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Start Over Author "Evelyn" Journal proceedings of the national academy of sciences of the united states of america
423 results on '"Evelyn"'

1. Decorating chromatin for enhanced genome editing using CRISPR-Cas9

Author

Chen, Evelyn, Lin-Shiao, Enrique, Trinidad, Marena, Doost, Mohammad Saffari, Colognori, David, and Doudna, Jennifer A

Subjects
Biochemistry and Cell Biology, Biological Sciences, Human Genome, Biotechnology, Genetics, 1.1 Normal biological development and functioning, Cancer, Generic health relevance, Humans, Chromatin, CRISPR-Cas Systems, Gene Editing, Recombinational DNA Repair, Homologous Recombination, Histone-Lysine N-Methyltransferase, CRISPR, genome editing, chromatin, epigenetics
Abstract

CRISPR-associated (Cas) enzymes have revolutionized biology by enabling RNA-guided genome editing. Homology-directed repair (HDR) in the presence of donor templates is currently the most versatile method to introduce precise edits following CRISPR-Cas-induced double-stranded DNA cuts, but HDR efficiency is generally low relative to end-joining pathways that lead to insertions and deletions (indels). We tested the hypothesis that HDR could be increased using a Cas9 construct fused to PRDM9, a chromatin remodeling factor that deposits histone methylations H3K36me3 and H3K4me3 to mediate homologous recombination in human cells. Our results show that the fusion protein contacts chromatin specifically at the Cas9 cut site in the genome to increase the observed HDR efficiency by threefold and HDR:indel ratio by fivefold compared with that induced by unmodified Cas9. HDR enhancement occurred in multiple cell lines with no increase in off-target genome editing. These findings underscore the importance of chromatin features for the balance between DNA repair mechanisms during CRISPR-Cas genome editing and provide a strategy to increase HDR efficiency.

Published
2022

2. Turning traditionally nonwetting surfaces wetting for even ultra-high surface energy liquids

Author

Wilke, Kyle L, Lu, Zhengmao, Song, Youngsup, and Wang, Evelyn N

Subjects
Cassie state, hemiwicking, omniphilic, omniphobic, reentrant structures
Abstract

We present a surface-engineering approach that turns all liquids highly wetting, including ultra-high surface tension fluids such as mercury. Previously, highly wetting behavior was only possible for intrinsically wetting liquid/material combinations through surface roughening to enable the so-called Wenzel and hemiwicking states, in which liquid fills the surface structures and causes a droplet to exhibit a low contact angle when contacting the surface. Here, we show that roughness made of reentrant structures allows for a metastable hemiwicking state even for nonwetting liquids. Our surface energy model reveals that with liquid filled in the structure, the reentrant feature creates a local energy barrier, which prevents liquid depletion from surface structures regardless of the intrinsic wettability. We experimentally demonstrated this concept with microfabricated reentrant channels. Notably, we show an apparent contact angle as low as 35° for mercury on structured silicon surfaces with fluorinated coatings, on which the intrinsic contact angle of mercury is 143°, turning a highly nonwetting liquid/material combination highly wetting through surface engineering. Our work enables highly wetting behavior for previously inaccessible material/liquid combinations and thus expands the design space for various thermofluidic applications.

Published
2022

6. Correction: Early life adversity promotes resilience to opioid addiction-related phenotypes in male rats and sex-specific transcriptional changes

Author

Sanchez, Evelyn Ordoñes, Bavley, Charlotte C., Deutschmann, Andre U., Carpenter, Rachel, Peterson, Drew R., Karbalaei, Reza, Flowers, James, Rogers, Charleanne M., Langrehr, Miranda G., Ardekani, Cory S., Famularo, Sydney T., Bongiovanni, Angela R., Knouse, Melissa C., Floresco, Stan B., Briand, Lisa A., Wimmer, Mathieu E., and Bangasser, Debra A.

Published
2022

8. Imaging the dynamic recruitment of monocytes to the blood–brain barrier and specific brain regions during Toxoplasma gondii infection

Author

Schneider, Christine A, Velez, Dario X Figueroa, Azevedo, Ricardo, Hoover, Evelyn M, Tran, Cuong J, Lo, Chelsie, Vadpey, Omid, Gandhi, Sunil P, and Lodoen, Melissa B

Subjects
Veterinary Sciences, Agricultural, Veterinary and Food Sciences, Physical Sciences, Neurosciences, Biodefense, Infectious Diseases, Foodborne Illness, Emerging Infectious Diseases, Biomedical Imaging, Infection, Animals, Antigens, Ly, Blood-Brain Barrier, Brain, CX3C Chemokine Receptor 1, Disease Models, Animal, Female, Male, Mice, Mice, Inbred C57BL, Monocytes, Receptors, CCR2, Toxoplasmosis, monocyte, Toxoplasma gondii, CNS infection, LPS, blood-brain barrier, blood–brain barrier
Abstract

Brain infection by the parasite Toxoplasma gondii in mice is thought to generate vulnerability to predation by mechanisms that remain elusive. Monocytes play a key role in host defense and inflammation and are critical for controlling T. gondii However, the dynamic and regional relationship between brain-infiltrating monocytes and parasites is unknown. We report the mobilization of inflammatory (CCR2+Ly6Chi) and patrolling (CX3CR1+Ly6Clo) monocytes into the blood and brain during T. gondii infection of C57BL/6J and CCR2RFP/+CX3CR1GFP/+ mice. Longitudinal analysis of mice using 2-photon intravital imaging of the brain through cranial windows revealed that CCR2-RFP monocytes were recruited to the blood-brain barrier (BBB) within 2 wk of T. gondii infection, exhibited distinct rolling and crawling behavior, and accumulated within the vessel lumen before entering the parenchyma. Optical clearing of intact T. gondii-infected brains using iDISCO+ and light-sheet microscopy enabled global 3D detection of monocytes. Clusters of T. gondii and individual monocytes across the brain were identified using an automated cell segmentation pipeline, and monocytes were found to be significantly correlated with sites of T. gondii clusters. Computational alignment of brains to the Allen annotated reference atlas [E. S. Lein et al., Nature 445:168-176 (2007)] indicated a consistent pattern of monocyte infiltration during T. gondii infection to the olfactory tubercle, in contrast to LPS treatment of mice, which resulted in a diffuse distribution of monocytes across multiple brain regions. These data provide insights into the dynamics of monocyte recruitment to the BBB and the highly regionalized localization of monocytes in the brain during T. gondii CNS infection.

Published
2019

10. Early life adversity promotes resilience to opioid addiction-related phenotypes in male rats and sex-specific transcriptional changes

Author

Sanchez, Evelyn Ordoñes, Bavley, Charlotte C., Deutschmann, Andre U., Carpenter, Rachel, Peterson, Drew R., Karbalaei, Reza, Flowers, James, Rogers, Charleanne M., Langrehr, Miranda G., Ardekani, Cory S., Famularo, Sydney T., Bongiovanni, Angela R., Knouse, Melissa C., Floresco, Stan B., Briand, Lisa A., Wimmer, Mathieu E., and Bangasser, Debra A.

Published
2021

13. Global trends in nature’s contributions to people

Author

Brauman, Kate A., Garibaldi, Lucas A., Polasky, Stephen, Aumeeruddy-Thomas, Yildiz, Brancalion, Pedro H. S., DeClerck, Fabrice, Jacob, Ute, Mastrangelo, Matias Enrique, Nkongolo, Nsalambi V., Palang, Hannes, Pérez-Méndez, Néstor, Shannon, Lynne J., Shrestha, Uttam Babu, Strombom, Evelyn, and Verma, Madhu

Published
2020

15. Modeling SHH-driven medulloblastoma with patient iPS cell-derived neural stem cells

Author

Susanto, Evelyn, Navarro, Ana Marin, Zhou, Leilei, Sundström, Anders, van Bree, Niek, Stantic, Marina, Moslem, Mohsen, Tailor, Jignesh, Rietdijk, Jonne, Zubillaga, Veronica, Hübner, Jens-Martin, Weishaupt, Holger, Wolfsberger, Johanna, Alafuzoff, Irina, Nordgren, Ann, Magnaldo, Thierry, Siesjö, Peter, Johnsen, John Inge, Kool, Marcel, Tammimies, Kristiina, Darabi, Anna, Swartling, Fredrik J., Falk, Anna, and Wilhelm, Margareta

Published
2020

21. Naturalized species drive functional trait shifts in plant communities.

Author

Garbowski, Magda, Laughlin, Daniel C., Blumenthal, Dana M., Sofaer, Helen R., Barnett, David T., Beaury, Evelyn M., Buonaiuto, Daniel M., Corbin, Jeffrey D., Dukes, Jeffrey S., Early, Regan, Nebhut, Andrea N., Petri, Laís, Vilà, Montserrat, and Pearse, Ian S.

Subjects
PLANT species, INVASIVE plants, PLANT communities, NATIVE plants, INTRODUCED species
Abstract

Despite decades of research documenting the consequences of naturalized and invasive plant species on ecosystem functions, our understanding of the functional underpinnings of these changes remains rudimentary. This is partially due to ineffective scaling of trait differences between native and naturalized species to whole plant communities. Working with data from over 75,000 plots and over 5,500 species from across the United States, we show that changes in the functional composition of communities associated with increasing abundance of naturalized species mirror the differences in traits between native and naturalized plants. We find that communities with greater abundance of naturalized species are more resource acquisitive aboveground and belowground, shorter, more shallowly rooted, and increasingly aligned with an independent strategy for belowground resource acquisition via thin fine roots with high specific root length. We observe shifts toward herbaceous-dominated communities but shifts within both woody and herbaceous functional groups follow community-level patterns for most traits. Patterns are remarkably similar across desert, grassland, and forest ecosystems. Our results demonstrate that the establishment and spread of naturalized species, likely in combination with underlying environmental shifts, leads to predictable and consistent changes in community-level traits that can alter ecosystem functions. [ABSTRACT FROM AUTHOR]

Published
2024
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22. Etiology of craniofacial and cardiac malformations in a mouse model of SF3B4-related syndromes.

Author

Kumar, Shruti, Bareke, Eric, Lee, Jimmy, Carlson, Emma, Merkuri, Fjodor, Schwager, Evelyn E., Maglio, Steven, Fish, Jennifer L., Majewski, Jacek, and Jerome-Majewska, Loydie A.

Subjects
RNA sequencing, NEURAL crest, GENE expression, LABORATORY mice, ANIMAL disease models
Abstract

Pathogenic variants in SF3B4, a component of the U2 snRNP complex important for branchpoint sequence recognition and splicing, are responsible for the acrofacial disorders Nager and Rodriguez Syndrome, also known as SF3B4-related syndromes. Patients exhibit malformations in the head, face, limbs, vertebrae as well as the heart. To uncover the etiology of craniofacial malformations found in SF3B4-related syndromes, mutant mouse lines with homozygous deletion of Sf3b4 in neural crest cells (NCC) were generated. Like in human patients, these embryos had craniofacial and cardiac malformations with variable expressivity and penetrance. The severity and survival of Sf3b4 NCC mutants was modified by the level of Sf3b4 in neighboring non-NCC. RNA sequencing analysis of heads of embryos prior to morphological abnormalities revealed significant changes in expression of genes forming the NCC regulatory network, as well as an increase in exon skipping. Additionally, several key histone modifiers involved in craniofacial and cardiac development showed increased exon skipping. Increased exon skipping was also associated with use of a more proximal branch point, as well as an enrichment in thymidine bases in the 50 bp around the branch points. We propose that decrease in Sf3b4 causes changes in the expression and splicing of transcripts required for proper craniofacial and cardiac development, leading to abnormalities. [ABSTRACT FROM AUTHOR]

Published
2024
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25. Exquisite sensitivity of adrenocortical carcinomas to induction of ferroptosis

Author

Belavgeni, Alexia, Bornstein, Stefan R., von Mässenhausen, Anne, Tonnus, Wulf, Stumpf, Julian, Meyer, Claudia, Othmar, Evelyn, Latk, Markus, Kanczkowski, Waldemar, Kroiss, Matthias, Hantel, Constanze, Hugo, Christian, Fassnacht, Martin, Ziegler, Christian G., Schally, Andrew V., Krone, Nils P., and Linkermann, Andreas

Published
2019

28. Intraarticular injection of relaxin-2 alleviates shoulder arthrofibrosis

Author

Blessing, William A., Okajima, Stephen M., Cubria, M. Belen, Villa-Camacho, Juan C., Perez-Viloria, Miguel, Williamson, Patrick M., Sabogal, Angie N., Suarez, Sebastian, Ang, Lay-Hong, White, Suzanne, Flynn, Evelyn, Rodriguez, Edward K., Grinstaff, Mark W., and Nazarian, Ara

Published
2019

30. Moving beyond panaceas in fisheries governance

Author

Young, Oran R., Webster, D. G., Cox, Michael E., Raakjær, Jesper, Blaxekjær, Lau Øfjord, Einarsson, Níels, Virginia, Ross A., Acheson, James, Bromley, Daniel, Cardwell, Emma, Carothers, Courtney, Eythórsson, Einar, Howarth, Richard B., Jentoft, Svein, McCay, Bonnie J., McCormack, Fiona, Osherenko, Gail, Pinkerton, Evelyn, van Ginkel, Rob, Wilson, James A., Rivers, Louie, and Wilson, Robyn S.

Published
2018

33. Mitochondrial Localization of Estrogen Receptor β

Author

Yang, Shao-Hua, Liu, Ran, Perez, Evelyn J., Wen, Yi, Stevens,, Stanley M., Valencia, Thomas, Brun-Zinkernagel, Anne-Marie, Prokai, Laszlo, Will, Yvonne, Dykens, James, Koulen, Peter, Simpkins, James W., and McEwen, Bruce S.

Published
2004

46. Timeless noncoding DNA contains cell-type preferential enhancers important for proper Drosophila circadian regulation.

Author

Dingbang Ma, Ojha, Pranav, Yu, Albert D., Araujo, Maisa S., Weifei Luo, Keefer, Evelyn, Díaz, Madelen M., Meilin Wu, Joiner, William J., Abruzzi, Katharine C., and Rosbash, Michael

Subjects
NON-coding DNA, GENE expression, MOLECULAR clock, CLOCK genes, DROSOPHILA, NATURAL products
Abstract

To address the contribution of transcriptional regulation to Drosophila clock gene expression and to behavior, we generated a series of CRISPR-mediated deletions within two regions of the circadian gene timeless (tim), an intronic E-box region and an upstream E-box region that are both recognized by the key transcription factor Clock (Clk) and its heterodimeric partner Cycle. The upstream deletions but not an intronic deletion dramatically impact tim expression in fly heads; the biggest upstream deletion reduces peak RNA levels and tim RNA cycling amplitude to about 15% of normal, and there are similar effects on tim protein (TIM). The cycling amplitude of other clock genes is also strongly reduced, in these cases due to increases in trough levels. These data underscore the important contribution of the upstream E-box enhancer region to tim expression and of TIM to clock gene transcriptional repression in fly heads. Surprisingly, tim expression in clock neurons is only modestly affected by the biggest upstream deletion and is similarly affected by a deletion of the intronic E-box region. This distinction between clock neurons and glia is paralleled by a dramatically enhanced accessibility of the intronic enhancer region within clock neurons. This distinctive feature of tim chromatin was revealed by ATAC-seq (assay for transposase-accessible chromatin with sequencing) assays of purified neurons and glia as well as of fly heads. The enhanced cell type-specific accessibility of the intronic enhancer region explains the resilience of clock neuron tim expression and circadian behavior to deletion of the otherwise more prominent upstream tim E-box region. [ABSTRACT FROM AUTHOR]

Published
2024
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