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2,213 results on '"Robert J"'

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

Author

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

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

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

Published
2024

2. Psychedelics promote neuroplasticity through the activation of intracellular 5-HT2A receptors

Author

Vargas, Maxemiliano V, Dunlap, Lee E, Dong, Chunyang, Carter, Samuel J, Tombari, Robert J, Jami, Shekib A, Cameron, Lindsay P, Patel, Seona D, Hennessey, Joseph J, Saeger, Hannah N, McCorvy, John D, Gray, John A, Tian, Lin, and Olson, David E

Subjects
Biological Psychology, Pharmacology and Pharmaceutical Sciences, Biomedical and Clinical Sciences, Psychology, Neurosciences, Hallucinogens, Neuronal Plasticity, Serotonin, Signal Transduction, Serotonin 5-HT2 Receptor Agonists, Receptor, Serotonin, 5-HT2A, Cerebral Cortex, Animals, Mice, Mice, Knockout, Antidepressive Agents, General Science & Technology
Abstract

Decreased dendritic spine density in the cortex is a hallmark of several neuropsychiatric diseases, and the ability to promote cortical neuron growth has been hypothesized to underlie the rapid and sustained therapeutic effects of psychedelics. Activation of 5-hydroxytryptamine (serotonin) 2A receptors (5-HT2ARs) is essential for psychedelic-induced cortical plasticity, but it is currently unclear why some 5-HT2AR agonists promote neuroplasticity, whereas others do not. We used molecular and genetic tools to demonstrate that intracellular 5-HT2ARs mediate the plasticity-promoting properties of psychedelics; these results explain why serotonin does not engage similar plasticity mechanisms. This work emphasizes the role of location bias in 5-HT2AR signaling, identifies intracellular 5-HT2ARs as a therapeutic target, and raises the intriguing possibility that serotonin might not be the endogenous ligand for intracellular 5-HT2ARs in the cortex.

Published
2023

3. Acrobatic squirrels learn to leap and land on tree branches without falling

Author

Hunt, Nathaniel H, Jinn, Judy, Jacobs, Lucia F, and Full, Robert J

Subjects
Basic Behavioral and Social Science, Behavioral and Social Science, Life on Land, Accidental Falls, Animals, Biomechanical Phenomena, Compliance, Locomotion, Sciuridae, Trees, General Science & Technology
Abstract

Arboreal animals often leap through complex canopies to travel and avoid predators. Their success at making split-second, potentially life-threatening decisions of biomechanical capability depends on their skillful use of acrobatic maneuvers and learning from past efforts. Here, we found that free-ranging fox squirrels (Sciurus niger) leaping across unfamiliar, simulated branches decided where to launch by balancing a trade-off between gap distance and branch-bending compliance. Squirrels quickly learned to modify impulse generation upon repeated leaps from unfamiliar, compliant beams. A repertoire of agile landing maneuvers enabled targeted leaping without falling. Unanticipated adaptive landing and leaping "parkour" behavior revealed an innovative solution for particularly challenging leaps. Squirrels deciding and learning how to launch and land demonstrates the synergistic roles of biomechanics and cognition in robust gap-crossing strategies.

Published
2021

4. De novo assembly, annotation, and comparative analysis of 26 diverse maize genomes

Author

Hufford, Matthew B, Seetharam, Arun S, Woodhouse, Margaret R, Chougule, Kapeel M, Ou, Shujun, Liu, Jianing, Ricci, William A, Guo, Tingting, Olson, Andrew, Qiu, Yinjie, Della Coletta, Rafael, Tittes, Silas, Hudson, Asher I, Marand, Alexandre P, Wei, Sharon, Lu, Zhenyuan, Wang, Bo, Tello-Ruiz, Marcela K, Piri, Rebecca D, Wang, Na, Kim, Dong Won, Zeng, Yibing, O'Connor, Christine H, Li, Xianran, Gilbert, Amanda M, Baggs, Erin, Krasileva, Ksenia V, Portwood, John L, Cannon, Ethalinda KS, Andorf, Carson M, Manchanda, Nancy, Snodgrass, Samantha J, Hufnagel, David E, Jiang, Qiuhan, Pedersen, Sarah, Syring, Michael L, Kudrna, David A, Llaca, Victor, Fengler, Kevin, Schmitz, Robert J, Ross-Ibarra, Jeffrey, Yu, Jianming, Gent, Jonathan I, Hirsch, Candice N, Ware, Doreen, and Dawe, R Kelly

Subjects
Genetics, Human Genome, Centromere, Chromosome Mapping, Chromosomes, Plant, DNA Methylation, Disease Resistance, Genes, Plant, Genetic Variation, Genome, Plant, Genotype, High-Throughput Nucleotide Sequencing, Molecular Sequence Annotation, Multifactorial Inheritance, Phenotype, Plant Diseases, Polymorphism, Single Nucleotide, Regulatory Sequences, Nucleic Acid, Sequence Analysis, DNA, Tetraploidy, Transcriptome, Whole Genome Sequencing, Zea mays, General Science & Technology
Abstract

We report de novo genome assemblies, transcriptomes, annotations, and methylomes for the 26 inbreds that serve as the founders for the maize nested association mapping population. The number of pan-genes in these diverse genomes exceeds 103,000, with approximately a third found across all genotypes. The results demonstrate that the ancient tetraploid character of maize continues to degrade by fractionation to the present day. Excellent contiguity over repeat arrays and complete annotation of centromeres revealed additional variation in major cytological landmarks. We show that combining structural variation with single-nucleotide polymorphisms can improve the power of quantitative mapping studies. We also document variation at the level of DNA methylation and demonstrate that unmethylated regions are enriched for cis-regulatory elements that contribute to phenotypic variation.

Published
2021

5. Lysosomal cholesterol activates mTORC1 via an SLC38A9–Niemann-Pick C1 signaling complex

Author

Castellano, Brian M, Thelen, Ashley M, Moldavski, Ofer, Feltes, McKenna, van der Welle, Reini EN, Mydock-McGrane, Laurel, Jiang, Xuntian, van Eijkeren, Robert J, Davis, Oliver B, Louie, Sharon M, Perera, Rushika M, Covey, Douglas F, Nomura, Daniel K, Ory, Daniel S, and Zoncu, Roberto

Subjects
Underpinning research, 1.1 Normal biological development and functioning, Amino Acid Motifs, Amino Acid Transport Systems, Animals, Biological Transport, CHO Cells, Carrier Proteins, Cholesterol, Cholesterol, HDL, Cricetulus, Enzyme Activation, Fibroblasts, HEK293 Cells, Humans, Lysosomes, Mechanistic Target of Rapamycin Complex 1, Mice, Multiprotein Complexes, Mutation, Nuclear Proteins, Signal Transduction, TOR Serine-Threonine Kinases, General Science & Technology
Abstract

The mechanistic target of rapamycin complex 1 (mTORC1) protein kinase is a master growth regulator that becomes activated at the lysosome in response to nutrient cues. Here, we identify cholesterol, an essential building block for cellular growth, as a nutrient input that drives mTORC1 recruitment and activation at the lysosomal surface. The lysosomal transmembrane protein, SLC38A9, is required for mTORC1 activation by cholesterol through conserved cholesterol-responsive motifs. Moreover, SLC38A9 enables mTORC1 activation by cholesterol independently from its arginine-sensing function. Conversely, the Niemann-Pick C1 (NPC1) protein, which regulates cholesterol export from the lysosome, binds to SLC38A9 and inhibits mTORC1 signaling through its sterol transport function. Thus, lysosomal cholesterol drives mTORC1 activation and growth signaling through the SLC38A9-NPC1 complex.

Published
2017

6. Response

Author

Biggs, Duan, Smith, Robert J., Adams, Vanessa M., Brink, Henry, Cook, Carly N., Cooney, Rosie, Holden, Matthew H., Maron, Martine, Phelps, Jacob, Possingham, Hugh P., Redford, Kent H., Scholes, Robert J., Sutherland, William J., Underwood, Fiona M., and Milner-Gulland, E. J.

Published
2018

7. Interplay of competition and facilitation in grazing succession by migrant Serengeti herbivores

Author

Anderson, T. Michael, primary, Hepler, Staci A., additional, Holdo, Ricardo M., additional, Donaldson, Jason E., additional, Erhardt, Robert J., additional, Hopcraft, J. Grant C., additional, Hutchinson, Matthew C., additional, Huebner, Sarah E., additional, Morrison, Thomas A., additional, Muday, Jeffry, additional, Munuo, Issack N., additional, Palmer, Meredith S., additional, Pansu, Johan, additional, Pringle, Robert M., additional, Sketch, Robert, additional, and Packer, Craig, additional

Published
2024
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8. Kinase-impaired BTK mutations are susceptible to clinical-stage BTK and IKZF1/3 degrader NX-2127

Author

Montoya, Skye, primary, Bourcier, Jessie, additional, Noviski, Mark, additional, Lu, Hao, additional, Thompson, Meghan C., additional, Chirino, Alexandra, additional, Jahn, Jacob, additional, Sondhi, Anya K., additional, Gajewski, Stefan, additional, Tan, Ying Siow (May), additional, Yung, Stephanie, additional, Urban, Aleksandra, additional, Wang, Eric, additional, Han, Cuijuan, additional, Mi, Xiaoli, additional, Kim, Won Jun, additional, Sievers, Quinlan, additional, Auger, Paul, additional, Bousquet, Hugo, additional, Brathaban, Nivetha, additional, Bravo, Brandon, additional, Gessner, Melissa, additional, Guiducci, Cristiana, additional, Iuliano, James N., additional, Kane, Tim, additional, Mukerji, Ratul, additional, Reddy, Panga Jaipal, additional, Powers, Janine, additional, Sanchez Garcia de los Rios, Mateo, additional, Ye, Jordan, additional, Barrientos Risso, Carla, additional, Tsai, Daniel, additional, Pardo, Gabriel, additional, Notti, Ryan Q., additional, Pardo, Alejandro, additional, Affer, Maurizio, additional, Nawaratne, Vindhya, additional, Totiger, Tulasigeri M., additional, Pena-Velasquez, Camila, additional, Rhodes, Joanna M., additional, Zelenetz, Andrew D., additional, Alencar, Alvaro, additional, Roeker, Lindsey E., additional, Mehta, Sanjoy, additional, Garippa, Ralph, additional, Linley, Adam, additional, Soni, Rajesh Kumar, additional, Skånland, Sigrid S., additional, Brown, Robert J., additional, Mato, Anthony R., additional, Hansen, Gwenn M., additional, Abdel-Wahab, Omar, additional, and Taylor, Justin, additional

Published
2024
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9. Integration of omic networks in a developmental atlas of maize

Author

Walley, Justin W, Sartor, Ryan C, Shen, Zhouxin, Schmitz, Robert J, Wu, Kevin J, Urich, Mark A, Nery, Joseph R, Smith, Laurie G, Schnable, James C, Ecker, Joseph R, and Briggs, Steven P

Subjects
Biological Sciences, Bioinformatics and Computational Biology, Genetics, Gene Regulatory Networks, Phosphoproteins, Phosphorylation, Plant Proteins, Proteome, Proteomics, RNA, Messenger, Transcriptome, Zea mays, General Science & Technology
Abstract

Coexpression networks and gene regulatory networks (GRNs) are emerging as important tools for predicting functional roles of individual genes at a system-wide scale. To enable network reconstructions, we built a large-scale gene expression atlas composed of 62,547 messenger RNAs (mRNAs), 17,862 nonmodified proteins, and 6227 phosphoproteins harboring 31,595 phosphorylation sites quantified across maize development. Networks in which nodes are genes connected on the basis of highly correlated expression patterns of mRNAs were very different from networks that were based on coexpression of proteins. Roughly 85% of highly interconnected hubs were not conserved in expression between RNA and protein networks. However, networks from either data type were enriched in similar ontological categories and were effective in predicting known regulatory relationships. Integration of mRNA, protein, and phosphoprotein data sets greatly improved the predictive power of GRNs.

Published
2016

10. Extinction filters mediate the global effects of habitat fragmentation on animals

Author

Betts, Matthew G., Wolf, Christopher, Pfeifer, Marion, Banks-Leite, Cristina, Arroyo-Rodríguez, Víctor, Ribeiro, Danilo Bandini, Barlow, Jos, Eigenbrod, Felix, Faria, Deborah, Fletcher, Robert J., Hadley, Adam S., Hawes, Joseph E., Holt, Robert D., Klingbeil, Brian, Kormann, Urs, Lens, Luc, Levi, Taal, Medina-Rangel, Guido F., Melles, Stephanie L., Mezger, Dirk, Morante-Filho, José Carlos, Orme, C. David L., Peres, Carlos A., Phalan, Benjamin T., Pidgeon, Anna, Possingham, Hugh, Ripple, William J., Slade, Eleanor M., Somarriba, Eduardo, A. Tobias, Joseph, Tylianakis, Jason M., Urbina-Cardona, J. Nicolás, Valente, Jonathon J., I. Watling, James, Wells, Konstans, Wearn, Oliver R., Wood, Eric, Young, Richard, and Ewers, Robert M.

Published
2019

11. Targeted selection of HIV-specific antibody mutations by engineering B cell maturation

Author

Saunders, Kevin O., Wiehe, Kevin, Tian, Ming, Acharya, Priyamvada, Bradley, Todd, Alam, S. Munir, Go, Eden P., Scearce, Richard, Sutherland, Laura, Henderson, Rory, Hsu, Allen L., Borgnia, Mario J., Chen, Haiyan, Lu, Xiaozhi, R. Wu, Nelson, Watts, Brian, Jiang, Chuancang, Easterhoff, David, Cheng, Hwei-Ling, McGovern, Kelly, Waddicor, Peyton, Chapdelaine-Williams, Aimee, Eaton, Amanda, Zhang, Jinsong, Rountree, Wes, Verkoczy, Laurent, Tomai, Mark, Lewis, Mark G., Desaire, Heather R., Edwards, Robert J., Cain, Derek W., Bonsignori, Mattia, Montefiori, David, Alt, Frederick W., and Haynes, Barton F.

Published
2019

16. The Influence of CCL3L1 Gene-Containing Segmental Duplications on HIV-1/AIDS Susceptibility

Author

Gonzalez, Enrique, Kulkarni, Hemant, Bolivar, Hector, Mangano, Andrea, Sanchez, Racquel, Catano, Gabriel, Nibbs, Robert J., Freedman, Barry I., Quinones, Marlon P., Bamshad, Michael J., Murthy, Krishna K., Rovin, Brad H., Bradley, William, Clark, Robert A., Anderson, Stephanie A., O'Connell, Robert J., Agan, Brian K., Ahuja, Seema S., Bologna, Rosa, Sen, Luisa, Dolan, Matthew J., and Ahuja, Sunil K.

Published
2005

17. Ultraviolet surprise: Efficient soft x-ray high-harmonic generation in multiply ionized plasmas

Author

Popmintchev, Dimitar, Hernández-García, Carlos, Dollar, Franklin, Mancuso, Christopher, Pérez-Hernández, Jose A, Chen, Ming-Chang, Hankla, Amelia, Gao, Xiaohui, Shim, Bonggu, Gaeta, Alexander L, Tarazkar, Maryam, Romanov, Dmitri A, Levis, Robert J, Gaffney, Jim A, Foord, Mark, Libby, Stephen B, Jaron-Becker, Agnieszka, Becker, Andreas, Plaja, Luis, Murnane, Margaret M, Kapteyn, Henry C, and Popmintchev, Tenio

Subjects
Quantum Physics, Atomic, Molecular and Optical Physics, Physical Sciences, General Science & Technology
Abstract

High-harmonic generation is a universal response of matter to strong femtosecond laser fields, coherently upconverting light to much shorter wavelengths. Optimizing the conversion of laser light into soft x-rays typically demands a trade-off between two competing factors. Because of reduced quantum diffusion of the radiating electron wave function, the emission from each species is highest when a short-wavelength ultraviolet driving laser is used. However, phase matching--the constructive addition of x-ray waves from a large number of atoms--favors longer-wavelength mid-infrared lasers. We identified a regime of high-harmonic generation driven by 40-cycle ultraviolet lasers in waveguides that can generate bright beams in the soft x-ray region of the spectrum, up to photon energies of 280 electron volts. Surprisingly, the high ultraviolet refractive indices of both neutral atoms and ions enabled effective phase matching, even in a multiply ionized plasma. We observed harmonics with very narrow linewidths, while calculations show that the x-rays emerge as nearly time-bandwidth-limited pulse trains of ~100 attoseconds.

Published
2015

18. Breaking the deadlock on ivory

Author

Biggs, Duan, Holden, Matthew H., Braczkowski, Alex, Cook, Carly N., Milner-Gulland, E. J., Phelps, Jacob, Scholes, Robert J., Smith, Robert J., Underwood, Fiona M., Adams, Vanessa M., Allan, James, Brink, Henry, Cooney, Rosie, Gao, Yufang, Hutton, Jon, Macdonald-Madden, Eve, Maron, Martine, Redford, Kent H., Sutherland, William J., and Possingham, Hugh P.

Published
2017

22. Predicting global killer whale population collapse from PCB pollution

Author

Desforges, Jean-Pierre, Hall, Ailsa, McConnell, Bernie, Rosing-Asvid, Aqqalu, Barber, Jonathan L., Brownlow, Andrew, De Guise, Sylvain, Eulaers, Igor, Jepson, Paul D., Letcher, Robert J., Levin, Milton, Ross, Peter S., Samarra, Filipa, Víkingson, Gísli, Sonne, Christian, and Dietz, Rune

Published
2018

23. Pollution threatens toothed whales

Author

Sills, Jennifer, Sonne, Christian, Jepson, Paul D., Desforges, Jean-Pierre, Alstrup, Aage K. O., Olsen, Morten T., Eulaers, Igor, Hansen, Martin, Letcher, Robert J., McKinney, Melissa A., and Dietz, Rune

Published
2018

28. Genomic correlates of response to immune checkpoint therapies in clear cell renal cell carcinoma

Author

Miao, Diana, Margolis, Claire A., Gao, Wenhua, Voss, Martin H., Li, Wei, Martini, Dylan J., Norton, Craig, Bossé, Dominick, Wankowicz, Stephanie M., Cullen, Dana, Horak, Christine, Wind-Rotolo, Megan, Tracy, Adam, Giannakis, Marios, Hodi, Frank Stephen, Drake, Charles G., Ball, Mark W., Allaf, Mohamad E., Snyder, Alexandra, Hellmann, Matthew D., Ho, Thai, Motzer, Robert J., Signoretti, Sabina, Kaelin, William G., Choueiri, Toni K., and Van Allen, Eliezer M.

Published
2018

29. Psychedelics promote neuroplasticity through the activation of intracellular 5-HT2A receptors

Author

Maxemiliano V. Vargas, Lee E. Dunlap, Chunyang Dong, Samuel J. Carter, Robert J. Tombari, Shekib A. Jami, Lindsay P. Cameron, Seona D. Patel, Joseph J. Hennessey, Hannah N. Saeger, John D. McCorvy, John A. Gray, Lin Tian, and David E. Olson

Subjects
Multidisciplinary
Abstract

Decreased dendritic spine density in the cortex is a hallmark of several neuropsychiatric diseases, and the ability to promote cortical neuron growth has been hypothesized to underlie the rapid and sustained therapeutic effects of psychedelics. Activation of 5-hydroxytryptamine (serotonin) 2A receptors (5-HT2ARs) is essential for psychedelic-induced cortical plasticity, but it is currently unclear why some 5-HT2AR agonists promote neuroplasticity, whereas others do not. We used molecular and genetic tools to demonstrate that intracellular 5-HT2ARs mediate the plasticity-promoting properties of psychedelics; these results explain why serotonin does not engage similar plasticity mechanisms. This work emphasizes the role of location bias in 5-HT2AR signaling, identifies intracellular 5-HT2ARs as a therapeutic target, and raises the intriguing possibility that serotonin might not be the endogenous ligand for intracellular 5-HT2ARs in the cortex.

Published
2023
Full Text
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33. Complement Factor H Polymorphism in Age-Related Macular Degeneration

Author

Klein, Robert J., Zeiss, Caroline, Chew, Emily Y., Tsai, Jen-Yue, Sackler, Richard S., Haynes, Chad, Henning, Alice K., SanGiovanni, John Paul, Mane, Shrikant M., Mayne, Susan T., Bracken, Michael B., Ferris, Frederick L., Ott, Jurg, Barnstable, Colin, and Hoh, Josephine

Published
2005

35. Genome Sequence of the PCE-Dechlorinating Bacterium Dehalococcoides ethenogenes

Author

Seshadri, Rekha, Adrian, Lorenz, Fouts, Derrick E., Eisen, Jonathan A., Phillippy, Adam M., Methe, Barbara A., Ward, Naomi L., Nelson, William C., Deboy, Robert T., Khouri, Hoda M., Kolonay, James F., Dodson, Robert J., Daugherty, Sean C., Brinkac, Lauren M., Sullivan, Steven A., Madupu, Ramana, Nelson, Karen E., Kang, Katherine H., Impraim, Marjorie, Tran, Kevin, Robinson, Jeffrey M., Forberger, Heather A., Fraser, Claire M., Zinder, Stephen H., and Heidelberg, John F.

Published
2005

49. Late Pliocene Homo and Hominid Land Use from Western Olduvai Gorge, Tanzania

Author

Blumenschine, Robert J., Peters, Charles R., Masao, Fidelis T., Clarke, Ronald J., Deino, Alan L., Hay, Richard L., Swisher, Carl C., Stanistreet, Ian G., Ashley, Gail M., McHenry, Lindsay J., Sikes, Nancy E., van der Merwe, Nikolaas J., Tactikos, Joanne C., Cushing, Amy E., Deocampo, Daniel M., Njau, Jackson K., and Ebert, James I.

Published
2003

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