Article
Engineering, Electrical & Electronic
Qianqian Zhang, Ying-Chang Liang, Hong-Chuan Yang, H. Vincent Poor
Summary: This paper investigates the mutualistic mechanism between primary and secondary transmissions in symbiotic radio. The condition for mutualistic symbiosis is derived and the performance of the system is evaluated in high SNR regime.
IEEE TRANSACTIONS ON WIRELESS COMMUNICATIONS
(2022)
Article
Chemistry, Multidisciplinary
Mengjie Chen, Si-Min Lu, Hao-Wei Wang, Yi-Tao Long
Summary: By statistically analyzing time-resolved current transients, we can quantitatively determine the dynamic chemical potential difference and interparticle communication between populations of large and small Ag NPs, enabling in situ investigation of chemical communication-dependent transformation kinetics of NPs in the photochemical process with the high sensitivity of stochastic collision electrochemistry, shedding light on designing nanomaterials.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2023)
Article
Biodiversity Conservation
Yaya Rayadin, Zuzana Burivalova
Summary: This research reflects on the challenges faced by researchers in multi-national collaborations where there is unequal financial and institutional support amongst their respective countries. Four key aspects of the research cycle are outlined as opportunities to build more equitable partnerships: defining a shared research agenda, obtaining funding, publication, and effective communication. Recommendations are given for both visiting and local scientists, as well as institutions involved in conservation science, with the hope of fostering productive and mutually beneficial collaborations leading to positive outcomes in conservation.
CONSERVATION SCIENCE AND PRACTICE
(2022)
Article
Biotechnology & Applied Microbiology
Nadia Rostami, Robert C. Shields, Hannah J. Serrage, Catherine Lawler, Jane L. Brittan, Sufian Yassin, Halah Ahmed, Achim Treumann, Paul Thompson, Kevin J. Waldron, Angela H. Nobbs, Nicholas S. Jakubovics
Summary: Extracellular DNA is a crucial component of microbial biofilms, but the role of extracellular DNase enzymes in biofilms remains unclear. This study identifies and characterizes SsnA, a protein in Streptococcus gordonii, that is responsible for extracellular DNase activity. SsnA plays a key role in oral biofilms.
NPJ BIOFILMS AND MICROBIOMES
(2022)
Article
Management
Katherine C. Kellogg
Summary: This study highlights the challenges faced by less powerful actors during the introduction and integration of digital technology in a U.S. medical center, and proposes the use of experimentalist governance to achieve mutually beneficial role reconfiguration. This approach allows for local experimentation followed by central revision, enabling the adaptation of digital technologies to specific contexts and negotiation of shared understandings for different groups of actors. Through this iterative process, problems and possibilities are addressed, leading to a more collaborative and adaptive approach to digital technology integration.
ORGANIZATION SCIENCE
(2022)
Article
Plant Sciences
Beatriz Moreno-Garcia, Patricia E. Lopez-Calcagno, Christine A. Raines, Lee J. Sweetlove
Summary: The communication between chloroplasts and mitochondria is crucial for efficient respiratory metabolism and photosynthesis, which relies on the inter-organellar exchange of carbon skeletons, energy, and reducing equivalents. Manipulating leaf energy and redox balance through a multi-transgene approach significantly affects cytosolic NADH:NAD+ levels and plant growth parameters. Interventions in gene expression pathways suggest a key role for the dual 2-oxoglutarate/malate and oxaloacetate/malate transporter (pOMT) in supporting photosynthesis and growth.
JOURNAL OF PLANT PHYSIOLOGY
(2022)
Article
Multidisciplinary Sciences
Shannon M. Hoffman, Makoto A. Lalwani, Jose L. Avalos
Summary: Microbial cell factories provide a sustainable solution for producing chemicals and recombinant proteins. Optogenetics offers a method of dynamically regulating gene expression, improving fermentation performance and productivity.
JOVE-JOURNAL OF VISUALIZED EXPERIMENTS
(2022)
Article
Biochemical Research Methods
He-Ryun Choi, Sung-Seen Choi
Summary: This study explores the ionization process of six isomers of aminonitrotoluene (ANT), revealing differences in ionization efficiency and types and abundances of product ions in positive and negative ion modes, which can aid in the differentiation and identification of these compounds.
RAPID COMMUNICATIONS IN MASS SPECTROMETRY
(2022)
Article
Biochemistry & Molecular Biology
Samagya Banskota, Aditya Raguram, Susie Suh, Samuel W. Du, Jessie R. Davis, Elliot H. Choi, Xiao Wang, Sarah C. Nielsen, Gregory A. Newby, Peyton B. Randolph, Mark J. Osborn, Kiran Musunuru, Krzysztof Palczewski, David R. Liu
Summary: We have developed and applied engineered DNA-free virus-like particles (eVLPs) for efficient delivery of gene editing tools, achieving high levels of base editing. By overcoming the limitations of cargo packaging, release, and localization, the fourth-generation eVLPs demonstrated efficient base editing in mouse and human cells. In addition, the off-target effects of eVLPs were significantly reduced compared to other delivery methods such as AAV or plasmid.
Article
Biotechnology & Applied Microbiology
Friederike Knipping, Gregory A. Newby, Cindy R. Eide, Amber N. McElroy, Sarah C. Nielsen, Kyle Smith, Yongxing Fang, Tatjana Cornu, Caroline Costa, Alejandra Gutierrez-Guerrero, Samuel P. Bingea, Colby J. Feser, Benjamin Steinbeck, Keli L. Hippen, Bruce R. Blazar, Anton McCaffrey, Claudio Mussolino, Els Verhoeyen, Jakub Tolar, David R. Liu, Mark J. Osborn
Summary: The disruption of CCR5 and CXCR4 co-receptors using base editing techniques has been shown to protect CD4(+) T cells from HIV-1 infection. The base editing strategies effectively introduce targeted mutations to inactivate the genes without causing double stranded DNA breaks. This study demonstrates the potential of base-editing strategies in preventing viral transduction and maintaining cellular functionality.
Review
Oncology
Anupam K. Chakravarty, Daniel J. McGrail, Thomas M. Lozanoski, Brandon S. Dunn, David J. H. Shih, Kara M. Cirillo, Sueda H. Cetinkaya, Wenjin Jim Zheng, Gordon B. Mills, S. Stephen Yi, Daniel F. Jarosz, Nidhi Sahni
Summary: Multicellularity was a crucial development in evolution, but it also led to the occurrence of cancer as individual cells can evade regulatory mechanisms. Recent research has shown that many biomolecules can undergo phase separation and reorganize cellular biochemistry, which has sparked a surge in studying the mechanistic connections between phase separation and cancer.
Article
Microbiology
Steven T. Denham, Brianna Brammer, Krystal Y. Chung, Morgan A. Wambaugh, Joseph M. Bednarek, Li Guo, Christian T. Moreau, Jessica C. S. Brown
Summary: This research reveals the critical role of seed cells, a small morphotype of Cryptococcus neoformans, in the invasion of extrapulmonary organs. The formation of seed cells is triggered by environmental factors, and they exhibit enhanced interaction with macrophages. Phosphate from pigeon guano plays a central role in the formation of seed cells.
CELL HOST & MICROBE
(2022)
Article
Biotechnology & Applied Microbiology
Monica E. Neugebauer, Alvin Hsu, Mandana Arbab, Nicholas A. Krasnow, Amber N. McElroy, Smriti Pandey, Jordan L. Doman, Tony P. Huang, Aditya Raguram, Samagya Banskota, Gregory A. Newby, Jakub Tolar, Mark J. Osborn, David R. Liu
Summary: Improved cytosine base editors are generated by phage-assisted evolution of a deoxyadenosine deaminase, which exhibit small size, low off-target activity, and high on-target activity. These modified base editors have significant application potential in cell and gene editing.
NATURE BIOTECHNOLOGY
(2023)
Article
Multidisciplinary Sciences
Adam Sheriff, Ina Guri, Paulina Zebrowska, Virginia Llopis-Hernandez, Imogen R. Brooks, Stavroula Tekkela, Kavita Subramaniam, Ruta Gebrezgabher, Gaetano Naso, Anastasia Petrova, Katarzyna Balon, Alexandros Onoufriadis, Dorota Kujawa, Martyna Kotulska, Gregory Newby, Lukasz Laczmanski, David R. Liu, John A. McGrath, Joanna Jackow
Summary: This study demonstrates the use of the adenine base editor ABE8e to correct gene mutations in RDEB patient fibroblasts. The results show efficient correction of the pathogenic allele and restoration of protein expression. This research lays the foundation for developing base editing strategies to treat RDEB patients.
SCIENTIFIC REPORTS
(2022)
Article
Biotechnology & Applied Microbiology
Zackery A. Ely, Nicolas Mathey-Andrews, Santiago Naranjo, Samuel I. Gould, Kim L. Mercer, Gregory A. Newby, Christina M. Cabana, William M. Rideout III, Grissel Cervantes Jaramillo, Jennifer M. Khirallah, Katie Holland, Peyton B. Randolph, William A. Freed-Pastor, Jessie R. Davis, Zachary Kulstad, Peter M. K. Westcott, Lin Lin, Andrew V. Anzalone, Brendan L. Horton, Nimisha B. Pattada, Sean-Luc Shanahan, Zhongfeng Ye, Stefani Spranger, Qiaobing Xu, Francisco J. Sanchez-Rivera, David R. Liu, Tyler Jacks
Summary: Genetically engineered mouse models have limitations in capturing the full range of genetic lesions that drive human cancer. However, a new CRISPR-Cas9 model has been developed to expand this scope through in vivo prime editing. This system allows for precise engineering of various mutations in cell lines and organoids derived from primary tissues, making it possible to study cancer-associated mutations and complex genetic combinations that are challenging with traditional models.
NATURE BIOTECHNOLOGY
(2023)
Article
Biotechnology & Applied Microbiology
Jessie R. Davis, Samagya Banskota, Jonathan M. Levy, Gregory A. Newby, Xiao Wang, Andrew V. Anzalone, Andrew T. Nelson, Peter J. Chen, Andrew D. Hennes, Meirui An, Heejin Roh, Peyton B. Randolph, Kiran Musunuru, David R. Liu
Summary: Efficient methods for delivering prime editors (PEs) in vivo are needed to realize the promise of prime editing for the study and treatment of genetic disorders. This study describes the identification of bottlenecks limiting adeno-associated virus (AAV)-mediated prime editing in vivo and the development of AAV-PE vectors with increased efficiency. The optimized PE-AAV systems support high levels of in vivo prime editing and enable therapeutically relevant editing in mouse organs.
NATURE BIOTECHNOLOGY
(2023)
Article
Multidisciplinary Sciences
Mandana Arbab, Zaneta Matuszek, Kaitlyn M. Kray, Ailing Du, Gregory A. Newby, Anton J. Blatnik, Aditya Raguram, Michelle F. Richter, Kevin T. Zhao, Jonathan M. Levy, Max W. Shen, W. David Arnold, Dan Wang, Jun Xie, Guangping Gao, Arthur H. M. Burghes, David R. Liu
Summary: Spinal muscular atrophy (SMA), a leading genetic cause of infant mortality, can be treated by genome editing of SMN2 to restore SMN protein levels and rescue SMA phenotypes, demonstrating the potential of a one-time base editing treatment for SMA.
Article
Engineering, Biomedical
Kelcee A. Everette, Gregory A. Newby, Rachel M. Levine, Kalin Mayberry, Yoonjeong Jang, Thiyagaraj Mayuranathan, Nikitha Nimmagadda, Erin Dempsey, Yichao Li, Senthil Velan Bhoopalan, Xiong Liu, Jessie R. Davis, Andrew T. Nelson, Peter J. Chen, Alexander A. Sousa, Yong Cheng, John F. Tisdale, Mitchell J. Weiss, Jonathan S. Yen, David R. Liu
Summary: Prime editing efficiently corrects the sickle-cell allele in patient haematopoietic stem cells, resulting in erythrocytes resistant to hypoxia-induced sickling. This correction was achieved at frequencies of 15%-41% in patients with sickle-cell disease. After transplantation into mice, the prime-edited cells maintained normal gene expression and displayed similar differentiation and maturation as unedited stem cells from healthy donors.
NATURE BIOMEDICAL ENGINEERING
(2023)
Article
Genetics & Heredity
Thiyagaraj Mayuranathan, Gregory A. Newby, Ruopeng Feng, Yu Yao, Kalin D. Mayberry, Cicera R. Lazzarotto, Yichao Li, Rachel M. Levine, Nikitha Nimmagadda, Erin Dempsey, Guolian Kang, Shaina N. Porter, Phillip A. Doerfler, Jingjing Zhang, Yoonjeong Jang, Jingjing Chen, Henry W. Bell, Merlin Crossley, Senthil Velan Bhoopalan, Akshay Sharma, John F. Tisdale, Shondra M. Pruett-Miller, Yong Cheng, Shengdar Q. Tsai, David R. Liu, Mitchell J. Weiss, Jonathan S. Yen
Summary: A comparison of gene editing strategies using sickle cell disease cells and in vivo transplantation reveals that adenine base editing of the -175A>G site in the γ-globin gene promoters yields durable and potent expression. This approach provides insights into γ-globin gene regulation and offers a potential strategy for inducing HbF. The study also highlights the unexpected phenotypic variation caused by Cas9-generated diverse indels, which can be avoided by base editing.
Article
Multidisciplinary Sciences
Swarnendu Tripathi, Hazheen K. Shirnekhi, Scott D. Gorman, Bappaditya Chandra, David W. Baggett, Cheon-Gil Park, Ramiz Somjee, Benjamin Lang, Seyed Mohammad Hadi Hosseini, Brittany J. Pioso, Yongsheng Li, Ilaria Iacobucci, Qingsong Gao, Michael N. Edmonson, Stephen V. Rice, Xin Zhou, John Bollinger, Diana M. Mitrea, Michael R. White, Daniel J. McGrail, Daniel F. Jarosz, S. Stephen Yi, M. Madan Babu, Charles G. Mullighan, Jinghui Zhang, Nidhi Sahni, Richard W. Kriwacki
Summary: Fusion oncoproteins have been found to form condensates with distinct physicochemical features, subcellular localization, and biological function. By Machine Learning, a predictor of condensation behavior was developed and it was discovered that approximately 67% of additional fusion oncoproteins likely form condensates.
NATURE COMMUNICATIONS
(2023)
Article
Medicine, Research & Experimental
Meha Kabra, Pawan K. Shahi, Yuyuan Wang, Divya Sinha, Allison Spillane, Gregory A. Newby, Shivani Saxena, Yao Tong, Yu Chang, Amr A. Abdeen, Kimberly L. Edwards, Cole O. Theisen, David R. Liu, David M. Gamm, Shaoqin Gong, Krishanu Saha, Bikash R. Pattnaik
Summary: Clinical genome editing is being used to treat rare diseases, but the delivery of CRISPR editors remains a challenge. In this study, we used silica nanocapsules to deliver base editors to the retinal pigmented epithelium for the treatment of retinal degeneration. The base editor effectively corrected point mutations in the KCNJ13 gene and restored functional channels. This preclinical validation of targeted ion channel functional rescue demonstrates the effectiveness of nonviral genome-editing therapy for rare inherited disorders.
JOURNAL OF CLINICAL INVESTIGATION
(2023)
Meeting Abstract
Biophysics
Theodore Yang, Daniel Jarosz, Roseanna N. Zia
BIOPHYSICAL JOURNAL
(2022)
Correction
Biotechnology & Applied Microbiology
James W. Nelson, Peyton B. Randolph, Simon P. Shen, Kelcee A. Everette, Peter J. Chen, Andrew V. Anzalone, Meirui An, Gregory A. Newby, Jonathan C. Chen, Alvin Hsu, David R. Liu
NATURE BIOTECHNOLOGY
(2022)
