heteropolymer ensembles as mixtures of disordered, partially folded and folded proteins. For each heteropolymer ensemble, the level of segmental similarity to that of natural proteins determines its ability to replicate many functions of biological fluids including assisting protein folding during translation, preserving the viability of fetal bovine serum without refrigeration, enhancing the thermal stability of proteins and behaving like synthetic cytosol under biologically relevant conditions. Molecular studies further translated protein sequence information at the segmental level into intermolecular interactions with a defined range, degree of diversity and temporal and spatial availability. This framework provides valuable guiding principles to synthetically realize protein properties, engineer bio/abiotic hybrid materials and, ultimately, realize matter-to-life transformations.
Published: 2023

3. Pan-cancer analysis of whole genomes

Author: Campbell, Peter J, Getz, Gad, Korbel, Jan O, Stuart, Joshua M, Jennings, Jennifer L, Stein, Lincoln D, Perry, Marc D, Nahal-Bose, Hardeep K, Ouellette, BF Francis, Li, Constance H, Rheinbay, Esther, Nielsen, G Petur, Sgroi, Dennis C, Wu, Chin-Lee, Faquin, William C, Deshpande, Vikram, Boutros, Paul C, Lazar, Alexander J, Hoadley, Katherine A, Louis, David N, Dursi, L Jonathan, Yung, Christina K, Bailey, Matthew H, Saksena, Gordon, Raine, Keiran M, Buchhalter, Ivo, Kleinheinz, Kortine, Schlesner, Matthias, Zhang, Junjun, Wang, Wenyi, Wheeler, David A, Ding, Li, Simpson, Jared T, O'Connor, Brian D, Yakneen, Sergei, Ellrott, Kyle, Miyoshi, Naoki, Butler, Adam P, Royo, Romina, Shorser, Solomon I, Vazquez, Miguel, Rausch, Tobias, Tiao, Grace, Waszak, Sebastian M, Rodriguez-Martin, Bernardo, Shringarpure, Suyash, Wu, Dai-Ying, Demidov, German M, Delaneau, Olivier, Hayashi, Shuto, Imoto, Seiya, Habermann, Nina, Segre, Ayellet V, Garrison, Erik, Cafferkey, Andy, Alvarez, Eva G, Maria Heredia-Genestar, Jose, Muyas, Francesc, Drechsel, Oliver, Bruzos, Alicia L, Temes, Javier, Zamora, Jorge, Baez-Ortega, Adrian, Kim, Hyung-Lae, Mashl, R Jay, Ye, Kai, DiBiase, Anthony, Huang, Kuan-lin, Letunic, Ivica, McLellan, Michael D, Newhouse, Steven J, Shmaya, Tal, Kumar, Sushant, Wedge, David C, Wright, Mark H, Yellapantula, Venkata D, Gerstein, Mark, Khurana, Ekta, Marques-Bonet, Tomas, Navarro, Arcadi, Bustamante, Carlos D, Siebert, Reiner, Nakagawa, Hidewaki, Easton, Douglas F, Ossowski, Stephan, Tubio, Jose MC, De La Vega, Francisco M, Estivill, Xavier, Yuen, Denis, Mihaiescu, George L, Omberg, Larsson, Ferretti, Vincent, Sabarinathan, Radhakrishnan, Pich, Oriol, Gonzalez-Perez, Abel, Weiner, Amaro Taylor, Fittall, Matthew W, Demeulemeester, Jonas, Tarabichi, Maxime, and Roberts, Nicola D
Subjects: Biological Sciences, Biomedical and Clinical Sciences, Bioinformatics and Computational Biology, Genetics, Oncology and Carcinogenesis, Cancer Genomics, Biotechnology, Human Genome, Cancer, Prevention, 2.1 Biological and endogenous factors, Cell Proliferation, Cellular Senescence, Chromothripsis, Cloud Computing, DNA Mutational Analysis, Evolution, Molecular, Female, Genome, Human, Genomics, Germ-Line Mutation, High-Throughput Nucleotide Sequencing, Humans, Information Dissemination, Male, Mutagenesis, Mutation, Neoplasms, Oncogenes, Promoter Regions, Genetic, RNA Splicing, Reproducibility of Results, Telomerase, Telomere, ICGC/TCGA Pan-Cancer Analysis of Whole Genomes Consortium, General Science & Technology
Abstract: Cancer is driven by genetic change, and the advent of massively parallel sequencing has enabled systematic documentation of this variation at the whole-genome scale1-3. Here we report the integrative analysis of 2,658 whole-cancer genomes and their matching normal tissues across 38 tumour types from the Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium of the International Cancer Genome Consortium (ICGC) and The Cancer Genome Atlas (TCGA). We describe the generation of the PCAWG resource, facilitated by international data sharing using compute clouds. On average, cancer genomes contained 4-5 driver mutations when combining coding and non-coding genomic elements; however, in around 5% of cases no drivers were identified, suggesting that cancer driver discovery is not yet complete. Chromothripsis, in which many clustered structural variants arise in a single catastrophic event, is frequently an early event in tumour evolution; in acral melanoma, for example, these events precede most somatic point mutations and affect several cancer-associated genes simultaneously. Cancers with abnormal telomere maintenance often originate from tissues with low replicative activity and show several mechanisms of preventing telomere attrition to critical levels. Common and rare germline variants affect patterns of somatic mutation, including point mutations, structural variants and somatic retrotransposition. A collection of papers from the PCAWG Consortium describes non-coding mutations that drive cancer beyond those in the TERT promoter4; identifies new signatures of mutational processes that cause base substitutions, small insertions and deletions and structural variation5,6; analyses timings and patterns of tumour evolution7; describes the diverse transcriptional consequences of somatic mutation on splicing, expression levels, fusion genes and promoter activity8,9; and evaluates a range of more-specialized features of cancer genomes8,10-18.
Published: 2020

4. Genetic analyses of diverse populations improves discovery for complex traits.

Author: Wojcik, Genevieve L, Graff, Mariaelisa, Nishimura, Katherine K, Tao, Ran, Haessler, Jeffrey, Gignoux, Christopher R, Highland, Heather M, Patel, Yesha M, Sorokin, Elena P, Avery, Christy L, Belbin, Gillian M, Bien, Stephanie A, Cheng, Iona, Cullina, Sinead, Hodonsky, Chani J, Hu, Yao, Huckins, Laura M, Jeff, Janina, Justice, Anne E, Kocarnik, Jonathan M, Lim, Unhee, Lin, Bridget M, Lu, Yingchang, Nelson, Sarah C, Park, Sung-Shim L, Poisner, Hannah, Preuss, Michael H, Richard, Melissa A, Schurmann, Claudia, Setiawan, Veronica W, Sockell, Alexandra, Vahi, Karan, Verbanck, Marie, Vishnu, Abhishek, Walker, Ryan W, Young, Kristin L, Zubair, Niha, Acuña-Alonso, Victor, Ambite, Jose Luis, Barnes, Kathleen C, Boerwinkle, Eric, Bottinger, Erwin P, Bustamante, Carlos D, Caberto, Christian, Canizales-Quinteros, Samuel, Conomos, Matthew P, Deelman, Ewa, Do, Ron, Doheny, Kimberly, Fernández-Rhodes, Lindsay, Fornage, Myriam, Hailu, Benyam, Heiss, Gerardo, Henn, Brenna M, Hindorff, Lucia A, Jackson, Rebecca D, Laurie, Cecelia A, Laurie, Cathy C, Li, Yuqing, Lin, Dan-Yu, Moreno-Estrada, Andres, Nadkarni, Girish, Norman, Paul J, Pooler, Loreall C, Reiner, Alexander P, Romm, Jane, Sabatti, Chiara, Sandoval, Karla, Sheng, Xin, Stahl, Eli A, Stram, Daniel O, Thornton, Timothy A, Wassel, Christina L, Wilkens, Lynne R, Winkler, Cheryl A, Yoneyama, Sachi, Buyske, Steven, Haiman, Christopher A, Kooperberg, Charles, Le Marchand, Loic, Loos, Ruth JF, Matise, Tara C, North, Kari E, Peters, Ulrike, Kenny, Eimear E, and Carlson, Christopher S
Subjects: Humans, Body Height, Cohort Studies, Genetics, Medical, Multifactorial Inheritance, Minority Groups, African Continental Ancestry Group, Asian Continental Ancestry Group, Hispanic Americans, Women's Health, United States, Female, Male, Health Status Disparities, Genome-Wide Association Study, Health Equity, Genetics, Medical, General Science & Technology
Abstract: Genome-wide association studies (GWAS) have laid the foundation for investigations into the biology of complex traits, drug development and clinical guidelines. However, the majority of discovery efforts are based on data from populations of European ancestry1-3. In light of the differential genetic architecture that is known to exist between populations, bias in representation can exacerbate existing disease and healthcare disparities. Critical variants may be missed if they have a low frequency or are completely absent in European populations, especially as the field shifts its attention towards rare variants, which are more likely to be population-specific4-10. Additionally, effect sizes and their derived risk prediction scores derived in one population may not accurately extrapolate to other populations11,12. Here we demonstrate the value of diverse, multi-ethnic participants in large-scale genomic studies. The Population Architecture using Genomics and Epidemiology (PAGE) study conducted a GWAS of 26 clinical and behavioural phenotypes in 49,839 non-European individuals. Using strategies tailored for analysis of multi-ethnic and admixed populations, we describe a framework for analysing diverse populations, identify 27 novel loci and 38 secondary signals at known loci, as well as replicate 1,444 GWAS catalogue associations across these traits. Our data show evidence of effect-size heterogeneity across ancestries for published GWAS associations, substantial benefits for fine-mapping using diverse cohorts and insights into clinical implications. In the United States-where minority populations have a disproportionately higher burden of chronic conditions13-the lack of representation of diverse populations in genetic research will result in inequitable access to precision medicine for those with the highest burden of disease. We strongly advocate for continued, large genome-wide efforts in diverse populations to maximize genetic discovery and reduce health disparities.
Published: 2019

5. Role of IL-27 in Epstein–Barr virus infection revealed by IL-27RA deficiency

Author: Martin, Emmanuel, primary, Winter, Sarah, additional, Garcin, Cécile, additional, Tanita, Kay, additional, Hoshino, Akihiro, additional, Lenoir, Christelle, additional, Fournier, Benjamin, additional, Migaud, Mélanie, additional, Boutboul, David, additional, Simonin, Mathieu, additional, Fernandes, Alicia, additional, Bastard, Paul, additional, Le Voyer, Tom, additional, Roupie, Anne-Laure, additional, Ben Ahmed, Yassine, additional, Leruez-Ville, Marianne, additional, Burgard, Marianne, additional, Rao, Geetha, additional, Ma, Cindy S., additional, Masson, Cécile, additional, Soudais, Claire, additional, Picard, Capucine, additional, Bustamante, Jacinta, additional, Tangye, Stuart G., additional, Cheikh, Nathalie, additional, Seppänen, Mikko, additional, Puel, Anne, additional, Daly, Mark, additional, Casanova, Jean-Laurent, additional, Neven, Bénédicte, additional, Fischer, Alain, additional, and Latour, Sylvain, additional
Published: 2024
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6. Genetic effects on gene expression across human tissues

Author: Aguet, François, Brown, Andrew A, Castel, Stephane E, Davis, Joe R, He, Yuan, Jo, Brian, Mohammadi, Pejman, Park, YoSon, Parsana, Princy, Segrè, Ayellet V, Strober, Benjamin J, Zappala, Zachary, Cummings, Beryl B, Gelfand, Ellen T, Hadley, Kane, Huang, Katherine H, Lek, Monkol, Li, Xiao, Nedzel, Jared L, Nguyen, Duyen Y, Noble, Michael S, Sullivan, Timothy J, Tukiainen, Taru, MacArthur, Daniel G, Getz, Gad, Addington, Anjene, Guan, Ping, Koester, Susan, Little, A Roger, Lockhart, Nicole C, Moore, Helen M, Rao, Abhi, Struewing, Jeffery P, Volpi, Simona, Brigham, Lori E, Hasz, Richard, Hunter, Marcus, Johns, Christopher, Johnson, Mark, Kopen, Gene, Leinweber, William F, Lonsdale, John T, McDonald, Alisa, Mestichelli, Bernadette, Myer, Kevin, Roe, Bryan, Salvatore, Michael, Shad, Saboor, Thomas, Jeffrey A, Walters, Gary, Washington, Michael, Wheeler, Joseph, Bridge, Jason, Foster, Barbara A, Gillard, Bryan M, Karasik, Ellen, Kumar, Rachna, Miklos, Mark, Moser, Michael T, Jewell, Scott D, Montroy, Robert G, Rohrer, Daniel C, Valley, Dana, Mash, Deborah C, Davis, David A, Sobin, Leslie, Barcus, Mary E, Branton, Philip A, Abell, Nathan S, Balliu, Brunilda, Delaneau, Olivier, Frésard, Laure, Gamazon, Eric R, Garrido-Martín, Diego, Gewirtz, Ariel DH, Gliner, Genna, Gloudemans, Michael J, Han, Buhm, He, Amy Z, Hormozdiari, Farhad, Li, Xin, Liu, Boxiang, Kang, Eun Yong, McDowell, Ian C, Ongen, Halit, Palowitch, John J, Peterson, Christine B, Quon, Gerald, Ripke, Stephan, Saha, Ashis, Shabalin, Andrey A, Shimko, Tyler C, Sul, Jae Hoon, Teran, Nicole A, Tsang, Emily K, Zhang, Hailei, Zhou, Yi-Hui, Bustamante, Carlos D, Cox, Nancy J, and Guigó, Roderic
Subjects: Human Genome, Genetics, Biotechnology, 1.1 Normal biological development and functioning, 2.1 Biological and endogenous factors, Aetiology, Underpinning research, Generic health relevance, Alleles, Chromosomes, Human, Disease, Female, Gene Expression Profiling, Gene Expression Regulation, Genetic Variation, Genome, Human, Genotype, Humans, Male, Organ Specificity, Quantitative Trait Loci, GTEx Consortium, Laboratory, Data Analysis &Coordinating Center (LDACC)—Analysis Working Group, Statistical Methods groups—Analysis Working Group, Enhancing GTEx (eGTEx) groups, NIH Common Fund, NIH/NCI, NIH/NHGRI, NIH/NIMH, NIH/NIDA, Biospecimen Collection Source Site—NDRI, Biospecimen Collection Source Site—RPCI, Biospecimen Core Resource—VARI, Brain Bank Repository—University of Miami Brain Endowment Bank, Leidos Biomedical—Project Management, ELSI Study, Genome Browser Data Integration &Visualization—EBI, Genome Browser Data Integration &Visualization—UCSC Genomics Institute, University of California Santa Cruz, Lead analysts:, Laboratory, Data Analysis &Coordinating Center (LDACC):, NIH program management:, Biospecimen collection:, Pathology:, eQTL manuscript working group:, General Science & Technology
Abstract: Characterization of the molecular function of the human genome and its variation across individuals is essential for identifying the cellular mechanisms that underlie human genetic traits and diseases. The Genotype-Tissue Expression (GTEx) project aims to characterize variation in gene expression levels across individuals and diverse tissues of the human body, many of which are not easily accessible. Here we describe genetic effects on gene expression levels across 44 human tissues. We find that local genetic variation affects gene expression levels for the majority of genes, and we further identify inter-chromosomal genetic effects for 93 genes and 112 loci. On the basis of the identified genetic effects, we characterize patterns of tissue specificity, compare local and distal effects, and evaluate the functional properties of the genetic effects. We also demonstrate that multi-tissue, multi-individual data can be used to identify genes and pathways affected by human disease-associated variation, enabling a mechanistic interpretation of gene regulation and the genetic basis of disease.
Published: 2017

7. Tuberculosis in otherwise healthy adults with inherited TNF deficiency

Author: Arias, Andrés A., Neehus, Anna-Lena, Ogishi, Masato, Meynier, Vincent, Krebs, Adam, Lazarov, Tomi, Lee, Angela M., Arango-Franco, Carlos A., Yang, Rui, Orrego, Julio, Corcini Berndt, Melissa, Rojas, Julian, Li, Hailun, Rinchai, Darawan, Erazo-Borrás, Lucia, Han, Ji Eun, Pillay, Bethany, Ponsin, Khoren, Chaldebas, Matthieu, Philippot, Quentin, Bohlen, Jonathan, Rosain, Jérémie, Le Voyer, Tom, Janotte, Till, Amarajeeva, Krishnajina, Soudée, Camille, Brollo, Marion, Wiegmann, Katja, Marquant, Quentin, Seeleuthner, Yoann, Lee, Danyel, Lainé, Candice, Kloos, Doreen, Bailey, Rasheed, Bastard, Paul, Keating, Narelle, Rapaport, Franck, Khan, Taushif, Moncada-Vélez, Marcela, Carmona, María Camila, Obando, Catalina, Alvarez, Jesús, Cataño, Juan Carlos, Martínez-Rosado, Larry Luber, Sanchez, Juan P., Tejada-Giraldo, Manuela, L’Honneur, Anne-Sophie, Agudelo, María L., Perez-Zapata, Lizet J., Arboleda, Diana M., Alzate, Juan Fernando, Cabarcas, Felipe, Zuluaga, Alejandra, Pelham, Simon J., Ensser, Armin, Schmidt, Monika, Velásquez-Lopera, Margarita M., Jouanguy, Emmanuelle, Puel, Anne, Krönke, Martin, Ghirardello, Stefano, Borghesi, Alessandro, Pahari, Susanta, Boisson, Bertrand, Pittaluga, Stefania, Ma, Cindy S., Emile, Jean-François, Notarangelo, Luigi D., Tangye, Stuart G., Marr, Nico, Lachmann, Nico, Salvator, Hélène, Schlesinger, Larry S., Zhang, Peng, Glickman, Michael S., Nathan, Carl F., Geissmann, Frédéric, Abel, Laurent, Franco, José Luis, Bustamante, Jacinta, Casanova, Jean-Laurent, and Boisson-Dupuis, Stéphanie
Abstract: Severe defects in human IFNγ immunity predispose individuals to both Bacillus Calmette–Guérin disease and tuberculosis, whereas milder defects predispose only to tuberculosis1. Here we report two adults with recurrent pulmonary tuberculosis who are homozygous for a private loss-of-function TNFvariant. Neither has any other clinical phenotype and both mount normal clinical and biological inflammatory responses. Their leukocytes, including monocytes and monocyte-derived macrophages (MDMs) do not produce TNF, even after stimulation with IFNγ. Blood leukocyte subset development is normal in these patients. However, an impairment in the respiratory burst was observed in granulocyte–macrophage colony-stimulating factor (GM-CSF)-matured MDMs and alveolar macrophage-like (AML) cells2from both patients with TNF deficiency, TNF- or TNFR1-deficient induced pluripotent stem (iPS)-cell-derived GM-CSF-matured macrophages, and healthy control MDMs and AML cells differentiated with TNF blockers in vitro, and in lung macrophages treated with TNF blockers ex vivo. The stimulation of TNF-deficient iPS-cell-derived macrophages with TNF rescued the respiratory burst. These findings contrast with those for patients with inherited complete deficiency of the respiratory burst across all phagocytes, who are prone to multiple infections, including both Bacillus Calmette–Guérin disease and tuberculosis3. Human TNF is required for respiratory-burst-dependent immunity to Mycobacterium tuberculosisin macrophages but is surprisingly redundant otherwise, including for inflammation and immunity to weakly virulent mycobacteria and many other infectious agents.
Published: 2024
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8. Genome-wide associations for birth weight and correlations with adult disease

Author: Horikoshi, Momoko, Beaumont, Robin N, Day, Felix R, Warrington, Nicole M, Kooijman, Marjolein N, Fernandez-Tajes, Juan, Feenstra, Bjarke, van Zuydam, Natalie R, Gaulton, Kyle J, Grarup, Niels, Bradfield, Jonathan P, Strachan, David P, Li-Gao, Ruifang, Ahluwalia, Tarunveer S, Kreiner, Eskil, Rueedi, Rico, Lyytikäinen, Leo-Pekka, Cousminer, Diana L, Wu, Ying, Thiering, Elisabeth, Wang, Carol A, Have, Christian T, Hottenga, Jouke-Jan, Vilor-Tejedor, Natalia, Joshi, Peter K, Boh, Eileen Tai Hui, Ntalla, Ioanna, Pitkänen, Niina, Mahajan, Anubha, van Leeuwen, Elisabeth M, Joro, Raimo, Lagou, Vasiliki, Nodzenski, Michael, Diver, Louise A, Zondervan, Krina T, Bustamante, Mariona, Marques-Vidal, Pedro, Mercader, Josep M, Bennett, Amanda J, Rahmioglu, Nilufer, Nyholt, Dale R, Ma, Ronald CW, Tam, Claudia HT, Tam, Wing Hung, Ganesh, Santhi K, van Rooij, Frank JA, Jones, Samuel E, Loh, Po-Ru, Ruth, Katherine S, Tuke, Marcus A, Tyrrell, Jessica, Wood, Andrew R, Yaghootkar, Hanieh, Scholtens, Denise M, Paternoster, Lavinia, Prokopenko, Inga, Kovacs, Peter, Atalay, Mustafa, Willems, Sara M, Panoutsopoulou, Kalliope, Wang, Xu, Carstensen, Lisbeth, Geller, Frank, Schraut, Katharina E, Murcia, Mario, van Beijsterveldt, Catharina EM, Willemsen, Gonneke, Appel, Emil VR, Fonvig, Cilius E, Trier, Caecilie, Tiesler, Carla MT, Standl, Marie, Kutalik, Zoltán, Bonàs-Guarch, Sílvia, Hougaard, David M, Sánchez, Friman, Torrents, David, Waage, Johannes, Hollegaard, Mads V, de Haan, Hugoline G, Rosendaal, Frits R, Medina-Gomez, Carolina, Ring, Susan M, Hemani, Gibran, McMahon, George, Robertson, Neil R, Groves, Christopher J, Langenberg, Claudia, Luan, Jian’an, Scott, Robert A, Zhao, Jing Hua, Mentch, Frank D, MacKenzie, Scott M, Reynolds, Rebecca M, Lowe, William L, Tönjes, Anke, Stumvoll, Michael, Lindi, Virpi, Lakka, Timo A, and van Duijn, Cornelia M
Subjects: Nutrition, Perinatal Period - Conditions Originating in Perinatal Period, Human Genome, Genetics, Clinical Research, Preterm, Low Birth Weight and Health of the Newborn, Obesity, Prevention, Pediatric, Infant Mortality, 2.1 Biological and endogenous factors, Aetiology, Adult, Aging, Anthropometry, Birth Weight, Blood Pressure, Chromatin Assembly and Disassembly, Cohort Studies, Coronary Artery Disease, Datasets as Topic, Diabetes Mellitus, Type 2, Female, Fetus, Genetic Loci, Genetic Predisposition to Disease, Genetic Variation, Genome-Wide Association Study, Genomic Imprinting, Genotype, Glucose, Glycogen, Humans, Insulin, Male, Phenotype, Signal Transduction, CHARGE Consortium Hematology Working Group, Early Growth Genetics (EGG) Consortium, General Science & Technology
Abstract: Birth weight (BW) has been shown to be influenced by both fetal and maternal factors and in observational studies is reproducibly associated with future risk of adult metabolic diseases including type 2 diabetes (T2D) and cardiovascular disease. These life-course associations have often been attributed to the impact of an adverse early life environment. Here, we performed a multi-ancestry genome-wide association study (GWAS) meta-analysis of BW in 153,781 individuals, identifying 60 loci where fetal genotype was associated with BW (P
Published: 2016

9. A global reference for human genetic variation

Author: Auton, Adam, Abecasis, Gonçalo R, Altshuler, David M, Durbin, Richard M, Bentley, David R, Chakravarti, Aravinda, Clark, Andrew G, Donnelly, Peter, Eichler, Evan E, Flicek, Paul, Gabriel, Stacey B, Gibbs, Richard A, Green, Eric D, Hurles, Matthew E, Knoppers, Bartha M, Korbel, Jan O, Lander, Eric S, Lee, Charles, Lehrach, Hans, Mardis, Elaine R, Marth, Gabor T, McVean, Gil A, Nickerson, Deborah A, Schmidt, Jeanette P, Sherry, Stephen T, Wang, Jun, Wilson, Richard K, Barnes, Kathleen C, Beiswanger, Christine, Burchard, Esteban G, Bustamante, Carlos D, Cai, Hongyu, Cao, Hongzhi, Gerry, Norman P, Gharani, Neda, Gignoux, Christopher R, Gravel, Simon, Henn, Brenna, Jones, Danielle, Jorde, Lynn, Kaye, Jane S, Keinan, Alon, Kent, Alastair, Kerasidou, Angeliki, Li, Yingrui, Mathias, Rasika, Moreno-Estrada, Andres, Ossorio, Pilar N, Parker, Michael, Resch, Alissa M, Rotimi, Charles N, Royal, Charmaine D, Sandoval, Karla, Su, Yeyang, Sudbrak, Ralf, Tian, Zhongming, Tishkoff, Sarah, Toji, Lorraine H, Tyler-Smith, Chris, Via, Marc, Wang, Yuhong, Yang, Huanming, Yang, Ling, Zhu, Jiayong, Brooks, Lisa D, Felsenfeld, Adam L, McEwen, Jean E, Vaydylevich, Yekaterina, Duncanson, Audrey, Dunn, Michael, Schloss, Jeffery A, Garrison, Erik P, Min Kang, Hyun, Marchini, Jonathan L, and McCarthy, Shane
Subjects: Human Genome, Genetics, Biotechnology, 2.1 Biological and endogenous factors, Aetiology, Datasets as Topic, Demography, Disease Susceptibility, Exome, Genetic Variation, Genetics, Medical, Genetics, Population, Genome, Human, Genome-Wide Association Study, Genomics, Genotype, Haplotypes, High-Throughput Nucleotide Sequencing, Humans, INDEL Mutation, Internationality, Physical Chromosome Mapping, Polymorphism, Single Nucleotide, Quantitative Trait Loci, Rare Diseases, Reference Standards, Sequence Analysis, DNA, Genomes Project Consortium, General Science & Technology
Abstract: The 1000 Genomes Project set out to provide a comprehensive description of common human genetic variation by applying whole-genome sequencing to a diverse set of individuals from multiple populations. Here we report completion of the project, having reconstructed the genomes of 2,504 individuals from 26 populations using a combination of low-coverage whole-genome sequencing, deep exome sequencing, and dense microarray genotyping. We characterized a broad spectrum of genetic variation, in total over 88 million variants (84.7 million single nucleotide polymorphisms (SNPs), 3.6 million short insertions/deletions (indels), and 60,000 structural variants), all phased onto high-quality haplotypes. This resource includes >99% of SNP variants with a frequency of >1% for a variety of ancestries. We describe the distribution of genetic variation across the global sample, and discuss the implications for common disease studies.
Published: 2015

10. The ancestry and affiliations of Kennewick Man

Author: Rasmussen, Morten, Sikora, Martin, Albrechtsen, Anders, Korneliussen, Thorfinn Sand, Moreno-Mayar, J Víctor, Poznik, G David, Zollikofer, Christoph PE, Ponce de León, Marcia S, Allentoft, Morten E, Moltke, Ida, Jónsson, Hákon, Valdiosera, Cristina, Malhi, Ripan S, Orlando, Ludovic, Bustamante, Carlos D, Stafford, Thomas W, Meltzer, David J, Nielsen, Rasmus, and Willerslev, Eske
Subjects: Biological Sciences, Anthropology, History, Heritage and Archaeology, Human Society, Clinical Research, Americas, Genome, Human, Genomics, Humans, Indians, North American, Male, Phylogeny, Skeleton, Skull, Washington, General Science & Technology
Abstract: Kennewick Man, referred to as the Ancient One by Native Americans, is a male human skeleton discovered in Washington state (USA) in 1996 and initially radiocarbon dated to 8,340-9,200 calibrated years before present (BP). His population affinities have been the subject of scientific debate and legal controversy. Based on an initial study of cranial morphology it was asserted that Kennewick Man was neither Native American nor closely related to the claimant Plateau tribes of the Pacific Northwest, who claimed ancestral relationship and requested repatriation under the Native American Graves Protection and Repatriation Act (NAGPRA). The morphological analysis was important to judicial decisions that Kennewick Man was not Native American and that therefore NAGPRA did not apply. Instead of repatriation, additional studies of the remains were permitted. Subsequent craniometric analysis affirmed Kennewick Man to be more closely related to circumpacific groups such as the Ainu and Polynesians than he is to modern Native Americans. In order to resolve Kennewick Man's ancestry and affiliations, we have sequenced his genome to ∼1× coverage and compared it to worldwide genomic data including for the Ainu and Polynesians. We find that Kennewick Man is closer to modern Native Americans than to any other population worldwide. Among the Native American groups for whom genome-wide data are available for comparison, several seem to be descended from a population closely related to that of Kennewick Man, including the Confederated Tribes of the Colville Reservation (Colville), one of the five tribes claiming Kennewick Man. We revisit the cranial analyses and find that, as opposed to genome-wide comparisons, it is not possible on that basis to affiliate Kennewick Man to specific contemporary groups. We therefore conclude based on genetic comparisons that Kennewick Man shows continuity with Native North Americans over at least the last eight millennia.
Published: 2015

11. The genome of a Late Pleistocene human from a Clovis burial site in western Montana.

Author: Rasmussen, Morten, Anzick, Sarah, Waters, Michael, Skoglund, Pontus, DeGiorgio, Michael, Stafford, Thomas, Rasmussen, Simon, Moltke, Ida, Albrechtsen, Anders, Doyle, Shane, Poznik, G, Gudmundsdottir, Valborg, Yadav, Rachita, Malaspinas, Anna-Sapfo, White, Samuel, Allentoft, Morten, Tambets, Kristiina, Eriksson, Anders, Heintzman, Peter, Karmin, Monika, Korneliussen, Thorfinn, Meltzer, David, Pierre, Tracey, Stenderup, Jesper, Saag, Lauri, Warmuth, Vera, Lopes, Margarida, Malhi, Ripan, Brunak, Søren, Sicheritz-Ponten, Thomas, Barnes, Ian, Collins, Matthew, Orlando, Ludovic, Balloux, Francois, Manica, Andrea, Gupta, Ramneek, Metspalu, Mait, Bustamante, Carlos, Jakobsson, Mattias, Willerslev, Eske, Nielsen, Rasmus, and Cornejo, Omar
Subjects: Archaeology, Asia, Bone and Bones, Burial, Chromosomes, Human, Y, DNA, Mitochondrial, Emigration and Immigration, Europe, Gene Flow, Genome, Human, Haplotypes, History, Ancient, Humans, Indians, North American, Infant, Male, Models, Genetic, Molecular Sequence Data, Montana, Phylogeny, Population Dynamics, Radiometric Dating
Abstract: Clovis, with its distinctive biface, blade and osseous technologies, is the oldest widespread archaeological complex defined in North America, dating from 11,100 to 10,700 (14)C years before present (bp) (13,000 to 12,600 calendar years bp). Nearly 50 years of archaeological research point to the Clovis complex as having developed south of the North American ice sheets from an ancestral technology. However, both the origins and the genetic legacy of the people who manufactured Clovis tools remain under debate. It is generally believed that these people ultimately derived from Asia and were directly related to contemporary Native Americans. An alternative, Solutrean, hypothesis posits that the Clovis predecessors emigrated from southwestern Europe during the Last Glacial Maximum. Here we report the genome sequence of a male infant (Anzick-1) recovered from the Anzick burial site in western Montana. The human bones date to 10,705 ± 35 (14)C years bp (approximately 12,707-12,556 calendar years bp) and were directly associated with Clovis tools. We sequenced the genome to an average depth of 14.4× and show that the gene flow from the Siberian Upper Palaeolithic Malta population into Native American ancestors is also shared by the Anzick-1 individual and thus happened before 12,600 years bp. We also show that the Anzick-1 individual is more closely related to all indigenous American populations than to any other group. Our data are compatible with the hypothesis that Anzick-1 belonged to a population directly ancestral to many contemporary Native Americans. Finally, we find evidence of a deep divergence in Native American populations that predates the Anzick-1 individual.
Published: 2014

12. Making cities mental health friendly for adolescents and young adults.

Author: Collins, Pamela Y., Sinha, Moitreyee, Concepcion, Tessa, Patton, George, Way, Thaisa, McCay, Layla, Mensa-Kwao, Augustina, Herrman, Helen, de Leeuw, Evelyne, Anand, Nalini, Atwoli, Lukoye, Bardikoff, Nicole, Booysen, Chantelle, Bustamante, Inés, Chen, Yajun, Davis, Kelly, Dua, Tarun, Foote, Nathaniel, Hughsam, Matthew, and Juma, Damian
Abstract: Urban life shapes the mental health of city dwellers, and although cities provide access to health, education and economic gain, urban environments are often detrimental to mental health1,2. Increasing urbanization over the next three decades will be accompanied by a growing population of children and adolescents living in cities3. Shaping the aspects of urban life that influence youth mental health could have an enormous impact on adolescent well-being and adult trajectories4. We invited a multidisciplinary, global group of researchers, practitioners, advocates and young people to complete sequential surveys to identify and prioritize the characteristics of a mental health-friendly city for young people. Here we show a set of ranked characteristic statements, grouped by personal, interpersonal, community, organizational, policy and environmental domains of intervention. Life skills for personal development, valuing and accepting young people’s ideas and choices, providing safe public space for social connection, employment and job security, centring youth input in urban planning and design, and addressing adverse social determinants were priorities by domain. We report the adversities that COVID-19 generated and link relevant actions to these data. Our findings highlight the need for intersectoral, multilevel intervention and for inclusive, equitable, participatory design of cities that support youth mental health.A study examining how cities can foster well-being and positive mental health in young residents synthesizes opinions from researchers, practitioners, advocates and young people, highlighting factors that policymakers and urban planners should consider. [ABSTRACT FROM AUTHOR]
Published: 2024
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13. Population-based heteropolymer design to mimic protein mixtures

Author: Zhiyuan Ruan, Shuni Li, Alexandra Grigoropoulos, Hossein Amiri, Shayna L. Hilburg, Haotian Chen, Ivan Jayapurna, Tao Jiang, Zhaoyi Gu, Alfredo Alexander-Katz, Carlos Bustamante, Haiyan Huang, and Ting Xu
Subjects: Multidisciplinary
Published: 2023
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14. Great ape genetic diversity and population history.

Author: Prado-Martinez, Javier, Sudmant, Peter H, Kidd, Jeffrey M, Li, Heng, Kelley, Joanna L, Lorente-Galdos, Belen, Veeramah, Krishna R, Woerner, August E, O'Connor, Timothy D, Santpere, Gabriel, Cagan, Alexander, Theunert, Christoph, Casals, Ferran, Laayouni, Hafid, Munch, Kasper, Hobolth, Asger, Halager, Anders E, Malig, Maika, Hernandez-Rodriguez, Jessica, Hernando-Herraez, Irene, Prüfer, Kay, Pybus, Marc, Johnstone, Laurel, Lachmann, Michael, Alkan, Can, Twigg, Dorina, Petit, Natalia, Baker, Carl, Hormozdiari, Fereydoun, Fernandez-Callejo, Marcos, Dabad, Marc, Wilson, Michael L, Stevison, Laurie, Camprubí, Cristina, Carvalho, Tiago, Ruiz-Herrera, Aurora, Vives, Laura, Mele, Marta, Abello, Teresa, Kondova, Ivanela, Bontrop, Ronald E, Pusey, Anne, Lankester, Felix, Kiyang, John A, Bergl, Richard A, Lonsdorf, Elizabeth, Myers, Simon, Ventura, Mario, Gagneux, Pascal, Comas, David, Siegismund, Hans, Blanc, Julie, Agueda-Calpena, Lidia, Gut, Marta, Fulton, Lucinda, Tishkoff, Sarah A, Mullikin, James C, Wilson, Richard K, Gut, Ivo G, Gonder, Mary Katherine, Ryder, Oliver A, Hahn, Beatrice H, Navarro, Arcadi, Akey, Joshua M, Bertranpetit, Jaume, Reich, David, Mailund, Thomas, Schierup, Mikkel H, Hvilsom, Christina, Andrés, Aida M, Wall, Jeffrey D, Bustamante, Carlos D, Hammer, Michael F, Eichler, Evan E, and Marques-Bonet, Tomas
Subjects: Animals, Animals, Wild, Animals, Zoo, Hominidae, Gorilla gorilla, Humans, Pan paniscus, Pan troglodytes, Inbreeding, Genetics, Population, Population Density, Evolution, Molecular, Phylogeny, Polymorphism, Single Nucleotide, Genome, Africa, Asia, Southeastern, Gene Flow, Genetic Variation, General Science & Technology
Abstract: Most great ape genetic variation remains uncharacterized; however, its study is critical for understanding population history, recombination, selection and susceptibility to disease. Here we sequence to high coverage a total of 79 wild- and captive-born individuals representing all six great ape species and seven subspecies and report 88.8 million single nucleotide polymorphisms. Our analysis provides support for genetically distinct populations within each species, signals of gene flow, and the split of common chimpanzees into two distinct groups: Nigeria-Cameroon/western and central/eastern populations. We find extensive inbreeding in almost all wild populations, with eastern gorillas being the most extreme. Inferred effective population sizes have varied radically over time in different lineages and this appears to have a profound effect on the genetic diversity at, or close to, genes in almost all species. We discover and assign 1,982 loss-of-function variants throughout the human and great ape lineages, determining that the rate of gene loss has not been different in the human branch compared to other internal branches in the great ape phylogeny. This comprehensive catalogue of great ape genome diversity provides a framework for understanding evolution and a resource for more effective management of wild and captive great ape populations.
Published: 2013

15. Erratum: The Amazon basin in transition (Nature (2012) 481 (321-328))

Author: Davidson, EA, De Araújo, AC, Artaxo, P, Balch, JK, Brown, IF, Bustamante, MMC, Coe, MT, Defries, RS, Keller, M, Longo, M, Munger, JW, Schroeder, W, Soares-Filho, BS, Souza, CM, and Wofsy, SC
Subjects: General Science & Technology
Published: 2012

16. Correction: Corrigendum: The Amazon basin in transition

Author: Davidson, Eric A, de Araújo, Alessandro C, Artaxo, Paulo, Balch, Jennifer K, Brown, I Foster, Bustamante, Mercedes MC, Coe, Michael T, DeFries, Ruth S, Keller, Michael, Longo, Marcos, Munger, J William, Schroeder, Wilfrid, Soares-Filho, Britaldo S, Souza, Carlos M, and Wofsy, Steven C
Subjects: General Science & Technology
Published: 2012

17. Publisher Correction: Population-based heteropolymer design to mimic protein mixtures

Author: Ruan, Zhiyuan, primary, Li, Shuni, additional, Grigoropoulos, Alexandra, additional, Amiri, Hossein, additional, Hilburg, Shayna L., additional, Chen, Haotian, additional, Jayapurna, Ivan, additional, Jiang, Tao, additional, Gu, Zhaoyi, additional, Alexander-Katz, Alfredo, additional, Bustamante, Carlos, additional, Huang, Haiyan, additional, and Xu, Ting, additional
Published: 2023
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18. Author Correction: Comparative and demographic analysis of orang-utan genomes

Author: Locke, Devin P., primary, Hillier, LaDeana W., additional, Warren, Wesley C., additional, Worley, Kim C., additional, Nazareth, Lynne V., additional, Muzny, Donna M., additional, Yang, Shiaw-Pyng, additional, Wang, Zhengyuan, additional, Chinwalla, Asif T., additional, Minx, Pat, additional, Mitreva, Makedonka, additional, Cook, Lisa, additional, Delehaunty, Kim D., additional, Fronick, Catrina, additional, Schmidt, Heather, additional, Fulton, Lucinda A., additional, Fulton, Robert S., additional, Nelson, Joanne O., additional, Magrini, Vincent, additional, Pohl, Craig, additional, Graves, Tina A., additional, Markovic, Chris, additional, Cree, Andy, additional, Dinh, Huyen H., additional, Hume, Jennifer, additional, Kovar, Christie L., additional, Fowler, Gerald R., additional, Lunter, Gerton, additional, Meader, Stephen, additional, Heger, Andreas, additional, Ponting, Chris P., additional, Marques-Bonet, Tomas, additional, Alkan, Can, additional, Chen, Lin, additional, Cheng, Ze, additional, Kidd, Jeffrey M., additional, Eichler, Evan E., additional, White, Simon, additional, Searle, Stephen, additional, Vilella, Albert J., additional, Chen, Yuan, additional, Flicek, Paul, additional, Ma, Jian, additional, Raney, Brian, additional, Suh, Bernard, additional, Burhans, Richard, additional, Herrero, Javier, additional, Haussler, David, additional, Faria, Rui, additional, Fernando, Olga, additional, Darré, Fleur, additional, Farré, Domènec, additional, Gazave, Elodie, additional, Oliva, Meritxell, additional, Navarro, Arcadi, additional, Roberto, Roberta, additional, Capozzi, Oronzo, additional, Archidiacono, Nicoletta, additional, Della Valle, Giuliano, additional, Purgato, Stefania, additional, Rocchi, Mariano, additional, Konkel, Miriam K., additional, Walker, Jerilyn A., additional, Ullmer, Brygg, additional, Batzer, Mark A., additional, Smit, Arian F. A., additional, Hubley, Robert, additional, Casola, Claudio, additional, Schrider, Daniel R., additional, Hahn, Matthew W., additional, Quesada, Victor, additional, Puente, Xose S., additional, Ordoñez, Gonzalo R., additional, López-Otín, Carlos, additional, Vinar, Tomas, additional, Brejova, Brona, additional, Ratan, Aakrosh, additional, Harris, Robert S., additional, Miller, Webb, additional, Kosiol, Carolin, additional, Lawson, Heather A., additional, Taliwal, Vikas, additional, Martins, André L., additional, Siepel, Adam, additional, RoyChoudhury, Arindam, additional, Ma, Xin, additional, Degenhardt, Jeremiah, additional, Bustamante, Carlos D., additional, Gutenkunst, Ryan N., additional, Mailund, Thomas, additional, Dutheil, Julien Y., additional, Hobolth, Asger, additional, Schierup, Mikkel H., additional, Ryder, Oliver A., additional, Yoshinaga, Yuko, additional, de Jong, Pieter J., additional, Weinstock, George M., additional, Rogers, Jeffrey, additional, Mardis, Elaine R., additional, Gibbs, Richard A., additional, and Wilson, Richard K., additional
Published: 2022
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19. 700,000 years of tropical Andean glaciation

Author: Rodbell, D. T., primary, Hatfield, R. G., additional, Abbott, M. B., additional, Chen, C. Y., additional, Woods, A., additional, Stoner, J. S., additional, McGee, D., additional, Tapia, P. M., additional, Bush, M., additional, Valero-Garcés, B. L., additional, Lehmann, S. B., additional, Mark, S. Z., additional, Weidhaas, N. C., additional, Hillman, A. L., additional, Larsen, D. J., additional, Delgado, G., additional, Katz, S. A., additional, Solada, K. E., additional, Morey, A. E., additional, Finkenbinder, M., additional, Valencia, B., additional, Rozas-Davila, A., additional, Wattrus, N., additional, Colman, S. M., additional, Bustamante, M. G., additional, Kück, J., additional, and Pierdominici, S., additional
Published: 2022
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20. The heat released during catalytic turnover enhances the diffusion of an enzyme

Author: Riedel, Clement, Gabizon, Ronen, Wilson, Christian A.M., Hamadani, Kambiz, Tsekouras, Konstantinos, Marqusee, Susan, Presse, Steve, and Bustamante, Carlos
Subjects: Catalysis -- Research, Heat -- Physiological aspects, Protein research, Enzymes -- Physiological aspects, Environmental issues, Science and technology, Zoology and wildlife conservation
Abstract: Recent studies have shown that the diffusivity of enzymes increases in a substrate-dependent manner during catalysis (1,2). Although this observation has been reported and characterized for several different systems (3-10), the precise origin of this phenomenon is unknown. Calorimetric methods are often used to determine enthalpies from enzyme-catalysed reactions and can therefore provide important insight into their reaction mechanisms (11,12). The ensemble averages involved in traditional bulk calorimetry cannot probe the transient effects that the energy exchanged in a reaction may have on the catalyst. Here we obtain single-molecule fluorescence correlation spectroscopy data and analyse them within the framework of a stochastic theory to demonstrate a mechanistic link between the enhanced diffusion of a single enzyme molecule and the heat released in the reaction. We propose that the heat released during catalysis generates an asymmetric pressure wave that results in a differential stress at the protein-solvent interface that transiently displaces the centre-of-mass of the enzyme (chemoacoustic effect). This novel perspective on how enzymes respond to the energy released during catalysis suggests a possible effect of the heat of reaction on the structural integrity and internal degrees of freedom of the enzyme., Externally induced temperature spikes--through the use of laser pulses, for example--can have dramatic effects on enzyme catalysis and protein conformations (13). Thus, pyramine and green fluorescent protein have been shown [...]
Published: 2015

21. Paths and timings of the peopling of Polynesia inferred from genomic networks

Author: Ioannidis, Alexander G., primary, Blanco-Portillo, Javier, additional, Sandoval, Karla, additional, Hagelberg, Erika, additional, Barberena-Jonas, Carmina, additional, Hill, Adrian V. S., additional, Rodríguez-Rodríguez, Juan Esteban, additional, Fox, Keolu, additional, Robson, Kathryn, additional, Haoa-Cardinali, Sonia, additional, Quinto-Cortés, Consuelo D., additional, Miquel-Poblete, Juan Francisco, additional, Auckland, Kathryn, additional, Parks, Tom, additional, Sofro, Abdul Salam M., additional, Ávila-Arcos, María C., additional, Sockell, Alexandra, additional, Homburger, Julian R., additional, Eng, Celeste, additional, Huntsman, Scott, additional, Burchard, Esteban G., additional, Gignoux, Christopher R., additional, Verdugo, Ricardo A., additional, Moraga, Mauricio, additional, Bustamante, Carlos D., additional, Mentzer, Alexander J., additional, and Moreno-Estrada, Andrés, additional
Published: 2021
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22. Author Correction: Comparative and demographic analysis of orang-utan genomes

Author: Devin P. Locke, LaDeana W. Hillier, Wesley C. Warren, Kim C. Worley, Lynne V. Nazareth, Donna M. Muzny, Shiaw-Pyng Yang, Zhengyuan Wang, Asif T. Chinwalla, Pat Minx, Makedonka Mitreva, Lisa Cook, Kim D. Delehaunty, Catrina Fronick, Heather Schmidt, Lucinda A. Fulton, Robert S. Fulton, Joanne O. Nelson, Vincent Magrini, Craig Pohl, Tina A. Graves, Chris Markovic, Andy Cree, Huyen H. Dinh, Jennifer Hume, Christie L. Kovar, Gerald R. Fowler, Gerton Lunter, Stephen Meader, Andreas Heger, Chris P. Ponting, Tomas Marques-Bonet, Can Alkan, Lin Chen, Ze Cheng, Jeffrey M. Kidd, Evan E. Eichler, Simon White, Stephen Searle, Albert J. Vilella, Yuan Chen, Paul Flicek, Jian Ma, Brian Raney, Bernard Suh, Richard Burhans, Javier Herrero, David Haussler, Rui Faria, Olga Fernando, Fleur Darré, Domènec Farré, Elodie Gazave, Meritxell Oliva, Arcadi Navarro, Roberta Roberto, Oronzo Capozzi, Nicoletta Archidiacono, Giuliano Della Valle, Stefania Purgato, Mariano Rocchi, Miriam K. Konkel, Jerilyn A. Walker, Brygg Ullmer, Mark A. Batzer, Arian F. A. Smit, Robert Hubley, Claudio Casola, Daniel R. Schrider, Matthew W. Hahn, Victor Quesada, Xose S. Puente, Gonzalo R. Ordoñez, Carlos López-Otín, Tomas Vinar, Brona Brejova, Aakrosh Ratan, Robert S. Harris, Webb Miller, Carolin Kosiol, Heather A. Lawson, Vikas Taliwal, André L. Martins, Adam Siepel, Arindam RoyChoudhury, Xin Ma, Jeremiah Degenhardt, Carlos D. Bustamante, Ryan N. Gutenkunst, Thomas Mailund, Julien Y. Dutheil, Asger Hobolth, Mikkel H. Schierup, Oliver A. Ryder, Yuko Yoshinaga, Pieter J. de Jong, George M. Weinstock, Jeffrey Rogers, Elaine R. Mardis, Richard A. Gibbs, and Richard K. Wilson
Subjects: Multidisciplinary
Published: 2022
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23. A global reference for human genetic variation

Author: Altshuler, David M., (Co-Chair), Durbin, Richard M., (Co-Chair, Principal Investigator), Donnelly, Peter, Green, Eric D., Nickerson, Deborah A., Boerwinkle, Eric, Doddapaneni, Harsha, Han, Yi, Korchina, Viktoriya, Kovar, Christie, Lee, Sandra, Muzny, Donna, Reid, Jeffrey G., Zhu, Yiming, Wang, Jun, (Principal Investigator), Chang, Yuqi, Feng, Qiang, Fang, Xiaodong, Guo, Xiaosen, Jian, Min, Jiang, Hui, Jin, Xin, Lan, Tianming, Li, Guoqing, Li, Jingxiang, Li, Yingrui, Liu, Shengmao, Liu, Xiao, Lu, Yao, Ma, Xuedi, Tang, Meifang, Wang, Bo, Wang, Guangbiao, Wu, Honglong, Wu, Renhua, Xu, Xun, Yin, Ye, Zhang, Dandan, Zhang, Wenwei, Zhao, Jiao, Zhao, Meiru, Zheng, Xiaole, Lander, Eric S., (Principal Investigator), Gabriel, Stacey B., (Co-Chair), Gupta, Namrata, Gharani, Neda, Toji, Lorraine H., Gerry, Norman P., Resch, Alissa M., Barker, Jonathan, Gil, Laurent, Hunt, Sarah E., Kelman, Gavin, Kulesha, Eugene, Leinonen, Rasko, McLaren, William M., Radhakrishnan, Rajesh, Roa, Asier, Smirnov, Dmitriy, Smith, Richard E., Streeter, Ian, Thormann, Anja, Toneva, Iliana, Vaughan, Brendan, Zheng-Bradley, Xiangqun, Bentley, David R., (Principal Investigator), Grocock, Russell, Humphray, Sean, James, Terena, Kingsbury, Zoya, Lehrach, Hans, (Principal Investigator), Sudbrak, Ralf, (Project Leader), Albrecht, Marcus W., Amstislavskiy, Vyacheslav S., Borodina, Tatiana A., Lienhard, Matthias, Mertes, Florian, Sultan, Marc, Timmermann, Bernd, Yaspo, Marie-Laure, Mardis, Elaine R., (Co-Principal Investigator) (Co-Chair), Wilson, Richard K., (Co-Principal Investigator), Fulton, Lucinda, Fulton, Robert, Ananiev, Victor, Belaia, Zinaida, Beloslyudtsev, Dimitriy, Bouk, Nathan, Chen, Chao, Church, Deanna, Cohen, Robert, Cook, Charles, Garner, John, Hefferon, Timothy, Kimelman, Mikhail, Liu, Chunlei, Lopez, John, Meric, Peter, O’Sullivan, Chris, Ostapchuk, Yuri, Phan, Lon, Ponomarov, Sergiy, Schneider, Valerie, Shekhtman, Eugene, Sirotkin, Karl, Slotta, Douglas, Zhang, Hua, Balasubramaniam, Senduran, Burton, John, Danecek, Petr, Keane, Thomas M., Kolb-Kokocinski, Anja, McCarthy, Shane, Stalker, James, Quail, Michael, Schmidt, Jeanette P., (Principal Investigator), Davies, Christopher J., Gollub, Jeremy, Webster, Teresa, Wong, Brant, Zhan, Yiping, Auton, Adam, (Principal Investigator), Campbell, Christopher L., Kong, Yu, Marcketta, Anthony, Yu, Fuli, (Project Leader), Antunes, Lilian, Bainbridge, Matthew, Sabo, Aniko, Huang, Zhuoyi, Coin, Lachlan J. M., Fang, Lin, Li, Qibin, Li, Zhenyu, Lin, Haoxiang, Liu, Binghang, Luo, Ruibang, Shao, Haojing, Xie, Yinlong, Ye, Chen, Yu, Chang, Zhang, Fan, Zheng, Hancheng, Zhu, Hongmei, Alkan, Can, Dal, Elif, Kahveci, Fatma, Garrison, Erik P., (Project Lead), Kural, Deniz, Lee, Wan-Ping, Leong, Wen Fung, Stromberg, Michael, Ward, Alistair N., Wu, Jiantao, Zhang, Mengyao, Daly, Mark J., (Principal Investigator), DePristo, Mark A., (Project Leader), Handsaker, Robert E., (Project Leader), Banks, Eric, Bhatia, Gaurav, del Angel, Guillermo, Genovese, Giulio, Li, Heng, Kashin, Seva, Nemesh, James C., Poplin, Ryan E., Yoon, Seungtai C., (Principal Investigator), Lihm, Jayon, Makarov, Vladimir, Clark, Andrew G., (Principal Investigator), Gottipati, Srikanth, Keinan, Alon, Rodriguez-Flores, Juan L., Rausch, Tobias, (Project Leader), Fritz, Markus H., Stütz, Adrian M., Beal, Kathryn, Datta, Avik, Herrero, Javier, Ritchie, Graham R. S., Zerbino, Daniel, Sabeti, Pardis C., (Principal Investigator), Shlyakhter, Ilya, Schaffner, Stephen F., Vitti, Joseph, Cooper, David N., (Principal Investigator), Ball, Edward V., Stenson, Peter D., Barnes, Bret, Bauer, Markus, Cheetham, Keira R., Cox, Anthony, Eberle, Michael, Kahn, Scott, Murray, Lisa, Peden, John, Shaw, Richard, Kenny, Eimear E., (Principal Investigator), Batzer, Mark A., (Principal Investigator), Konkel, Miriam K., Walker, Jerilyn A., MacArthur, Daniel G., (Principal Investigator), Lek, Monkol, Herwig, Ralf, Koboldt, Daniel C., Larson, David, Ye, Kai, Gravel, Simon, Swaroop, Anand, Chew, Emily, Lappalainen, Tuuli, (Principal Investigator), Erlich, Yaniv, (Principal Investigator), Gymrek, Melissa, Willems, Thomas Frederick, Simpson, Jared T., Shriver, Mark D., (Principal Investigator), Rosenfeld, Jeffrey A., (Principal Investigator), Montgomery, Stephen B., (Principal Investigator), De La Vega, Francisco M., (Principal Investigator), Byrnes, Jake K., Carroll, Andrew W., DeGorter, Marianne K., Lacroute, Phil, Maples, Brian K., Martin, Alicia R., Moreno-Estrada, Andres, Shringarpure, Suyash S., Zakharia, Fouad, Halperin, Eran, (Principal Investigator), Baran, Yael, Cerveira, Eliza, Hwang, Jaeho, Malhotra, Ankit, (Co-Project Lead), Plewczynski, Dariusz, Radew, Kamen, Romanovitch, Mallory, Zhang, Chengsheng, (Co-Project Lead), Hyland, Fiona C. L., Craig, David W., (Principal Investigator), Christoforides, Alexis, Homer, Nils, Izatt, Tyler, Kurdoglu, Ahmet A., Sinari, Shripad A., Squire, Kevin, Xiao, Chunlin, Sebat, Jonathan, (Principal Investigator), Antaki, Danny, Gujral, Madhusudan, Noor, Amina, Ye, Kenny, Burchard, Esteban G., (Principal Investigator), Hernandez, Ryan D., (Principal Investigator), Gignoux, Christopher R., Haussler, David, (Principal Investigator), Katzman, Sol J., Kent, James W., Howie, Bryan, Ruiz-Linares, Andres, (Principal Investigator), Dermitzakis, Emmanouil T., (Principal Investigator), Devine, Scott E., (Principal Investigator), Abecasis, Gonçalo R., (Principal Investigator) (Co-Chair), Kang, Hyun Min, (Project Leader), Kidd, Jeffrey M., (Principal Investigator), Blackwell, Tom, Caron, Sean, Chen, Wei, Emery, Sarah, Fritsche, Lars, Fuchsberger, Christian, Jun, Goo, Li, Bingshan, Lyons, Robert, Scheller, Chris, Sidore, Carlo, Song, Shiya, Sliwerska, Elzbieta, Taliun, Daniel, Tan, Adrian, Welch, Ryan, Wing, Mary Kate, Zhan, Xiaowei, Awadalla, Philip, (Principal Investigator), Hodgkinson, Alan, Li, Yun, Shi, Xinghua, (Principal Investigator), Quitadamo, Andrew, Lunter, Gerton, (Principal Investigator), McVean, Gil A., (Principal Investigator) (Co-Chair), Marchini, Jonathan L., (Principal Investigator), Myers, Simon, (Principal Investigator), Churchhouse, Claire, Delaneau, Olivier, Gupta-Hinch, Anjali, Kretzschmar, Warren, Iqbal, Zamin, Mathieson, Iain, Menelaou, Androniki, Rimmer, Andy, Xifara, Dionysia K., Oleksyk, Taras K., (Principal Investigator), Fu, Yunxin, (Principal Investigator), Liu, Xiaoming, Xiong, Momiao, Jorde, Lynn, (Principal Investigator), Witherspoon, David, Xing, Jinchuan, Browning, Brian L., (Principal Investigator), Browning, Sharon R., (Principal Investigator), Hormozdiari, Fereydoun, Sudmant, Peter H., Khurana, Ekta, (Principal Investigator), Hurles, Matthew E., (Principal Investigator), Albers, Cornelis A., Ayub, Qasim, Chen, Yuan, Colonna, Vincenza, Jostins, Luke, Walter, Klaudia, Xue, Yali, Abyzov, Alexej, Balasubramanian, Suganthi, Chen, Jieming, Clarke, Declan, Fu, Yao, Harmanci, Arif O., Jin, Mike, Lee, Donghoon, Liu, Jeremy, Mu, Xinmeng Jasmine, Zhang, Jing, Zhang, Yan, McCarroll, Steven A., (Principal Investigator), Hartl, Chris, Shakir, Khalid, Degenhardt, Jeremiah, Korbel, Jan O., (Principal Investigator) (Co-Chair), Meiers, Sascha, Raeder, Benjamin, Casale, Francesco Paolo, Stegle, Oliver, Lameijer, Eric-Wubbo, Ding, Li, (Principal Investigator), Hall, Ira, Lee, Charles, (Principal Investigator) (Co-Chair), Bafna, Vineet, Michaelson, Jacob, Gardner, Eugene J., (Project Leader), Mills, Ryan E., (Principal Investigator), Dayama, Gargi, Chen, Ken, (Principle Investigator), Fan, Xian, Chong, Zechen, Chen, Tenghui, Eichler, Evan E., (Principal Investigator) (Co-Chair), Chaisson, Mark J., Huddleston, John, Malig, Maika, Nelson, Bradley J., Parrish, Nicholas F., Blackburne, Ben, Lindsay, Sarah J., Ning, Zemin, Zhang, Yujun, Lam, Hugo, Sisu, Cristina, Gibbs, Richard A., (Principal Investigator) (Co-Chair), Challis, Danny, Evani, Uday S., Lu, James, Nagaswamy, Uma, Yu, Jin, Li, Wangshen, Marth, Gabor T., (Principal Investigator) (Co-Chair), Habegger, Lukas, Yu, Haiyuan, (Principal Investigator), Cunningham, Fiona, Dunham, Ian, Lage, Kasper, (Principal Investigator), Jespersen, Jakob Berg, Horn, Heiko, Tyler-Smith, Chris, (Principal Investigator) (Co-Chair), Gerstein, Mark B., (Principal Investigator) (Co-Chair), Kim, Donghoon, Desalle, Rob, Narechania, Apurva, Wilson Sayres, Melissa A., Bustamante, Carlos D., (Principal Investigator) (Co-Chair), Mendez, Fernando L., Poznik, David G., Underhill, Peter A., Coin, Lachlan, (Principal Investigator), Mittelman, David, Banerjee, Ruby, Cerezo, Maria, Fitzgerald, Thomas W., Louzada, Sandra, Massaia, Andrea, Ritchie, Graham R., Yang, Fengtang, Kalra, Divya, Hale, Walker, Dan, Xu, Flicek, Paul, (Principal Investigator) (Co-Chair), Clarke, Laura, (Project Lead), Sherry, Stephen T., (Principal Investigator) (Co-Chair), Chakravarti, Aravinda, (Co-Chair), Knoppers, Bartha M., (Co-Chair), Barnes, Kathleen C., Beiswanger, Christine, Cai, Hongyu, Cao, Hongzhi, Henn, Brenna, Jones, Danielle, Kaye, Jane S., Kent, Alastair, Kerasidou, Angeliki, Mathias, Rasika, Ossorio, Pilar N., Parker, Michael, Rotimi, Charles N., Royal, Charmaine D., Sandoval, Karla, Su, Yeyang, Tian, Zhongming, Tishkoff, Sarah, Via, Marc, Wang, Yuhong, Yang, Ling, Zhu, Jiayong, Bodmer, Walter, Bedoya, Gabriel, Cai, Zhiming, Gao, Yang, Chu, Jiayou, Peltonen, Leena, Garcia-Montero, Andres, Orfao, Alberto, Dutil, Julie, Martinez-Cruzado, Juan C., Mathias, Rasika A., Hennis, Anselm, Watson, Harold, McKenzie, Colin, Qadri, Firdausi, LaRocque, Regina, Deng, Xiaoyan, Asogun, Danny, Folarin, Onikepe, Happi, Christian, Omoniwa, Omonwunmi, Stremlau, Matt, Tariyal, Ridhi, Jallow, Muminatou, Joof, Fatoumatta Sisay, Corrah, Tumani, Rockett, Kirk, Kwiatkowski, Dominic, Kooner, Jaspal, Hiê`n, Trâ`n Tinh, Dunstan, Sarah J., Hang, Nguyen Thuy, Fonnie, Richard, Garry, Robert, Kanneh, Lansana, Moses, Lina, Schieffelin, John, Grant, Donald S., Gallo, Carla, Poletti, Giovanni, Saleheen, Danish, Rasheed, Asif, Brooks, Lisa D., Felsenfeld, Adam L., McEwen, Jean E., Vaydylevich, Yekaterina, Duncanson, Audrey, Dunn, Michael, Schloss, Jeffery A., and Yang, Huanming
Published: 2015
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24. Human intracellular ISG15 prevents interferon-α/β over-amplification and auto-inflammation

Author: Zhang, Xianqin, Bogunovic, Dusan, Payelle-Brogard, Béatrice, Francois-Newton, Véronique, Speer, Scott D., Yuan, Chao, Volpi, Stefano, Li, Zhi, Sanal, Ozden, Mansouri, Davood, Tezcan, Ilhan, Rice, Gillian I., Chen, Chunyuan, Mansouri, Nahal, Mahdaviani, Seyed Alireza, Itan, Yuval, Boisson, Bertrand, Okada, Satoshi, Zeng, Lu, Wang, Xing, Jiang, Hui, Liu, Wenqiang, Han, Tiantian, Liu, Delin, Ma, Tao, Wang, Bo, Liu, Mugen, Liu, Jing-Yu, Wang, Qing K., Yalnizoglu, Dilek, Radoshevich, Lilliana, Uzé, Gilles, Gros, Philippe, Rozenberg, Flore, Zhang, Shen-Ying, Jouanguy, Emmanuelle, Bustamante, Jacinta, García-Sastre, Adolfo, Abel, Laurent, Lebon, Pierre, Notarangelo, Luigi D., Crow, Yanick J., Boisson-Dupuis, Stéphanie, Casanova, Jean-Laurent, and Pellegrini, Sandra
Published: 2015
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25. An integrated map of genetic variation from 1,092 human genomes

Author: McVean, Gil A., Altshuler, David M., Durbin, Richard M., Abecasis, Gonçalo R., Bentley, David R., Chakravarti, Aravinda, Clark, Andrew G., Donnelly, Peter, Eichler, Evan E., Flicek, Paul, Gabriel, Stacey B., Gibbs, Richard A., Green, Eric D., Hurles, Matthew E., Knoppers, Bartha M., Korbel, Jan O., Lander, Eric S., Lee, Charles, Lehrach, Hans, Mardis, Elaine R., Marth, Gabor T., Nickerson, Deborah A., Schmidt, Jeanette P., Sherry, Stephen T., Wang, Jun, Wilson, Richard K., Dinh, Huyen, Kovar, Christie, Lee, Sandra, Lewis, Lora, Muzny, Donna, Reid, Jeff, Wang, Min, Wang, Jun, Fang, Xiaodong, Guo, Xiaosen, Jian, Min, Jiang, Hui, Jin, Xin, Li, Guoqing, Li, Jingxiang, Li, Yingrui, Li, Zhuo, Liu, Xiao, Lu, Yao, Ma, Xuedi, Su, Zhe, Tai, Shuaishuai, Tang, Meifang, Wang, Bo, Wang, Guangbiao, Wu, Honglong, Wu, Renhua, Yin, Ye, Zhang, Wenwei, Zhao, Jiao, Zhao, Meiru, Zheng, Xiaole, Zhou, Yan, Lander, Eric S., Gabriel, Stacey B., Gupta, Namrata, Flicek, Paul, Clarke, Laura, Leinonen, Rasko, Smith, Richard E., Zheng-Bradley, Xiangqun, Bentley, David R., Grocock, Russell, Humphray, Sean, James, Terena, Kingsbury, Zoya, Lehrach, Hans, Sudbrak, Ralf, Albrecht, Marcus W., Amstislavskiy, Vyacheslav S., Borodina, Tatiana A., Lienhard, Matthias, Mertes, Florian, Sultan, Marc, Timmermann, Bernd, Yaspo, Marie-Laure, Sherry, Stephen T., McVean, Gil A., Mardis, Elaine R., Wilson, Richard K., Fulton, Lucinda, Fulton, Robert, Weinstock, George M., Durbin, Richard M., Balasubramaniam, Senduran, Burton, John, Danecek, Petr, Keane, Thomas M., Kolb-Kokocinski, Anja, McCarthy, Shane, Stalker, James, Quail, Michael, Schmidt, Jeanette P., Davies, Christopher J., Gollub, Jeremy, Webster, Teresa, Wong, Brant, Zhan, Yiping, Auton, Adam, Yu, Fuli, Bainbridge, Matthew, Challis, Danny, Evani, Uday S., Lu, James, Nagaswamy, Uma, Sabo, Aniko, Wang, Yi, Yu, Jin, Coin, Lachlan J. M., Fang, Lin, Li, Qibin, Li, Zhenyu, Lin, Haoxiang, Liu, Binghang, Luo, Ruibang, Qin, Nan, Shao, Haojing, Wang, Bingqiang, Xie, Yinlong, Ye, Chen, Yu, Chang, Zhang, Fan, Zheng, Hancheng, Zhu, Hongmei, Garrison, Erik P., Kural, Deniz, Lee, Wan-Ping, Fung Leong, Wen, Ward, Alistair N., Wu, Jiantao, Zhang, Mengyao, Lee, Charles, Griffin, Lauren, Hsieh, Chih-Heng, Mills, Ryan E., Shi, Xinghua, von Grotthuss, Marcin, Zhang, Chengsheng, Daly, Mark J., DePristo, Mark A., Banks, Eric, Bhatia, Gaurav, Carneiro, Mauricio O., del Angel, Guillermo, Genovese, Giulio, Handsaker, Robert E., Hartl, Chris, McCarroll, Steven A., Nemesh, James C., Poplin, Ryan E., Schaffner, Stephen F., Shakir, Khalid, Yoon, Seungtai C., Lihm, Jayon, Makarov, Vladimir, Jin, Hanjun, Kim, Wook, Cheol Kim, Ki, Korbel, Jan O., Rausch, Tobias, Beal, Kathryn, Cunningham, Fiona, Herrero, Javier, McLaren, William M., Ritchie, Graham R. S., Clark, Andrew G., Gottipati, Srikanth, Keinan, Alon, Rodriguez-Flores, Juan L., Sabeti, Pardis C., Grossman, Sharon R., Tabrizi, Shervin, Tariyal, Ridhi, Cooper, David N., Ball, Edward V., Stenson, Peter D., Barnes, Bret, Bauer, Markus, Keira Cheetham, R., Cox, Tony, Eberle, Michael, Kahn, Scott, Murray, Lisa, Peden, John, Shaw, Richard, Ye, Kai, Batzer, Mark A., Konkel, Miriam K., Walker, Jerilyn A., MacArthur, Daniel G., Lek, Monkol, Sudbrak, Herwig, Ralf, Shriver, Mark D., Bustamante, Carlos D., Byrnes, Jake K., De La Vega, Francisco M., Gravel, Simon, Kenny, Eimear E., Kidd, Jeffrey M., Lacroute, Phil, Maples, Brian K., Moreno-Estrada, Andres, Zakharia, Fouad, Halperin, Eran, Baran, Yael, Craig, David W., Christoforides, Alexis, Homer, Nils, Izatt, Tyler, Kurdoglu, Ahmet A., Sinari, Shripad A., Squire, Kevin, Xiao, Chunlin, Sebat, Jonathan, Bafna, Vineet, Ye, Kenny, Burchard, Esteban G., Hernandez, Ryan D., Gignoux, Christopher R., Haussler, David, Katzman, Sol J., James Kent, W., Howie, Bryan, Ruiz-Linares, Andres, Dermitzakis, Emmanouil T., Lappalainen, Tuuli, Devine, Scott E., Liu, Xinyue, Maroo, Ankit, Tallon, Luke J., Rosenfeld, Jeffrey A., Min Kang, Hyun, Anderson, Paul, Angius, Andrea, Bigham, Abigail, Blackwell, Tom, Busonero, Fabio, Cucca, Francesco, Fuchsberger, Christian, Jones, Chris, Jun, Goo, Li, Yun, Lyons, Robert, Maschio, Andrea, Porcu, Eleonora, Reinier, Fred, Sanna, Serena, Schlessinger, David, Sidore, Carlo, Tan, Adrian, Kate Trost, Mary, Awadalla, Philip, Hodgkinson, Alan, Lunter, Gerton, McVean, Gil A., Marchini, Jonathan L., Myers, Simon, Churchhouse, Claire, Delaneau, Olivier, Gupta-Hinch, Anjali, Iqbal, Zamin, Mathieson, Iain, Rimmer, Andy, Xifara, Dionysia K., Oleksyk, Taras K., Fu, Yunxin, Liu, Xiaoming, Xiong, Momiao, Jorde, Lynn, Witherspoon, David, Xing, Jinchuan, Eichler, Evan E., Browning, Brian L., Alkan, Can, Hajirasouliha, Iman, Hormozdiari, Fereydoun, Ko, Arthur, Sudmant, Peter H., Mardis, Elaine R., Chen, Ken, Chinwalla, Asif, Ding, Li, Dooling, David, Koboldt, Daniel C., McLellan, Michael D., Wallis, John W., Wendl, Michael C., Zhang, Qunyuan, Hurles, Matthew E., Tyler-Smith, Chris, Albers, Cornelis A., Ayub, Qasim, Chen, Yuan, Coffey, Alison J., Colonna, Vincenza, Huang, Ni, Jostins, Luke, Li, Heng, Scally, Aylwyn, Walter, Klaudia, Xue, Yali, Zhang, Yujun, Gerstein, Mark B., Abyzov, Alexej, Balasubramanian, Suganthi, Chen, Jieming, Clarke, Declan, Fu, Yao, Habegger, Lukas, Harmanci, Arif O., Jin, Mike, Khurana, Ekta, Jasmine Mu, Xinmeng, Sisu, Cristina, Lee, Charles, McCarroll, Steven A., Degenhardt, Jeremiah, Korbel, Jan O., Stütz, Adrian M., Church, Deanna, Michaelson, Jacob J., Eichler, Evan E., Hurles, Matthew E., Blackburne, Ben, Lindsay, Sarah J., Ning, Zemin, DePristo, Mark A., Min Kang, Hyun, Mardis, Elaine R., Yu, Fuli, Michelson, Leslie P., Tyler-Smith, Chris, Frankish, Adam, Harrow, Jennifer, Fowler, Gerald, Hale, Walker, Kalra, Divya, Flicek, Paul, Clarke, Laura, Barker, Jonathan, Kelman, Gavin, Kulesha, Eugene, Radhakrishnan, Rajesh, Roa, Asier, Smirnov, Dmitriy, Streeter, Ian, Toneva, Iliana, Vaughan, Brendan, Sherry, Stephen T., Ananiev, Victor, Belaia, Zinaida, Beloslyudtsev, Dimitriy, Bouk, Nathan, Chen, Chao, Cohen, Robert, Cook, Charles, Garner, John, Hefferon, Timothy, Kimelman, Mikhail, Liu, Chunlei, Lopez, John, Meric, Peter, OʼSullivan, Chris, Ostapchuk, Yuri, Phan, Lon, Ponomarov, Sergiy, Schneider, Valerie, Shekhtman, Eugene, Sirotkin, Karl, Slotta, Douglas, Zhang, Hua, Chakravarti, Aravinda, Knoppers, Bartha M., Barnes, Kathleen C., Beiswanger, Christine, Burchard, Esteban G., Bustamante, Carlos D., Cai, Hongyu, Cao, Hongzhi, Durbin, Richard M., Gharani, Neda, Henn, Brenna, Jones, Danielle, Jorde, Lynn, Kaye, Jane S., Kent, Alastair, Kerasidou, Angeliki, Mathias, Rasika, Ossorio, Pilar N., Parker, Michael, Reich, David, Rotimi, Charles N., Royal, Charmaine D., Sandoval, Karla, Su, Yeyang, Sudbrak, Ralf, Tian, Zhongming, Tishkoff, Sarah, Toji, Lorraine H., Tyler-Smith, Chris, Via, Marc, Wang, Yuhong, Yang, Huanming, Yang, Ling, Zhu, Jiayong, Bodmer, Walter, Bedoya, Gabriel, Ruiz-Linares, Andres, Zhi Ming, Cai, Yang, Gao, Jia You, Chu, Peltonen, Leena, Garcia-Montero, Andres, Orfao, Alberto, Dutil, Julie, Martinez-Cruzado, Juan C., Oleksyk, Taras K., Brooks, Lisa D., Felsenfeld, Adam L., McEwen, Jean E., Clemm, Nicholas C., Duncanson, Audrey, Dunn, Michael, Guyer, Mark S., Peterson, Jane L., Abecasis, Goncalo R., and Auton, Adam
Published: 2012
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26. The Amazon basin in transition

Author: Davidson, Eric A., de Araujo, Alessandro C., Artaxo, Paulo, Balch, Jennifer K., Brown, I. Foster, Bustamante, Mercedes M.C., Coe, Michael T., DeFries, Ruth S., Keller, Michael, Longo, Marcos, Munger, J. William, Schroeder, Wilfrid, Soares-Filho, Britaldo S., Souza, Jr., Carlos M., and Wofsy, Steven C.
Subjects: Biogeochemical cycles -- Research, Deforestation -- Methods -- Brazil, Precipitation (Meteorology) -- Environmental aspects -- Research, Environmental issues, Science and technology, Zoology and wildlife conservation
Abstract: Agricultural expansion and climate variability have become important agents of disturbance in the Amazon basin. Recent studies have demonstrated considerable resilience of Amazonian forests to moderate annual drought, but they also show that interactions between deforestation, fire and drought potentially lead to losses of carbon storage and changes in regional precipitation patterns and river discharge. Although the basin-wide impacts of land use and drought may not yet surpass the magnitude of natural variability of hydrologic and biogeochemical cycles, there are some signs of a transition to a disturbance-dominated regime. These signs include changing energy and water cycles in the southern and eastern portions of the Amazon basin., Humans have been part of the vast forest-river system of the Amazon basin for many thousands of years, but expansion and intensification of agriculture, logging and urban footprints during the [...]
Published: 2012
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27. A map of human genome variation from population-scale sequencing

Author: Durbin, Richard M., Altshuler, David L., Durbin, Richard M., Abecasis, Gonçalo R., Bentley, David R., Chakravarti, Aravinda, Clark, Andrew G., Collins, Francis S., De La Vega, Francisco M., Donnelly, Peter, Egholm, Michael, Flicek, Paul, Gabriel, Stacey B., Gibbs, Richard A., Knoppers, Bartha M., Lander, Eric S., Lehrach, Hans, Mardis, Elaine R., McVean, Gil A., Nickerson, Debbie A., Peltonen, Leena, Schafer, Alan J., Sherry, Stephen T., Wang, Jun, Wilson, Richard K., Gibbs, Richard A., Deiros, David, Metzker, Mike, Muzny, Donna, Reid, Jeff, Wheeler, David, Wang, Jun, Li, Jingxiang, Jian, Min, Li, Guoqing, Li, Ruiqiang, Liang, Huiqing, Tian, Geng, Wang, Bo, Wang, Jian, Wang, Wei, Yang, Huanming, Zhang, Xiuqing, Zheng, Huisong, Lander, Eric S., Altshuler, David L., Ambrogio, Lauren, Bloom, Toby, Cibulskis, Kristian, Fennell, Tim J., Gabriel, Stacey B., Jaffe, David B., Shefler, Erica, Sougnez, Carrie L., Bentley, David R., Gormley, Niall, Humphray, Sean, Kingsbury, Zoya, Koko-Gonzales, Paula, Stone, Jennifer, McKernan, Kevin J., Costa, Gina L., Ichikawa, Jeffry K., Lee, Clarence C., Sudbrak, Ralf, Lehrach, Hans, Borodina, Tatiana A., Dahl, Andreas, Davydov, Alexey N., Marquardt, Peter, Mertes, Florian, Nietfeld, Wilfiried, Rosenstiel, Philip, Schreiber, Stefan, Soldatov, Aleksey V., Timmermann, Bernd, Tolzmann, Marius, Egholm, Michael, Affourtit, Jason, Ashworth, Dana, Attiya, Said, Bachorski, Melissa, Buglione, Eli, Burke, Adam, Caprio, Amanda, Celone, Christopher, Clark, Shauna, Conners, David, Desany, Brian, Gu, Lisa, Guccione, Lorri, Kao, Kalvin, Kebbel, Andrew, Knowlton, Jennifer, Labrecque, Matthew, McDade, Louise, Mealmaker, Craig, Minderman, Melissa, Nawrocki, Anne, Niazi, Faheem, Pareja, Kristen, Ramenani, Ravi, Riches, David, Song, Wanmin, Turcotte, Cynthia, Wang, Shally, Mardis, Elaine R., Wilson, Richard K., Dooling, David, Fulton, Lucinda, Fulton, Robert, Weinstock, George, Durbin, Richard M., Burton, John, Carter, David M., Churcher, Carol, Coffey, Alison, Cox, Anthony, Palotie, Aarno, Quail, Michael, Skelly, Tom, Stalker, James, Swerdlow, Harold P., Turner, Daniel, De Witte, Anniek, Giles, Shane, Bainbridge, Matthew, Challis, Danny, Sabo, Aniko, Yu, Fuli, Yu, Jin, Fang, Xiaodong, Guo, Xiaosen, Li, Yingrui, Luo, Ruibang, Tai, Shuaishuai, Wu, Honglong, Zheng, Hancheng, Zheng, Xiaole, Zhou, Yan, Marth, Gabor T., Garrison, Erik P., Huang, Weichun, Indap, Amit, Kural, Deniz, Lee, Wan-Ping, Fung Leong, Wen, Quinlan, Aaron R., Stewart, Chip, Stromberg, Michael P., Ward, Alistair N., Wu, Jiantao, Lee, Charles, Mills, Ryan E., Shi, Xinghua, Daly, Mark J., DePristo, Mark A., Ball, Aaron D., Banks, Eric, Browning, Brian L., Garimella, Kiran V., Grossman, Sharon R., Handsaker, Robert E., Hanna, Matt, Hartl, Chris, Kernytsky, Andrew M., Korn, Joshua M., Li, Heng, Maguire, Jared R., McCarroll, Steven A., McKenna, Aaron, Nemesh, James C., Philippakis, Anthony A., Poplin, Ryan E., Price, Alkes, Rivas, Manuel A., Sabeti, Pardis C., Schaffner, Stephen F., Shlyakhter, Ilya A., Cooper, David N., Ball, Edward V., Mort, Matthew, Phillips, Andrew D., Stenson, Peter D., Sebat, Jonathan, Makarov, Vladimir, Ye, Kenny, Yoon, Seungtai C., Bustamante, Carlos D., Clark, Andrew G., Boyko, Adam, Degenhardt, Jeremiah, Gravel, Simon, Gutenkunst, Ryan N., Kaganovich, Mark, Keinan, Alon, Lacroute, Phil, Ma, Xin, Reynolds, Andy, Clarke, Laura, Flicek, Paul, Cunningham, Fiona, Herrero, Javier, Keenen, Stephen, Kulesha, Eugene, Leinonen, Rasko, McLaren, William M., Radhakrishnan, Rajesh, Smith, Richard E., Zalunin, Vadim, Zheng-Bradley, Xiangqun, Korbel, Jan O., Stütz, Adrian M., Humphray, Sean, Bauer, Markus, Cheetham, Keira R., Cox, Tony, Eberle, Michael, James, Terena, Kahn, Scott, Murray, Lisa, Ye, Kai, De La Vega, Francisco M., Fu, Yutao, Hyland, Fiona C. L., Manning, Jonathan M., McLaughlin, Stephen F., Peckham, Heather E., Sakarya, Onur, Sun, Yongming A., Tsung, Eric F., Batzer, Mark A., Konkel, Miriam K., Walker, Jerilyn A., Albrecht, Marcus W., Amstislavskiy, Vyacheslav S., Herwig, Ralf, Parkhomchuk, Dimitri V., Sherry, Stephen T., Agarwala, Richa, Khouri, Hoda M., Morgulis, Aleksandr O., Paschall, Justin E., Phan, Lon D., Rotmistrovsky, Kirill E., Sanders, Robert D., Shumway, Martin F., Xiao, Chunlin, McVean, Gil A., Auton, Adam, Iqbal, Zamin, Lunter, Gerton, Marchini, Jonathan L., Moutsianas, Loukas, Myers, Simon, Tumian, Afidalina, Desany, Brian, Knight, James, Winer, Roger, Craig, David W., Beckstrom-Sternberg, Steve M., Christoforides, Alexis, Kurdoglu, Ahmet A., Pearson, John V., Sinari, Shripad A., Tembe, Waibhav D., Haussler, David, Hinrichs, Angie S., Katzman, Sol J., Kern, Andrew, Kuhn, Robert M., Przeworski, Molly, Hernandez, Ryan D., Howie, Bryan, Kelley, Joanna L., Cord Melton, S., Abecasis, Gonçalo R., Li, Yun, Anderson, Paul, Blackwell, Tom, Chen, Wei, Cookson, William O., Ding, Jun, Min Kang, Hyun, Lathrop, Mark, Liang, Liming, Moffatt, Miriam F., Scheet, Paul, Sidore, Carlo, Snyder, Matthew, Zhan, Xiaowei, Zöllner, Sebastian, Awadalla, Philip, Casals, Ferran, Idaghdour, Youssef, Keebler, John, Stone, Eric A., Zilversmit, Martine, Jorde, Lynn, Xing, Jinchuan, Eichler, Evan E., Aksay, Gozde, Alkan, Can, Hajirasouliha, Iman, Hormozdiari, Fereydoun, Sahinalp, Cenk S., Sudmant, Peter H., Mardis, Elaine R., Chen, Ken, Chinwalla, Asif, Ding, Li, Koboldt, Daniel C., McLellan, Mike D., Wallis, John W., Wendl, Michael C., Zhang, Qunyuan, Albers, Cornelis A., Ayub, Qasim, Balasubramaniam, Senduran, Barrett, Jeffrey C., Chen, Yuan, Conrad, Donald F., Danecek, Petr, Dermitzakis, Emmanouil T., Hu, Min, Huang, Ni, Hurles, Matt E., Jin, Hanjun, Jostins, Luke, Keane, Thomas M., Quang Le, Si, Lindsay, Sarah, Long, Quan, MacArthur, Daniel G., Montgomery, Stephen B., Parts, Leopold, Tyler-Smith, Chris, Walter, Klaudia, Zhang, Yujun, Gerstein, Mark B., Snyder, Michael, Abyzov, Alexej, Balasubramanian, Suganthi, Bjornson, Robert, Du, Jiang, Grubert, Fabian, Habegger, Lukas, Haraksingh, Rajini, Jee, Justin, Khurana, Ekta, Lam, Hugo Y. K., Leng, Jing, Jasmine Mu, Xinmeng, Urban, Alexander E., Zhang, Zhengdong, Lee, Charles, McCarroll, Steven A., DePristo, Mark A., Korbel, Jan O., De La Vega, Francisco M., Blackwell, Tom, Eichler, Evan E., Kidd, Jeffrey M., Hurles, Matt E., Gibbs, Richard A., Coafra, Cristian, Dinh, Huyen, Kovar, Christie, Lee, Sandy, Nazareth, Lynne, Marth, Gabor T., Wilkinson, Jane, Flicek, Paul, Sherry, Stephen T., Abecasis, Gonçalo R., Mardis, Elaine R., Coffey, Allison, Scott, Carol, Gerstein, Mark B., Chakravarti, Aravinda, Knoppers, Bartha M., Bustamante, Carlos D., Gharani, Neda, Jorde, Lynn, Kaye, Jane S., Kent, Alastair, Li, Taosha, McGuire, Amy L., Ossorio, Pilar N., Rotimi, Charles N., Su, Yeyang, Toji, Lorraine H., Brooks, Lisa D., Felsenfeld, Adam L., McEwen, Jean E., Abdallah, Assya, Juenger, Christopher R., Clemm, Nicholas C., Duncanson, Audrey, Green, Eric D., Guyer, Mark S., and Peterson, Jane L.
Published: 2010
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28. Basigin is a receptor essential for erythrocyte invasion by plasmodium Falciparum

Author: Crosnier, Cecile, Bustamante, Leyla Y., Bartholdson, S. Josefin, Bei, Amy K., Theron, Michel, Uchikawa, Makoto, Mboup, Souleymane, Ndir, Omar, Kwiatkowski, Dominic P., Duraisingh, Manoj T., Rayner, Julian C., and Wright, Gavin J.
Subjects: Malaria -- Causes of -- Research, Plasmodium falciparum -- Physiological aspects -- Research, Environmental issues, Science and technology, Zoology and wildlife conservation
Abstract: Erythrocyte invasion by Plasmodium falciparum is central to the pathogenesis of malaria. Invasion requires a series of extracellular recognition events between erythrocyte receptors and ligands on the merozoite, the invasive [...]
Published: 2011

29. The ribosome uses two active mechanisms to unwind messenger RNA during translation

Author: Qu, Xiaohui, Wen, Jin-Der, Lancaster, Laura, Noller, Harry F., Bustamante, Carlos, and Tinoco, Jr., Ignacio
Subjects: Ribosomes -- Physiological aspects -- Research, Messenger RNA -- Physiological aspects -- Research, Genetic regulation -- Research, Environmental issues, Science and technology, Zoology and wildlife conservation
Abstract: The ribosome translates the genetic information encoded in messenger RNA into protein. Folded structures in the coding region of an mRNA represent a kinetic barrier that lowers the peptide elongation rate, as the ribosome must disrupt structures it encounters in the mRNA at its entry site to allow translocation to the next codon. Such structures are exploited by the cell to create diverse strategies for translation regulation, such as programmed frameshifting (1,2), the modulation of protein expression levels (3,4), ribosome localization (5) and co-translational protein folding (6). Although strand separation activity is inherent to the ribosome, requiring no exogenous helicases (7),its mechanism is still unknown. Here, using a single-molecule optical tweezers assay on mRNA hairpins, we find that the translation rate of identical codons at the decoding centre is greatly influenced by the GC content of folded structures at the mRNA entry site. Furthermore, force applied to the ends of the hairpin to favour its unfolding significantly speeds translation. Quantitative analysis of the force dependence of its helicase activity reveals that the ribosome, unlike previously studied helicases, uses two distinct active mechanisms to unwind mRNA structure: it destabilizes the helical junction at the mRNA entry site by biasing its thermal fluctuations towards the open state, increasing the probability of the ribosome translocating unhindered; and it mechanically pulls apart the mRNA single strands of the closed junction during the conformational changes that accompany ribosome translocation. The second of these mechanisms ensures a minimal basal rate of translation in the cell; specialized, mechanically stable structures are required to stall the ribosome temporarily (1,2). Our results establish a quantitative mechanical basis for understanding the mechanism of regulation of the elongation rate of translation by structured mRNAs., To monitor ribosome translation and mRNA unwinding with optical tweezers, we use a hairpin-forming mRNA which has a single-stranded 5' overhang that includes the Shine-Dalgarno sequence and the start codon [...]
Published: 2011
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30. TFH-derived dopamine accelerates productive synapses in germinal centres

Author: Salvatore Valvo, Pablo F. Canete, Ilenia Papa, Michael Meyer-Hermann, David Saliba, Claudio Doglioni, Carola G. Vinuesa, Maurilio Ponzoni, Hayley A. McNamara, Michele A. Grimbaldeston, Paula Gonzalez-Figueroa, Rebecca A. Sweet, Ian A. Cockburn, Harpreet Vohra, Sonia Bustamante, Michael L. Dustin, Papa, Ilenia, Saliba, David, Ponzoni, Maurilio, Bustamante, Sonia, Canete, Pablo F., Gonzalez-Figueroa, Paula, Mcnamara, Hayley A., Valvo, Salvatore, Grimbaldeston, Michele, Sweet, Rebecca A., Vohra, Harpreet, Cockburn, Ian A., Meyer-Hermann, Michael, Dustin, Michael L., Doglioni, Claudio, Vinuesa, Carola G., Canete, Pablo F, McNamara, Hayley A, Sweet, Rebecca A, Cockburn, Ian A, Dustin, Michael L, and Vinuesa, Carola G
Subjects: 0301 basic medicine, medicine.medical_specialty, Immunological Synapses, Secretory Vesicle, Dopamine, CD40 Ligand, Immunological Synapse, Neurotransmission, Article, germinal centres, immunology, Synapse, Inducible T-Cell Co-Stimulator Ligand, Mice, Neurotransmitter Agent, 03 medical and health sciences, Internal medicine, medicine, Animals, Humans, Child, Receptor, B-Lymphocytes, Neurotransmitter Agents, Multidisciplinary, CD40, biology, Animal, Secretory Vesicles, B-Lymphocyte, Models, Immunological, Germinal center, T-Lymphocytes, Helper-Inducer, Germinal Center, Up-Regulation, Cell biology, 030104 developmental biology, Endocrinology, biology.protein, Female, Chromogranin B, Human, medicine.drug
Abstract: Protective high-affinity antibody responses depend on competitive selection of B cells carrying somatically mutated B-cell receptors by follicular helper T (T FH ) cells in germinal centres. The rapid T-B-cell interactions that occur during this process are reminiscent of neural synaptic transmission pathways. Here we show that a proportion of human T FH cells contain dense-core granules marked by chromogranin B, which are normally found in neuronal presynaptic terminals storing catecholamines such as dopamine. T FH cells produce high amounts of dopamine and release it upon cognate interaction with B cells. Dopamine causes rapid translocation of intracellular ICOSL (inducible T-cell co-stimulator ligand, also known as ICOSLG) to the B-cell surface, which enhances accumulation of CD40L and chromogranin B granules at the human T FH cell synapse and increases the synapse area. Mathematical modelling suggests that faster dopamine-induced T-B-cell interactions increase total germinal centre output and accelerate it by days. Delivery of neurotransmitters across the T-B-cell synapse may be advantageous in the face of infection. Refereed/Peer-reviewed
Published: 2017
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31. The folding cooperativity of a protein is controlled by its chain topology

Author: Shank, Elizabeth A., Cecconi, Ciro, Dill, Jesse W., Marqusee, Susan, and Bustamante, Carlos
Subjects: Nucleotide sequencing -- Methods, Protein folding -- Observations -- Methods, Proteins -- Structure, Polypeptides -- Properties -- Methods, DNA sequencing -- Methods
Abstract: The three-dimensional structures of proteins often show a modular architecture comprised of discrete structural regions or domains. Cooperative communication between these regions is important for catalysis, regulation and efficient folding; lack of coupling has been implicated in the formation of fibrils and other misfolding pathologies (1). How different structural regions of a protein communicate and contribute to a protein's overall energetics and folding, however, is still poorly understood. Here we use a single-molecule optical tweezers approach to induce the selective unfolding of particular regions of T4 lysozyme and monitor the effect on other regions not directly acted on by force. We investigate how the topological organization of a protein (the order of structural elements along the sequence) affects the coupling and folding cooperativity between its domains. To probe the status of the regions not directly subjected to force, we determine the free energy changes during mechanical unfolding using Crooks' fluctuation theorem. We pull on topological variants (circular permutants) and find that the topological organization of the polypeptide chain critically determines the folding cooperativity between domains and thus what parts of the folding/unfolding landscape are explored. We speculate that proteins may have evolved to select certain topologies that increase coupling between regions to avoid areas of the landscape that lead to kinetic trapping and misfolding., Most mechanical unfolding studies have focused on small globular domains, using either the atomic force microscope (AFM) (2-4) or optical tweezers (5). By grabbing the molecule at specific residues, one [...]
Published: 2010
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32. 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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33. Substrate interactions and promiscuity in a viral DNA packaging motor

Author: Aathavant, K., Politzer, Adam T., Kaplan, Ariel, Moffitt, Jeffrey R., Chemla, Yann R., Grimes, Shelley, Jardine, Paul J., Andersons, Dwight L., and Bustamante, Carlos
Subjects: DNA -- Physiological aspects -- Research -- Genetic aspects, Biological transport -- Genetic aspects -- Research -- Physiological aspects, Viral genetics -- Research -- Genetic aspects -- Physiological aspects, Carrier proteins -- Physiological aspects -- Genetic aspects -- Research, Environmental issues, Science and technology, Zoology and wildlife conservation
Abstract: The ASCE (additional strand, conserved E) superfamily of proteins consists of structurally similar ATPases associated with diverse cellular activities involving metabolism and transport of proteins and nucleic acids in all forms of life (1). A subset of these enzymes consists of multimeric ringed pumps responsible for DNA transport in processes including genome packaging in adenoviruses, herpesviruses, poxviruses and tailed bacteriophages (2). Although their mechanism of mechanochemical conversion is beginning to be understood (3), little is known about how these motors engage their nucleic acid substrates. Questions remain as to whether the motors contact a single DNA element, such as a phosphate or a base, or whether contacts are distributed over several parts of the DNA. Furthermore, the role of these contacts in the mechanochemical rycle is unknown. Here we use the genome packaging motor of the Bacillus subtilis bacteriophage φ29 (ref. 4) to address these questions. The full mechanochemical cycle of the motor, in which the ATPase is a pentameric-ring (5) of gene product 16 (gp16), involves two phases-an ATP-loading dwell followed by a translocation burst of four 2.5-base-pair (bp) steps (6) triggered by hydrolysis product release (7). By challenging the motor with a variety of modified DNA substrates, we show that during the dwell phase important contacts are made with adjacent phosphates every 10-bp on the 5'-3' strand in the direction of packaging. As well as providing stable, long-lived contacts, these phosphate interactions also regulate the chemical cycle. In contrast, during the burst phase, we find that DNA translocation is driven against large forces by extensive contacts, some of which are not specific to the chemical moieties of DNA. Such promiscuous, nonspecific contacts may reflect common translocase-substrate interactions for both the nucleic acid and protein translocases of the ASCE superfamily (1)., To test the role of the phosphate backbone charge in motor-DNA interactions we inserted a 10-bp region of double-stranded methyl-phosphonate DNA (dsMeP) into the middle of an ~8-kilobase-pair (kb) native [...]
Published: 2009

34. Intersubunit coordination in a homomeric ring ATPase

Author: Moffitt, Jeffrey R., Chemla, Yann R., Aathavan, K., Grimes, Shelley, Jardine, Paul J., Anderson, Dwight L., and Bustamante, Carlos
Subjects: DNA -- Physiological aspects -- Research, Adenosine triphosphatase -- Physiological aspects -- Research, Hydrolysis -- Research -- Physiological aspects, Environmental issues, Science and technology, Zoology and wildlife conservation, Physiological aspects, Research
Abstract: Homomeric ring ATPases perform many vital and varied tasks in the cell, ranging from chromosome segregation to protein degradation. Here we report the direct observation of the intersubunit coordination and step size of such a ring ATPase, the double-stranded-DNA packaging motor in the bacteriophage φ29. Using high-resolution optical tweezers, we find that packaging occurs in increments of 10 base pairs (bp). Statistical analysis of the preceding dwell times reveals that multiple ATPs bind during each dwell, and application of high force reveals that these 10-bp increments are composed of four 2.5-bp steps. These results indicate that the hydrolysis cycles of the individual subunits are highly coordinated by means of a mechanism novel for ring ATPases. Furthermore, a step size that is a non-integer number of base pairs demands new models for motor-DNA interactions., Multimeric ring ATPases of the ASCE (additional strand, conserved E) superfamily represent a structurally homologous yet functionally diverse group of proteins involved in such varied tasks as ATP synthesis, protein [...]
Published: 2009

35. Genes mirror geography within Europe

Author: Novembre, John, Johnson, Toby, Bryc, Katarzyna, Kutalik, Zoltan, Boyko, Adam R., Auton, Adam, Indap, Amit, King, Karen S., Bergmann, Sven, Nelson, Matthew R., Stephens, Matthew, and Bustamante, Carlos D.
Subjects: Europeans -- Genetic aspects -- Research, Human population genetics -- Research -- Genetic aspects, Environmental issues, Science and technology, Zoology and wildlife conservation, Genetic aspects, Research
Abstract: Understanding the genetic structure of human populations is of fundamental interest to medical, forensic and anthropological sciences. Advances in high-throughput genotyping technology have markedly improved our understanding of global patterns [...]
Published: 2008

36. Following translation by single ribosomes one codon at a time

Author: Wen, Jin-Der, Lancaster, Laura, Hodges, Courtney, Zeri, Ana-Carolina, Yoshimura, Shige H., Noller, Harry F., Bustamante, Carlos, and Tinoco, Jr., Ignacio
Subjects: Environmental issues, Science and technology, Zoology and wildlife conservation
Abstract: We have followed individual ribosomes as they translate single messenger RNA hairpins tethered by the ends to optical tweezers. Here we reveal that translation occurs through successive translocation-and-pause cycles. The [...]
Published: 2008

37. Proportionally more deleterious genetic variation in European than in African populations

Author: Lohmueller, Kirk E., Indap, Amit R., Schmidt, Steffen, Boyko, Adam R., Hernandez, Ryan D., Hubisz, Melissa J., Sninsky, John J., White, Thomas J., Sunyaev, Shamil R., Nielsen, Rasmus, Clark, Andrew G., and Bustamante, Carlos D.
Subjects: Environmental issues, Science and technology, Zoology and wildlife conservation
Abstract: Quantifying the number of deleterious mutations per diploid human genome is of crucial concern to both evolutionary and medical geneticists (1-3). Here we combine genome-wide polymorphism data from PCR-based exon [...]
Published: 2008

38. TFH-derived dopamine accelerates productive synapses in germinal centres

Author: Papa, Ilenia, Saliba, David, Ponzoni, Maurilio, Bustamante, Sonia, Canete, Pablo F., Gonzalez-Figueroa, Paula, McNamara, Hayley A., Valvo, Salvatore, Grimbaldeston, Michele, Sweet, Rebecca A., Vohra, Harpreet, Cockburn, Ian A., Meyer-Hermann, Michael, Dustin, Michael L., Doglioni, Claudio, and Vinuesa, Carola G.
Subjects: Synapses -- Physiological aspects, Dopamine -- Physiological aspects, T cells -- Physiological aspects, Environmental issues, Science and technology, Zoology and wildlife conservation
Abstract: Protective high-affinity antibody responses depend on competitive selection of B cells carrying somatically mutated B-cell receptors by follicular helper T (T[sub.FH]) cells in germinal centres. The rapid TB-cell interactions that occur during this process are reminiscent of neural synaptic transmission pathways. Here we show that a proportion of human T[sub.FH] cells contain dense-core granules marked by chromogranin B, which are normally found in neuronal presynaptic terminals storing catecholamines such as dopamine. T[sub.FH] cells produce high amounts of dopamine and release it upon cognate interaction with B cells. Dopamine causes rapid translocation of intracellular ICOSL (inducible T-cell co-stimulator ligand, also known as ICOSLG) to the B-cell surface, which enhances accumulation of CD40L and chromogranin B granules at the human T[sub.FH] cell synapse and increases the synapse area. Mathematical modelling suggests that faster dopamine-induced TB-cell interactions increase total germinal centre output and accelerate it by days. Delivery of neurotransmitters across the TB-cell synapse may be advantageous in the face of infection., Author(s): Ilenia Papa [1]; David Saliba [2]; Maurilio Ponzoni [3]; Sonia Bustamante [4]; Pablo F. Canete [1]; Paula Gonzalez-Figueroa [1]; Hayley A. McNamara [1]; Salvatore Valvo [2]; Michele Grimbaldeston [5, [...]
Published: 2017
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39. Widespread amphibian extinctions from epidemic disease driven by global warming

Author: Alan Pounds, J., Bustamante, Martin R., Coloma, Luis A., Consuegra, Jamie A., Fogden, Michael P. L., Foster, Pru N., La Marca, Enrique, Masters, Karen L., Merino-Viteri, Andres, Puschendorf, Robert, Ron, Santiago R., Sanchez-Azofeifa, G. Arturo, Still, Christopher J., and Young, Bruce E.
Subjects: Environmental issues, Science and technology, Zoology and wildlife conservation
Abstract: Author(s): J. Alan Pounds (corresponding author) [1]; MartÃn R. Bustamante [2]; Luis A. Coloma [2]; Jamie A. Consuegra [3]; Michael P. L. Fogden [1]; Pru N. Foster [4, 12]; Enrique [...]
Published: 2006
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40. 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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41. RNA translocation and unwinding mechanism of HCV NS3 helicase and its coordination by ATP

Author: Dumont, Sophie, Cheng, Wei, Serebrov, Victor, Beran, Rudolf K., Tinoco, Jr, Ignacio, Pyle, Anna Marie, and Bustamante, Carlos
Subjects: Environmental issues, Science and technology, Zoology and wildlife conservation
Abstract: Author(s): Sophie Dumont [1, 7]; Wei Cheng [2, 7]; Victor Serebrov [5]; Rudolf K. Beran [5]; Ignacio Tinoco, Jr [3]; Anna Marie Pyle [5]; Carlos Bustamante (corresponding author) [1, 2, [...]
Published: 2006
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42. Natural selection on protein-coding genes in the human genome

Author: Bustamante, Carlos D., Fledel-Alon, Adi, Williamson, Scott, Nielsen, Rasmus, Todd Hubisz, Melissa, Glanowski, Stephen, Tanenbaum, David M., White, Thomas J., Sninsky, John J., Hernandez, Ryan D., Civello, Daniel, Adams, Mark D., Cargill, Michele, and Clark, Andrew G.
Subjects: Environmental issues, Science and technology, Zoology and wildlife conservation
Abstract: Author(s): Carlos D. Bustamante (corresponding author) [1]; Adi Fledel-Alon [1]; Scott Williamson [1]; Rasmus Nielsen [1, 2]; Melissa Todd Hubisz [1]; Stephen Glanowski [3]; David M. Tanenbaum [3]; Thomas J. [...]
Published: 2005
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43. Verification of the Crooks fluctuation theorem and recovery of RNA folding free energies

Author: Collin, D., Ritort, F., Jarzynski, C., Smith, S. B., Tinoco, Jr, I., and Bustamante, C.
Subjects: Environmental issues, Science and technology, Zoology and wildlife conservation
Abstract: Author(s): D. Collin [1, 7]; F. Ritort (corresponding author) [2, 7]; C. Jarzynski [3]; S. B. Smith [4]; I. Tinoco, Jr [5]; C. Bustamante (corresponding author) [4, 6] Atomic force [...]
Published: 2005
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44. Fisheries: Broaden the arguments

Author: Hobday, Alistair J., Bustamante, Rodrigo H., and Plagányi, Éva E.
Published: 2013
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45. 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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46. 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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47. The cost of inbreeding in Arabidopsis

Author: Bustamante, Carlos D., Nielsen, Rasmus, Sawyer, Stanley A., Olsen, Kenneth M., Purugganan, Michael D., and Hartl, Daniel L.
Subjects: Arabidopsis -- Genetic aspects -- Analysis, Inbreeding -- Analysis -- Genetic aspects, Environmental issues, Science and technology, Zoology and wildlife conservation, Analysis, Genetic aspects
Abstract: Author(s): Carlos D. Bustamante [1, 2]; Rasmus Nielsen [3]; Stanley A. Sawyer [4]; Kenneth M. Olsen [5]; Michael D. Purugganan [5]; Daniel L. Hartl (corresponding author) [1] Population geneticists have [...]
Published: 2002
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48. Corrigendum: The Amazon basin in transition

Author: Davidson, Eric A., de Araújo, Alessandro C., Artaxo, Paulo, Balch, Jennifer K., Brown, Foster I., Bustamante, Mercedes M. C., Coe, Michael T., DeFries, Ruth S., Keller, Michael, Longo, Marcos, Munger, William J., Schroeder, Wilfrid, Soares-Filho, Britaldo S., Souza, Carlos M., and Wofsy, Steven C.
Published: 2012
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49. The bacteriophage [straight phi]29 portal motor can package DNA against a large internal force

Author: Smith, Douglas E., Tans, Sander J., Smith, Steven B., Grimes, Shelley, Anderson, Dwight L., and Bustamante, Carlos
Subjects: Environmental issues, Science and technology, Zoology and wildlife conservation
Abstract: Author(s): Douglas E. Smith [1, 2]; Sander J. Tans [1, 2]; Steven B. Smith [3]; Shelley Grimes [4]; Dwight L. Anderson [4]; Carlos Bustamante (corresponding author) [2, 3, 5, 6] [...]
Published: 2001
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50. Genomics for the world

Author: Bustamante, Carlos D., De La Vega, Francisco M., and Burchard, Esteban G.
Published: 2011
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