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17 results on '"Kyle E"'

1. An ultrapotent synthetic nanobody neutralizes SARS-CoV-2 by stabilizing inactive Spike

Author

Schoof, Michael, Faust, Bryan, Saunders, Reuben A, Sangwan, Smriti, Rezelj, Veronica, Hoppe, Nick, Boone, Morgane, Billesbølle, Christian B, Puchades, Cristina, Azumaya, Caleigh M, Kratochvil, Huong T, Zimanyi, Marcell, Deshpande, Ishan, Liang, Jiahao, Dickinson, Sasha, Nguyen, Henry C, Chio, Cynthia M, Merz, Gregory E, Thompson, Michael C, Diwanji, Devan, Schaefer, Kaitlin, Anand, Aditya A, Dobzinski, Niv, Zha, Beth Shoshana, Simoneau, Camille R, Leon, Kristoffer, White, Kris M, Chio, Un Seng, Gupta, Meghna, Jin, Mingliang, Li, Fei, Liu, Yanxin, Zhang, Kaihua, Bulkley, David, Sun, Ming, Smith, Amber M, Rizo, Alexandrea N, Moss, Frank, Brilot, Axel F, Pourmal, Sergei, Trenker, Raphael, Pospiech, Thomas, Gupta, Sayan, Barsi-Rhyne, Benjamin, Belyy, Vladislav, Barile-Hill, Andrew W, Nock, Silke, Liu, Yuwei, Krogan, Nevan J, Ralston, Corie Y, Swaney, Danielle L, García-Sastre, Adolfo, Ott, Melanie, Vignuzzi, Marco, Walter, Peter, Manglik, Aashish, Braxton, Julian R, Lopez, Kyle E, Melo, Arthur, Paulino, Joana, Pospiech, Thomas H, Thomas, Paul V, Wang, Feng, Yu, Zanlin, Dickinson, Miles Sasha, Asarnow, Daniel, Campbell, Melody G, Li, Junrui, Tsui, Tsz Kin Martin, Trinidad, Donovan, Tse, Eric, Zhou, Fengbo, Herrera, Nadia, and Schulze-Gahmen, Ursula

Subjects
Biochemistry and Cell Biology, Biological Sciences, Lung, Vaccine Related, Prevention, Infectious Diseases, Pneumonia, Pneumonia & Influenza, Biodefense, Emerging Infectious Diseases, Angiotensin-Converting Enzyme 2, Animals, Antibodies, Neutralizing, Antibodies, Viral, Antibody Affinity, Chlorocebus aethiops, Cryoelectron Microscopy, Humans, Neutralization Tests, Protein Binding, Protein Stability, Single-Domain Antibodies, Spike Glycoprotein, Coronavirus, Vero Cells, QCRG Structural Biology Consortium, General Science & Technology
Abstract

The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) virus enters host cells via an interaction between its Spike protein and the host cell receptor angiotensin-converting enzyme 2 (ACE2). By screening a yeast surface-displayed library of synthetic nanobody sequences, we developed nanobodies that disrupt the interaction between Spike and ACE2. Cryo-electron microscopy (cryo-EM) revealed that one nanobody, Nb6, binds Spike in a fully inactive conformation with its receptor binding domains locked into their inaccessible down state, incapable of binding ACE2. Affinity maturation and structure-guided design of multivalency yielded a trivalent nanobody, mNb6-tri, with femtomolar affinity for Spike and picomolar neutralization of SARS-CoV-2 infection. mNb6-tri retains function after aerosolization, lyophilization, and heat treatment, which enables aerosol-mediated delivery of this potent neutralizer directly to the airway epithelia.

Published
2020

2. Comparative host-coronavirus protein interaction networks reveal pan-viral disease mechanisms

Author

Gordon, David E, Hiatt, Joseph, Bouhaddou, Mehdi, Rezelj, Veronica V, Ulferts, Svenja, Braberg, Hannes, Jureka, Alexander S, Obernier, Kirsten, Guo, Jeffrey Z, Batra, Jyoti, Kaake, Robyn M, Weckstein, Andrew R, Owens, Tristan W, Gupta, Meghna, Pourmal, Sergei, Titus, Erron W, Cakir, Merve, Soucheray, Margaret, McGregor, Michael, Cakir, Zeynep, Jang, Gwendolyn, O’Meara, Matthew J, Tummino, Tia A, Zhang, Ziyang, Foussard, Helene, Rojc, Ajda, Zhou, Yuan, Kuchenov, Dmitry, Hüttenhain, Ruth, Xu, Jiewei, Eckhardt, Manon, Swaney, Danielle L, Fabius, Jacqueline M, Ummadi, Manisha, Tutuncuoglu, Beril, Rathore, Ujjwal, Modak, Maya, Haas, Paige, Haas, Kelsey M, Naing, Zun Zar Chi, Pulido, Ernst H, Shi, Ying, Barrio-Hernandez, Inigo, Memon, Danish, Petsalaki, Eirini, Dunham, Alistair, Marrero, Miguel Correa, Burke, David, Koh, Cassandra, Vallet, Thomas, Silvas, Jesus A, Azumaya, Caleigh M, Billesbølle, Christian, Brilot, Axel F, Campbell, Melody G, Diallo, Amy, Dickinson, Miles Sasha, Diwanji, Devan, Herrera, Nadia, Hoppe, Nick, Kratochvil, Huong T, Liu, Yanxin, Merz, Gregory E, Moritz, Michelle, Nguyen, Henry C, Nowotny, Carlos, Puchades, Cristina, Rizo, Alexandrea N, Schulze-Gahmen, Ursula, Smith, Amber M, Sun, Ming, Young, Iris D, Zhao, Jianhua, Asarnow, Daniel, Biel, Justin, Bowen, Alisa, Braxton, Julian R, Chen, Jen, Chio, Cynthia M, Chio, Un Seng, Deshpande, Ishan, Doan, Loan, Faust, Bryan, Flores, Sebastian, Jin, Mingliang, Kim, Kate, Lam, Victor L, Li, Fei, Li, Junrui, Li, Yen-Li, Li, Yang, Liu, Xi, Lo, Megan, Lopez, Kyle E, Melo, Arthur A, Moss, Frank R, Nguyen, Phuong, Paulino, Joana, Pawar, Komal Ishwar, and Peters, Jessica K

Subjects
Biological Sciences, Bioinformatics and Computational Biology, Infectious Diseases, Coronaviruses Therapeutics and Interventions, Lung, Coronaviruses, Pneumonia, Emerging Infectious Diseases, Genetics, Biodefense, Pneumonia & Influenza, Generic health relevance, Infection, Good Health and Well Being, COVID-19, Conserved Sequence, Coronavirus Nucleocapsid Proteins, Cryoelectron Microscopy, Host Microbial Interactions, Humans, Mitochondrial Membrane Transport Proteins, Mitochondrial Precursor Protein Import Complex Proteins, Phosphoproteins, Protein Conformation, Protein Interaction Maps, Severe acute respiratory syndrome-related coronavirus, SARS-CoV-2, Severe Acute Respiratory Syndrome, QCRG Structural Biology Consortium, Zoonomia Consortium, General Science & Technology
Abstract

The COVID-19 pandemic, caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), is a grave threat to public health and the global economy. SARS-CoV-2 is closely related to the more lethal but less transmissible coronaviruses SARS-CoV-1 and Middle East respiratory syndrome coronavirus (MERS-CoV). Here, we have carried out comparative viral-human protein-protein interaction and viral protein localization analyses for all three viruses. Subsequent functional genetic screening identified host factors that functionally impinge on coronavirus proliferation, including Tom70, a mitochondrial chaperone protein that interacts with both SARS-CoV-1 and SARS-CoV-2 ORF9b, an interaction we structurally characterized using cryo-electron microscopy. Combining genetically validated host factors with both COVID-19 patient genetic data and medical billing records identified molecular mechanisms and potential drug treatments that merit further molecular and clinical study.

Published
2020

3. Systematic discovery of natural CRISPR-Cas12a inhibitors

Author

Watters, Kyle E, Fellmann, Christof, Bai, Hua B, Ren, Shawn M, and Doudna, Jennifer A

Subjects
Microbiology, Biological Sciences, Human Genome, Genetics, Emerging Infectious Diseases, Biotechnology, Stem Cell Research, Development of treatments and therapeutic interventions, 5.1 Pharmaceuticals, Good Health and Well Being, Bacterial Proteins, CRISPR-Cas Systems, Cell Line, Computational Biology, DNA Cleavage, Endonucleases, Gene Editing, Genome, Bacterial, Humans, Moraxella, General Science & Technology
Abstract

Cas12a (Cpf1) is a CRISPR-associated nuclease with broad utility for synthetic genome engineering, agricultural genomics, and biomedical applications. Although bacteria harboring CRISPR-Cas9 or CRISPR-Cas3 adaptive immune systems sometimes acquire mobile genetic elements encoding anti-CRISPR proteins that inhibit Cas9, Cas3, or the DNA-binding Cascade complex, no such inhibitors have been found for CRISPR-Cas12a. Here we use a comprehensive bioinformatic and experimental screening approach to identify three different inhibitors that block or diminish CRISPR-Cas12a-mediated genome editing in human cells. We also find a widespread connection between CRISPR self-targeting and inhibitor prevalence in prokaryotic genomes, suggesting a straightforward path to the discovery of many more anti-CRISPRs from the microbial world.

Published
2018

4. The Importance of Demographic Niches to Tree Diversity

Author

Condit, Richard, Ashton, Peter, Bunyavejchewin, Sarayudh, Dattaraja, H. S., Davies, Stuart, Esufali, Shameema, Ewango, Corneille, Foster, Robin, Gunatilleke, C. V. S., Hall, Pamela, Harms, Kyle E., Hart, Terese, Hernandez, Consuelo, Hubbell, Stephen, Itoh, Akira, Kiratiprayoon, Somboon, LaFrankie, James, de Lao, Suzanne Loo, Makana, Jean-Remy, Kassim, Abdul Rahman, Russo, Sabrina, Sukumar, Raman, Samper, Cristián, Suresh, Hebbalalu S., Tan, Sylvester, Thomas, Sean, Valencia, Renato, Vallejo, Martha, Villa, Gorky, and Zillio, Tommaso

Published
2006

5. Nonrandom Processes Maintain Diversity in Tropical Forests

Author

Wills, Christopher, Harms, Kyle E., Condit, Richard, King, David, Thompson, Jill, He, Fangliang, Muller-Landau, Helene C., Ashton, Peter, Losos, Elizabeth, Comita, Liza, Hubbell, Stephen, LaFrankie, James, Bunyavejchewin, Sarayudh, Dattaraja, H. S., Davies, Stuart, Esufali, Shameema, Foster, Robin, Gunatilleke, Nimal, Gunatilleke, Savitri, Hall, Pamela, Itoh, Akira, John, Robert, Kiratiprayoon, Somboon, de Lao, Suzanne Loo, Massa, Marie, Nath, Cheryl, Kassim, Abdul Rahman, Sukumar, Raman, Suresh, Hebbalalu Satyanarayana, Tan, Sylvester, Yamakura, Takuo, and Zimmerman, Jess

Published
2006

9. Autologous grafting of cryopreserved prepubertal rhesus testis produces sperm and offspring

Author

Gunapala Shetty, Victoria H. J. Roberts, Marvin L. Meistrich, Hanna Valli-Pulaski, Adetunji P. Fayomi, Cathy Ramsey, Carol B. Hanna, Jon D. Hennebold, Ina Dobrinski, Nicola Robertson, Meena Sukhwani, Karen A. Peters, Kyle E. Orwig, and Lisa A Houser

Subjects
Male, 0301 basic medicine, Offspring, Transplantation, Autologous, Cryopreservation, Andrology, 03 medical and health sciences, 0302 clinical medicine, Testis, medicine, Animals, Sexual Maturation, Autografts, Spermatogenesis, Testosterone, Pregnancy, 030219 obstetrics & reproductive medicine, Multidisciplinary, business.industry, Reproduction, Embryogenesis, Fertility Preservation, medicine.disease, Macaca mulatta, Spermatozoa, Sperm, Transplantation, 030104 developmental biology, Fertilization, business
Abstract

Preserving male fertility Before chemotherapy or radiation treatment, sperm from adult men can be cryopreserved for future use. However, this is not possible for prepubertal boys. Fayomi et al. grafted cryopreserved testicular tissue from castrated pubertal rhesus macaques, placing each animal's own testis sections under the skin of the back or scrotum (see the Perspective by Neuhaus and Schlatt). Grafts grew, produced testosterone, and were able to generate sperm that could fertilize oocytes, in one case resulting in a successful pregnancy. The results hold promise for preserving human fertility, for example, after childhood cancer treatments. Science , this issue p. 1314 ; see also p. 1283

Published
2019

11. Systematic discovery of natural CRISPR-Cas12a inhibitors

Author

Jennifer A. Doudna, Hua B. Bai, Shawn M. Ren, Christof Fellmann, and Kyle E. Watters

Subjects
0301 basic medicine, General Science & Technology, Genomics, Computational biology, Genome, Article, Cell Line, Genome engineering, 03 medical and health sciences, 0302 clinical medicine, Bacterial Proteins, Genome editing, MD Multidisciplinary, Humans, Moraxella, CRISPR, DNA Cleavage, Gene Editing, Nuclease, Multidisciplinary, biology, Cas9, Bacterial, Computational Biology, Endonucleases, 030104 developmental biology, biology.protein, CRISPR-Cas Systems, Mobile genetic elements, Genome, Bacterial, 030217 neurology & neurosurgery
Abstract

Cas12 inhibitors join the anti-CRISPR family Bacteria and their phages continually coevolve in a molecular arms race. For example, phages use anti-CRISPR proteins to inhibit the bacterial type I and II CRISPR systems (see the Perspective by Koonin and Makarova). Watters et al. and Marino et al. used bioinformatic and experimental approaches to identify inhibitors of type V CRISPR-Cas12a. Cas12a has been successfully engineered for gene editing and nucleic acid detection. Some of the anti-Cas12a proteins identified in these studies had broad-spectrum inhibitory effects on Cas12a orthologs and could block Cas12a-mediated genome editing in human cells. Science , this issue p. 236 , p. 240 ; see also p. 156

Published
2018

12. Autologous grafting of cryopreserved prepubertal rhesus testis produces sperm and offspring

Author

Fayomi, Adetunji P., primary, Peters, Karen, additional, Sukhwani, Meena, additional, Valli-Pulaski, Hanna, additional, Shetty, Gunapala, additional, Meistrich, Marvin L., additional, Houser, Lisa, additional, Robertson, Nicola, additional, Roberts, Victoria, additional, Ramsey, Cathy, additional, Hanna, Carol, additional, Hennebold, Jon D., additional, Dobrinski, Ina, additional, and Orwig, Kyle E., additional

Published
2019
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13. Light-Gap Disturbances, Recruitment Limitation, and Tree Diversity in a Neotropical Forest

Author

Robin B. Foster, Richard Condit, S. J. Wright, Kyle E. Harms, B. Wechsler, Sean T. O'Brien, S. Loo de Lao, and Stephen P. Hubbell

Subjects
Panama, Multidisciplinary, Ecology, Seedling, Gap dynamics, Species richness, Biology, Tropical forest, biology.organism_classification, Tree species, Light gap, Tree diversity
Abstract

Light gap disturbances have been postulated to play a major role in maintaining tree diversity in species-rich tropical forests. This hypothesis was tested in more than 1200 gaps in a tropical forest in Panama over a 13-year period. Gaps increased seedling establishment and sapling densities, but this effect was nonspecific and broad-spectrum, and species richness per stem was identical in gaps and in nongap control sites. Spatial and temporal variation in the gap disturbance regime did not explain variation in species richness. The species composition of gaps was unpredictable even for pioneer tree species. Strong recruitment limitation appears to decouple the gap disturbance regime from control of tree diversity in this tropical forest.

Published
1999

15. Caterpillars and Polymorphisms

Author

Stanley H. Faeth and Kyle E. Hammon

Subjects
Lepidoptera genitalia, Larva, Text mining, Multidisciplinary, Nemoria arizonaria, business.industry, Zoology, Computational biology, Biology, business, biology.organism_classification
Published
1989

16. Large-Pore Apertures in a Series of Metal-Organic Frameworks.

Author

Hexiang Deng, Grunder, Sergio, Cordova, Kyle E., Valente, Cory, Furukawa, Hiroyasu, Hmadeh, Mohamad, Gándara, Felipe, Whalley, Adam C., Zheng Liu, Asahina, Shunsuke, Kazumori, Hiroyoshi, O'Keeffe, Michael, Terasaki, Osamu, Stoddart, J. Fraser, and Yaghi, 0mar M.

Subjects
*POROUS metals, *ORGANOMETALLIC compounds, *ORGANOMETALLIC chemistry, *PHENYLENE compounds, *POROSITY, *CRYSTAL structure, *CHARTS, diagrams, etc.
Abstract

The article discusses large-pore apertures in a series of metal-organic frameworks. Topics include the team's strategy for expanding the pore aperture of metal-organic frameworks (MOFs) into a previously unattained size regime of (>32 angstroms), the results of the systematic expansion of a well-known MOF structure, MOF-74, from its original link of one phenylene ring (I) to two, three, four, five, six, seven, nine, and eleven (II to XI, respectively), and a diagram illustrating the crystal structure of MOF-74.

Published
2012
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17. Soft Microfluidic Assemblies of Sensors, Circuits, and Radios for the Skin.

Author

Sheng Xu, Yihui Zhang, Lin Jia, Mathewson, Kyle E., Kyung-In Jang, Jeonghyun Kim, Haoran Fu, Xian Huang, Chava, Pranav, Renhan Wang, Bhole, Sanat, Lizhe Wang, Yoon Joo Na, Yue Guan, Flavin, Matthew, Zheshen Han, Yonggang Huang, and Rogers, John A.

Subjects
*MICROFLUIDIC devices, *MICROTECHNOLOGY, *ADHESIVES, *PATIENT monitoring equipment, *INTEGRATED circuits, *ELASTOMERS, *RADIOS
Abstract

The article discusses research describing experimental and theoretical approaches for the development of soft microfluidic assemblies of sensors, circuits, and radios for the skin using various ideas in materials science, such as structured adhesive surfaces. Topics include the device's multifunctional operation for physiological monitoring in a wireless mode and the key concept behind the technology. Schematic illustrations of the soft microfluidic assemblies are also presented.

Published
2014
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