Article
Biochemical Research Methods
David Feldman, Luke Funk, Anna Le, Rebecca J. Carlson, Michael D. Leiken, FuNien Tsai, Brian Soong, Avtar Singh, Paul C. Blainey
Summary: The combination of efficient genetic engineering and high-resolution phenotypic readouts has greatly accelerated the discovery of genetic components underlying fundamental and disease-related processes. Optical pooled screens using in situ sequencing provide a scalable integration of barcoded lentiviral libraries with high-content imaging assays, enabling single-cell resolution and accurate sequence reads for large-scale genetic screens.
Article
Plant Sciences
Saminathan Subburaj, Caroline Bedin Zanatta, Jennifer A. L. Nunn, Aline Martins Hoepers, Rubens Onofre Nodari, Sarah Zanon Agapito-Tenfen
Summary: This study developed a method that allows genetic screens in knockout gene-edited soybeans without the transfection of DNA vectors by delivering Cas9 RNPs directly to soybean protoplasts. The results showed that this DNA-free delivery approach is a useful tool for early-stage genetic screens and anticipated analysis of Cas9 activity in soybeans.
FRONTIERS IN PLANT SCIENCE
(2022)
Article
Biotechnology & Applied Microbiology
Noa Liscovitch-Brauer, Antonino Montalbano, Jiale Deng, Alejandro Mendez-Mancilla, Hans-Hermann Wessels, Nicholas G. Moss, Chia-Yu Kung, Akash Sookdeo, Xinyi Guo, Evan Geller, Suma Jaini, Peter Smibert, Neville E. Sanjana
Summary: Researchers have developed a single-cell combinatorial indexing assay called CRISPR-sciATAC, which links genetic perturbations to genome-wide chromatin accessibility in a large number of cells. By targeting 105 chromatin-related genes in human myelogenous leukemia cells, they found that loss of specific chromatin remodelers affects chromatin accessibility and triggers gene expression.
NATURE BIOTECHNOLOGY
(2021)
Article
Plant Sciences
Tao Yao, Guoliang Yuan, Haiwei Lu, Yang Liu, Jin Zhang, Gerald A. Tuskan, Wellington Muchero, Jin-Gui Chen, Xiaohan Yang
Summary: The genus Populus is widely used for various purposes and has become a desirable crop for biofuel production and research. Modern biotechnologies, including CRISPR/Cas9, have been applied to improve its genetic and genomic traits. In this study, CRISPRa and CBE technologies were successfully used for gene expression regulation and precise gene engineering in two Populus species.
HORTICULTURE RESEARCH
(2023)
Review
Plant Sciences
K. T. Ravikiran, R. Thribhuvan, Seema Sheoran, Sandeep Kumar, Amar Kant Kushwaha, T. V. Vineeth, Manisha Saini
Summary: This review discusses the use of genome editing to alter the quality traits in important crops and the challenges faced in maintaining the crop products' quality. Improving product quality is as important as high yield for consumer acceptance and end use. Conventional plant breeding approaches have achieved significant progress, but at a slower rate. To keep up with changing consumer tastes and industry demands, these efforts need to be supplemented with biotechnological tools. Genome editing, particularly with the CRISPR/Cas9 system, has revolutionized trait manipulation and has been applied in various crops for desirable modifications in quality attributes.
Article
Biochemistry & Molecular Biology
Yingbo Cui, Xiaolong Cheng, Qing Chen, Bicna Song, Anthony Chiu, Yuan Gao, Tyson Dawson, Lumen Chao, Wubing Zhang, Dian Li, Zexiang Zeng, Jijun Yu, Zexu Li, Teng Fei, Shaoliang Peng, Wei Li
Summary: CRISP-view is a comprehensive database containing high-throughput genetic screening datasets based on CRISPR/Cas9 and RNAi, covering various phenotypes. It has collected 10,321 human samples and 825 mouse samples from 167 papers, with curated and processed datasets available for visualization and exploration on a user-friendly webserver.
NUCLEIC ACIDS RESEARCH
(2021)
Article
Plant Sciences
Biyun Huang, Renying Zhuo, Huijin Fan, Yujun Wang, Jing Xu, Kangming Jin, Guirong Qiao
Summary: In this study, a plant regeneration system and genetic transformation system were successfully established in moso bamboo, along with an efficient CRISPR/Cas9 genome-editing system. These technical systems will contribute to gene functional validation and accelerate the molecular breeding process of moso bamboo.
FRONTIERS IN PLANT SCIENCE
(2022)
Article
Chemistry, Multidisciplinary
Wenliang Hao, Wenjing Cui, Feiya Suo, Laichuang Han, Zhongyi Cheng, Zhemin Zhou
Summary: In this study, a genomic diversification platform was constructed using CRISPR-ABE8e-CDA-nCas9 technology to rapidly evolve bacterial chassis. The platform allows for adjustable conversion efficiency and editable window, enabling editing of any pre-defined genomic loci and generating a diverse repertoire of genomic sequence mutants.
Review
Biotechnology & Applied Microbiology
Jacob S. Antony, John M. Hinz, John J. Wyrick
Summary: The versatile CRISPR-Cas genome editing technology has become a popular tool for research and biotechnology. In this article, the applications and challenges of using CRISPR genome editing in Saccharomyces cerevisiae are discussed.
FRONTIERS IN BIOENGINEERING AND BIOTECHNOLOGY
(2022)
Article
Multidisciplinary Sciences
Zechen Wang, Limei Li, Lejun Ouyang
Summary: Plantation forestry of Eucalyptus urophylla x Eucalyptus grandis provides high-quality raw materials for various industries and reduces pressures on native forests. Genetic engineering can effectively improve germplasm resources, with transgenic technology becoming increasingly important for enhancing plantation productivity and wood quality. The fluorescence labelling method established in this study using CRISPR/Cas9 technology allows for easy identification of positive transformed progenies and may be beneficial for editing Eucalyptus genetic resources.
Article
Multidisciplinary Sciences
Nicole M. Wong, Elizabeth Frias, Frederic D. Sigoillot, Justin H. Letendre, Marc Hild, Wilson W. Wong
Summary: Cell-based transcriptional reporters are crucial in high-throughput screening, but many of them have weak or transient responses. This article introduces a digitizer circuit for amplifying reporter activity, increasing sensitivity, and retaining memory of pathway activation.
NATURE COMMUNICATIONS
(2021)
Article
Biochemical Research Methods
Saba Parvez, Zachary J. J. Brandt, Randall T. T. Peterson
Summary: MIC-Drop is a method for large-scale CRISPR screening in zebrafish, using microfluidics to create droplets containing Cas9, multiplexed single-guide RNAs, and corresponding DNA barcodes. This method allows genetic screens to be performed in F0 zebrafish, targeting tens to hundreds of genes simultaneously during injection. MIC-Drop is valuable for developmental biologists, zebrafish geneticists, and researchers interested in in vivo functional genetic screens in a vertebrate model system. It is also useful for chemical biologists seeking to identify targets of small molecules causing phenotype changes in zebrafish. Using MIC-Drop, a typical screen of 100 genes can be completed within 2-3 weeks by a single user.
Article
Cell Biology
Xiaowei Yan, Nico Stuurman, Susana A. Ribeiro, Marvin E. Tanenbaum, Max A. Horlbeck, Christina R. Liem, Marco Jost, Jonathan S. Weissman, Ronald D. Vale
Summary: A microscopy-based optical enrichment approach was developed for selecting and marking cells displaying specific CRISPR-induced phenotypes, followed by isolation using fluorescence-activated cell sorting (FAG). Automated phenotypic identification and photoactivation of cells were achieved through a plugin developed for the open source software mu Manager, allowing screening of approximately 1.5 million individual cells in 8 hours. This scalable approach facilitated the identification of 14 bona fide hits out of 6,092 sgRNAs targeting 544 genes in terms of their effects on nuclear size regulation.
JOURNAL OF CELL BIOLOGY
(2021)
Review
Plant Sciences
Lu Shi, Jing Su, Myeong-Je Cho, Hao Song, Xiaoou Dong, Ying Liang, Zhiyong Zhang
Summary: Gene expression plays a crucial role in crop plant regulation. Genome editing of plant promoters offers the potential to modify gene expression patterns and create favorable traits. This can be done by precise generation of nucleotide sequences or by generating random mutations in the promoter region to select elite alleles based on phenotypic effects.
JOURNAL OF EXPERIMENTAL BOTANY
(2023)
Article
Biochemistry & Molecular Biology
Nina Reuven, Julia Adler, Nadav Myers, Yosef Shaul
Summary: This study presents a method to enrich HDR-dependent edited cells in genome editing by using a co-editing strategy. By using repair of a temperature-sensitive mutation as a selectable marker, selection for edited cells is scarless since editing restores the wild-type sequence. This approach offers a rapid, efficient, and scarless method for selecting genome-edited cells requiring HDR.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Review
Neurosciences
Nathalie Jurisch-Yaksi, Emre Yaksi, Caghan Kizil
Article
Multidisciplinary Sciences
Stephanie Fore, Francisca Acuna-Hinrichsen, Kadir Aytac Mutlu, Ewelina Magdalena Bartoszek, Bram Serneels, Nicholas Guy Faturos, Khac Thanh Phong Chau, Mehmet Ilyas Cosacak, Carmen Diaz Verdugo, Fabrizio Palumbo, Christa Ringers, Nathalie Jurisch-Yaksi, Caghan Kizil, Emre Yaksi
Article
Biochemistry & Molecular Biology
Emre Yaksi, Ahmed Jamali, Carmen Diaz Verdugo, Nathalie Jurisch-Yaksi
Summary: Animal models, including zebrafish, have played a significant role in epilepsy research, providing mechanistic insights into the disease and potential strategies for prevention. Zebrafish, in particular, offer great untapped potential for expanding our understanding of epilepsy and developing new treatments.
Article
Biochemistry & Molecular Biology
Ewelina Magdalena Bartoszek, Anna Maria Ostenrath, Suresh Kumar Jetti, Bram Serneels, Aytac Kadir Mutlu, Khac Thanh Phong Chau, Emre Yaksi
Summary: The ongoing neural activity in the brain, representing internal states, is modulated by sensory information. The habenular circuits in the brain act as a major hub integrating ongoing limbic forebrain activity and olfactory information. Olfactory stimuli can modulate specific habenular neuron activity driven by the forebrain circuitry, highlighting the role of the olfactory system in regulating brain activity.
Article
Neurosciences
Adriana L. Hotz, Ahmed Jamali, Nicolas N. Rieser, Stephanie Niklaus, Ecem Aydin, Sverre Myren-Svelstad, Laetitia Lalla, Nathalie Jurisch-Yaksi, Emre Yaksi, Stephan C. F. Neuhauss
Summary: The loss of function in the astroglia predominant eaat2a gene in zebrafish leads to altered neuronal and astroglial networks, resulting in epileptic seizures and increased extracellular glutamate levels. Interestingly, while hyperexcitability is observed during seizures, basal neuronal and astroglial activity is reduced, leading to decreased overall locomotion in eaat2a(-/-) mutant animals.
Article
Cell Biology
Percival P. D'Gama, Tao Qiu, Mehmet Ilyas Cosacak, Dheeraj Rayamajhi, Ahsen Konac, Jan Niklas Hansen, Christa Ringers, Francisca Acuna-Hinrichsen, Subhra P. Hui, Emilie W. Olstad, Yan Ling Chong, Charlton Kang An Lim, Astha Gupta, Chee Peng Ng, Benedikt S. Nilges, Nachiket D. Kashikar, Dagmar Wachten, David Liebl, Kazu Kikuchi, Caghan Kizil, Emre Yaksi, Sudipto Roy, Nathalie Jurisch-Yaksi
Summary: Through studying motile ciliated cells in zebrafish brain ventricles, it was found that the ventricles undergo restructuring during development from mono- to multiciliated cells, which generate directional flow patterns. These ciliated cells have different developmental origins and genetic heterogeneity, but do not affect overall brain or spine morphogenesis, only resulting in enlarged ventricles.
Article
Cell Biology
Luis M. Franco, Emre Yaksi
Summary: This study reveals that the projection neurons in the fruit fly antennal lobe exhibit spatiotemporally organized ongoing activity, which can be influenced by repeated odor experience leading to changes in the amplitude and number of calcium events and the correlation between olfactory glomeruli. These plastic changes result in decreased trial-to-trial variability and enhanced specificity of odor representations.
Article
Clinical Neurology
Sverre Myren-Svelstad, Ahmed Jamali, Sunniva S. Ophus, Percival P. D'gama, Anna M. Ostenrath, Aytac Kadir Mutlu, Helene Homme Hoffshagen, Adriana L. Hotz, Stephan C. F. Neuhauss, Nathalie Jurisch-Yaksi, Emre Yaksi
Summary: This study investigated neural excitability and dynamics in multiple zebrafish seizure and epilepsy models. The researchers found divergent and convergent features in spontaneous and photically evoked neural and locomotor activity. The study suggests that understanding the interplay between elevated and depressed excitability states could lead to tailored epilepsy therapies.
Article
Cell Biology
Nicole Kirchhammer, Marcel P. Trefny, Marina Natoli, Dominik Bruecher, Sheena N. Smith, Franziska Werner, Victoria Koch, David Schreiner, Ewelina Bartoszek, Melanie Buchi, Markus Schmid, Daniel Breu, K. Patricia Hartmann, Polina Zaytseva, Daniela S. Thommen, Heinz Laeubli, Jan P. Boettcher, Michal A. Stanczak, Abhishek S. Kashyap, Andreas Plueckthun, Alfred Zippelius
Summary: This study demonstrates that therapeutic targeting of the IFN-gamma-IL-12 pathway relies on tissue-resident NK cells to orchestrate an anti-tumor microenvironment. By inducing the expression of CCL5, IFN-gamma-inducing therapies and PD-1 blockade can increase the infiltration of NK cells and enhance immune cell interactions, leading to improved anti-tumor immunity and overcoming treatment resistance.
SCIENCE TRANSLATIONAL MEDICINE
(2022)
Article
Multidisciplinary Sciences
Tala Shekarian, Carl P. Zinner, Ewelina M. Bartoszek, Wandrille Duchemin, Anna T. Wachnowicz, Sabrina Hogan, Manina M. Etter, Julia Flammer, Chiara Paganetti, Tomas A. Martins, Philip Schmassmann, Steven Zanganeh, Francois Le Goff, Manuele G. Muraro, Marie-Francoise Ritz, Darci Phillips, Salil S. Bhate, Graham L. Barlow, Garry P. Nolan, Christian M. Schuerch, Gregor Hutter
Summary: This study demonstrated that ex vivo immunotherapy of GBM explants can induce an active antitumoral immune response within the tumor center, providing a framework for multidimensional personalized assessment of tumor response to immunotherapy.
Article
Gastroenterology & Hepatology
Sarp Uzun, Carl P. Zinner, Amke C. Beenen, Ilaria Alborelli, Ewelina M. Bartoszek, Jason Yeung, Byron Calgua, Matthias Reinscheid, Peter Bronsert, Anna K. Stalder, Jasmin D. Haslbauer, Juerg Vosbeck, Luca Mazzucchelli, Tobias Hoffmann, Luigi M. Terracciano, Gregor Hutter, Michael Manz, Isabelle Panne, Tobias Boettler, Maike Hofmann, Bertram Bengsch, Markus H. Heim, Christine Bernsmeier, Sizun Jiang, Alexandar Tzankov, Benedetta Terziroli Beretta-Piccoli, Matthias S. Matter
Summary: Liver injury after COVID-19 vaccination, known as vaccine-induced liver injury (VILI), shares similarities with autoimmune hepatitis (AIH) but also exhibits distinct differences in histomorphology, pathway activation, immune infiltrates, and TCR usage. VILI may be considered a separate entity closely related to drug-induced autoimmune-like hepatitis.
JOURNAL OF HEPATOLOGY
(2023)
Article
Biochemical Research Methods
Fabrizio Palumbo, Bram Serneels, Emre Yaksi
Summary: Conditioned place avoidance assays are widely used in mammals to study operant learning, and this study introduces experimental designs for training juvenile zebrafish in short-term and long-term assays. The aim is to promote standardization of animal handling procedures and setup conditions to enhance animal welfare and reproducibility in studying operant learning behaviors in juvenile zebrafish.
Meeting Abstract
Endocrinology & Metabolism
Emre Yaksi
NEUROENDOCRINOLOGY
(2021)
Meeting Abstract
Endocrinology & Metabolism
Emre Yaksi
NEUROENDOCRINOLOGY
(2021)
