Author: "Singer, A." / Journal: nature - Searchworks@Jio Institute Digital Library Search Results

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798 results on '"Singer, A."'

1. Groundwater-dependent ecosystem map exposes global dryland protection needs

Author: Rohde, Melissa M, Albano, Christine M, Huggins, Xander, Klausmeyer, Kirk R, Morton, Charles, Sharman, Ali, Zaveri, Esha, Saito, Laurel, Freed, Zach, Howard, Jeanette K, Job, Nancy, Richter, Holly, Toderich, Kristina, Rodella, Aude-Sophie, Gleeson, Tom, Huntington, Justin, Chandanpurkar, Hrishikesh A, Purdy, Adam J, Famiglietti, James S, Singer, Michael Bliss, Roberts, Dar A, Caylor, Kelly, and Stella, John C
Subjects: Climate Change Impacts and Adaptation, Environmental Sciences, Generic health relevance, Life on Land, Biodiversity, Conservation of Natural Resources, Culture, Ecosystem, Geographic Mapping, Groundwater, Socioeconomic Factors, Sustainable Development, Agriculture, Animals, General Science & Technology
Abstract: Groundwater is the most ubiquitous source of liquid freshwater globally, yet its role in supporting diverse ecosystems is rarely acknowledged1,2. However, the location and extent of groundwater-dependent ecosystems (GDEs) are unknown in many geographies, and protection measures are lacking1,3. Here, we map GDEs at high-resolution (roughly 30 m) and find them present on more than one-third of global drylands analysed, including important global biodiversity hotspots4. GDEs are more extensive and contiguous in landscapes dominated by pastoralism with lower rates of groundwater depletion, suggesting that many GDEs are likely to have already been lost due to water and land use practices. Nevertheless, 53% of GDEs exist within regions showing declining groundwater trends, which highlights the urgent need to protect GDEs from the threat of groundwater depletion. However, we found that only 21% of GDEs exist on protected lands or in jurisdictions with sustainable groundwater management policies, invoking a call to action to protect these vital ecosystems. Furthermore, we examine the linkage of GDEs with cultural and socio-economic factors in the Greater Sahel region, where GDEs play an essential role in supporting biodiversity and rural livelihoods, to explore other means for protection of GDEs in politically unstable regions. Our GDE map provides critical information for prioritizing and developing policies and protection mechanisms across various local, regional or international scales to safeguard these important ecosystems and the societies dependent on them.
Published: 2024

2. Single-molecule imaging of transcription dynamics in somatic stem cells

Author: Wheat, Justin C., Sella, Yehonatan, Willcockson, Michael, Skoultchi, Arthur I., Bergman, Aviv, Singer, Robert H., and Steidl, Ulrich
Subjects: Stem cells -- Physiological aspects, Somatic cells -- Physiological aspects -- Methods, Genetic transcription -- Observations -- Physiological aspects -- Methods, Imaging systems -- Methods -- Physiological aspects, Environmental issues, Science and technology, Zoology and wildlife conservation
Abstract: Molecular noise is a natural phenomenon that is inherent to all biological systems.sup.1,2. How stochastic processes give rise to the robust outcomes that support tissue homeostasis remains unclear. Here we use single-molecule RNA fluorescent in situ hybridization (smFISH) on mouse stem cells derived from haematopoietic tissue to measure the transcription dynamics of three key genes that encode transcription factors: PU.1 (also known as Spi1), Gata1 and Gata2. We find that infrequent, stochastic bursts of transcription result in the co-expression of these antagonistic transcription factors in the majority of haematopoietic stem and progenitor cells. Moreover, by pairing smFISH with time-lapse microscopy and the analysis of pedigrees, we find that although individual stem-cell clones produce descendants that are in transcriptionally related states--akin to a transcriptional priming phenomenon--the underlying transition dynamics between states are best captured by stochastic and reversible models. As such, a stochastic process can produce cellular behaviours that may be incorrectly inferred to have arisen from deterministic dynamics. We propose a model whereby the intrinsic stochasticity of gene expression facilitates, rather than impedes, the concomitant maintenance of transcriptional plasticity and stem cell robustness. Single-molecule fluorescence in situ hybridization and live-cell imaging are used to study the contribution of transcriptional noise to stem cell heterogeneity, revealing that stochastic transcription dynamics are conducive to concomitant stem-cell maintenance and tissue homeostasis., Author(s): Justin C. Wheat [sup.1] [sup.2] , Yehonatan Sella [sup.3] , Michael Willcockson [sup.1] , Arthur I. Skoultchi [sup.1] , Aviv Bergman [sup.3] [sup.4] [sup.5] [sup.6] , Robert H. Singer [...]
Published: 2020
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3. Transcript expression-aware annotation improves rare variant interpretation

Author: Cummings, Beryl B., Karczewski, Konrad J., Kosmicki, Jack A., Seaby, Eleanor G., Watts, Nicholas A., Singer-Berk, Moriel, and Mudge, Jonathan M.
Subjects: Genetic variation -- Analysis -- Usage, Human genome -- Identification and classification -- Analysis -- Usage, Genetic transcription -- Usage -- Analysis, Citation indexes -- Management -- Analysis -- Usage, Company business management, Environmental issues, Science and technology, Zoology and wildlife conservation
Abstract: The acceleration of DNA sequencing in samples from patients and population studies has resulted in extensive catalogues of human genetic variation, but the interpretation of rare genetic variants remains problematic. A notable example of this challenge is the existence of disruptive variants in dosage-sensitive disease genes, even in apparently healthy individuals. Here, by manual curation of putative loss-of-function (pLoF) variants in haploinsufficient disease genes in the Genome Aggregation Database (gnomAD).sup.1, we show that one explanation for this paradox involves alternative splicing of mRNA, which allows exons of a gene to be expressed at varying levels across different cell types. Currently, no existing annotation tool systematically incorporates information about exon expression into the interpretation of variants. We develop a transcript-level annotation metric known as the 'proportion expressed across transcripts', which quantifies isoform expression for variants. We calculate this metric using 11,706 tissue samples from the Genotype Tissue Expression (GTEx) project.sup.2 and show that it can differentiate between weakly and highly evolutionarily conserved exons, a proxy for functional importance. We demonstrate that expression-based annotation selectively filters 22.8% of falsely annotated pLoF variants found in haploinsufficient disease genes in gnomAD, while removing less than 4% of high-confidence pathogenic variants in the same genes. Finally, we apply our expression filter to the analysis of de novo variants in patients with autism spectrum disorder and intellectual disability or developmental disorders to show that pLoF variants in weakly expressed regions have similar effect sizes to those of synonymous variants, whereas pLoF variants in highly expressed exons are most strongly enriched among cases. Our annotation is fast, flexible and generalizable, making it possible for any variant file to be annotated with any isoform expression dataset, and will be valuable for the genetic diagnosis of rare diseases, the analysis of rare variant burden in complex disorders, and the curation and prioritization of variants in recall-by-genotype studies. A novel variant annotation metric that quantifies the level of expression of genetic variants across tissues is validated in the Genome Aggregation Database (gnomAD) and is shown to improve rare variant interpretation., Author(s): Beryl B. Cummings [sup.1] [sup.2] [sup.3] , Konrad J. Karczewski [sup.1] [sup.2] , Jack A. Kosmicki [sup.1] [sup.2] [sup.4] , Eleanor G. Seaby [sup.1] [sup.2] [sup.5] , Nicholas A. [...]
Published: 2020
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4. Discriminating [alpha]-synuclein strains in Parkinson's disease and multiple system atrophy

Author: Shahnawaz, Mohammad, Mukherjee, Abhisek, Pritzkow, Sandra, Mendez, Nicolas, Rabadia, Prakruti, Liu, Xiangan, Hu, Bo, Schmeichal, Ann, Singer, Wolfgang, Wu, Gang, Tsai, Ah-Lim, Shirani, Hamid, Nilsson, K. Peter R., Low, Philip A., and Soto, Claudio
Subjects: Atrophy -- Development and progression, Parkinson's disease -- Development and progression, Nerve proteins -- Physiological aspects, Environmental issues, Science and technology, Zoology and wildlife conservation
Abstract: Synucleinopathies are neurodegenerative diseases that are associated with the misfolding and aggregation of [alpha]-synuclein, including Parkinson's disease, dementia with Lewy bodies and multiple system atrophy.sup.1. Clinically, it is challenging to differentiate Parkinson's disease and multiple system atrophy, especially at the early stages of disease.sup.2. Aggregates of [alpha]-synuclein in distinct synucleinopathies have been proposed to represent different conformational strains of [alpha]-synuclein that can self-propagate and spread from cell to cell.sup.3-6. Protein misfolding cyclic amplification (PMCA) is a technique that has previously been used to detect [alpha]-synuclein aggregates in samples of cerebrospinal fluid with high sensitivity and specificity.sup.7,8. Here we show that the [alpha]-synuclein-PMCA assay can discriminate between samples of cerebrospinal fluid from patients diagnosed with Parkinson's disease and samples from patients with multiple system atrophy, with an overall sensitivity of 95.4%. We used a combination of biochemical, biophysical and biological methods to analyse the product of [alpha]-synuclein-PMCA, and found that the characteristics of the [alpha]-synuclein aggregates in the cerebrospinal fluid could be used to readily distinguish between Parkinson's disease and multiple system atrophy. We also found that the properties of aggregates that were amplified from the cerebrospinal fluid were similar to those of aggregates that were amplified from the brain. These findings suggest that [alpha]-synuclein aggregates that are associated with Parkinson's disease and multiple system atrophy correspond to different conformational strains of [alpha]-synuclein, which can be amplified and detected by [alpha]-synuclein-PMCA. Our results may help to improve our understanding of the mechanism of [alpha]-synuclein misfolding and the structures of the aggregates that are implicated in different synucleinopathies, and may also enable the development of a biochemical assay to discriminate between Parkinson's disease and multiple system atrophy. Protein misfolding cyclic amplification (PMCA) technology can discriminate between patients with Parkinson's disease and patients with multiple system atrophy on the basis of the characteristics of the [alpha]-synuclein aggregates in the cerebrospinal fluid., Author(s): Mohammad Shahnawaz [sup.1] , Abhisek Mukherjee [sup.1] , Sandra Pritzkow [sup.1] , Nicolas Mendez [sup.1] , Prakruti Rabadia [sup.1] , Xiangan Liu [sup.2] , Bo Hu [sup.2] , Ann [...]
Published: 2020
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5. Comprehensive molecular profiling of lung adenocarcinoma

Author: Collisson, Eric A, Campbell, Joshua D, Brooks, Angela N, Berger, Alice H, Lee, William, Chmielecki, Juliann, Beer, David G, Cope, Leslie, Creighton, Chad J, Danilova, Ludmila, Ding, Li, Getz, Gad, Hammerman, Peter S, Neil Hayes, D, Hernandez, Bryan, Herman, James G, Heymach, John V, Jurisica, Igor, Kucherlapati, Raju, Kwiatkowski, David, Ladanyi, Marc, Robertson, Gordon, Schultz, Nikolaus, Shen, Ronglai, Sinha, Rileen, Sougnez, Carrie, Tsao, Ming-Sound, Travis, William D, Weinstein, John N, Wigle, Dennis A, Wilkerson, Matthew D, Chu, Andy, Cherniack, Andrew D, Hadjipanayis, Angela, Rosenberg, Mara, Weisenberger, Daniel J, Laird, Peter W, Radenbaugh, Amie, Ma, Singer, Stuart, Joshua M, Averett Byers, Lauren, Baylin, Stephen B, Govindan, Ramaswamy, Meyerson, Matthew, Gabriel, Stacey B, Cibulskis, Kristian, Kim, Jaegil, Stewart, Chip, Lichtenstein, Lee, Lander, Eric S, Lawrence, Michael S, Kandoth, Cyriac, Fulton, Robert, Fulton, Lucinda L, McLellan, Michael D, Wilson, Richard K, Ye, Kai, Fronick, Catrina C, Maher, Christopher A, Miller, Christopher A, Wendl, Michael C, Cabanski, Christopher, Mardis, Elaine, Wheeler, David, Balasundaram, Miruna, Butterfield, Yaron SN, Carlsen, Rebecca, Chuah, Eric, Dhalla, Noreen, Guin, Ranabir, Hirst, Carrie, Lee, Darlene, Li, Haiyan I, Mayo, Michael, Moore, Richard A, Mungall, Andrew J, Schein, Jacqueline E, Sipahimalani, Payal, Tam, Angela, Varhol, Richard, Gordon Robertson, A, Wye, Natasja, Thiessen, Nina, Holt, Robert A, Jones, Steven JM, Marra, Marco A, Imielinski, Marcin, Onofrio, Robert C, Hodis, Eran, and Zack, Travis
Subjects: Rare Diseases, Genetics, Biotechnology, Clinical Research, Lung Cancer, Human Genome, Cancer, Lung, Aetiology, 2.1 Biological and endogenous factors, Adenocarcinoma, Adenocarcinoma of Lung, Cell Cycle Proteins, Female, Gene Dosage, Gene Expression Regulation, Neoplastic, Genomics, Humans, Lung Neoplasms, Male, Molecular Typing, Mutation, Oncogenes, Sex Factors, Transcriptome, Cancer Genome Atlas Research Network, General Science & Technology
Abstract: Adenocarcinoma of the lung is the leading cause of cancer death worldwide. Here we report molecular profiling of 230 resected lung adenocarcinomas using messenger RNA, microRNA and DNA sequencing integrated with copy number, methylation and proteomic analyses. High rates of somatic mutation were seen (mean 8.9 mutations per megabase). Eighteen genes were statistically significantly mutated, including RIT1 activating mutations and newly described loss-of-function MGA mutations which are mutually exclusive with focal MYC amplification. EGFR mutations were more frequent in female patients, whereas mutations in RBM10 were more common in males. Aberrations in NF1, MET, ERBB2 and RIT1 occurred in 13% of cases and were enriched in samples otherwise lacking an activated oncogene, suggesting a driver role for these events in certain tumours. DNA and mRNA sequence from the same tumour highlighted splicing alterations driven by somatic genomic changes, including exon 14 skipping in MET mRNA in 4% of cases. MAPK and PI(3)K pathway activity, when measured at the protein level, was explained by known mutations in only a fraction of cases, suggesting additional, unexplained mechanisms of pathway activation. These data establish a foundation for classification and further investigations of lung adenocarcinoma molecular pathogenesis.
Published: 2014

6. Aridity is expressed in river topography globally

Author: Chen, Shiuan-An, Michaelides, Katerina, Grieve, Stuart W. D., and Singer, Michael Bliss
Subjects: Environmental issues, Science and technology, Zoology and wildlife conservation
Abstract: It has long been suggested that climate shapes land surface topography through interactions between rainfall, runoff and erosion in drainage basins.sup.1-4. The longitudinal profile of a river (elevation versus distance downstream) is a key morphological attribute that reflects the history of drainage basin evolution, so its form should be diagnostic of the regional expression of climate and its interaction with the land surface.sup.5-9. However, both detecting climatic signatures in longitudinal profiles and deciphering the climatic mechanisms of their development have been challenging, owing to the lack of relevant global data and to the variable effects of tectonics, lithology, land surface properties and human activities.sup.10,11. Here we present a global dataset of 333,502 river longitudinal profiles, and use it to explore differences in overall profile shape (concavity) across climate zones. We show that river profiles are systematically straighter with increasing aridity. Through simple numerical modelling, we demonstrate that these global patterns in longitudinal profile shape can be explained by hydrological controls that reflect rainfall-runoff regimes in different climate zones. The most important of these is the downstream rate of change in streamflow, independent of the area of the drainage basin. Our results illustrate that river topography expresses a signature of aridity, suggesting that climate is a first-order control on the evolution of the drainage basin. A global dataset of river longitudinal profiles shows that river profiles become straighter with increasing aridity and numerical modelling suggests that this can be explained by rainfall-runoff regimes in different climate zones., Author(s): Shiuan-An Chen [sup.1] , Katerina Michaelides [sup.1] [sup.2] , Stuart W. D. Grieve [sup.3] , Michael Bliss Singer [sup.2] [sup.4] [sup.5] Author Affiliations: (1) School of Geographical Sciences, University [...]
Published: 2019
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7. Mitochondrial complex III is essential for suppressive function of regulatory T cells

Author: Weinberg, Samuel E., Singer, Benjamin D., Steinert, Elizabeth M., Martinez, Carlos A., Mehta, Manan M., MartÃnez-Reyes, Inmaculada, and Gao, Peng
Subjects: T cells -- Research, Cytochrome bc1 complex -- Research, Suppressor mutation -- Research, Genetic research, Methylation, Metabolites, Gene expression, Resveratrol, Genes, DNA, Cytochrome b, Environmental issues, Science and technology, Zoology and wildlife conservation
Abstract: Regulatory T cells (T.sub.reg cells), a distinct subset of CD4.sup.+ T cells, are necessary for the maintenance of immune self-tolerance and homeostasis.sup.1,2. Recent studies have demonstrated that T.sub.reg cells exhibit a unique metabolic profile, characterized by an increase in mitochondrial metabolism relative to other CD4.sup.+ effector subsets.sup.3,4. Furthermore, the T.sub.reg cell lineage-defining transcription factor, Foxp3, has been shown to promote respiration.sup.5,6; however, it remains unknown whether the mitochondrial respiratory chain is required for the T cell-suppression capacity, stability and survival of T.sub.reg cells. Here we report that T.sub.reg cell-specific ablation of mitochondrial respiratory chain complex III in mice results in the development of fatal inflammatory disease early in life, without affecting T.sub.reg cell number. Mice that lack mitochondrial complex III specifically in T.sub.reg cells displayed a loss of T cell-suppression capacity without altering T.sub.reg cell proliferation and survival. T.sub.reg cells deficient in complex III showed decreased expression of genes associated with T.sub.reg function, whereas Foxp3 expression remained stable. Loss of complex III in T.sub.reg cells increased DNA methylation as well as the metabolites 2-hydroxyglutarate (2-HG) and succinate that inhibit the ten-eleven translocation (TET) family of DNA demethylases.sup.7. Thus, T.sub.reg cells require mitochondrial complex III to maintain immune regulatory gene expression and suppressive function.Specific ablation of mitochondrial complex III subunits in T.sub.reg cells in mice results in inflammatory disease, altered T.sub.reg gene expression and defective T.sub.reg function, indicating a key functional role for mitochondrial complex III in T.sub.reg cells., Author(s): Samuel E. Weinberg [sup.1] , Benjamin D. Singer [sup.1] [sup.2] , Elizabeth M. Steinert [sup.1] , Carlos A. Martinez [sup.2] , Manan M. Mehta [sup.1] , Inmaculada Martínez-Reyes [sup.1] [...]
Published: 2019
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8. A first update on mapping the human genetic architecture of COVID-19

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

9. A phylogeny-driven genomic encyclopaedia of Bacteria and Archaea

Author: Wu, D, Hugenholtz, P, Mavromatis, K, Pukall, R, Dalin, E, Ivanova, NN, Kunin, V, Goodwin, L, Wu, M, Tindall, BJ, Hooper, SD, Pati, A, Lykidis, A, Spring, S, Anderson, IJ, Dhaeseleer, P, Zemla, A, Singer, M, Lapidus, A, Nolan, M, Copeland, A, Han, C, Chen, F, Cheng, JF, Lucas, S, Kerfeld, C, Lang, E, Gronow, S, Chain, P, Bruce, D, Rubin, EM, Kyrpides, NC, Klenk, HP, and Eisen, JA
Subjects: General Science & Technology
Abstract: Sequencing of bacterial and archaeal genomes has revolutionized our understanding of the many roles played by microorganisms. There are now nearly 1,000 completed bacterial and archaeal genomes available, most of which were chosen for sequencing on the basis of their physiology. As a result, the perspective provided by the currently available genomes is limited by a highly biased phylogenetic distribution. To explore the value added by choosing microbial genomes for sequencing on the basis of their evolutionary relationships, we have sequenced and analysed the genomes of 56 culturable species of Bacteria and Archaea selected to maximize phylogenetic coverage. Analysis of these genomes demonstrated pronounced benefits (compared to an equivalent set of genomes randomly selected from the existing database) in diverse areas including the reconstruction of phylogenetic history, the discovery of new protein families and biological properties, and the prediction of functions for known genes from other organisms. Our results strongly support the need for systematic phylogenomic efforts to compile a phylogeny-driven Genomic Encyclopedia of Bacteria and Archaea in order to derive maximum knowledge from existing microbial genome data as well as from genome sequences to come. © 2009 Macmillan Publishers Limited. All rights reserved.
Published: 2009

10. Induction and transcriptional regulation of the co-inhibitory gene module in T cells

Author: Chihara, Norio, Madi, Asaf, Kondo, Takaaki, Zhang, Huiyuan, Acharya, Nandini, Singer, Meromit, and Nyman, Jackson
Subjects: Transcription (Genetics) -- Observations, T cells -- Genetic aspects, DNA binding proteins, Homeostasis, Protein C, Virus diseases, Tumors, Infection, Genes, Autoimmunity, RNA, Criminal investigation, Fatigue, Environmental issues, Science and technology, Zoology and wildlife conservation
Abstract: The expression of co-inhibitory receptors, such as CTLA-4 and PD-1, on effector T cells is a key mechanism for ensuring immune homeostasis. Dysregulated expression of co-inhibitory receptors on CD4.sup.+ T cells promotes autoimmunity, whereas sustained overexpression on CD8.sup.+ T cells promotes T cell dysfunction or exhaustion, leading to impaired ability to clear chronic viral infections and diseases such as cancer.sup.1,2. Here, using RNA and protein expression profiling at single-cell resolution in mouse cells, we identify a module of co-inhibitory receptors that includes not only several known co-inhibitory receptors (PD-1, TIM-3, LAG-3 and TIGIT) but also many new surface receptors. We functionally validated two new co-inhibitory receptors, activated protein C receptor (PROCR) and podoplanin (PDPN). The module of co-inhibitory receptors is co-expressed in both CD4.sup.+ and CD8.sup.+ T cells and is part of a larger co-inhibitory gene program that is shared by non-responsive T cells in several physiological contexts and is driven by the immunoregulatory cytokine IL-27. Computational analysis identified the transcription factors PRDM1 and c-MAF as cooperative regulators of the co-inhibitory module, and this was validated experimentally. This molecular circuit underlies the co-expression of co-inhibitory receptors in T cells and identifies regulators of T cell function with the potential to control autoimmunity and tumour immunity.A module of co-inhibitory T cell receptors, driven by the cytokine IL-27, is identified in mice that is regulated by the transcription factors PRDM1 and c-MAF., Author(s): Norio Chihara [sup.1] , Asaf Madi [sup.1] [sup.2] , Takaaki Kondo [sup.1] , Huiyuan Zhang [sup.1] , Nandini Acharya [sup.1] , Meromit Singer [sup.2] , Jackson Nyman [sup.2] , [...]
Published: 2018
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11. A mildly relativistic wide-angle outflow in the neutron-star merger event GW170817

Author: Mooley, K. P., Nakar, E., Hotokezaka, K., Hallinan, G., Corsi, A., Frail, D. A., Horesh, A., Murphy, T., Lenc, E., Kaplan, D. L., De, K., Dobie, D., Chandra, P., Deller, A., Gottlieb, O., Kasliwal, M. M., Kulkarni, S. R., Myers, S. T., Nissanke, S., Piran, T., Lynch, C., Bhalerao, V., Bourke, S., Bannister, K. W., and Singer, L. P.
Subjects: Gravitational waves -- Observations, Neutron stars -- Observations, Environmental issues, Science and technology, Zoology and wildlife conservation
Abstract: Author(s): K. P. Mooley (corresponding author) [1, 2, 3]; E. Nakar [4]; K. Hotokezaka [5]; G. Hallinan [3]; A. Corsi [6]; D. A. Frail [2]; A. Horesh [7]; T. Murphy [...]
Published: 2018
Full Text: View/download PDF

12. A gravitational-wave standard siren measurement of the Hubble constant

Author: Abbott, B. P., Abbott, R., Abbott, T. D., Acernese, F., Ackley, K., Adams, C., Adams, T., Addesso, P., Adhikari, R. X., Adya, V. B., Affeldt, C., Afrough, M., Agarwal, B., Agathos, M., Agatsuma, K., Aggarwal, N., Aguiar, O. D., Aiello, L., Ain, A., Ajith, P., Allen, B., Allen, G., Allocca, A., Altin, P. A., Amato, A., Ananyeva, A., Anderson, S. B., Anderson, W. G., Angelova, S. V., Antier, S., Appert, S., Arai, K., Araya, M. C., Areeda, J. S., Arnaud, N., Arun, K. G., Ascenzi, S., Ashton, G., Ast, M., Aston, S. M., Astone, P., Atallah, D. V., Aufmuth, P., Aulbert, C., AultONeal, K., Austin, C., Avila-Alvarez, A., Babak, S., Bacon, P., Bader, M. K. M., Bae, S., Baker, P. T., Baldaccini, F., Ballardin, G., Ballmer, S. W., Banagiri, S., Barayoga, J. C., Barclay, S. E., Barish, B. C., Barker, D., Barkett, K., Barone, F., Barr, B., Barsotti, L., Barsuglia, M., Barta, D., Bartlett, J., Bartos, I., Bassiri, R., Basti, A., Batch, J. C., Bawaj, M., Bayley, J. C., Bazzan, M., Bcsy, B., Beer, C., Bejger, M., Belahcene, I., Bell, A. S., Berger, B. K., Bergmann, G., Bero, J. J., Berry, C. P. L., Bersanetti, D., Bertolini, A., Betzwieser, J., Bhagwat, S., Bhandare, R., Bilenko, I. A., Billingsley, G., Billman, C. R., Birch, J., Birney, R., Birnholtz, O., Biscans, S., Biscoveanu, S., Bisht, A., Bitossi, M., Biwer, C., Bizouard, M. A., Blackburn, J. K., Blackman, J., Blair, C. D., Blair, D. G., Blair, R. M., Bloemen, S., Bock, O., Bode, N., Boer, M., Bogaert, G., Bohe, A., Bondu, F., Bonilla, E., Bonnand, R., Boom, B. A., Bork, R., Boschi, V., Bose, S., Bossie, K., Bouffanais, Y., Bozzi, A., Bradaschia, C., Brady, P. R., Branchesi, M., Brau, J. E., Briant, T., Brillet, A., Brinkmann, M., Brisson, V., Brockill, P., Broida, J. E., Brooks, A. F., Brown, D. A., Brown, D. D., Brunett, S., Buchanan, C. C., Buikema, A., Bulik, T., Bulten, H. J., Buonanno, A., Buskulic, D., Buy, C., Byer, R. L., Cabero, M., Cadonati, L., Cagnoli, G., Cahillane, C., Bustillo, J. Caldern, Callister, T. A., Calloni, E., Camp, J. B., Canepa, M., Canizares, P., Cannon, K. C., Cao, H., Cao, J., Capano, C. D., Capocasa, E., Carbognani, F., Caride, S., Carney, M. F., Diaz, J. Casanueva, Casentini, C., Caudill, S., Cavagli, M., Cavalier, F., Cavalieri, R., Cella, G., Cepeda, C. B., Cerd-Durn, P., Cerretani, G., Cesarini, E., Chamberlin, S. J., Chan, M., Chao, S., Charlton, P., Chase, E., Chassande-Mottin, E., Chatterjee, D., Chatziioannou, K., Cheeseboro, B. D., Chen, H. Y., Chen, X., Chen, Y., Cheng, H.-P., Chia, H., Chincarini, A., Chiummo, A., Chmiel, T., Cho, H. S., Cho, M., Chow, J. H., Christensen, N., Chu, Q., Chua, A. J. K., Chua, S., Chung, A. K. W., Chung, S., Ciani, G., Ciolfi, R., Cirelli, C. E., Cirone, A., Clara, F., Clark, J. A., Clearwater, P., Cleva, F., Cocchieri, C., Coccia, E., Cohadon, P.-F., Cohen, D., Colla, A., Collette, C. G., Cominsky, L. R., Constancio, M., Jr., Conti, L., Cooper, S. J., Corban, P., Corbitt, T. R., Cordero-Carrin, I., Corley, K. R., Cornish, N., Corsi, A., Cortese, S., Costa, C. A., Coughlin, M. W., Coughlin, S. B., Coulon, J.-P., Countryman, S. T., Couvares, P., Covas, P. B., Cowan, E. E., Coward, D. M., Cowart, M. J., Coyne, D. C., Coyne, R., Creighton, J. D. E., Creighton, T. D., Cripe, J., Crowder, S. G., Cullen, T. J., Cumming, A., Cunningham, L., Cuoco, E., Dal Canton, T., Dlya, G., Danilishin, S. L., DAntonio, S., Danzmann, K., Dasgupta, A., Da Silva Costa, C. F., Datrier, L. E. H., Dattilo, V., Dave, I., Davier, M., Davis, D., Daw, E. J., Day, B., De, S., DeBra, D., Degallaix, J., De Laurentis, M., Delglise, S., Del Pozzo, W., Demos, N., Denker, T., Dent, T., De Pietri, R., Dergachev, V., De Rosa, R., DeRosa, R. T., De Rossi, C., DeSalvo, R., de Varona, O., Devenson, J., Dhurandhar, S., Daz, M. C., Di Fiore, L., Di Giovanni, M., Di Girolamo, T., Di Lieto, A., Di Pace, S., Di Palma, I., Di Renzo, F., Doctor, Z., Dolique, V., Donovan, F., Dooley, K. L., Doravari, S., Dorrington, I., Douglas, R., Dovale lvarez, M., Downes, T. P., Drago, M., Dreissigacker, C., Driggers, J. C., Du, Z., Ducrot, M., Dupej, P., Dwyer, S. E., Edo, T. B., Edwards, M. C., Effler, A., Eggenstein, H.-B., Ehrens, P., Eichholz, J., Eikenberry, S. S., Eisenstein, R. A., Essick, R. C., Estevez, D., Etienne, Z. B., Etzel, T., Evans, M., Evans, T. M., Factourovich, M., Fafone, V., Fair, H., Fairhurst, S., Fan, X., Farinon, S., Farr, B., Farr, W. M., Fauchon-Jones, E. J., Favata, M., Fays, M., Fee, C., Fehrmann, H., Feicht, J., Fejer, M. M., Fernandez-Galiana, A., Ferrante, I., Ferreira, E. C., Ferrini, F., Fidecaro, F., Finstad, D., Fiori, I., Fiorucci, D., Fishbach, M., Fisher, R. P., Fitz-Axen, M., Flaminio, R., Fletcher, M., Fong, H., Font, J. A., Forsyth, P. W. F., Forsyth, S. S., Fournier, J.-D., Frasca, S., Frasconi, F., Frei, Z., Freise, A., Frey, R., Frey, V., Fries, E. M., Fritschel, P., Frolov, V. V., Fulda, P., Fyffe, M., Gabbard, H., Gadre, B. U., Gaebel, S. M., Gair, J. R., Gammaitoni, L., Ganija, M. R., Gaonkar, S. G., Garcia-Quiros, C., Garufi, F., Gateley, B., Gaudio, S., Gaur, G., Gayathri, V., Gehrels, N., Gemme, G., Genin, E., Gennai, A., George, D., George, J., Gergely, L., Germain, V., Ghonge, S., Ghosh, Abhirup, Ghosh, Archisman, Ghosh, S., Giaime, J. A., Giardina, K. D., Giazotto, A., Gill, K., Glover, L., Goetz, E., Goetz, R., Gomes, S., Goncharov, B., Gonzlez, G., Castro, J. M. Gonzalez, Gopakumar, A., Gorodetsky, M. L., Gossan, S. E., Gosselin, M., Gouaty, R., Grado, A., Graef, C., Granata, M., Grant, A., Gras, S., Gray, C., Greco, G., Green, A. C., Gretarsson, E. M., Groot, P., Grote, H., Grunewald, S., Gruning, P., Guidi, G. M., Guo, X., Gupta, A., Gupta, M. K., Gushwa, K. E., Gustafson, E. K., Gustafson, R., Halim, O., Hall, B. R., Hall, E. D., Hamilton, E. Z., Hammond, G., Haney, M., Hanke, M. M., Hanks, J., Hanna, C., Hannam, M. D., Hannuksela, O. A., Hanson, J., Hardwick, T., Harms, J., Harry, G. M., Harry, I. W., Hart, M. J., Haster, C.-J., Haughian, K., Healy, J., Heidmann, A., Heintze, M. C., Heitmann, H., Hello, P., Hemming, G., Hendry, M., Heng, I. S., Hennig, J., Heptonstall, A. W., Heurs, M., Hild, S., Hinderer, T., Hoak, D., Hofman, D., Holt, K., Holz, D. E., Hopkins, P., Horst, C., Hough, J., Houston, E. A., Howell, E. J., Hreibi, A., Hu, Y. M., Huerta, E. A., Huet, D., Hughey, B., Husa, S., Huttner, S. H., Huynh-Dinh, T., Indik, N., Inta, R., Intini, G., Isa, H. N., Isac, J.-M., Isi, M., Iyer, B. R., Izumi, K., Jacqmin, T., Jani, K., Jaranowski, P., Jawahar, S., Jimnez-Forteza, F., Johnson, W. W., Jones, D. I., Jones, R., Jonker, R. J. G., Ju, L., Junker, J., Kalaghatgi, C. V., Kalogera, V., Kamai, B., Kandhasamy, S., Kang, G., Kanner, J. B., Kapadia, S. J., Karki, S., Karvinen, K. S., Kasprzack, M., Katolik, M., Katsavounidis, E., Katzman, W., Kaufer, S., Kawabe, K., Kflian, F., Keitel, D., Kemball, A. J., Kennedy, R., Kent, C., Key, J. S., Khalili, F. Y., Khan, I., Khan, S., Khan, Z., Khazanov, E. A., Kijbunchoo, N., Kim, Chunglee, Kim, J. C., Kim, K., Kim, W., Kim, W. S., Kim, Y.-M., Kimbrell, S. J., King, E. J., King, P. J., Kinley-Hanlon, M., Kirchhoff, R., Kissel, J. S., Kleybolte, L., Klimenko, S., Knowles, T. D., Koch, P., Koehlenbeck, S. M., Koley, S., Kondrashov, V., Kontos, A., Korobko, M., Korth, W. Z., Kowalska, I., Kozak, D. B., Krmer, C., Kringel, V., Krishnan, B., Krlak, A., Kuehn, G., Kumar, P., Kumar, R., Kumar, S., Kuo, L., Kutynia, A., Kwang, S., Lackey, B. D., Lai, K. H., Landry, M., Lang, R. N., Lange, J., Lantz, B., Lanza, R. K., Lartaux-Vollard, A., Lasky, P. D., Laxen, M., Lazzarini, A., Lazzaro, C., Leaci, P., Leavey, S., Lee, C. H., Lee, H. K., Lee, H. M., Lee, H. W., Lee, K., Lehmann, J., Lenon, A., Leonardi, M., Leroy, N., Letendre, N., Levin, Y., Li, T. G. F., Linker, S. D., Littenberg, T. B., Liu, J., Liu, X., Lo, R. K. L., Lockerbie, N. A., London, L. T., Lord, J. E., Lorenzini, M., Loriette, V., Lormand, M., Losurdo, G., Lough, J. D., Lousto, C. O., Lovelace, G., Lck, H., Lumaca, D., Lundgren, A. P., Lynch, R., Ma, Y., Macas, R., Macfoy, S., Machenschalk, B., MacInnis, M., Macleod, D. M., Hernandez, I. Magaa, Magaa-Sandoval, F., Zertuche, L. Magaa, Magee, R. M., Majorana, E., Maksimovic, I., Man, N., Mandic, V., Mangano, V., Mansell, G. L., Manske, M., Mantovani, M., Marchesoni, F., Marion, F., Mrka, S., Mrka, Z., Markakis, C., Markosyan, A. S., Markowitz, A., Maros, E., Marquina, A., Martelli, F., Martellini, L., Martin, I. W., Martin, R. M., Martynov, D. V., Mason, K., Massera, E., Masserot, A., Massinger, T. J., Masso-Reid, M., Mastrogiovanni, S., Matas, A., Matichard, F., Matone, L., Mavalvala, N., Mazumder, N., McCarthy, R., McClelland, D. E., McCormick, S., McCuller, L., McGuire, S. C., McIntyre, G., McIver, J., McManus, D. J., McNeill, L., McRae, T., McWilliams, S. T., Meacher, D., Meadors, G. D., Mehmet, M., Meidam, J., Mejuto-Villa, E., Melatos, A., Mendell, G., Mercer, R. A., Merilh, E. L., Merzougui, M., Meshkov, S., Messenger, C., Messick, C., Metzdorff, R., Meyers, P. M., Miao, H., Michel, C., Middleton, H., Mikhailov, E. E., Milano, L., Miller, A. L., Miller, B. B., Miller, J., Millhouse, M., Milovich-Goff, M. C., Minazzoli, O., Minenkov, Y., Ming, J., Mishra, C., Mitra, S., Mitrofanov, V. P., Mitselmakher, G., Mittleman, R., Moffa, D., Moggi, A., Mogushi, K., Mohan, M., Mohapatra, S. R. P., Montani, M., Moore, C. J., Moraru, D., Moreno, G., Morriss, S. R., Mours, B., Mow-Lowry, C. M., Mueller, G., Muir, A. W., Mukherjee, Arunava, Mukherjee, D., Mukherjee, S., Mukund, N., Mullavey, A., Munch, J., Muiz, E. A., Muratore, M., Murray, P. G., Napier, K., Nardecchia, I., Naticchioni, L., Nayak, R. K., Neilson, J., Nelemans, G., Nelson, T. J. N., Nery, M., Neunzert, A., Nevin, L., Newport, J. M., Newton, G., Ng, K. K. Y., Nguyen, T. T., Nichols, D., Nielsen, A. B., Nissanke, S., Nitz, A., Noack, A., Nocera, F., Nolting, D., North, C., Nuttall, L. K., Oberling, J., ODea, G. D., Ogin, G. H., Oh, J. J., Oh, S. H., Ohme, F., Okada, M. A., Oliver, M., Oppermann, P., Oram, Richard J., OReilly, B., Ormiston, R., Ortega, L. F., OShaughnessy, R., Ossokine, S., Ottaway, D. J., Overmier, H., Owen, B. J., Pace, A. E., Page, J., Page, M. A., Pai, A., Pai, S. A., Palamos, J. R., Palashov, O., Palomba, C., Pal-Singh, A., Pan, Howard, Pan, Huang-Wei, Pang, B., Pang, P. T. H., Pankow, C., Pannarale, F., Pant, B. C., Paoletti, F., Paoli, A., Papa, M. 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D., Ricci, F., Ricker, P. M., Rieger, S., Riles, K., Rizzo, M., Robertson, N. A., Robie, R., Robinet, F., Rocchi, A., Rolland, L., Rollins, J. G., Roma, V. J., Romano, J. D., Romano, R., Romel, C. L., Romie, J. H., Rosiska, D., Ross, M. P., Rowan, S., Rdiger, A., Ruggi, P., Rutins, G., Ryan, K., Sachdev, S., Sadecki, T., Sadeghian, L., Sakellariadou, M., Salconi, L., Saleem, M., Salemi, F., Samajdar, A., Sammut, L., Sampson, L. M., Sanchez, E. J., Sanchez, L. E., Sanchis-Gual, N., Sandberg, V., Sanders, J. R., Sassolas, B., Sathyaprakash, B. S., Saulson, P. R., Sauter, O., Savage, R. L., Sawadsky, A., Schale, P., Scheel, M., Scheuer, J., Schmidt, J., Schmidt, P., Schnabel, R., Schofield, R. M. S., Schnbeck, A., Schreiber, E., Schuette, D., Schulte, B. W., Schutz, B. F., Schwalbe, S. G., Scott, J., Scott, S. M., Seidel, E., Sellers, D., Sengupta, A. S., Sentenac, D., Sequino, V., Sergeev, A., Shaddock, D. A., Shaffer, T. J., Shah, A. A., Shahriar, M. S., Shaner, M. B., Shao, L., Shapiro, B., Shawhan, P., Sheperd, A., Shoemaker, D. H., Shoemaker, D. M., Siellez, K., Siemens, X., Sieniawska, M., Sigg, D., Silva, A. D., Singer, L. P., Singh, A., Singhal, A., Sintes, A. M., Slagmolen, B. J. J., Smith, B., Smith, J. R., Smith, R. J. E., Somala, S., Son, E. J., Sonnenberg, J. A., Sorazu, B., Sorrentino, F., Souradeep, T., Spencer, A. P., Srivastava, A. K., Staats, K., Staley, A., Steer, D., Steinke, M., Steinlechner, J., Steinlechner, S., Steinmeyer, D., Stevenson, S. P., Stone, R., Stops, D. J., Strain, K. A., Stratta, G., Strigin, S. E., Strunk, A., Sturani, R., Stuver, A. L., Summerscales, T. Z., Sun, L., Sunil, S., Suresh, J., Sutton, P. J., Swinkels, B. L., Szczepaczyk, M. J., Tacca, M., Tait, S. C., Talbot, C., Talukder, D., Tanner, D. B., Tpai, M., Taracchini, A., Tasson, J. D., Taylor, J. A., Taylor, R., Tewari, S. V., Theeg, T., Thies, F., Thomas, E. G., Thomas, M., Thomas, P., Thorne, K. A., Thrane, E., Tiwari, S., Tiwari, V., Tokmakov, K. 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X., Ramirez-Ruiz, E., Rest, A., Rojas-Bravo, C., Shappee, B. J., Siebert, M. R., Simon, J. D., Ulloa, N., Annis, J., Soares-Santos, M., Brout, D., Scolnic, D., Diehl, H. T., Frieman, J., Berger, E., Alexander, K. D., Allam, S., Balbinot, E., Blanchard, P., Butler, R. E., Chornock, R., Cook, E. R., Cowperthwaite, P., Drlica-Wagner, A., Durret, F., Eftekhari, T., Finley, D. A., Fong, W., Fryer, C. L., Garca-Bellido, J., Gill, M. S. S., Gruendl, R. A., Hartley, W., Herner, K., Huterer, D., Kessler, R., Li, T. S., Lin, H., Lopes, P. A. A., Loureno, A. C. C., Margutti, R., Marriner, J., Marshall, J. L., Matheson, T., Medina, G. E., Metzger, B. D., Muoz, R. R., Muir, J., Nicholl, M., Nugent, P., Palmese, A., Paz-Chinchn, F., Quataert, E., Sako, M., Sauseda, M., Schlegel, D. J., Secco, L. F., Smith, N., Sobreira, F., Stebbins, A., Villar, V. A., Vivas, A. K., Wester, W., Williams, P. K. G., Yanny, B., Zenteno, A., Abbott, T. M. C., Abdalla, F. B., Bechtol, K., Benoit-Lvy, A., Bertin, E., Bridle, S. L., Brooks, D., Buckley-Geer, E., Burke, D. L., Rosell, A. Carnero, Kind, M. Carrasco, Carretero, J., Castander, F. J., Cunha, C. E., DAndrea, C. B., da Costa, L. N., Davis, C., DePoy, D. L., Desai, S., Dietrich, J. P., Estrada, J., Fernandez, E., Flaugher, B., Fosalba, P., Gaztanaga, E., Gerdes, D. W., Giannantonio, T., Goldstein, D. A., Gruen, D., Gutierrez, G., Hartley, W. G., Honscheid, K., Jain, B., James, D. J., Jeltema, T., Johnson, M. W. G., Kent, S., Krause, E., Kron, R., Kuehn, K., Kuhlmann, S., Kuropatkin, N., Lahav, O., Lima, M., Maia, M. A. G., March, M., Miller, C. J., Miquel, R., Neilsen, E., Nord, B., Ogando, R. L. C., Plazas, A. A., Romer, A. K., Roodman, A., Rykoff, E. S., Sanchez, E., Scarpine, V., Schubnell, M., Sevilla-Noarbe, I., Smith, M., Smith, R. C., Suchyta, E., Tarle, G., Thomas, D., Thomas, R. C., Troxel, M. A., Tucker, D. L., Vikram, V., Walker, A. R., Weller, J., Zhang, Y., Haislip, J. B., Kouprianov, V. V., Reichart, D. E., Tartaglia, L., Sand, D. J., Valenti, S., Yang, S., Arcavi, Iair, Hosseinzadeh, Griffin, Howell, D. Andrew, McCully, Curtis, Poznanski, Dovi, Vasylyev, Sergiy, Tanvir, N. R., Levan, A. J., Hjorth, J., Cano, Z., Copperwheat, C., de Ugarte-Postigo, A., Evans, P. A., Fynbo, J. P. U., Gonzlez-Fernndez, C., Greiner, J., Irwin, M., Lyman, J., Mandel, I., McMahon, R., Milvang-Jensen, B., OBrien, P., Osborne, J. P., Perley, D. A., Pian, E., Palazzi, E., Rol, E., Rosetti, S., Rosswog, S., Rowlinson, A., Schulze, S., Steeghs, D. T. H., Thne, C. C., Ulaczyk, K., Watson, D., Wiersema, K., Lipunov, V. M., Gorbovskoy, E., Kornilov, V. G., Tyurina, N., Balanutsa, P., Vlasenko, D., Gorbunov, I., Podesta, R., Levato, H., Saffe, C., Buckley, D. A. H., Budnev, N. M., Gress, O., Yurkov, V., Rebolo, R., and Serra-Ricart, M.
Subjects: Gravitational waves -- Measurement, Hubble constant -- Measurement, Environmental issues, Science and technology, Zoology and wildlife conservation
Abstract: Author(s): The LIGO Scientific Collaboration and The Virgo Collaboration; B. P. Abbott [1]; R. Abbott [1]; T. D. Abbott [2]; F. Acernese [3, 4]; K. Ackley [5, 6]; C. Adams [...]
Published: 2017
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13. Reply to: Climate versus tectonics as controls on river profiles

Author: Michaelides, Katerina, primary, Chen, Shiuan-An, additional, Grieve, Stuart, additional, and Singer, Michael Bliss, additional
Published: 2022
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14. Synthetic recording and in situ readout of lineage information in single cells

Author: Frieda, Kirsten L., Linton, James M., Hormoz, Sahand, Choi, Joonhyuk, Chow, Ke-Huan K., Singer, Zakary S., Budde, Mark W., Elowitz, Michael B., and Cai, Long
Subjects: Cell interactions -- Observations, Environmental issues, Science and technology, Zoology and wildlife conservation
Abstract: Author(s): Kirsten L. Frieda [1]; James M. Linton [1]; Sahand Hormoz [1]; Joonhyuk Choi [2]; Ke-Huan K. Chow [1]; Zakary S. Singer [1]; Mark W. Budde [1]; Michael B. Elowitz [...]
Published: 2017
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15. Reply to: Climate versus tectonics as controls on river profiles

Author: Katerina Michaelides, Shiuan-An Chen, Stuart Grieve, and Michael Bliss Singer
Subjects: Multidisciplinary
Published: 2022

16. Gamma frequency entrainment attenuates amyloid load and modifies microglia

Author: Iaccarino, Hannah F., Singer, Annabelle C., Martorell, Anthony J., Rudenko, Andrii, Gao, Fan, Gillingham, Tyler Z., Mathys, Hansruedi, Seo, Jinsoo, Kritskiy, Oleg, Abdurrob, Fatema, Adaikkan, Chinnakkaruppan, Canter, Rebecca G., Rueda, Richard, Brown, Emery N., Boyden, Edward S., and Tsai, Li-Huei
Subjects: Neural oscillations -- Health aspects, Microglia -- Health aspects, Alzheimer's disease -- Development and progression, Amyloid beta-protein -- Health aspects, Environmental issues, Science and technology, Zoology and wildlife conservation
Abstract: Changes in gamma oscillations (2050Hz) have been observed in several neurological disorders. However, the relationship between gamma oscillations and cellular pathologies is unclear. Here we show reduced, behaviourally driven gamma oscillations before the onset of plaque formation or cognitive decline in a mouse model of Alzheimers disease. Optogenetically driving fast-spiking parvalbumin-positive (FS-PV)-interneurons at gamma (40Hz), but not other frequencies, reduces levels of amyloid- (A)[sub.140] and A [sub.142] isoforms. Gene expression profiling revealed induction of genes associated with morphological transformation of microglia, and histological analysis confirmed increased microglia co-localization with A. Subsequently, we designed a non-invasive 40Hz light-flickering regime that reduced A[sub.140] and A[sub.142] levels in the visual cortex of pre-depositing mice and mitigated plaque load in aged, depositing mice. Our findings uncover a previously unappreciated function of gamma rhythms in recruiting both neuronal and glial responses to attenuate Alzheimers-disease-associated pathology., Author(s): Hannah F. Iaccarino [1, 3]; Annabelle C. Singer [2, 3, 4]; Anthony J. Martorell [1, 3]; Andrii Rudenko [1, 3]; Fan Gao [1, 3]; Tyler Z. Gillingham [1, 3]; [...]
Published: 2016
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17. Convection in a volatile nitrogen-ice-rich layer drives Plutos geological vigour

Author: McKinnon, William B., Nimmo, Francis, Wong, Teresa, Schenk, Paul M., White, Oliver L., Roberts, J. H., Moore, J. M., Spencer, J. R., Howard, A. D., Umurhan, O. M., Stern, S. A., Weaver, H. A., Olkin, C. B., Young, L. A., Smith, K. E., McKinnon, W. B., Beyer, R., Buie, M., Buratti, B., Cheng, A., Cruikshank, D., Dalle Ore, C., Gladstone, R., Grundy, W., Lauer, T., Linscott, I., Olkin, C., Parker, J., Porter, S., Reitsema, H., Reuter, D., Robbins, S., Schenk, P. M., Showalter, M., Singer, K., Strobel, D., Summers, M., Tyler, L., Weaver, H., White, O. L., Banks, M., Barnouin, O., Bray, V., Carcich, B., Chaikin, A., Chavez, C., Conrad, C., Hamilton, D., Howett, C., Hofgartner, J., Kammer, J., Lisse, C., Marcotte, A., Parker, A., Retherford, K., Saina, M., Runyon, K., Schindhelm, E., Stansberry, J., Steffl, A., Stryk, T., Throop, H., Tsang, C., Verbiscer, A., Winters, H., and Zangari, A.
Subjects: Pluto (Dwarf planet) -- Observations, Astrogeology -- Methods, Environmental issues, Science and technology, Zoology and wildlife conservation
Abstract: Author(s): William B. McKinnon (corresponding author) [1]; Francis Nimmo [2]; Teresa Wong [1]; Paul M. Schenk [3]; Oliver L. White [4]; J. H. Roberts [5]; J. M. Moore [4]; J. [...]
Published: 2016
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18. Author Correction: Aridity is expressed in river topography globally

Author: Chen, Shiuan-An, primary, Michaelides, Katerina, additional, Grieve, Stuart W. D., additional, and Singer, Michael Bliss, additional
Published: 2022
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19. SARS-CoV-2 evolution during treatment of chronic infection

Author: Kemp, S. A., Collier, D. A., Datir, R. P., Ferreira, I. A. T. M., Gayed, S., Jahun, A., Hosmillo, M., Rees-Spear, C., Mlcochova, P., Lumb, I. U., Roberts, D. J., Chandra, A., Temperton, N., Baker, S., Dougan, G., Hess, C., Kingston, N., Lehner, P. J., Lyons, P. A., Matheson, N. J., Owehand, W. H., Saunders, C., Summers, C., Thaventhiran, J. E. D., Toshner, M., Weekes, M. P., Bucke, A., Calder, J., Canna, L., Domingo, J., Elmer, A., Fuller, S., Harris, J., Hewitt, S., Kennet, J., Jose, S., Kourampa, J., Meadows, A., O'Brien, C., Price, J., Publico, C., Rastall, R., Ribeiro, C., Rowlands, J., Ruffolo, V., Tordesillas, H., Bullman, B., Dunmore, B. J., Fawke, S., Graf, S., Hodgson, J., Huang, C., Hunter, K., Jones, E., Legchenko, E., Matara, C., Martin, J., Mescia, F., O'Donnell, C., Pointon, L., Pond, N., Shih, J., Sutcliffe, R., Tilly, T., Treacy, C., Tong, Z., Wood, J., Wylot, M., Bergamaschi, L., Betancourt, A., Bower, G., Cossetti, C., De Sa, A., Epping, M., Gleadall, N., Grenfell, R., Hinch, A., Huhn, O., Jackson, S., Jarvis, I., Lewis, D., Marsden, J., Nice, F., Okecha, G., Omarjee, O., Perera, M., Richoz, N., Romashova, V., Yarkoni, N. S., Sharma, R., Stefanucci, L., Stephens, J., Strezlecki, M., Turner, L., De Bie, E. M. D. D., Bunclark, K., Josipovic, M., Mackay, M., Rossi, S., Selvan, M., Spencer, S., Yong, C., Ansaripour, A., Michael, A., Mwaura, L., Patterson, C., Polwarth, G., Polgarova, P., di Stefano, G., Fahey, C., Michel, R., Bong, S. -H., Coudert, J. D., Holmes, E., Allison, J., Butcher, H., Caputo, D., Clapham-Riley, D., Dewhurst, E., Furlong, A., Graves, B., Gray, J., Ivers, T., Kasanicki, M., Le Gresley, E., Linger, R., Meloy, S., Muldoon, F., Ovington, N., Papadia, S., Phelan, I., Stark, H., Stirrups, K. E., Townsend, P., Walker, N., Webster, J., Robson, S. C., Loman, N. J., Connor, T. R., Golubchik, T., Martinez Nunez, R. T., Ludden, C., Corden, S., Johnston, I., Bonsall, D., Smith, C. P., Awan, A. R., Bucca, G., Estee Torok, M., Saeed, K., Prieto, J. A., Jackson, D. K., Hamilton, W. L., Snell, L. B., Moore, C., Harrison, E. M., Goncalves, S., Fairley, D. J., Loose, M. W., Watkins, J., Livett, R., Moses, S., Amato, R., Nicholls, S., Bull, M., Smith, D. L., Barrett, J., Aanensen, D. M., Curran, M. D., Parmar, S., Aggarwal, D., Shepherd, J. G., Parker, M. D., Glaysher, S., Bashton, M., Underwood, A. P., Pacchiarini, N., Loveson, K. F., Carabelli, A. M., Templeton, K. E., Langford, C. F., Sillitoe, J., de Silva, T. I., Wang, D., Kwiatkowski, D., Rambaut, A., O'Grady, J., Cottrell, S., Holden, M. T. G., Thomson, E. C., Osman, H., Andersson, M., Chauhan, A. J., Hassan-Ibrahim, M. O., Lawniczak, M., Alderton, A., Chand, M., Constantinidou, C., Unnikrishnan, M., Darby, A. C., Hiscox, J. A., Paterson, S., Martincorena, I., Robertson, D. L., Volz, E. M., Page, A. J., Pybus, O. G., Bassett, A. R., Ariani, C. V., Spencer Chapman, M. H., K. K., Li, Shah, R. N., Jesudason, N. G., Taha, Y., Mchugh, M. P., Dewar, R., Jahun, A. S., Mcmurray, C., Pandey, S., Mckenna, J. P., Nelson, A., Young, G. R., Mccann, C. M., Elliott, S., Lowe, H., Temperton, B., Roy, S., Price, A., Rey, S., Wyles, M., Rooke, S., Shaaban, S., de Cesare, M., Letchford, L., Silveira, S., Pelosi, E., Wilson-Davies, E., O'Toole, A., Hesketh, A. R., Stark, R., du Plessis, L., Ruis, C., Adams, H., Bourgeois, Y., Michell, S. L., Gramatopoulos, D., Edgeworth, J., Breuer, J., Todd, J. A., Fraser, C., Buck, D., John, M., Kay, G. L., Palmer, S., Peacock, S. J., Heyburn, D., Weldon, D., Robinson, E., Mcnally, A., Muir, P., Vipond, I. B., Boyes, J., Sivaprakasam, V., Salluja, T., Dervisevic, S., Meader, E. J., Park, N. R., Oliver, K., Jeffries, A. R., Ott, S., da Silva Filipe, A., Simpson, D. A., Williams, C., Masoli, J. A. H., Knight, B. A., Jones, C. R., Koshy, C., Ash, A., Casey, A., Bosworth, A., Ratcliffe, L., Xu-McCrae, L., Pymont, H. M., Hutchings, S., Berry, L., Jones, K., Halstead, F., Davis, T., Holmes, C., Iturriza-Gomara, M., Lucaci, A. O., Randell, P. A., Cox, A., Madona, P., Harris, K. A., Brown, J. R., Mahungu, T. W., Irish-Tavares, D., Haque, T., Hart, J., Witele, E., Fenton, M. L., Liggett, S., Graham, C., Swindells, E., Collins, J., Eltringham, G., Campbell, S., Mcclure, P. C., Clark, G., Sloan, T. J., Jones, C., Lynch, J., Warne, B., Leonard, S., Durham, J., Williams, T., Haldenby, S. T., Storey, N., Alikhan, N. -F., Holmes, N., Carlile, M., Perry, M., Craine, N., Lyons, R. A., Beckett, A. H., Goudarzi, S., Fearn, C., Cook, K., Dent, H., Paul, H., Davies, R., Blane, B., Girgis, S. T., Beale, M. A., Bellis, K. L., Dorman, M. J., Drury, E., Kane, L., Kay, S., Mcguigan, S., Nelson, R., Prestwood, L., Rajatileka, S., Batra, R., Williams, R. J., Kristiansen, M., Green, A., Justice, A., Mahanama, A. I. K., Samaraweera, B., Hadjirin, N. F., Quick, J., Poplawski, R., Kermack, L. M., Reynolds, N., Hall, G., Chaudhry, Y., Pinckert, M. L., Georgana, I., Moll, R. J., Thornton, A., Myers, R., Stockton, J., Williams, C. A., Yew, W. C., Trotter, A. J., Trebes, A., MacIntyre-Cockett, G., Birchley, A., Adams, A., Plimmer, A., Gatica-Wilcox, B., Mckerr, C., Hilvers, E., Jones, H., Asad, H., Coombes, J., Evans, J. M., Fina, L., Gilbert, L., Graham, L., Cronin, M., Kumziene-Summerhayes, S., Taylor, S., Jones, S., Groves, D. C., Zhang, P., Gallis, M., Louka, S. F., Starinskij, I., Jackson, C., Gourtovaia, M., Tonkin-Hill, G., Lewis, K., Tovar-Corona, J. M., James, K., Baxter, L., Alam, M. T., Orton, R. J., Hughes, J., Vattipally, S., Ragonnet-Cronin, M., Nascimento, F. F., Jorgensen, D., Boyd, O., Geidelberg, L., Zarebski, A. E., Raghwani, J., Kraemer, M. U. G., Southgate, J., Lindsey, B. B., Freeman, T. M., Keatley, J. -P., Singer, J. B., de Oliveira Martins, L., Yeats, C. A., Abudahab, K., Taylor, B. E. W., Menegazzo, M., Danesh, J., Hogsden, W., Eldirdiri, S., Kenyon, A., Mason, J., Robinson, T. I., Holmes, A., Hartley, J. A., Curran, T., Mather, A. E., Shankar, G., Jones, R., Howe, R., Morgan, S., Wastenge, E., Chapman, M. R., Mookerjee, S., Stanley, R., Smith, W., Peto, T., Eyre, D., Crook, D., Vernet, G., Kitchen, C., Gulliver, H., Merrick, I., Guest, M., Munn, R., Bradley, D. T., Wyatt, T., Beaver, C., Foulser, L., Churcher, C. M., Brooks, E., Smith, K. S., Galai, K., Mcmanus, G. M., Bolt, F., Coll, F., Meadows, L., Attwood, S. W., Davies, A., De Lacy, E., Downing, F., Edwards, S., Scarlett, G. P., Jeremiah, S., Smith, N., Leek, D., Sridhar, S., Forrest, S., Cormie, C., Gill, H. K., Dias, J., Higginson, E. E., Maes, M., Young, J., Wantoch, M., Jamrozy, D., Lo, S., Patel, M., Hill, V., Bewshea, C. M., Ellard, S., Auckland, C., Harrison, I., Bishop, C., Chalker, V., Richter, A., Beggs, A., Best, A., Percival, B., Mirza, J., Megram, O., Mayhew, M., Crawford, L., Ashcroft, F., Moles-Garcia, E., Cumley, N., Hopes, R., Asamaphan, P., Niebel, M. O., Gunson, R. N., Bradley, A., Maclean, A., Mollett, G., Blacow, R., Bird, P., Helmer, T., Fallon, K., Tang, J., Hale, A. D., Macfarlane-Smith, L. R., Harper, K. L., Carden, H., Machin, N. W., Jackson, K. A., Ahmad, S. S. Y., George, R. P., Turtle, L., O'Toole, E., Watts, J., Breen, C., Cowell, A., Alcolea-Medina, A., Charalampous, T., Patel, A., Levett, L. J., Heaney, J., Rowan, A., Taylor, G. P., Shah, D., Atkinson, L., Lee, J. C. D., Westhorpe, A. P., Jannoo, R., Lowe, H. L., Karamani, A., Ensell, L., Chatterton, W., Pusok, M., Dadrah, A., Symmonds, A., Sluga, G., Molnar, Z., Baker, P., Bonner, S., Essex, S., Barton, E., Padgett, D., Scott, G., Greenaway, J., Payne, B. A. I., Burton-Fanning, S., Waugh, S., Raviprakash, V., Sheriff, N., Blakey, V., Williams, L. -A., Moore, J., Stonehouse, S., Smith, L., Davidson, R. K., Bedford, L., Coupland, L., Wright, V., Chappell, J. G., Tsoleridis, T., Ball, J., Khakh, M., Fleming, V. M., Lister, M. M., Howson-Wells, H. C., Boswell, T., Joseph, A., Willingham, I., Duckworth, N., Walsh, S., Wise, E., Moore, N., Mori, M., Cortes, N., Kidd, S., Williams, R., Gifford, L., Bicknell, K., Wyllie, S., Lloyd, A., Impey, R., Malone, C. S., Cogger, B. J., Levene, N., Monaghan, L., Keeley, A. J., Partridge, D. G., Raza, M., Evans, C., Johnson, K., Abnizova, I., Aigrain, L., Ali, M., Allen, L., Anderson, R., Ariani, C., Austin-Guest, S., Bala, S., Bassett, A., Battleday, K., Beal, J., Beale, M., Bellany, S., Bellerby, T., Bellis, K., Berger, D., Berriman, M., Betteridge, E., Bevan, P., Binley, S., Bishop, J., Blackburn, K., Bonfield, J., Boughton, N., Bowker, S., Brendler-Spaeth, T., Bronner, I., Brooklyn, T., Buddenborg, S. K., Bush, R., Caetano, C., Cagan, A., Carter, N., Cartwright, J., Monteiro, T. C., Chapman, L., Chillingworth, T. -J., Clapham, P., Clark, R., Clarke, A., Clarke, C., Cole, D., Cook, E., Coppola, M., Cornell, L., Cornwell, C., Corton, C., Crackett, A., Cranage, A., Craven, H., Craw, S., Crawford, M., Cutts, T., Dabrowska, M., Davies, M., Dawson, J., Day, C., Densem, A., Dibling, T., Dockree, C., Dodd, D., Dogga, S., Dougherty, M., Dove, A., Drummond, L., Dudek, M., Durrant, L., Easthope, E., Eckert, S., Ellis, P., Farr, B., Fenton, M., Ferrero, M., Flack, N., Fordham, H., Forsythe, G., Francis, M., Fraser, A., Freeman, A., Galvin, A., Garcia-Casado, M., Gedny, A., Girgis, S., Glover, J., Goodwin, S., Gould, O., Gray, A., Gray, E., Griffiths, C., Gu, Y., Guerin, F., Hamilton, W., Hanks, H., Harrison, E., Harrott, A., Harry, E., Harvison, J., Heath, P., Hernandez-Koutoucheva, A., Hobbs, R., Holland, D., Holmes, S., Hornett, G., Hough, N., Huckle, L., Hughes-Hallet, L., Hunter, A., Inglis, S., Iqbal, S., Jackson, A., Jackson, D., Verdejo, C. J., Jones, M., Kallepally, K., Kay, K., Keatley, J., Keith, A., King, A., Kitchin, L., Kleanthous, M., Klimekova, M., Korlevic, P., Krasheninnkova, K., Lane, G., Langford, C., Laverack, A., Law, K., Lensing, S., Lewis-Wade, A., Liddle, J., Lin, Q., Lindsay, S., Linsdell, S., Long, R., Lovell, J., Mack, J., Maddison, M., Makunin, A., Mamun, I., Mansfield, J., Marriott, N., Martin, M., Mayho, M., Mccarthy, S., Mcclintock, J., Mchugh, S., Mcminn, L., Meadows, C., Mobley, E., Moll, R., Morra, M., Morrow, L., Murie, K., Nash, S., Nathwani, C., Naydenova, P., Neaverson, A., Nerou, E., Nicholson, J., Nimz, T., Noell, G. G., O'Meara, S., Ohan, V., Olney, C., Ormond, D., Oszlanczi, A., Pang, Y. F., Pardubska, B., Park, N., Parmar, A., Patel, G., Payne, M., Peacock, S., Petersen, A., Plowman, D., Preston, T., Puethe, C., Quail, M., Rajan, D., Rance, R., Rawlings, S., Redshaw, N., Reynolds, J., Reynolds, M., Rice, S., Richardson, M., Roberts, C., Robinson, K., Robinson, M., Robinson, D., Rogers, H., Rojo, E. M., Roopra, D., Rose, M., Rudd, L., Sadri, R., Salmon, N., Saul, D., Schwach, F., Scott, C., Seekings, P., Shirley, L., Simms, A., Sinnott, M., Sivadasan, S., Siwek, B., Sizer, D., Skeldon, K., Skelton, J., Slater-Tunstill, J., Sloper, L., Smerdon, N., Smith, C., Smith, J., Smith, K., Smith, M., Smith, S., Smith, T., Sneade, L., Soria, C. D., Sousa, C., Souster, E., Sparkes, A., Spencer-Chapman, M., Squares, J., Steed, C., Stickland, T., Still, I., Stratton, M., Strickland, M., Swann, A., Swiatkowska, A., Sycamore, N., Swift, E., Symons, E., Szluha, S., Taluy, E., Tao, N., Taylor, K., Thompson, S., Thompson, M., Thomson, M., Thomson, N., Thurston, S., Toombs, D., Topping, B., Tovar-Corona, J., Ungureanu, D., Uphill, J., Urbanova, J., Jansen Van, P., Vancollie, V., Voak, P., Walker, D., Walker, M., Waller, M., Ward, G., Weatherhogg, C., Webb, N., Wells, A., Wells, E., Westwood, L., Whipp, T., Whiteley, T., Whitton, G., Whitwham, A., Widaa, S., Williams, M., Wilson, M., Wright, S., Farr, B. W., Quail, M. A., Thurston, S. A. J., Bronner, I. F., Redshaw, N. M., Lensing, S. V., Balcazar, C. E., Gallagher, M. D., Williamson, K. A., Stanton, T. D., Michelsen, M. L., Warwick-Dugdale, J., Manley, R., Farbos, A., Harrison, J. W., Sambles, C. M., Studholme, D. J., Lackenby, A., Mbisa, T., Platt, S., Miah, S., Bibby, D., Manso, C., Hubb, J., Dabrera, G., Ramsay, M., Bradshaw, D., Schaefer, U., Groves, N., Gallagher, E., Lee, D., Williams, D., Ellaby, N., Hartman, H., Manesis, N., Patel, V., Ledesma, J., Twohig, K. A., Allara, E., Pearson, C., Cheng, J. K. J., Bridgewater, H. E., Frost, L. R., Taylor-Joyce, G., Brown, P. E., Tong, L., Broos, A., Mair, D., Nichols, J., Carmichael, S. N., Smollett, K. L., Nomikou, K., Aranday-Cortes, E., Johnson, N., Nickbakhsh, S., Vamos, E. E., Hughes, M., Rainbow, L., Eccles, R., Nelson, C., Whitehead, M., Gregory, R., Gemmell, M., Wierzbicki, C., Webster, H. J., Fisher, C. L., Signell, A. W., Betancor, G., Wilson, H. D., Nebbia, G., Flaviani, F., Cerda, A. C., Merrill, T. V., Wilson, R. E., Cotic, M., Bayzid, N., Thompson, T., Acheson, E., Rushton, S., O'Brien, S., Baker, D. J., Rudder, S., Aydin, A., Sang, F., Debebe, J., Francois, S., Vasylyeva, T. I., Zamudio, M. E., Gutierrez, B., Marchbank, A., Maksimovic, J., Spellman, K., Mccluggage, K., Morgan, M., Beer, R., Afifi, S., Workman, T., Fuller, W., Bresner, C., Angyal, A., Green, L. R., Parsons, P. J., Tucker, R. M., Brown, R., Whiteley, M., Rowe, W., Siveroni, I., Le-Viet, T., Gaskin, A., Johnson, R., Sharrocks, K., Blane, E., Modis, Y., Leigh, K. E., Briggs, J. A. G., van Gils, M. J., Smith, K. G. C., Bradley, J. R., Doffinger, R., Ceron-Gutierrez, L., Barcenas-Morales, G., Pollock, D. D., Goldstein, R. A., Smielewska, A., Skittrall, J. P., Gouliouris, T., Goodfellow, I. G., Gkrania-Klotsas, E., Illingworth, C. J. R., Mccoy, L. E., Gupta, R. K., Medical Microbiology and Infection Prevention, AII - Infectious diseases, Collier, Dami A [0000-0001-5446-4423], Jahun, Aminu [0000-0002-4585-1701], Temperton, Nigel [0000-0002-7978-3815], Modis, Yorgo [0000-0002-6084-0429], Briggs, John AG [0000-0003-3990-6910], Goldstein, Richard A [0000-0001-5148-4672], Skittrall, Jordan P [0000-0002-8228-3758], Gkrania-Klotsas, Effrossyni [0000-0002-0930-8330], McCoy, Laura E [0000-0001-9503-7946], Gupta, Ravindra K [0000-0001-9751-1808], and Apollo - University of Cambridge Repository
Subjects: 0301 basic medicine, Male, Time Factors, viruses, Passive, Antibodies, Viral, CITIID-NIHR BioResource COVID-19 Collaboration, 2.1 Biological and endogenous factors, Viral, Aetiology, Neutralizing, Lung, Phylogeny, neutralising antibodies, Infectivity, education.field_of_study, Genome, Multidisciplinary, Alanine, biology, High-Throughput Nucleotide Sequencing, Viral Load, Spike Glycoprotein, Virus Shedding, Adenosine Monophosphate, Aged, Antibodies, Neutralizing, COVID-19, Chronic Disease, Genome, Viral, Humans, Immune Evasion, Immune Tolerance, Immunization, Passive, Immunosuppression Therapy, Mutagenesis, Mutant Proteins, Mutation, SARS-CoV-2, Spike Glycoprotein, Coronavirus, Evolution, Molecular, Infectious Diseases, Pneumonia & Influenza, Antibody, Infection, Viral load, Biotechnology, Evolution, General Science & Technology, antibody escape, Convalescent plasma, 030106 microbiology, Population, evasion, Antibodies, Virus, Article, Vaccine Related, resistance, 03 medical and health sciences, Immune system, COVID-19 Genomics UK (COG-UK) Consortium, Biodefense, Genetics, Viral shedding, education, COVID-19 Serotherapy, QR355, Prevention, Wild type, Molecular, Pneumonia, Virology, COVID-19 Drug Treatment, Coronavirus, Emerging Infectious Diseases, Good Health and Well Being, 030104 developmental biology, biology.protein, Immunization, immune suppression, mutation
Abstract: The spike protein of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is critical for virus infection through the engagement of the human ACE2 protein1 and is a major antibody target. Here we show that chronic infection with SARS-CoV-2 leads to viral evolution and reduced sensitivity to neutralizing antibodies in an immunosuppressed individual treated with convalescent plasma, by generating whole-genome ultra-deep sequences for 23 time points that span 101 days and using in vitro techniques to characterize the mutations revealed by sequencing. There was little change in the overall structure of the viral population after two courses of remdesivir during the first 57 days. However, after convalescent plasma therapy, we observed large, dynamic shifts in the viral population, with the emergence of a dominant viral strain that contained a substitution (D796H) in the S2 subunit and a deletion (ΔH69/ΔV70) in the S1 N-terminal domain of the spike protein. As passively transferred serum antibodies diminished, viruses with the escape genotype were reduced in frequency, before returning during a final, unsuccessful course of convalescent plasma treatment. In vitro, the spike double mutant bearing both ΔH69/ΔV70 and D796H conferred modestly decreased sensitivity to convalescent plasma, while maintaining infectivity levels that were similar to the wild-type virus.The spike substitution mutant D796H appeared to be the main contributor to the decreased susceptibility to neutralizing antibodies, but this mutation resulted in an infectivity defect. The spike deletion mutant ΔH69/ΔV70 had a twofold higher level of infectivity than wild-type SARS-CoV-2, possibly compensating for the reduced infectivity of the D796H mutation. These data reveal strong selection on SARS-CoV-2 during convalescent plasma therapy, which is associated with the emergence of viral variants that show evidence of reduced susceptibility to neutralizing antibodies in immunosuppressed individuals.
Published: 2021

20. Circuits between infected macrophages and T cells in SARS-CoV-2 pneumonia

Author: Darryl A. Abbott, Sean B. Smith, Ali Shilatifard, Daniel Schneider, Benjamin D. Singer, Alexander V. Misharin, Luisa Morales-Nebreda, NU Script Study Investigators, Lango Sichizya, Nikolay S. Markov, G. R. Scott Budinger, Hiam Abdala-Valencia, Ankit Bharat, Chao Qi, Elizabeth S. Malsin, Prasanth Nannapaneni, Anna Pawlowski, Helen K. Donnelly, Alvaro Donayre, Cara J. Gottardi, Yuliya Politanska, Zasu M Klug, Melissa Querrey, Suchitra Swaminathan, Mengjia Kang, Richard G Wunderink, Chiagozie O Pickens, Jacqueline M. Kruser, Hermon Kihshen, James M. Walter, Estefany R Guzman, Ziyan Lu, Nicole Borkowski, Rogan A. Grant, Isaac Goldberg, A. Christine Argento, and Jon W. Lomasney
Subjects: 0301 basic medicine, ARDS, Time Factors, T-Lymphocytes, viruses, medicine.medical_treatment, T cell, Pneumonia, Viral, Inflammation, Article, Cohort Studies, Interferon-gamma, 03 medical and health sciences, 0302 clinical medicine, Immune system, Macrophages, Alveolar, medicine, Humans, RNA-Seq, Respiratory system, Multidisciplinary, medicine.diagnostic_test, SARS-CoV-2, business.industry, COVID-19, respiratory system, medicine.disease, respiratory tract diseases, Pneumonia, 030104 developmental biology, Bronchoalveolar lavage, Cytokine, medicine.anatomical_structure, 030220 oncology & carcinogenesis, Immunology, Interferons, Single-Cell Analysis, medicine.symptom, business, Bronchoalveolar Lavage Fluid, Signal Transduction
Abstract: Some patients infected with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) develop severe pneumonia and acute respiratory distress syndrome1 (ARDS). Distinct clinical features in these patients have led to speculation that the immune response to virus in the SARS-CoV-2-infected alveolus differs from that in other types of pneumonia2. Here we investigate SARS-CoV-2 pathobiology by characterizing the immune response in the alveoli of patients infected with the virus. We collected bronchoalveolar lavage fluid samples from 88 patients with SARS-CoV-2-induced respiratory failure and 211 patients with known or suspected pneumonia from other pathogens, and analysed them using flow cytometry and bulk transcriptomic profiling. We performed single-cell RNA sequencing on 10 bronchoalveolar lavage fluid samples collected from patients with severe coronavirus disease 2019 (COVID-19) within 48 h of intubation. In the majority of patients with SARS-CoV-2 infection, the alveolar space was persistently enriched in T cells and monocytes. Bulk and single-cell transcriptomic profiling suggested that SARS-CoV-2 infects alveolar macrophages, which in turn respond by producing T cell chemoattractants. These T cells produce interferon-γ to induce inflammatory cytokine release from alveolar macrophages and further promote T cell activation. Collectively, our results suggest that SARS-CoV-2 causes a slowly unfolding, spatially limited alveolitis in which alveolar macrophages containing SARS-CoV-2 and T cells form a positive feedback loop that drives persistent alveolar inflammation. Analysis of bronchoalveolar lavage fluid samples from patients with SARS-CoV-2-induced respiratory failure suggests that SARS-CoV-2 infects alveolar macrophages to cause release of T cell chemoattractants, thereby inducing local inflammatory cytokine release and further T cell activation, ultimately resulting in a positive feedback loop that drives alveolar inflammation.
Published: 2021

21. Genetic diversity fuels gene discovery for tobacco and alcohol use

Author: Saunders, Gretchen R. B., Wang, Xingyan, Chen, Fang, Jang, Seon-Kyeong, Liu, Mengzhen, Wang, Chen, Gao, Shuang, Jiang, Yu, Khunsriraksakul, Chachrit, Otto, Jacqueline M., Addison, Clifton, Akiyama, Masato, Albert, Christine M., Aliev, Fazil, Alonso, Alvaro, Arnett, Donna K., Ashley-Koch, Allison E., Ashrani, Aneel A., Barnes, Kathleen C., Barr, R. Graham, Bartz, Traci M., Becker, Diane M., Bielak, Lawrence F., Benjamin, Emelia J., Bis, Joshua C., Bjornsdottir, Gyda, Blangero, John, Bleecker, Eugene R., Boardman, Jason D., Boerwinkle, Eric, Boomsma, Dorret, Boorgula, Meher Preethi, Bowden, Donald W., Brody, Jennifer A., Cade, Brian E., Chasman, Daniel, Chavan, Sameer, Chen, Yii-Der Ida, Chen, Zhengming, Cheng, Iona, Cho, Michael H., Choquet, Helene, Cole, John W., Cornelis, Marilyn C., Cucca, Francesco, Curran, Joanne E., de Andrade, Mariza, Dick, Danielle M., Docherty, Anna R., Duggirala, Ravindranath, Eaton, Charles B., Ehringer, Marissa A., Esko, Tonu, Faul, Jessica D., Silva, Lilian Fernandes, Fiorillo, Edoardo, Fornage, Myriam, Freedman, Barry, Gabrielsen, Maiken E., Garrett, Melanie E., Gharib, Sina A., Gieger, Christian, Gillespie, Nathan, Glahn, David C., Gordon, Scott D., Gu, Charles C., Gu, Dongfeng, Gudbjartsson, Daniel F., Guo, Xiuqing, Haessler, Jeffrey, Hall, Michael E., Haller, Toomas, Harris, Kathleen Mullan, He, Jiang, Herd, Pamela, Hewitt, John K., Hickie, Ian, Hidalgo, Bertha, Hokanson, John E., Hopfer, Christian, Hottenga, JoukeJan, Hou, Lifang, Huang, Hongyan, Hung, Yi-Jen, Hunter, David J., Hveem, Kristian, Hwang, Shih-Jen, Hwu, Chii-Min, Iacono, William, Irvin, Marguerite R., Jee, Yon Ho, Johnson, Eric O., Joo, Yoonjung Y., Jorgenson, Eric, Justice, Anne E., Kamatani, Yoichiro, Kaplan, Robert C., Kaprio, Jaakko, Kardia, Sharon L. R., Keller, Matthew C., Kelly, Tanika N., Kooperberg, Charles, Korhonen, Tellervo, Kraft, Peter, Krauter, Kenneth, Kuusisto, Johanna, Laakso, Markku, Lasky-Su, Jessica, Lee, Wen-Jane, Lee, James J., Levy, Daniel, Li, Liming, Li, Kevin, Li, Yuqing, Lin, Kuang, Lind, Penelope A., Liu, Chunyu, Lloyd-Jones, Donald M., Lutz, Sharon M., Ma, Jiantao, Magi, Reedik, Manichaikul, Ani, Martin, Nicholas G., Mathur, Ravi, Matoba, Nana, McArdle, Patrick F., McGue, Matt, McQueen, Matthew B., Medland, Sarah E., Metspalu, Andres, Meyers, Deborah A., Millwood, Iona Y., Mitchell, Braxton D., Mohlke, Karen L., Moll, Matthew, Montasser, May E., Morrison, Alanna C., Mulas, Antonella, Nielsen, Jonas B., North, Kari E., Oelsner, Elizabeth C., Okada, Yukinori, Orru, Valeria, Palmer, Nicholette D., Palviainen, Teemu, Pandit, Anita, Park, S. Lani, Peters, Ulrike, Peters, Annette, Peyser, Patricia A., Polderman, Tinca J. C., Rafaels, Nicholas, Redline, Susan, Reed, Robert M., Reiner, Alex P., Rice, John P., Rich, Stephen S., Richmond, Nicole E., Roan, Carol, Rotter, Jerome, Rueschman, Michael N., Runarsdottir, Valgerdur, Saccone, Nancy L., Schwartz, David A., Shadyab, Aladdin H., Shi, Jingchunzi, Shringarpure, Suyash S., Sicinski, Kamil, Skogholt, Anne Heidi, Smith, Jennifer A., Smith, Nicholas L., Sotoodehnia, Nona, Stallings, Michael C., Stefansson, Hreinn, Stefansson, Kari, Stitzel, Jerry A., Sun, Xiao, Syed, Moin, Tal-Singer, Ruth, Taylor, Amy E., Taylor, Kent D., Telen, Marilyn J., Thai, Khanh K., Tiwari, Hemant, Turman, Constance, Tyrfingsson, Thorarinn, Wall, Tamara L., Walters, Robin G., Weir, David R., Weiss, Scott T., White, Wendy B., Whitfield, John B., Wiggins, Kerri L., Willemsen, Gonneke, Willer, Cristen J., Winsvold, Bendik S., Xu, Huichun, Yanek, Lisa R., Yin, Jie, Young, Kristin L., Young, Kendra A., Yu, Bing, Zhao, Wei, Zhou, Wei, Zollner, Sebastian, Zuccolo, Luisa, Project, The Biobank Japan, Batini, Chiara, Bergen, Andrew W., Bierut, Laura J., David, Sean P., Taliun, Sarah A. Gagliano, Hancock, Dana B., Jiang, Bibo, Munafo, Marcus R., Thorgeirsson, Thorgeir E., Liu, Dajiang J., Vrieze, Scott, Pediatrics, Amsterdam Neuroscience - Complex Trait Genetics, Amsterdam Neuroscience - Compulsivity, Impulsivity & Attention, Biological Psychology, Amsterdam Reproduction & Development, APH - Mental Health, APH - Methodology, APH - Health Behaviors & Chronic Diseases, APH - Personalized Medicine, Clinical Developmental Psychology, Institute for Molecular Medicine Finland, University Management, Tellervo Korhonen / Principal Investigator, Genetic Epidemiology, and University of Helsinki
Subjects: Multidisciplinary, Internationality, Protein, Genetic Predisposition to Disease/genetics, 1184 Genetics, developmental biology, physiology, Neurotrophic factors, Alcohol Drinking/genetics, Europe/ethnology, Genetic Variation/genetics, Tobacco Use/genetics, SDG 3 - Good Health and Well-being, Risk Factors, Sample Size, Genetic Loci/genetics, Genome-Wide Association Study/methods, Humans, Disease, 3111 Biomedicine, Prediction, Transcriptome, Multifactorial Inheritance/genetics, Model
Abstract: Tobacco and alcohol use are heritable behaviours associated with 15% and 5.3% of worldwide deaths, respectively, due largely to broad increased risk for disease and injury1–4. These substances are used across the globe, yet genome-wide association studies have focused largely on individuals of European ancestries5. Here we leveraged global genetic diversity across 3.4 million individuals from four major clines of global ancestry (approximately 21% non-European) to power the discovery and fine-mapping of genomic loci associated with tobacco and alcohol use, to inform function of these loci via ancestry-aware transcriptome-wide association studies, and to evaluate the genetic architecture and predictive power of polygenic risk within and across populations. We found that increases in sample size and genetic diversity improved locus identification and fine-mapping resolution, and that a large majority of the 3,823 associated variants (from 2,143 loci) showed consistent effect sizes across ancestry dimensions. However, polygenic risk scores developed in one ancestry performed poorly in others, highlighting the continued need to increase sample sizes of diverse ancestries to realize any potential benefit of polygenic prediction.
Published: 2022

22. Clinical targeting of HIV capsid protein with a long-acting small molecule

Author: Qi Liu, Chien-Hung Chou, Eda Canales, Roman Sakowicz, Steven Bondy, Tomas Cihlar, Albert Liclican, Diana M. Brainard, Anita Niedziela-Majka, William Rowe, Nikolai Novikov, Shekeba Ahmadyar, John R. Somoza, Randall L. Halcomb, Cheryl K. McDonald, Carina E. Cannizzaro, Nicolas Margot, Debi Jin, George Stepan, Qiaoyin Wu, Eric Hu, Judy Mwangi, Stephanie A. Leavitt, Todd C. Appleby, Robert L. Anderson, Scott E. Lazerwith, Schroeder Scott D, Tse Winston C, Gediminas Brizgys, Rebecca Begley, Yili Xu, Scott Sellers, Scott A. Wolckenhauer, Wesley I. Sundquist, Derek Hansen, Philip Morganelli, Andrew Mulato, Sheila Clancy, Xiaohong Liu, Anna Chiu, Eric S. Daar, Renee R. Ram, S. Swaminathan, Anne E. Chester, Melanie H. Wong, Ya-Pei Liu, John O. Link, Michael Graupe, Luong K. Tsai, Christian Callebaut, Latesh Lad, William E. Lee, Rujuta A. Bam, Terrence Z. Cai, Bing Lu, John K. Ling, Roland D. Saito, Magdeleine Hung, Armando G. Villaseñor, Peter Ruane, Nikos Pagratis, Martin S. Rhee, David Koditek, Gordon Crofoot, Giuseppe A. Papalia, Stephen R. Yant, Rob Hyland, Helen Yu, Jim Zheng, Jennifer R. Zhang, Gary I. Sinclair, Jiayao Li, and Eric Singer
Subjects: Adult, Male, Models, Molecular, 0301 basic medicine, Adolescent, Anti-HIV Agents, 030106 microbiology, Drug resistance, Virus Replication, Article, Cell Line, Young Adult, 03 medical and health sciences, Subcutaneous injection, In vivo, Drug Resistance, Viral, Humans, Medicine, Cells, Cultured, Multidisciplinary, business.industry, Drug discovery, Middle Aged, Small molecule, Virology, 030104 developmental biology, Capsid, Viral replication, Drug development, HIV-1, Capsid Proteins, Female, business
Abstract: Oral antiretroviral agents provide life-saving treatments for millions of people living with HIV, and can prevent new infections via pre-exposure prophylaxis1–5. However, some people living with HIV who are heavily treatment-experienced have limited or no treatment options, owing to multidrug resistance6. In addition, suboptimal adherence to oral daily regimens can negatively affect the outcome of treatment—which contributes to virologic failure, resistance generation and viral transmission—as well as of pre-exposure prophylaxis, leading to new infections1,2,4,7–9. Long-acting agents from new antiretroviral classes can provide much-needed treatment options for people living with HIV who are heavily treatment-experienced, and additionally can improve adherence10. Here we describe GS-6207, a small molecule that disrupts the functions of HIV capsid protein and is amenable to long-acting therapy owing to its high potency, low in vivo systemic clearance and slow release kinetics from the subcutaneous injection site. Drawing on X-ray crystallographic information, we designed GS-6207 to bind tightly at a conserved interface between capsid protein monomers, where it interferes with capsid-protein-mediated interactions between proteins that are essential for multiple phases of the viral replication cycle. GS-6207 exhibits antiviral activity at picomolar concentrations against all subtypes of HIV-1 that we tested, and shows high synergy and no cross-resistance with approved antiretroviral drugs. In phase-1 clinical studies, monotherapy with a single subcutaneous dose of GS-6207 (450 mg) resulted in a mean log10-transformed reduction of plasma viral load of 2.2 after 9 days, and showed sustained plasma exposure at antivirally active concentrations for more than 6 months. These results provide clinical validation for therapies that target the functions of HIV capsid protein, and demonstrate the potential of GS-6207 as a long-acting agent to treat or prevent infection with HIV. The small molecule GS-6207, which disrupts the function of the HIV capsid protein, shows potential as a long-acting therapeutic agent for the treatment and prevention of HIV infection.
Published: 2020

23. Single-molecule imaging of transcription dynamics in somatic stem cells

Author: Arthur I. Skoultchi, Justin C. Wheat, Michael A. Willcockson, Robert H. Singer, Ulrich Steidl, Yehonatan Sella, and Aviv Bergman
Subjects: Male, 0301 basic medicine, Transcription, Genetic, Gene regulatory network, Biology, Article, Mice, 03 medical and health sciences, 0302 clinical medicine, Proto-Oncogene Proteins, Animals, GATA1 Transcription Factor, Gene Regulatory Networks, RNA, Messenger, Progenitor cell, Transcription factor, Cells, Cultured, In Situ Hybridization, Fluorescence, Tissue homeostasis, Stochastic Processes, Multidisciplinary, GATA2, Single Molecule Imaging, Clone Cells, Pedigree, Cell biology, GATA2 Transcription Factor, Mice, Inbred C57BL, Adult Stem Cells, Haematopoiesis, 030104 developmental biology, Gene Expression Regulation, 030220 oncology & carcinogenesis, Trans-Activators, Female, Stem cell, Adult stem cell
Abstract: Summary Molecular noise is a natural phenomenon inherent to all biological systems1,2. How stochastic processes give rise to the robust outcomes supportive of tissue homeostasis is a conundrum. Here, to quantitatively investigate this issue, we use single-molecule mRNA FISH (smFISH) on stem cells derived from hematopoietic tissue to measure the transcription dynamics of three key transcription factor (TF) genes: PU.1, Gata1 and Gata2. Our results indicate that infrequent, stochastic bursts of transcription result in the co-expression of these antagonistic TF in the majority of hematopoietic stem and progenitor cells. Moreover, by pairing smFISH to time-lapse microscopy and the analysis of pedigrees, we find that while individual stem cell clones produce offspring that are in transcriptionally related states, akin to a transcriptional priming phenomenon, the underlying transition dynamics between states are nevertheless best captured by stochastic and reversible models. As such, the outcome of a stochastic process can produce cellular behaviors that may be incorrectly inferred to have arisen from deterministic dynamics. In light of our findings, we propose a model whereby the intrinsic stochasticity of gene expression facilitates, rather than impedes, concomitant maintenance of transcriptional plasticity and stem cell robustness.
Published: 2020

24. The UN needs a new mission: get stuff done.

Author: Singer, Peter
Abstract: The United Nations has just listed more things the world needs to accomplish. It should be asking why it hasn’t reached its current goals. [ABSTRACT FROM AUTHOR]
Published: 2024
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25. To combat antimicrobial resistance, invest in test-to-treat strategies.

Author: McKendry, Rachel A., Rogers, Elliott, Singer, Mervyn, and Brown, Colin S.
Abstract: Letter to the Editor [ABSTRACT FROM AUTHOR]
Published: 2024
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26. The Formation of Charon's Red Poles from Seasonally Cold-Trapped Volatiles

Author: Grundy, W. M, Cruikshank, D. P, Gladstone, D. R, Howett, C. J. A, Lauer, T. R, Spencer, J. R, Summers, M. E, Buie, M. W, Earle, A. M, Ennico, K, Parker, J. Wm, Porter, S. B, Singer, K. N, Stern, S. A, Verbiscer, A. J, Beyer, R. A, Binzel, R. P, Buratti, B. J, Cook, J. C, Ore, C. M. Dalle, Olkin, C. B, Parker, A. H, Protopapa, S, Quirico, E, Moore, J. M, and Reuter, D. C
Subjects: Lunar And Planetary Science And Exploration
Abstract: A unique feature of Plutos large satellite Charon is its dark red northern polar cap. Similar colours on Plutos surface have been attributed to tholin-like organic macromolecules produced by energetic radiation processing of hydrocarbons. The polar location on Charon implicates the temperature extremes that result from Charons high obliquity and long seasons in the production of this material. The escape of Pluto's atmosphere provides a potential feedstock for a complex chemistry. Gas from Pluto that is transiently cold-trapped and processed at Charon's winter pole was proposed as an explanation for the dark coloration on the basis of an image of Charon's northern hemisphere, but not modelled quantitatively. Here we report images of the southern hemisphere illuminated by Pluto-shine and also images taken during the approach phase that show the northern polar cap over a range of longitudes. We model the surface thermal environment on Charon and the supply and temporary cold-trapping of material escaping from Pluto, as well as the photolytic processing of this material into more complex and less volatile molecules while cold-trapped. The model results are consistent with the proposed mechanism for producing the observed colour pattern on Charon.
Published: 2016
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27. Lethal trap created by adaptive evolutionary response to an exotic resource

Author: Singer, Michael C. and Parmesan, Camille
Subjects: Insect-plant relationships -- Research, Biological research, Local extinction, Biodiversity conservation, Hostages, Grasses, Land management, Butterflies, Insects, Cattle feed, Beef cattle, Cattle industry, Cattle, Environmental issues, Science and technology, Zoology and wildlife conservation
Abstract: Global transport of organisms by humans provides novel resources to wild species, which often respond maladaptively. Native herbivorous insects have been killed feeding on toxic exotic plants, which acted as 'ecological traps'.sup.1-4. We document a novel 'eco-evolutionary trap' stemming from the opposite effect; that is, high fitness on an exotic resource despite lack of adaptation to it. Plantago lanceolata was introduced to western North America by cattle-ranching. Feeding on this exotic plant released a large, isolated population of the native butterfly Euphydryas editha from a longstanding trade-off between maternal fecundity and offspring mortality. Because of this release--and despite a reduced insect developmental rate when feeding on this exotic--Plantago immediately supported higher larval survival than did the insects' traditional host, Collinsia parviflora.sup.5. Previous work from the 1980s documented an evolving preference for Plantago by ovipositing adults.sup.6. We predicted that if this trend continued the insects could endanger themselves, because the availability of Plantago to butterflies is controlled by humans, who change land management practices faster than butterflies evolve.sup.6. Here we report the fulfilment of this prediction. The butterflies abandoned Collinsia and evolved total dependence on Plantago. The trap was set. In 2005, humans withdrew their cattle, springing the trap. Grasses grew around the Plantago, cooling the thermophilic insects, which then went extinct. This local extinction could have been prevented if the population had retained partial use of Collinsia, which occupied drier microhabitats unaffected by cattle removal. The flush of grasses abated quickly, rendering the meadow once again suitable for Euphydryas feeding on either host, but no butterflies were observed from 2008 to 2012. In 2013-2014, the site was naturally recolonized by Euphydryas feeding exclusively on Collinsia, returning the system to its starting point and setting the stage for a repeat of the anthropogenic evolutionary cycle.Local extinction of the butterfly Euphydryas editha occurred after the population was caught in an eco-evolutionary trap set when the insects evolved unanimous preference for an exotic host, Plantago lanceolata, and sprung when that host became embedded in grasses after humans removed cattle., Author(s): Michael C. Singer [sup.1] [sup.2] , Camille Parmesan [sup.1] [sup.2] [sup.3] Author Affiliations:(1) Biological and Marine Sciences, University of Plymouth, Plymouth, UK(2) Theoretical and Experimental Ecology Station, CNRS, Université [...]
Published: 2018
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28. Neutrophils escort circulating tumour cells to enable cell cycle progression

Author: Nicola Aceto, Walter P. Weber, Ramona Scherrer, Niko Beerenwinkel, Christian Kurzeder, Julia Landin, Christian Beisel, Marcus Vetter, Francesc Castro-Giner, Jochen Singer, Ilona Krol, Viola Heinzelmann-Schwarz, Barbara Maria Szczerba, Cinzia Donato, Manuel C. Scheidmann, Christoph Rochlitz, and Sofia Gkountela
Subjects: 0301 basic medicine, Multidisciplinary, Innate immune system, Cell growth, Cancer, Biology, medicine.disease, Metastasis, Gene expression profiling, 03 medical and health sciences, 030104 developmental biology, 0302 clinical medicine, Immune system, Breast cancer, 030220 oncology & carcinogenesis, Cancer cell, Cancer research, medicine
Abstract: A better understanding of the features that define the interaction between cancer cells and immune cells is important for the development of new cancer therapies1. However, focus is often given to interactions that occur within the primary tumour and its microenvironment, whereas the role of immune cells during cancer dissemination in patients remains largely uncharacterized2,3. Circulating tumour cells (CTCs) are precursors of metastasis in several types of cancer4–6, and are occasionally found within the bloodstream in association with non-malignant cells such as white blood cells (WBCs)7,8. The identity and function of these CTC-associated WBCs, as well as the molecular features that define the interaction between WBCs and CTCs, are unknown. Here we isolate and characterize individual CTC-associated WBCs, as well as corresponding cancer cells within each CTC–WBC cluster, from patients with breast cancer and from mouse models. We use single-cell RNA sequencing to show that in the majority of these cases, CTCs were associated with neutrophils. When comparing the transcriptome profiles of CTCs associated with neutrophils against those of CTCs alone, we detect a number of differentially expressed genes that outline cell cycle progression, leading to more efficient metastasis formation. Further, we identify cell–cell junction and cytokine–receptor pairs that define CTC–neutrophil clusters, representing key vulnerabilities of the metastatic process. Thus, the association between neutrophils and CTCs drives cell cycle progression within the bloodstream and expands the metastatic potential of CTCs, providing a rationale for targeting this interaction in treatment of breast cancer. The authors show that circulating tumour cells can be found in association with neutrophils, an interaction which supports their proliferation and their ability to seed metastasis.
Published: 2019

29. Mitochondrial complex III is essential for regulatory T cell suppressive function

Author: Manan M. Mehta, Paul T. Schumacker, Samuel E. Weinberg, Carlos A. Martinez, Benjamin D. Singer, Inmaculada Martínez-Reyes, Navdeep S. Chandel, Elizabeth M. Steinert, Hiam Abdala-Valencia, Laurence A. Turka, Laura A. Sena, Kathryn A. Helmin, and Peng Gao
Subjects: 0301 basic medicine, Succinic Acid, Inflammation, chemical and pharmacologic phenomena, Biology, Mitochondrion, T-Lymphocytes, Regulatory, Article, Oxidative Phosphorylation, Electron Transport, Glutarates, 03 medical and health sciences, Electron Transport Complex III, Mice, 0302 clinical medicine, Immune system, medicine, Animals, Humans, Regulation of gene expression, Multidisciplinary, FOXP3, Forkhead Transcription Factors, hemic and immune systems, DNA Methylation, Mitochondrial respiratory chain complex III, Cell biology, Mitochondria, DNA Demethylation, Mice, Inbred C57BL, 030104 developmental biology, Mitochondrial respiratory chain, Self Tolerance, Gene Expression Regulation, 030220 oncology & carcinogenesis, DNA methylation, Mitochondrial Membranes, Female, medicine.symptom, Energy Metabolism
Abstract: Regulatory T cells (Treg cells), a distinct subset of CD4+ T cells, are necessary for the maintenance of immune self-tolerance and homeostasis1,2. Recent studies have demonstrated that Treg cells exhibit a unique metabolic profile, characterized by an increase in mitochondrial metabolism relative to other CD4+ effector subsets3,4. Furthermore, the Treg cell lineage-defining transcription factor, Foxp3, has been shown to promote respiration5,6; however, it remains unknown whether the mitochondrial respiratory chain is required for the T cell-suppression capacity, stability and survival of Treg cells. Here we report that Treg cell-specific ablation of mitochondrial respiratory chain complex III in mice results in the development of fatal inflammatory disease early in life, without affecting Treg cell number. Mice that lack mitochondrial complex III specifically in Treg cells displayed a loss of T cell-suppression capacity without altering Treg cell proliferation and survival. Treg cells deficient in complex III showed decreased expression of genes associated with Treg function, whereas Foxp3 expression remained stable. Loss of complex III in Treg cells increased DNA methylation as well as the metabolites 2-hydroxyglutarate (2-HG) and succinate that inhibit the ten-eleven translocation (TET) family of DNA demethylases7. Thus, Treg cells require mitochondrial complex III to maintain immune regulatory gene expression and suppressive function.
Published: 2019

30. Author Correction: Aridity is expressed in river topography globally

Author: Shiuan-An Chen, Katerina Michaelides, Stuart W. D. Grieve, and Michael Bliss Singer
Subjects: Multidisciplinary
Published: 2022

31. Sensitivity of SARS-CoV-2 B.1.1.7 to mRNA vaccine-elicited antibodies

Author: Collier, D. A., De Marco, A., Ferreira, I. A. T. M., Meng, B., Datir, R. P., Walls, A. C., Kemp, S. A., Bassi, J., Pinto, D., Silacci-Fregni, C., Bianchi, S., Tortorici, M. A., Bowen, J., Culap, K., Jaconi, S., Cameroni, E., Snell, G., Pizzuto, M. S., Pellanda, A. F., Garzoni, C., Riva, A., Baker, S., Dougan, G., Hess, C., Kingston, N., Lehner, P. J., Lyons, P. A., Matheson, N. J., Owehand, W. H., Saunders, C., Summers, C., Thaventhiran, J. E. D., Toshner, M., Weekes, M. P., Bucke, A., Calder, J., Canna, L., Domingo, J., Elmer, A., Fuller, S., Harris, J., Hewitt, S., Kennet, J., Jose, S., Kourampa, J., Meadows, A., O'Brien, C., Price, J., Publico, C., Rastall, R., Ribeiro, C., Rowlands, J., Ruffolo, V., Tordesillas, H., Bullman, B., Dunmore, B. J., Fawke, S., Graf, S., Hodgson, J., Huang, C., Hunter, K., Jones, E., Legchenko, E., Matara, C., Martin, J., Mescia, F., O'Donnell, C., Pointon, L., Pond, N., Shih, J., Sutcliffe, R., Tilly, T., Treacy, C., Tong, Z., Wood, J., Wylot, M., Bergamaschi, L., Betancourt, A., Bower, G., Cossetti, C., De Sa, A., Epping, M., Grenfell, R., Hinch, A., Huhn, O., Jackson, S., Jarvis, I., Lewis, D., Marsden, J., Nice, F., Okecha, G., Omarjee, O., Perera, M., Richoz, N., Romashova, V., Yarkoni, N. S., Sharma, R., Stefanucci, L., Stephens, J., Strezlecki, M., Turner, L., De Bie, E. M. D. D., Bunclark, K., Josipovic, M., Mackay, M., Rossi, S., Selvan, M., Spencer, S., Yong, C., Ansaripour, A., Michael, A., Mwaura, L., Patterson, C., Polwarth, G., Polgarova, P., di Stefano, G., Fahey, C., Michel, R., Bong, S. -H., Coudert, J. D., Holmes, E., Allison, J., Butcher, H., Caputo, D., Clapham-Riley, D., Dewhurst, E., Furlong, A., Graves, B., Gray, J., Ivers, T., Kasanicki, M., Le Gresley, E., Linger, R., Meloy, S., Muldoon, F., Ovington, N., Papadia, S., Phelan, I., Stark, H., Stirrups, K. E., Townsend, P., Walker, N., Webster, J., Mccoy, L. E., Smith, K. G. C., Bradley, J. R., Temperton, N., Ceron-Gutierrez, L., Barcenas-Morales, G., Robson, S. C., Loman, N. J., Connor, T. R., Golubchik, T., Martinez Nunez, R. T., Ludden, C., Corden, S., Johnston, I., Bonsall, D., Smith, C. P., Awan, A. R., Bucca, G., Torok, M. E., Saeed, K., Prieto, J. A., Jackson, D. K., Hamilton, W. L., Snell, L. B., Moore, C., Harrison, E. M., Goncalves, S., Fairley, D. J., Loose, M. W., Watkins, J., Livett, R., Moses, S., Amato, R., Nicholls, S., Bull, M., Smith, D. L., Barrett, J., Aanensen, D. M., Curran, M. D., Parmar, S., Aggarwal, D., Shepherd, J. G., Parker, M. D., Glaysher, S., Bashton, M., Underwood, A. P., Pacchiarini, N., Loveson, K. F., Carabelli, A. M., Templeton, K. E., Langford, C. F., Sillitoe, J., de Silva, T. I., Wang, D., Kwiatkowski, D., Rambaut, A., O'Grady, J., Cottrell, S., Holden, M. T. G., Thomson, E. C., Osman, H., Andersson, M., Chauhan, A. J., Hassan-Ibrahim, M. O., Lawniczak, M., Alderton, A., Chand, M., Constantinidou, C., Unnikrishnan, M., Darby, A. C., Hiscox, J. A., Paterson, S., Martincorena, I., Robertson, D. L., Volz, E. M., Page, A. J., Pybus, O. G., Bassett, A. R., Ariani, C. V., Spencer Chapman, M. H., K. K., Li, Shah, R. N., Jesudason, N. G., Taha, Y., Mchugh, M. P., Dewar, R., Jahun, A. S., Mcmurray, C., Pandey, S., Mckenna, J. P., Nelson, A., Young, G. R., Mccann, C. M., Elliott, S., Lowe, H., Temperton, B., Roy, S., Price, A., Rey, S., Wyles, M., Rooke, S., Shaaban, S., de Cesare, M., Letchford, L., Silveira, S., Pelosi, E., Wilson-Davies, E., Hosmillo, M., O'Toole, A., Hesketh, A. R., Stark, R., du Plessis, L., Ruis, C., Adams, H., Bourgeois, Y., Michell, S. L., Gramatopoulos, D., Edgeworth, J., Breuer, J., Todd, J. A., Fraser, C., Buck, D., John, M., Kay, G. L., Palmer, S., Peacock, S. J., Heyburn, D., Weldon, D., Robinson, E., Mcnally, A., Muir, P., Vipond, I. B., Boyes, J., Sivaprakasam, V., Salluja, T., Dervisevic, S., Meader, E. J., Park, N. R., Oliver, K., Jeffries, A. R., Ott, S., da Silva Filipe, A., Simpson, D. A., Williams, C., Masoli, J. A. H., Knight, B. A., Jones, C. R., Koshy, C., Ash, A., Casey, A., Bosworth, A., Ratcliffe, L., Xu-McCrae, L., Pymont, H. M., Hutchings, S., Berry, L., Jones, K., Halstead, F., Davis, T., Holmes, C., Iturriza-Gomara, M., Lucaci, A. O., Randell, P. A., Cox, A., Madona, P., Harris, K. A., Brown, J. R., Mahungu, T. W., Irish-Tavares, D., Haque, T., Hart, J., Witele, E., Fenton, M. L., Liggett, S., Graham, C., Swindells, E., Collins, J., Eltringham, G., Campbell, S., Mcclure, P. C., Clark, G., Sloan, T. J., Jones, C., Lynch, J., Warne, B., Leonard, S., Durham, J., Williams, T., Haldenby, S. T., Storey, N., Alikhan, N. -F., Holmes, N., Carlile, M., Perry, M., Craine, N., Lyons, R. A., Beckett, A. H., Goudarzi, S., Fearn, C., Cook, K., Dent, H., Paul, H., Davies, R., Blane, B., Girgis, S. T., Beale, M. A., Bellis, K. L., Dorman, M. J., Drury, E., Kane, L., Kay, S., Mcguigan, S., Nelson, R., Prestwood, L., Rajatileka, S., Batra, R., Williams, R. J., Kristiansen, M., Green, A., Justice, A., Mahanama, A. I. K., Samaraweera, B., Hadjirin, N. F., Quick, J., Poplawski, R., Kermack, L. M., Reynolds, N., Hall, G., Chaudhry, Y., Pinckert, M. L., Georgana, I., Moll, R. J., Thornton, A., Myers, R., Stockton, J., Williams, C. A., Yew, W. C., Trotter, A. J., Trebes, A., MacIntyre-Cockett, G., Birchley, A., Adams, A., Plimmer, A., Gatica-Wilcox, B., Mckerr, C., Hilvers, E., Jones, H., Asad, H., Coombes, J., Evans, J. M., Fina, L., Gilbert, L., Graham, L., Cronin, M., Kumziene-Summerhayes, S., Taylor, S., Jones, S., Groves, D. C., Zhang, P., Gallis, M., Louka, S. F., Starinskij, I., Jackson, C., Gourtovaia, M., Tonkin-Hill, G., Lewis, K., Tovar-Corona, J. M., James, K., Baxter, L., Alam, M. T., Orton, R. J., Hughes, J., Vattipally, S., Ragonnet-Cronin, M., Nascimento, F. F., Jorgensen, D., Boyd, O., Geidelberg, L., Zarebski, A. E., Raghwani, J., Kraemer, M. U. G., Southgate, J., Lindsey, B. B., Freeman, T. M., Keatley, J. -P., Singer, J. B., de Oliveira Martins, L., Yeats, C. A., Abudahab, K., Taylor, B. E. W., Menegazzo, M., Danesh, J., Hogsden, W., Eldirdiri, S., Kenyon, A., Mason, J., Robinson, T. I., Holmes, A., Hartley, J. A., Curran, T., Mather, A. E., Shankar, G., Jones, R., Howe, R., Morgan, S., Wastenge, E., Chapman, M. R., Mookerjee, S., Stanley, R., Smith, W., Peto, T., Eyre, D., Crook, D., Vernet, G., Kitchen, C., Gulliver, H., Merrick, I., Guest, M., Munn, R., Bradley, D. T., Wyatt, T., Beaver, C., Foulser, L., Churcher, C. M., Brooks, E., Smith, K. S., Galai, K., Mcmanus, G. M., Bolt, F., Coll, F., Meadows, L., Attwood, S. W., Davies, A., De Lacy, E., Downing, F., Edwards, S., Scarlett, G. P., Jeremiah, S., Smith, N., Leek, D., Sridhar, S., Forrest, S., Cormie, C., Gill, H. K., Dias, J., Higginson, E. E., Maes, M., Young, J., Wantoch, M., Jamrozy, D., Lo, S., Patel, M., Hill, V., Bewshea, C. M., Ellard, S., Auckland, C., Harrison, I., Bishop, C., Chalker, V., Richter, A., Beggs, A., Best, A., Percival, B., Mirza, J., Megram, O., Mayhew, M., Crawford, L., Ashcroft, F., Moles-Garcia, E., Cumley, N., Hopes, R., Asamaphan, P., Niebel, M. O., Gunson, R. N., Bradley, A., Maclean, A., Mollett, G., Blacow, R., Bird, P., Helmer, T., Fallon, K., Tang, J., Hale, A. D., Macfarlane-Smith, L. R., Harper, K. L., Carden, H., Machin, N. W., Jackson, K. A., Ahmad, S. S. Y., George, R. P., Turtle, L., O'Toole, E., Watts, J., Breen, C., Cowell, A., Alcolea-Medina, A., Charalampous, T., Patel, A., Levett, L. J., Heaney, J., Rowan, A., Taylor, G. P., Shah, D., Atkinson, L., Lee, J. C. D., Westhorpe, A. P., Jannoo, R., Lowe, H. L., Karamani, A., Ensell, L., Chatterton, W., Pusok, M., Dadrah, A., Symmonds, A., Sluga, G., Molnar, Z., Baker, P., Bonner, S., Essex, S., Barton, E., Padgett, D., Scott, G., Greenaway, J., Payne, B. A. I., Burton-Fanning, S., Waugh, S., Raviprakash, V., Sheriff, N., Blakey, V., Williams, L. -A., Moore, J., Stonehouse, S., Smith, L., Davidson, R. K., Bedford, L., Coupland, L., Wright, V., Chappell, J. G., Tsoleridis, T., Ball, J., Khakh, M., Fleming, V. M., Lister, M. M., Howson-Wells, H. C., Boswell, T., Joseph, A., Willingham, I., Duckworth, N., Walsh, S., Wise, E., Moore, N., Mori, M., Cortes, N., Kidd, S., Williams, R., Gifford, L., Bicknell, K., Wyllie, S., Lloyd, A., Impey, R., Malone, C. S., Cogger, B. J., Levene, N., Monaghan, L., Keeley, A. J., Partridge, D. G., Raza, M., Evans, C., Johnson, K., Betteridge, E., Farr, B. W., Goodwin, S., Quail, M. A., Scott, C., Shirley, L., Thurston, S. A. J., Rajan, D., Bronner, I. F., Aigrain, L., Redshaw, N. M., Lensing, S. V., Mccarthy, S., Makunin, A., Balcazar, C. E., Gallagher, M. D., Williamson, K. A., Stanton, T. D., Michelsen, M. L., Warwick-Dugdale, J., Manley, R., Farbos, A., Harrison, J. W., Sambles, C. M., Studholme, D. J., Lackenby, A., Mbisa, T., Platt, S., Miah, S., Bibby, D., Manso, C., Hubb, J., Dabrera, G., Ramsay, M., Bradshaw, D., Schaefer, U., Groves, N., Gallagher, E., Lee, D., Williams, D., Ellaby, N., Hartman, H., Manesis, N., Patel, V., Ledesma, J., Twohig, K. A., Allara, E., Pearson, C., Cheng, J. K. J., Bridgewater, H. E., Frost, L. R., Taylor-Joyce, G., Brown, P. E., Tong, L., Broos, A., Mair, D., Nichols, J., Carmichael, S. N., Smollett, K. L., Nomikou, K., Aranday-Cortes, E., Johnson, N., Nickbakhsh, S., Vamos, E. E., Hughes, M., Rainbow, L., Eccles, R., Nelson, C., Whitehead, M., Gregory, R., Gemmell, M., Wierzbicki, C., Webster, H. J., Fisher, C. L., Signell, A. W., Betancor, G., Wilson, H. D., Nebbia, G., Flaviani, F., Cerda, A. C., Merrill, T. V., Wilson, R. E., Cotic, M., Bayzid, N., Thompson, T., Acheson, E., Rushton, S., O'Brien, S., Baker, D. J., Rudder, S., Aydin, A., Sang, F., Debebe, J., Francois, S., Vasylyeva, T. I., Zamudio, M. E., Gutierrez, B., Marchbank, A., Maksimovic, J., Spellman, K., Mccluggage, K., Morgan, M., Beer, R., Afifi, S., Workman, T., Fuller, W., Bresner, C., Angyal, A., Green, L. R., Parsons, P. J., Tucker, R. M., Brown, R., Whiteley, M., Bonfield, J., Puethe, C., Whitwham, A., Liddle, J., Rowe, W., Siveroni, I., Le-Viet, T., Gaskin, A., Johnson, R., Abnizova, I., Ali, M., Allen, L., Anderson, R., Ariani, C., Austin-Guest, S., Bala, S., Bassett, A., Battleday, K., Beal, J., Beale, M., Bellany, S., Bellerby, T., Bellis, K., Berger, D., Berriman, M., Bevan, P., Binley, S., Bishop, J., Blackburn, K., Boughton, N., Bowker, S., Brendler-Spaeth, T., Bronner, I., Brooklyn, T., Buddenborg, S. K., Bush, R., Caetano, C., Cagan, A., Carter, N., Cartwright, J., Monteiro, T. C., Chapman, L., Chillingworth, T. -J., Clapham, P., Clark, R., Clarke, A., Clarke, C., Cole, D., Cook, E., Coppola, M., Cornell, L., Cornwell, C., Corton, C., Crackett, A., Cranage, A., Craven, H., Craw, S., Crawford, M., Cutts, T., Dabrowska, M., Davies, M., Dawson, J., Day, C., Densem, A., Dibling, T., Dockree, C., Dodd, D., Dogga, S., Dougherty, M., Dove, A., Drummond, L., Dudek, M., Durrant, L., Easthope, E., Eckert, S., Ellis, P., Farr, B., Fenton, M., Ferrero, M., Flack, N., Fordham, H., Forsythe, G., Francis, M., Fraser, A., Freeman, A., Galvin, A., Garcia-Casado, M., Gedny, A., Girgis, S., Glover, J., Gould, O., Gray, A., Gray, E., Griffiths, C., Gu, Y., Guerin, F., Hamilton, W., Hanks, H., Harrison, E., Harrott, A., Harry, E., Harvison, J., Heath, P., Hernandez-Koutoucheva, A., Hobbs, R., Holland, D., Holmes, S., Hornett, G., Hough, N., Huckle, L., Hughes-Hallet, L., Hunter, A., Inglis, S., Iqbal, S., Jackson, A., Jackson, D., Verdejo, C. J., Jones, M., Kallepally, K., Kay, K., Keatley, J., Keith, A., King, A., Kitchin, L., Kleanthous, M., Klimekova, M., Korlevic, P., Krasheninnkova, K., Lane, G., Langford, C., Laverack, A., Law, K., Lensing, S., Lewis-Wade, A., Lin, Q., Lindsay, S., Linsdell, S., Long, R., Lovell, J., Mack, J., Maddison, M., Mamun, I., Mansfield, J., Marriott, N., Martin, M., Mayho, M., Mcclintock, J., Mchugh, S., Mcminn, L., Meadows, C., Mobley, E., Moll, R., Morra, M., Morrow, L., Murie, K., Nash, S., Nathwani, C., Naydenova, P., Neaverson, A., Nerou, E., Nicholson, J., Nimz, T., Noell, G. G., O'Meara, S., Ohan, V., Olney, C., Ormond, D., Oszlanczi, A., Pang, Y. F., Pardubska, B., Park, N., Parmar, A., Patel, G., Payne, M., Peacock, S., Petersen, A., Plowman, D., Preston, T., Quail, M., Rance, R., Rawlings, S., Redshaw, N., Reynolds, J., Reynolds, M., Rice, S., Richardson, M., Roberts, C., Robinson, K., Robinson, M., Robinson, D., Rogers, H., Rojo, E. M., Roopra, D., Rose, M., Rudd, L., Sadri, R., Salmon, N., Saul, D., Schwach, F., Seekings, P., Simms, A., Sinnott, M., Sivadasan, S., Siwek, B., Sizer, D., Skeldon, K., Skelton, J., Slater-Tunstill, J., Sloper, L., Smerdon, N., Smith, C., Smith, J., Smith, K., Smith, M., Smith, S., Smith, T., Sneade, L., Soria, C. D., Sousa, C., Souster, E., Sparkes, A., Spencer-Chapman, M., Squares, J., Steed, C., Stickland, T., Still, I., Stratton, M., Strickland, M., Swann, A., Swiatkowska, A., Sycamore, N., Swift, E., Symons, E., Szluha, S., Taluy, E., Tao, N., Taylor, K., Thompson, S., Thompson, M., Thomson, M., Thomson, N., Thurston, S., Toombs, D., Topping, B., Tovar-Corona, J., Ungureanu, D., Uphill, J., Urbanova, J., Van, P. J., Vancollie, V., Voak, P., Walker, D., Walker, M., Waller, M., Ward, G., Weatherhogg, C., Webb, N., Wells, A., Wells, E., Westwood, L., Whipp, T., Whiteley, T., Whitton, G., Widaa, S., Williams, M., Wilson, M., Wright, S., Harvey, W., Virgin, H. W., Lanzavecchia, A., Piccoli, L., Doffinger, R., Wills, M., Veesler, D., Corti, D., and Gupta, R. K.
Subjects: 0301 basic medicine, Male, Models, Molecular, Passive, Antibodies, Viral, Neutralization, 0302 clinical medicine, Models, Monoclonal, 80 and over, Viral, Neutralizing antibody, Neutralizing, Aged, 80 and over, Vaccines, Vaccines, Synthetic, Multidisciplinary, biology, Antibodies, Monoclonal, C500, Middle Aged, C700, Spike Glycoprotein, Vaccination, Spike Glycoprotein, Coronavirus, Female, Angiotensin-Converting Enzyme 2, Antibody, Aged, Antibodies, Neutralizing, COVID-19, COVID-19 Vaccines, HEK293 Cells, Humans, Immune Evasion, Immunization, Passive, Mutation, Neutralization Tests, SARS-CoV-2, medicine.drug_class, B100, Monoclonal antibody, Antibodies, Virus, 03 medical and health sciences, Immune system, medicine, COVID-19 Serotherapy, QR355, Synthetic, Molecular, Virology, Coronavirus, 030104 developmental biology, Immunization, biology.protein, 030217 neurology & neurosurgery
Abstract: Transmission of SARS-CoV-2 is uncontrolled in many parts of the world; control is compounded in some areas by the higher transmission potential of the B.1.1.7 variant1, which has now been reported in 94 countries. It is unclear whether the response of the virus to vaccines against SARS-CoV-2 on the basis of the prototypic strain will be affected by the mutations found in B.1.1.7. Here we assess the immune responses of individuals after vaccination with the mRNA-based vaccine BNT162b22. We measured neutralizing antibody responses after the first and second immunizations using pseudoviruses that expressed the wild-type spike protein or a mutated spike protein that contained the eight amino acid changes found in the B.1.1.7 variant. The sera from individuals who received the vaccine exhibited a broad range of neutralizing titres against the wild-type pseudoviruses that were modestly reduced against the B.1.1.7 variant. This reduction was also evident in sera from some patients who had recovered from COVID-19. Decreased neutralization of the B.1.1.7 variant was also observed for monoclonal antibodies that target the N-terminal domain (9 out of 10) and the receptor-binding motif (5 out of 31), but not for monoclonal antibodies that recognize the receptor-binding domain that bind outside the receptor-binding motif. Introduction of the mutation that encodes the E484K substitution in the B.1.1.7 background to reflect a newly emerged variant of concern (VOC 202102/02) led to a more-substantial loss of neutralizing activity by vaccine-elicited antibodies and monoclonal antibodies (19 out of 31) compared with the loss of neutralizing activity conferred by the mutations in B.1.1.7 alone. The emergence of the E484K substitution in a B.1.1.7 background represents a threat to the efficacy of the BNT162b2 vaccine.
Published: 2021

32. BTB-ZF factors recruit the E3 ligase cullin 3 to regulate lymphoid effector programs

Author: Mathew, Rebecca, Seiler, Michael P., Scanlon, Seth T., Mao, Ai-ping, Constantinides, Michael G., Bertozzi-Villa, Clara, Singer, Jeffrey D., and Bendelac, Albert
Subjects: Zinc finger proteins -- Research, Ubiquitin-proteasome system -- Research, Lymphocyte transformation -- Research, Environmental issues, Science and technology, Zoology and wildlife conservation
Abstract: The differentiation of several T- and B-cell effector programs in the immune system is directed by signature transcription factors that induce rapid epigenetic remodelling. Here we report that promyelocytic leukaemia [...]
Published: 2012

33. ACE2 links amino acid malnutrition to microbial ecology and intestinal inflammation

Author: Hashimoto, Tatsuo, Perlot, Thomas, Rehman, Ateequr, Trichereau, Jean, Ishiguro, Hiroaki, Paolino, Magdalena, Sigl, Verena, Hanada, Toshikatsu, Hanada, Reiko, Lipinski, Simone, Wild, Birgit, Camargo, Simone M.R., Singer, Dustin, Richter, Andreas, Kuba, Keiji, Fukamizu, Akiyoshi, Schreiber, Stefan, Clevers, Hans, Verrey, Francois, Rosenstiel, Philip, and Penninger, Josef M.
Subjects: Angiotensin converting enzyme -- Physiological aspects -- Health aspects, Inflammation -- Physiological aspects -- Development and progression, Intestines -- Physiological aspects -- Health aspects, Microbial colonies -- Physiological aspects -- Health aspects, Amino acids -- Physiological aspects -- Health aspects, Environmental issues, Science and technology, Zoology and wildlife conservation
Abstract: Malnutrition affects up to one billion people in the world and is a major cause of mortality (1,2). In many cases malnutrition is associated with diarrhoea and intestinal inflammation, further [...]
Published: 2012
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34. Embryonic stem cell potency fluctuates with endogenous retrovirus activity

Author: Macfarlan, Todd S., Gifford, Wesley D., Driscoll, Shawn, Lettieri, Karen, Rowe, Helen M., Bonanomi, Dario, Firth, Amy, Singer, Oded, Trono, Didier, and Pfaff, Samuel L.
Subjects: Embryonic stem cells -- Physiological aspects -- Health aspects, Retroviruses -- Physiological aspects -- Health aspects, Disease transmission -- Research, Environmental issues, Science and technology, Zoology and wildlife conservation
Abstract: Embryonic stem (ES) cells are derived from blastocyst-stage embryos and are thought to be functionally equivalent to the inner cell mass, which lacks the ability to produce all extraembryonic tissues. Here we identify a rare transient cell population within mouse ES and induced pluripotent stem (iPS) cell cultures that expresses high levels of transcripts found in two-cell (2C) embryos in which the blastomeres are totipotent. We genetically tagged these 2C-like ES cells and show that they lack the inner cell mass pluripotency proteins Oct4 (also known as Pou5f1), Sox2 and Nanog, and have acquired the ability to contribute to both embryonic and extraembryonic tissues. We show that nearly all ES cells cycle in and out of this privileged state, which is partially controlled by histone-modifying enzymes. Transcriptome sequencing and bioinformatic analyses showed that many 2C transcripts are initiated from long terminal repeats derived from endogenous retroviruses, suggesting this foreign sequence has helped to drive cell-fate regulation in placental mammals., The zygote and its daughter cells are totipotent because they are able to develop into all embryonic and extraembryonic cell types (1,2). The progeny of these first two daughter cells [...]
Published: 2012
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35. Nuclear export dynamics of RNA-protein complexes

Author: Grunwald, David, Singer, Robert H., and Rout, Michael
Subjects: Electron microscopy -- Usage, RNA -- Physiological aspects -- Research, Proteins -- Physiological aspects -- Research, Environmental issues, Science and technology, Zoology and wildlife conservation
Abstract: The central dogma of molecular biology--DNA makes RNA makes proteins--is a flow of information that in eukaryotes encounters a physical barrier: the nuclear envelope, which encapsulates, organizes and protects the genome. Nuclear- pore complexes, embedded in the nuclear envelope, regulate the passage of molecules to and from the nucleus, including the poorly understood process of the export of RNAs from the nucleus. Recent imaging approaches focusing on single molecules have provided unexpected insight into this crucial step in the information flow. This review addresses the latest studies of RNA export and presents some models for how this complex process may work., Since its first description in electron micrographs (1), our understanding of the nuclear-pore complex (NPC), arguably the largest nanomachine in the cell, has increased steadily. We are now at the [...]
Published: 2011
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36. In vivo imaging of labelled endogenous β-actin mRNA during nucleocytoplasmic transport

Author: Grunwald, David and Singer, Robert H.
Subjects: Cytoplasm -- Chemical properties -- Genetic aspects, Messenger RNA -- Observations -- Chemical properties -- Genetic aspects, Cellular proteins -- Genetic aspects -- Properties -- Chemical properties, Fluorescent proteins -- Properties -- Chemical properties -- Genetic aspects, Environmental issues, Science and technology, Zoology and wildlife conservation
Abstract: Export of messenger RNA occurs via nuclear pores, which are large nanomachines with diameters of roughly 120 nm that are the only link between the nucleus and cytoplasm (1). Hence, mRNA export occurs over distances smaller than the optical resolution of conventional light microscopes. There is extensive knowledge on the physical structure and composition of the nuclear pore complex (2-7), but transport selectivity and the dynamics of mRNA export at nuclear pores remain unknown (8). Here we developed a super-registration approach using fluorescence microscopy that can overcome the current limitations of co-localization by means of measuring intermolecular distances of chromatically different fluorescent molecules with nanometre precision. With this method we achieve 20-ms time-precision and at least 26-nm spatial precision, enabling the capture of highly transient interactions in living cells. Using this approach we were able to spatially resolve the kinetics of mRNA transport in mammalian cells and present a three-step model consisting of docking (80 ms), transport (5-20 ms) and release (80 ms), totalling 180 ± 10 ms. Notably, the translocation through the channel was not the rate-limiting step, mRNAs can move bi-directionally in the pore complex and not all pores are equally active., We generated a stable cell line, derived from a transgenic mouse, where all β-actin mRNA is labelled by yellow fluorescent protein (YFP) fused to a MS2 protein tag (9,10) (Methods [...]
Published: 2010
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37. Author Correction: Transcript expression-aware annotation improves rare variant interpretation

Author: Cummings, Beryl B., Karczewski, Konrad J., Kosmicki, Jack A., Seaby, Eleanor G., Watts, Nicholas A., Singer-Berk, Moriel, and Mudge, Jonathan M.
Subjects: Environmental issues, Science and technology, Zoology and wildlife conservation
Abstract: A Correction to this paper has been published: https://doi.org/10.1038/s41586-020-03175-7, Author(s): Beryl B. Cummings [sup.1] [sup.2] [sup.3], Konrad J. Karczewski [sup.1] [sup.2], Jack A. Kosmicki [sup.1] [sup.2] [sup.4], Eleanor G. Seaby [sup.1] [sup.2] [sup.5], Nicholas A. Watts [sup.1] [sup.2], Moriel [...]
Published: 2021
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38. Arginine methylation at histone H3R2 controls deposition of H3K4 trimethylation

Author: Kirmizis, Antonis, Santos-Rosa, Helena, Penkett, Christopher J., Singer, Michael A., Vermeulen, Michiel, Mann, Matthias, Bahler, Jurg, Green, Roland D., and Kouzarides, Tony
Subjects: Gene expression -- Research, Methylation -- Research -- Control, Histones -- Research, Arginine -- Research, Environmental issues, Science and technology, Zoology and wildlife conservation, Control, Research
Abstract: Modifications on histones control important biological processes through their effects on chromatin structure (1-3). Methylation at lysine 4 on histone H3 (H3K4) is found at the 5' end of active [...]
Published: 2007

39. A tough transition

Author: Singer, Peter A., Berndtson, Kathryn, Tracy, C. Shawn, Cohen, Emma R. M., Masum, Hassan, Lavery, James V., and Daar, Abdallah S.
Subjects: Environmental issues, Science and technology, Zoology and wildlife conservation
Abstract: Author(s): Peter A. Singer [1]; Kathryn Berndtson [1]; C. Shawn Tracy [1]; Emma R. M. Cohen [1]; Hassan Masum [1]; James V. Lavery [2]; Abdallah S. Daar [1] The path [...]
Published: 2007
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40. Dating the origin of the Orchidaceae from a fossil orchid with its pollinator

Author: Ramirez, Santiago R., Gravendeel, Barbara, Singer, Rodrigo B., Marshall, Charles R., and Pierce, Naomi E.
Subjects: Environmental issues, Science and technology, Zoology and wildlife conservation
Abstract: Author(s): Santiago R. RamÃrez (corresponding author) [1]; Barbara Gravendeel [2]; Rodrigo B. Singer [3]; Charles R. Marshall [1, 4]; Naomi E. Pierce [1] Since the time of Darwin [1], evolutionary [...]
Published: 2007
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41. Host specificity of Lepidoptera in tropical and temperate forests

Author: Dyer, L. A., Singer, M. S., Lill, J. T., Stireman, J. O., Gentry, G. L., Marquis, R. J., Ricklefs, R. E., Greeney, H. F., Wagner, D. L., Morais, H. C., Diniz, I. R., Kursar, T. A., and Coley, P. D.
Subjects: Environmental issues, Science and technology, Zoology and wildlife conservation
Abstract: Author(s): L. A. Dyer (corresponding author) [1]; M. S. Singer [2]; J. T. Lill [3]; J. O. Stireman [4]; G. L. Gentry [1]; R. J. Marquis [5]; R. E. Ricklefs [...]
Published: 2007
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42. Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project

Author: Birney, Ewan, Stamatoyannopoulos, John A., Dutta, Anindya, Guigo, Roderic, Gingeras, Thomas R., Margulies, Elliott H., Weng, Zhiping, Snyder, Michael, Dermitzakis, Emmanouil T., Thurman, Robert E., Kuehn, Michael S., Taylor, Christopher M., Neph, Shane, Koch, Christoph M., Asthana, Saurabh, Malhotra, Ankit, Adzhubei, Ivan, Greenbaum, Jason A., Andrews, Robert M., Flicek, Paul, Boyle, Patrick J., Cao, Hua, Carter, Nigel P., Clelland, Gayle K., Davis, Sean, Day, Nathan, Dhami, Pawandeep, Dillon, Shane C., Dorschner, Michael O., Fiegler, Heike, Giresi, Paul G., Goldy, Jeff, Hawrylycz, Michael, Haydock, Andrew, Humbert, Richard, James, Keith D., Johnson, Brett E., Johnson, Ericka M., Frum, Tristan T., Rosenzweig, Elizabeth R., Karnani, Neerja, Lee, Kirsten, Lefebvre, Gregory C., Navas, Patrick A., Neri, Fidencio, Parker, Stephen C. J., Sabo, Peter J., Sandstrom, Richard, Shafer, Anthony, Vetrie, David, Weaver, Molly, Wilcox, Sarah, Yu1, Man, Collins, Francis S., Dekker, Job, Lieb, Jason D., Tullius, Thomas D., Crawford, Gregory E., Sunyaev, Shamil, Noble, William S., Dunham, Ian, Denoeud, France, Reymond, Alexandre, Kapranov, Philipp, Rozowsky, Joel, Zheng, Deyou, Castelo, Robert, Frankish, Adam, Harrow, Jennifer, Ghosh, Srinka, Sandelin, Albin, Hofacker, Ivo L., Baertsch, Robert, Keefe, Damian, Dike, Sujit, Cheng, Jill, Hirsch, Heather A., Sekinger, Edward A., Lagarde, Julien, Abril, Josep F., Shahab, Atif, Flamm, Christoph, Fried, Claudia, Hackermuller, Jorg, Hertel, Jana, Lindemeyer, Manja, Missal, Kristin, Tanzer, Andrea, Washietl, Stefan, Korbel, Jan, Emanuelsson, Olof, Pedersen, Jakob S., Holroyd, Nancy, Taylor, Ruth, Swarbreck, David, Matthews, Nicholas, Dickson, Mark C., Thomas, Daryl J., Weirauch, Matthew T., Gilbert, James, Drenkow, Jorg, Bell, Ian, Zhao, XiaoDong, Srinivasan, K.G., Sung, Wing-Kin, Ooi, Hong Sain, Chiu, Kuo Ping, Foissac, Sylvain, Alioto, Tyler, Brent, Michael, Pachter, Lior, Tress, Michael L., Valencia, Alfonso, Choo, Siew Woh, Choo, Chiou Yu, Ucla, Catherine, Manzano, Caroline, Wyss, Carine, Cheung, Evelyn, Clark, Taane G., Brown, James B., Ganesh, Madhavan, Patel, Sandeep, Tammana, Hari, Chrast, Jacqueline, Henrichsen, Charlotte N., Kai, Chikatoshi, Kawai, Jun, Nagalakshmi, Ugrappa, Wu, Jiaqian, Lian, Zheng, Lian, Jin, Newburger, Peter, Zhang, Xueqing, Bickel, Peter, Mattick, John S., Carninci, Piero, Hayashizaki, Yoshihide, Weissman, Sherman, Hubbard, Tim, Myers, Richard M., Rogers, Jane, Stadler, Peter F., Lowe, Todd M., Wei, Chia-Lin, Ruan, Yijun, Struhl, Kevin, Gerstein, Mark, Antonarakis, Stylianos E., Fu, Yutao, Green, Eric D., Karaoz, Ulaş, Siepel, Adam, Taylor, James, Liefer, Laura A., Wetterstrand, Kris A., Good, Peter J., Feingold, Elise A., Guyer, Mark S., Cooper, Gregory M., Asimenos, George, Dewey, Colin N., Hou, Minmei, Nikolaev, Sergey, Montoya-Burgos, Juan I., Loytynoja, Ari, Whelan, Simon, Pardi, Fabio, Massingham, Tim, Huang, Haiyan, Zhang, Nancy R., Holmes, Ian, Mullikin, James C., Ureta-Vidal, Abel, Paten, Benedict, Seringhaus, Michael, Church, Deanna, Rosenbloom, Kate, Kent, W. James, Stone, Eric A., Batzoglou, Serafim, Goldman, Nick, Hardison, Ross C., Haussler, David, Miller, Webb, Sidow, Arend, Trinklein, Nathan D., Zhang, Zhengdong D., Barrera, Leah, Stuart, Rhona, King, David C., Ameur, Adam, Enroth, Stefan, Bieda, Mark C., Kim, Jonghwan, Bhinge, Akshay A., Jiang, Nan, Liu, Jun, Yao, Fei, Vega, Vinsensius B., Lee, Charlie W.H., Ng, Patrick, Yang, Annie, Moqtaderi, Zarmik, Zhu, Zhou, Xu, Xiaoqin, Squazzo, Sharon, Oberley, Matthew J., Inman, David, Singer, Michael A., Richmond, Todd A., Munn, Kyle J., Rada-Iglesias, Alvaro, Wallerman, Ola, Komorowski, Jan, Fowler, Joanna C., Couttet, Phillippe, Bruce, Alexander W., Dovey, Oliver M., Ellis, Peter D., Langford, Cordelia F., Nix, David A., Euskirchen, Ghia, Hartman, Stephen, Urban, Alexander E., Kraus, Peter, Van Calcar, Sara, Heintzman, Nate, Hoon Kim, Tae, Wang, Kun, Qu, Chunxu, Hon, Gary, Luna, Rosa, Glass, Christopher K., Rosenfeld, M. Geoff, Aldred, Shelley Force, Cooper, Sara J., Halees, Anason, Lin, Jane M., Shulha, Hennady P., Zhang, Xiaoling, Xu, Mousheng, Haidar, Jaafar N. S., Yu, Yong, Birney*, Ewan, Iyer, Vishwanath R., Green, Roland D., Wadelius, Claes, Farnham, Peggy J., Ren, Bing, Harte, Rachel A., Hinrichs, Angie S., Trumbower, Heather, Clawson, Hiram, Hillman-Jackson, Jennifer, Zweig, Ann S., Smith, Kayla, Thakkapallayil, Archana, Barber, Galt, Kuhn, Robert M., Karolchik, Donna, Armengol, Lluis, Bird, Christine P., de Bakker, Paul I. W., Kern, Andrew D., Lopez-Bigas, Nuria, Martin, Joel D., Stranger, Barbara E., Woodroffe, Abigail, Davydov, Eugene, Dimas, Antigone, Eyras, Eduardo, Hallgrimsdottir, Ingileif B., Huppert, Julian, Zody, Michael C., Abecasis, Goncalo R., Estivill, Xavier, Bouffard, Gerard G., Guan, Xiaobin, Hansen, Nancy F., Idol, Jacquelyn R., Maduro, Valerie V.B., Maskeri, Baishali, McDowell, Jennifer C., Park, Morgan, Thomas, Pamela J., Young, Alice C., Blakesley, Robert W., Baylor College of Medicine, Human Genome Sequencing Center, Muzny, Donna M., Sodergren, Erica, Wheeler, David A., Worley, Kim C., Jiang, Huaiyang, Weinstock, George M., Gibbs, Richard A., Graves, Tina, Fulton, Robert, Mardis, Elaine R., Wilson, Richard K., Clamp, Michele, Cuff, James, Gnerre, Sante, Jaffe, David B., Chang, Jean L., Lindblad-Toh, Kerstin, Lander, Eric S., Koriabine, Maxim, Nefedov, Mikhail, Osoegawa, Kazutoyo, Yoshinaga, Yuko, Zhu, Baoli, and de Jong, Pieter J.
Subjects: Environmental issues, Science and technology, Zoology and wildlife conservation
Abstract: Author(s): The ENCODE Project Consortium; Analysis Coordination; Ewan Birney (corresponding author) [1]; John A. Stamatoyannopoulos (corresponding author) [2]; Anindya Dutta (corresponding author) [3]; Roderic GuigÃ³ (corresponding author) [4, 5]; Thomas [...]
Published: 2007
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43. Grand challenges in humanitarian aid

Author: Trillium Chang, Abdallah S. Daar, Angela Salomon, and Peter Singer
Subjects: Government, Multidisciplinary, Humanitarian aid, business.industry, Natural Disasters, 030231 tropical medicine, 05 social sciences, Social Sciences, Armed Conflicts, Public administration, Altruism, Conflict, Psychological, 03 medical and health sciences, Politics, 0302 clinical medicine, Political science, 0502 economics and business, Humans, business, Goals, 050203 business & management, Grand Challenges
Abstract: Fund and study these priorities for natural and social sciences to meet a gaping need, urge Abdallah S. Daar, Trillium Chang, Angela Salomon and Peter A. Singer. Fund and study these priorities for natural and social sciences to meet a gaping need.
Published: 2018

44. Induction and transcriptional regulation of the co-inhibitory gene module in T cells

Author: James Nevin, Jackson Nyman, Yasaman Etminan, Meromit Singer, Nemanja D. Marjanovic, Ana C. Anderson, Huiyuan Zhang, Aviv Regev, Takaaki Kondo, Travis Law, Patrick R. Burkett, Nandini Acharya, Jason D. Buenrostro, Christopher D. Buckley, Sema Kurtulus, Norio Chihara, Orit Rozenblatt-Rosen, Vijay K. Kuchroo, Asaf Madi, Monika S. Kowalczyk, and Chao Wang
Subjects: 0301 basic medicine, CD4-Positive T-Lymphocytes, Male, Interleukin-27, Transcription, Genetic, medicine.medical_treatment, T cell, Receptors, Cell Surface, Biology, CD8-Positive T-Lymphocytes, Article, Immune tolerance, 03 medical and health sciences, Mice, 0302 clinical medicine, Lymphocytes, Tumor-Infiltrating, TIGIT, PRDM1, medicine, Immune Tolerance, Animals, Gene Regulatory Networks, Receptor, Melanoma, Mice, Knockout, Endothelial protein C receptor, Multidisciplinary, Reproducibility of Results, Cell biology, Mice, Inbred C57BL, 030104 developmental biology, Cytokine, medicine.anatomical_structure, 030220 oncology & carcinogenesis, Proto-Oncogene Proteins c-maf, Female, Positive Regulatory Domain I-Binding Factor 1, CD8
Abstract: The expression of co-inhibitory receptors, such as CTLA-4 and PD-1, on effector T cells is a key mechanism for ensuring immune homeostasis. Dysregulated expression of co-inhibitory receptors on CD4+ T cells promotes autoimmunity, whereas sustained overexpression on CD8+ T cells promotes T cell dysfunction or exhaustion, leading to impaired ability to clear chronic viral infections and diseases such as cancer1,2. Here, using RNA and protein expression profiling at single-cell resolution in mouse cells, we identify a module of co-inhibitory receptors that includes not only several known co-inhibitory receptors (PD-1, TIM-3, LAG-3 and TIGIT) but also many new surface receptors. We functionally validated two new co-inhibitory receptors, activated protein C receptor (PROCR) and podoplanin (PDPN). The module of co-inhibitory receptors is co-expressed in both CD4+ and CD8+ T cells and is part of a larger co-inhibitory gene program that is shared by non-responsive T cells in several physiological contexts and is driven by the immunoregulatory cytokine IL-27. Computational analysis identified the transcription factors PRDM1 and c-MAF as cooperative regulators of the co-inhibitory module, and this was validated experimentally. This molecular circuit underlies the co-expression of co-inhibitory receptors in T cells and identifies regulators of T cell function with the potential to control autoimmunity and tumour immunity.
Published: 2018

45. Reorientation of Sputnik Planitia implies a subsurface ocean on Pluto

Author: Nimmo, F., Hamilton, D. P., McKinnon, W. B., Schenk, P. M., Binzel, R. P., Bierson, C. J., Beyer, R. A., Moore, J. M., Stern, S. A., Weaver, H. A., Olkin, C. B., Young, L. A., Smith, K. E., Spencer, J. R., Beyer, R., Buie, M., Buratti, B., Cheng, A., Cruikshank, D., Ore, C. Dalle, Earle, A., Gladstone, R., Grundy, W., Howard, A. D., Lauer, T., Linscott, I., Parker, J., Porter, S., Reitsema, H., Reuter, D., Roberts, J. H., Robbins, S., Showalter, M., Singer, K., Strobel, D., Summers, M., Tyler, L., White, O. L., Umurhan, O. M., Banks, M., Barnouin, O., Bray, V., Carcich, B., Chaikin, A., Chavez, C., Conrad, C., Howett, C., Hofgartner, J., Kammer, J., Lisse, C., Marcotte, A., Parker, A., Retherford, K., Saina, M., Runyon, K., Schindhelm, E., Stansberry, J., Steffl, A., Stryk, T., Throop, H., Tsang, C., Verbiscer, A., Winters, H., and Zangari, A.
Subjects: Pluto (Dwarf planet) -- Observations, Environmental issues, Science and technology, Zoology and wildlife conservation
Abstract: Author(s): F. Nimmo (corresponding author) [1]; D. P. Hamilton [2]; W. B. McKinnon [3]; P. M. Schenk [4]; R. P. Binzel [5]; C. J. Bierson [1]; R. A. Beyer [6]; [...]
Published: 2016
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46. Spatial regulation of [beta]-actin translation by Src-dependent phosphorylation of ZBP1

Author: Huttelmaier, Stefan, Zenklusen, Daniel, Lederer, Marcell, Dictenberg, Jason, Lorenz, Mike, Meng, XiuHua, Bassell, Gary J., Condeelis, John, and Singer, Robert H.
Subjects: Environmental issues, Science and technology, Zoology and wildlife conservation
Abstract: Author(s): Stefan HÃ¼ttelmaier (corresponding author) [1, 2]; Daniel Zenklusen [1]; Marcell Lederer [2]; Jason Dictenberg [3]; Mike Lorenz [1]; XiuHua Meng [1]; Gary J. Bassell [3]; John Condeelis [1]; Robert [...]
Published: 2005
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47. Structural and temporal requirements for geomagnetic field reversal deduced from lava flows

Author: Singer, Brad S., Hoffman, Kenneth A., Coe, Robert S., Brown, Laurie L., Jicha, Brian R., Pringle, Malcolm S., and Chauvin, Annick
Subjects: Environmental issues, Science and technology, Zoology and wildlife conservation
Abstract: Author(s): Brad S. Singer (corresponding author) [1]; Kenneth A. Hoffman [2]; Robert S. Coe [3]; Laurie L. Brown [4]; Brian R. Jicha [1]; Malcolm S. Pringle [5]; Annick Chauvin [6] [...]
Published: 2005
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48. Recurrent de novo point mutations in lamin A cause Hutchinson-Gilford progeria syndrome

Author: Eriksson, Maria, Brown, W. Ted, Gordon, Leslie B., Glynn, Michael W., Singer, Joel, Scott, Laura, Erdos, Michael R., Robbins, Christiane M., Moses, Tracy Y., Berglund, Peter, Dutra, Amalia, Pak, Evgenia, Durkin, Sandra, Csoka, Antonei B., Boehnke, Michael, Glover, Thomas W., and Collins, Francis S.
Subjects: Environmental issues, Science and technology, Zoology and wildlife conservation
Abstract: Author(s): Maria Eriksson [1]; W. Ted Brown [2]; Leslie B. Gordon [3]; Michael W. Glynn [4]; Joel Singer [5]; Laura Scott [5]; Michael R. Erdos [1]; Christiane M. Robbins [1]; [...]
Published: 2003
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49. Initial sequencing and comparative analysis of the mouse genome

Author: Chinwalla, Asif T., Cook, Lisa L., Delehaunty, Kimberly D., Fewell, Ginger A., Fulton, Lucinda A., Fulton, Robert S., Graves, Tina A., Hillier, LaDeana W., Mardis, Elaine R., McPherson, John D., Miner, Tracie L., Nash, William E., Nelson, Joanne O., Nhan, Michael N., Pepin, Kymberlie H., Pohl, Craig S., Ponce, Tracy C., Schultz, Brian, Thompson, Johanna, Trevaskis, Evanne, Waterston, Robert H., Wendl, Michael C., Wilson, Richard K., Yang, Shiaw-Pyng, An, Peter, Berry, Eric, Birren, Bruce, Bloom, Toby, Brown, Daniel G., Butler, Jonathan, Daly, Mark, David, Robert, Deri, Justin, Dodge, Sheila, Foley, Karen, Gage, Diane, Gnerre, Sante, Holzer, Timothy, Jaffe, David B., Kamal, Michael, Karlsson, Elinor K., Kells, Cristyn, Kirby, Andrew, Kulbokas, III, Edward J., Lander, Eric S., Landers, Tom, Leger, J. P., Levine, Rosie, Lindblad-Toh, Kerstin, Mauceli, Evan, Mayer, John H., McCarthy, Megan, Meldrim, Jim, Mesirov, Jill P., Nicol, Robert, Nusbaum, Chad, Seaman, Steven, Sharpe, Ted, Sheridan, Andrew, Singer, Jonathan B., Santos, Ralph, Spencer, Brian, Stange-Thomann, Nicole, Vinson, Jade P., Wade, Claire M., Wierzbowski, Jamey, Wyman, Dudley, Zody, Michael C., Birney, Ewan, Goldman, Nick, Kasprzyk, Arkadiusz, Mongin, Emmanuel, Rust, Alistair G., Slater, Guy, Stabenau, Arne, Ureta-Vidal, Abel, Whelan, Simon, Ainscough, Rachel, Attwood, John, Bailey, Jonathon, Barlow, Karen, Beck, Stephan, Burton, John, Clamp, Michele, Clee, Christopher, Coulson, Alan, Cuff, James, Curwen, Val, Cutts, Tim, Davies, Joy, Eyras, Eduardo, Grafham, Darren, Gregory, Simon, Hubbard, Tim, Hunt, Adrienne, Jones, Matthew, Joy, Ann, Leonard, Steven, Lloyd, Christine, Matthews, Lucy, McLaren, Stuart, McLay, Kirsten, Meredith, Beverley, Mullikin, James C., Ning, Zemin, Oliver, Karen, Overton-Larty, Emma, Plumb, Robert, Potter, Simon, Quail, Michael, Rogers, Jane, Scott, Carol, Searle, Steve, Shownkeen, Ratna, Sims, Sarah, Wall, Melanie, West, Anthony P., Willey, David, Williams, Sophie, Abril, Josep F., Guigo, Roderic, Parra, Genis, Agarwal, Pankaj, Agarwala, Richa, Church, Deanna M., Hlavina, Wratko, Maglott, Donna R., Sapojnikov, Victor, Alexandersson, Marina, Pachter, Lior, Antonarakis, Stylianos E., Dermitzakis, Emmanouil T., Reymond, Alexandre, Ucla, Catherine, Baertsch, Robert, Diekhans, Mark, Furey, Terrence S., Hinrichs, Angela, Hsu, Fan, Karolchik, Donna, Kent, W. James, Roskin, Krishna M., Schwartz, Matthias S., Sugnet, Charles, Weber, Ryan J., Bork, Peer, Letunic, Ivica, Suyama, Mikita, Torrents, David, Zdobnov, Evgeny M., Botcherby, Marc, Brown, Stephen D., Campbell, Robert D., Jackson, Ian, Bray, Nicolas, Couronne, Olivier, Dubchak, Inna, Poliakov, Alex, Rubin, Edward M., Brent, Michael R., Flicek, Paul, Keibler, Evan, Korf, Ian, Batalov, S., Bult, Carol, Frankel, Wayne N., Carninci, Piero, Hayashizaki, Yoshihide, Kawai, Jun, Okazaki, Yasushi, Cawley, Simon, Kulp, David, Wheeler, Raymond, Chiaromonte, Francesca, Collins, Francis S., Felsenfeld, Adam, Guyer, Mark, Peterson, Jane, Wetterstrand, Kris, Copley, Richard R., Mott, Richard, Dewey, Colin, Dickens, Nicholas J., Emes, Richard D., Goodstadt, Leo, Ponting, Chris P., Winter, Eitan, Dunn, Diane M., von Niederhausern, Andrew C., Weiss, Robert B., Eddy, Sean R., Johnson, L. Steven, Jones, Thomas A., Elnitski, Laura, Kolbe, Diana L., Eswara, Pallavi, Miller, Webb, O'Connor, Michael J., Schwartz, Scott, Muzny, Donna M., Glusman, Gustavo, Smit, Arian, Green, Eric D., Hardison, Ross C., Yang, Shan, Haussler, David, Hua, Axin, Roe, Bruce A., Kucherlapati, Raju S., Montgomery, Kate T., Li, Jia, Li, Ming, Lucas, Susan, Ma, Bin, McCombie, W. Richard, Morgan, Michael, Pevzner, Pavel, Tesler, Glenn, Schultz, Jorg, Smith, Douglas R., Tromp, John, and Worley, Kim C.
Subjects: Environmental issues, Science and technology, Zoology and wildlife conservation
Abstract: Author(s): Mouse Genome Sequencing Consortium ; Genome Sequencing Center: ; Asif T. Chinwalla [1, 47]; Lisa L. Cook [1]; Kimberly D. Delehaunty [1]; Ginger A. Fewell [1]; Lucinda A. Fulton [...]
Published: 2002
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50. Self-organization of supramolecular helical dendrimers into complex electronic materials

Author: Percec, V., Glodde, M., Bera, T. K., Miura, Y., Shiyanovskaya, I., Singer, K. D., Balagurusamy, V. S. K., Heiney, P. A., Schnell, I., Rapp, A., Spiess, H.-W., Hudson, S. D., and Duan, H.
Subjects: Environmental issues, Science and technology, Zoology and wildlife conservation
Abstract: Author(s): V. Percec (corresponding author) [1]; M. Glodde [1]; T. K. Bera [1]; Y. Miura [1]; I. Shiyanovskaya [2]; K. D. Singer [2]; V. S. K. Balagurusamy [1, 3]; P. [...]
Published: 2002
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