Article
Biochemical Research Methods
Stefan J. Tekel, Nicholas Brookhouser, Kylie Standage-Beier, Xiao Wang, David A. Brafman
Summary: The introduction of transient reporters of editing enrichment (TREE) has enabled highly efficient single-base editing of human cells using a transient episomal fluorescent reporter, allowing for rapid generation of clonal editing efficiencies exceeding 80% in biallelic or multiplexed edited isogenic human pluripotent stem cell lines within approximately 3-4 weeks.
Article
Biochemistry & Molecular Biology
Xiabing Sheng, Zhiyong Ai, Yanning Tan, Yuanyi Hu, Xiayu Guo, Xiaolin Liu, Zhizhong Sun, Dong Yu, Jin Chen, Ning Tang, Meijuan Duan, Dingyang Yuan
Summary: Climate change has led to increased salinity in many areas, particularly in coastal mud flats, which affects rice productivity. This study successfully developed new salt-tolerant rice germplasms through CRISPR/Cas9 gene editing technology combined with heterosis utilization. By developing hybrid rice varieties, a new generation of rice with high salinity tolerance was cultivated.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Agronomy
Fangquan Wang, Yang Xu, Wenqi Li, Zhihui Chen, Jun Wang, Fangjun Fan, Yajun Tao, Yanjie Jiang, Qian-Hao Zhu, Jie Yang
Summary: The novel herbicide-tolerance allele (G628W) created in rice using CRISPR/Cas9-mediated gene editing proved to be valuable for developing elite rice varieties with strong herbicide tolerance. A DNA marker for the G628W allele was developed to accurately distinguish homozygous from heterozygous segregants, facilitating its use and introgression into elite alleles for crop breeding. This study further demonstrates the feasibility of CRISPR/Cas9-mediated gene editing in generating novel genetic variation for crop improvement.
Article
Plant Sciences
Tianya Wang, Hongwei Xun, Wei Wang, Xiaoyang Ding, Hainan Tian, Saddam Hussain, Qianli Dong, Yingying Li, Yuxin Cheng, Chen Wang, Rao Lin, Guimin Li, Xueyan Qian, Jinsong Pang, Xianzhong Feng, Yingshan Dong, Bao Liu, Shucai Wang
Summary: This study demonstrates that mutation of GmAITR genes using CRISPR/Cas9 can enhance salinity tolerance in soybean, improving stress resistance at the molecular level. Targeting multiple GmAITR genes simultaneously successfully generated Cas9-free mutants, which showed increased ABA sensitivity and enhanced salt tolerance. These results highlight the efficiency of CRISPR/Cas9 in improving salinity tolerance in soybean.
FRONTIERS IN PLANT SCIENCE
(2021)
Article
Chemistry, Multidisciplinary
Valentin Bauer, Boris Schmidtgall, Gergo Gogl, Jozica Dolenc, Judit Osz, Yves Nomine, Camille Kostmann, Alexandra Cousido-Siah, Andre Mitschler, Natacha Rochel, Gilles Trave, Bruno Kieffer, Vladimir Torbeev
Summary: This study utilized a specific amino acid substitution pattern to modify the free activation domain of transcriptional coactivator ACTR, resulting in increased binding affinity to CREB-binding protein. The X-ray structure of the modified ACTR domain - NCBD complex revealed a unique conformation of ACTR, demonstrating a strategy for characterizing individual conformational states of IDPs.
Article
Multidisciplinary Sciences
Emmarie. C. C. Ryan, Leslie. M. M. Huggins, Joshua. D. D. Podlevsky
Summary: CRISPR arrays and Cas proteins are adaptive immune systems in bacteria and archaea, defending against genetic elements. The reprogrammable guide RNA of single effector CRISPR-Cas systems greatly facilitates gene-editing but complicates PCR tests. These systems are derived from human microflora and pathogens, making detection of gene-editor exposure difficult. To overcome false positives, a DNA displacement assay has been developed to specifically detect gene-editors without cross-reacting with bacterial CRISPRs.
SCIENTIFIC REPORTS
(2023)
Review
Biochemistry & Molecular Biology
Yulin Mu, Chengxiao Zhang, Taihua Li, Feng-Jie Jin, Yun-Ju Sung, Hee-Mock Oh, Hyung-Gwan Lee, Long Jin
Summary: Lactobacillus, important in food production and probiotics, can benefit from CRISPR/Cas9-based genome editing to improve strain efficiency and achieve traceless genome modification.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Multidisciplinary Sciences
Zsolt Bodai, Alena L. Bishop, Valentino M. Gantz, Alexis C. Komor
Summary: Programmable double-strand DNA breaks (DSBs) can be harnessed for precision genome editing through manipulation of the homology-directed repair (HDR) pathway. This study introduces a general strategy called the double tap method, which improves HDR-mediated precision editing efficiency by taking advantage of the reproducible nature of indel sequences. The method utilizes multiple gRNAs, including a primary gRNA that targets the wild-type genomic sequence and one or more secondary gRNAs that target the most common indel sequence(s).
NATURE COMMUNICATIONS
(2022)
Article
Biology
Zhiquan Liu, Siyu Chen, Wanhua Xie, Hao Yu, Liangxue Lai, Zhanjun Li
Summary: Researchers have revisited and engineered a compact Cas9 orthologue derived from Neisseria cinerea (NcCas9) for efficient genome editing in mammal cells. NcCas9 can recognize a PAM sequence (N4GYAT) that existing Cas9s cannot, and by optimizing its architecture and spacer length, editing efficacy is improved. NcCas9-derived Base editors can efficiently generate base conversions, and six anti-CRISPR proteins were identified as off-switches for NcCas9. NcCas9 successfully generated efficient editing of mouse embryos by microinjection of NcCas9 mRNA and the corresponding sgRNA.
COMMUNICATIONS BIOLOGY
(2022)
Review
Agriculture, Dairy & Animal Science
Julia Popova, Victoria Bets, Elena Kozhevnikova
Summary: Genome editing has practical applications in farm animals, improving production traits, economic value, and disease resistance. It also has potential in biomedical research and drug production, as well as xenograft donors. Recent advancements in site-specific nucleases and embryological delivery methods have revolutionized transgenesis, providing efficient and reliable tools for genome engineering in agriculture.
Article
Biotechnology & Applied Microbiology
Hui Kwon Kim, Goosang Yu, Jinman Park, Seonwoo Min, Sungtae Lee, Sungroh Yoon, Hyongbum Henry Kim
Summary: This study identified factors affecting PE2 efficiency through high-throughput evaluation and developed three computational models to predict pegRNA efficiency, which can be applied to edits of various types and positions. Spearman's correlations between 0.47 and 0.81 were found when testing the accuracy of the predictions using independent test data sets.
NATURE BIOTECHNOLOGY
(2021)
Review
Pharmacology & Pharmacy
Siwei Chen, Deng Chen, Bin Liu, Hidde J. Haisma
Summary: CRISPR/Cas9-mediated genome engineering has extensive applications in basic biology, biotechnology, and medicine. However, the low gene modification efficiency and uncontrollable prolonged Cas9 activity hinder its further use. Researchers have explored small molecules with clinical potential to precisely modulate CRISPR/Cas9 genome editing activity.
DRUG DISCOVERY TODAY
(2022)
Article
Chemistry, Physical
Juhee Lee, Yoo Kyung Kang, Eonju Oh, Juhee Jeong, San Hae Im, Duk Ki Kim, Haeshin Lee, Sang-Gyu Kim, Keehoon Jung, Hyun Jung Chung
Summary: The study presents a cancer gene therapy strategy based on NanoRNP that efficiently blocks the PD-L1 immune checkpoint and induces an antitumor effect in vivo without the need for combination therapy. In vivo results demonstrate that NanoRNP can induce indels in target cells at high frequencies, significantly suppressing tumor growth.
CHEMISTRY OF MATERIALS
(2022)
Article
Multidisciplinary Sciences
Beate Rieblinger, Hicham Sid, Denise Duda, Tarik Bozoglu, Romina Klinger, Antonina Schlickenrieder, Kamila Lengyel, Krzysztof Flisikowski, Tatiana Flisikowska, Nina Simm, Alessandro Grodziecki, Carolin Perleberg, Andrea Bahr, Lucie Carrier, Mayuko Kurome, Valeri Zakhartchenko, Barbara Kessler, Eckhard Wolf, Lutz Kettler, Harald Luksch, Ibrahim T. Hagag, Daniel Wise, Jim Kaufman, Benedikt B. Kaufer, Christian Kupatt, Angelika Schnieke, Benjamin Schusser
Summary: Research on genetically modified animals has mostly focused on mice, but also includes species like pigs that are more physiologically similar to humans, and cross-species comparisons with phylogenetically distant species like chickens. CRISPR-Cas9 is a versatile genetic editing method applicable across various species. The successful generation of transgenic chickens and pigs that express Cas9 in all organs has confirmed the functionality of Cas9 across different target genes, cell types, and in vivo applications.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2021)
Article
Chemistry, Multidisciplinary
William Shu Ching Ngai, Shaojun Yang, Xiangmei Zeng, Yanjun Liu, Feng Lin, Xin Wang, Heng Zhang, Xinyuan Fan, Peng R. Chen
Summary: This article reports a bioorthogonally activatable base editor called BaseBAC, which can initiate pyroptosis in specific cells in situ and on demand. By establishing a bioorthogonal blockage on the PAM-interacting residue to control the enzymatic activity of a cytosine base editor, BaseBAC enables control over pyroptosis.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2022)
Article
Multidisciplinary Sciences
Andrew C. Riley, Daniel A. Ashlock, Steffen P. Graether
Article
Plant Sciences
Stefania Short, Rommy Diaz, John Quinones, Jorge Beltran, Jorge G. Farias, Steffen P. Graether, Leon A. Bravo
JOURNAL OF EXPERIMENTAL BOTANY
(2020)
Article
Biochemistry & Molecular Biology
Natalia G. Li, Jantina Toxopeus, Martin Moos, Jesper G. Sorensen, Brent J. Sinclair
COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY A-MOLECULAR & INTEGRATIVE PHYSIOLOGY
(2020)
Article
Multidisciplinary Sciences
Karamjeet K. Singh, Steffen P. Graether
Article
Biochemistry & Molecular Biology
Karamjeet K. Singh, Steffen P. Graether
Summary: Late embryogenesis abundant (LEA) proteins play crucial roles in stress response and stress tolerance, with AtLEA3-4 showing specific binding abilities to metal ions and membrane mimic. Biochemical and structural analyses revealed that LEA3 proteins, although disordered in solution, possess regions with propensity for order.
Article
Entomology
Jacqueline E. Lebenzon, Jantina Toxopeus, Susan E. Anthony, Brent J. Sinclair
Summary: The study analyzed the transcriptome of the pseudoscorpion Wyochernes asiaticus from northern Canada and identified 1100 transcripts encoding proteins associated with stress tolerance, including heat shock proteins and antioxidants. Additionally, transcripts encoding putative venom proteins were discovered, with eight showing high sequence similarity to venom proteins described in other pseudoscorpions. The research provides important sequence information for understanding how W. asiaticus survives in Canadian polar environments.
CANADIAN ENTOMOLOGIST
(2021)
Article
Biochemistry & Molecular Biology
Jantina Toxopeus, Lahari Gadey, Lalitya Andaloori, Matin Sanaei, Gregory J. Ragland
Summary: The study showed that non- and post-diapause pupae can slowly achieve diapause-like metabolic rates when incubated at 4 degrees Celsius. While both diapause and quiescent pupae exhibited high tolerance of extreme low temperatures, quiescent pupae did not survive well when chilled for prolonged periods at 4 degrees Celsius.
COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY A-MOLECULAR & INTEGRATIVE PHYSIOLOGY
(2021)
Article
Biochemistry & Molecular Biology
Alicyia Walczyk-Mooradally, Jennifer Holborn, Karamjeet Singh, Marshall Tyler, Debasis Patnaik, Hendrik Wesseling, Nicholas J. Brandon, Judith Steen, Steffen P. Graether, Stephen J. Haggarty, Jasmin Lalonde
Summary: Arc is a protein crucial for cognitive function and memory formation, able to self-assemble into virus-like capsids for mRNA transportation. The study shows that TNIK kinase can modify Arc at Serine 67 and Threonine 278, influencing its subcellular distribution and self-assembly. Understanding the interaction between Arc and TNIK in neuronal cells could offer new insights into psychiatric disorders.
JOURNAL OF NEUROCHEMISTRY
(2021)
Article
Biology
Philip J. Freda, Jantina Toxopeus, Edwina J. Dowle, Zainab M. Ali, Nicholas Heter, Rebekah L. Collier, Isaiah Sower, Joseph C. Tucker, Theodore J. Morgan, Gregory J. Ragland
Summary: Organisms with complex life cycles have the ability to change their phenotypes across development, which is thought to be an evolutionary adaptation to variable environments. In this study, the researchers investigated the genetic decoupling of thermal physiology in the development of holometabolous insects. They found that there were stage-specific differences in gene expression related to thermal adaptation and that natural selection might be acting on different loci in different life stages.
JOURNAL OF EXPERIMENTAL BIOLOGY
(2022)
Review
Plant Sciences
Itzell E. Hernandez-Sanchez, Israel Maruri Lopez, Coral Martinez-Martinez, Brett Janis, Juan Francisco Jimenez-Bremont, Alejandra A. Covarrubias, Michael A. Menze, Steffen P. Graether, Anja Thalhammer
Summary: This review summarizes the physiological roles and potential molecular functions of late embryogenesis abundant (LEA) proteins in plants and other organisms. The structure-function relationship of LEA proteins, including their state in solution, self-assembly, and liquid-liquid phase separation, is also discussed. Furthermore, the promising potential of LEA proteins in biotechnological and agronomic applications is highlighted.
JOURNAL OF EXPERIMENTAL BOTANY
(2022)
Article
Biochemistry & Molecular Biology
Margaret A. Smith, Steffen P. Graether
Summary: This study investigates the importance of positive charges in dehydrin sequences on cryoprotection of two different proteins, indicating that alterations in positive charges can affect the ability of dehydrins to promote protein structure.
Article
Entomology
Trinity McIntyre, Lalitya Andaloori, Glen R. Hood, Jeffrey L. Feder, Daniel A. Hahn, Gregory J. Ragland, Jantina Toxopeus
Summary: Low temperatures in winter can have a negative impact on the survival of organisms, particularly ectotherms. This study investigates the variation in overwintering strategies among groups of closely interacting parasitoid species. The researchers found that different species of endoparasitoid wasps exhibited similar diapause phenotypes as their host insect, the apple maggot fly. The study also reveals a high level of cold tolerance and consistency in survival rates among the three wasp species.
JOURNAL OF INSECT PHYSIOLOGY
(2023)
Article
Multidisciplinary Sciences
Andrew C. Riley, Daniel A. Ashlock, Steffen P. Graether
Summary: Intrinsically disordered proteins (IDPs) are difficult to align due to lower sequence conservation, but their alignments can still produce accurate species trees.
Meeting Abstract
Zoology
James deMayo, Joseph Tucker, Jenna Tomkinson, Lahari Gadey, Phillip Freda, Jantina Toxopeus, Gregory Ragland
INTEGRATIVE AND COMPARATIVE BIOLOGY
(2023)
Meeting Abstract
Biophysics
Karamjeet K. Singh, Steffen P. Graether
BIOPHYSICAL JOURNAL
(2021)