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| Collection: Genetics |
| New papers are added as they are published. Explore this Cell Reports Methods collection. |
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| Table of Contents |
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| HazardPyMatch: A tool for identifying reproductive and other hazards in scientific laboratories |
| Emily M. Parker, Anastasia-Maria Zavitsanou, Clara Liff, Nour El Houda Mimouni, Isabella Succi, Eric Rogers, Marianna Liistro, Danique Jeurissen |
| Parker et al. present HazardPyMatch, an automated tool that identifies hazardous chemicals such as reproductive hazards using standardized classifications and adaptable search criteria. This workflow improves laboratory safety and supports researchers with exposure sensitivities by making chemical hazard information more transparent and easier to evaluate. |
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| Human neuromuscular organoids mimic cancer-induced muscle cachexia |
| Pietro Chiolerio, Beatrice Auletta, Camilla Pezzini, Luigi Sartore, Giorgia Gregolon, Onelia Gagliano, Cecilia Laterza, Valeria Roxana Balmaceda Valdez, Davide Cacchiarelli, Camilla Luni, Carlo Viscomi, Melanie Planque, Sarah-Maria Fendt, Marco Sandri, Roberta Sartori, Anna Urciuolo |
| Chiolerio et al. introduce neuromuscular organoids derived from human-induced pluripotent stem cells as an innovative in vitro platform to model cancer-induced muscle wasting. The organoids recapitulate key features of muscle cachexia, providing a multicellular, physiologically relevant human model to investigate underlying mechanisms and develop potential therapeutics. |
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| Using DIPA-CRISPR for simple and efficient endogenous protein tagging in insects |
| Alfonso Ferrández-Roldán, Maria-Dolors Piulachs |
| Ferrández-Roldán and Piulachs report a successful fluorescent knockin in cockroaches using DIPA-CRISPR and HDR. By inserting mCherry in-frame at the endogenous dll locus, they achieve robust in vivo visualization of protein localization in live embryos. This method enables accessible, precise genome editing in hemimetabolous insects without egg microinjection. |
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| High-efficiency transfection of Acanthamoeba castellanii using a cationic polymer |
| Anaísa B. Moreno, Viktor Ek, Jens Eriksson, Mikael E. Sellin, Lionel Guy |
| Moreno et al. present a robust, cost-effective transfection method for Acanthamoeba castellanii employing the common polymer polyethylenimine, yielding up to 100-fold improvement in genetic delivery efficiency. By overcoming a major technical limitation, this advance facilitates molecular genetic manipulation of an evolutionarily, ecologically, and clinically significant amoeba. |
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| A unified framework combining linear and 3D molecular features for robust drug-protein interaction prediction |
| Chang Sun, Zichen Qin, Minglei Li, Yanfei Li, Rong Tang, Shengquan Chen, Yuxiang Wang, Yanqiang Liu, Jinmao Wei, Jian Liu |
| Sun et al. develop PointDPI to predict drug-protein interactions (DPIs) by integrating linear and 3D molecular structures. PointDPI preserves inter-molecular relationships and predicts key regulatory sites, outperforming several state-of-the-art methods. |
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| Non-invasive ovulation tracking enables genetic engineering in wild rodents |
| Joanna Buchthal, Emma J. Chory, Zachary Hill, Christy Dennison, Boqiang Tu, Rick P. Wierenga, Çağrı Çevrim, Stefan Golas, Gabriel Meier, Tammy C.T. Lan, Hattie Chung, Magalie Boucher, Sam R. Telford, Kara L. McKinley, Styliani Markoulaki, Rudolf Jaenisch, Kevin M. Esvelt |
| Buchthal et al. develop a camera-based estrous-tracking method that reliably detects ovulation in wild rodents. This non-invasive approach overcomes barriers to genetic engineering in Peromyscus leucopus, enables transgenesis, generalizes to additional species, and identifies reproductive aging phenotypes through behavioral signatures. This work advances tools needed for disease-resistant reservoir models. |
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| African pygmy mouse iPSCs as a model for in vitro embryogenesis, interspecies chimerism, and blastocyst complementation |
| Pjeter Gjonlleshaj, Ajda Lenardič, Monika Tarnowska-Sengül, David Taborsky, Christine L. Trautmann, João Agostinho de Sousa, Nicola Bundschuh, Frédéric Veyrunes, Ataman Sendoel, Ori Bar-Nur |
| Gjonlleshaj et al. report chimera-competent induced pluripotent stem cells from the African pygmy mouse, a rodent with distinctive genetics and exceptionally small size. These iPSCs reveal principles of differentiation in non-laboratory rodents and enable interspecies chimerism and blastocyst complementation with the house mouse, thereby expanding models for developmental and regenerative research. |
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| A 3D multi-compartment assembloid to study combined immune cell infiltration and cytotoxicity |
| Eban A. Hanna, Ashleigh J. Crawford, Wenxuan Du, Adrian Johnston, David Schell, Zeqi Wan, Ting-Hsi Chen, Fan Wu, Kehan Ren, Yeongseo Lim, Vasco Queiroga, Praful Nair, Denis Wirtz |
| Hanna et al. develop a 3D model of the tumor microenvironment to study how immune cells migrate and infiltrate solid tumors. This approach allows researchers to evaluate how the movement of cell therapies through extracellular matrices influences their efficacy, particularly in challenging tumors like pancreatic cancer, thereby advancing treatment strategies. |
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| Dynamic estimation of metabolic state during CAR T cell production |
| N. Suhas Jagannathan, Wei-Xiang Sin, Denise Bei Lin Teo, Faris Kairi, Yen Hoon Luah, Francesca Lorraine Wei Inng Lim, Michaela Su-Fern Seng, Shui Yen Soh, Yie Hou Lee, Lisa Tucker-Kellogg, Michael E. Birnbaum, Rajeev J. Ram |
| In this work, Jagannathan et al. use computational modeling to estimate metabolic dynamics of healthy-donor and patient-derived CAR T cells during ex vivo culture in a bioreactor and use it to show that early metabolism could correlate with cellular attributes of the harvested cell therapy product. |
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| An integrative spatial multi-omic workflow for unified analysis of tumor tissue |
| Jurgen Kriel, Joel J.D. Moffet, Tianyao Lu, Oluwaseun E. Fatunla, Vinod K. Narayana, Adam Valkovic, Ana Maluenda, Malcolm J. McConville, Ellen Tsui, James R. Whittle, Sarah A. Best, Saskia Freytag |
| Kriel et al. introduce SMINT, a scalable method that aligns maps of gene expression with metabolite imaging in the same tissue to build single-cell multi-omic maps. SMINT integrates metabolite activity with cell neighborhoods, helping generate new ideas about tumor spatial architecture. |
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| 2P-FENDO-II: A fiber bundle microscope for all-optical, large field-of-view brain studies in freely moving mice |
| François G.C. Blot, Dimitri Decombe, Antonio Lorca-Cámara, Maya Anquetil, Vincent de Sars, Christophe Tourain, Benoît C. Forget, Nicolò Accanto, Valentina Emiliani |
| Studying the brain’s natural mechanisms requires tools to precisely manipulate widespread neuronal circuits in freely moving animals. Blot et al. present a new microscope that allows the recording and control of neural activity with high precision, down to the level of individual cells, across large brain areas during naturalistic behavior. |
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| DMC-BrainMap is an open-source, end-to-end tool for multi-feature brain mapping in different species |
| Felix Jung, Xiao Cao, Loran Heymans, Marie Carlén |
| In this study, Jung et al. present DMC-BrainMap, a software for performing mapping of anatomical data (e.g., cell bodies, axonal densities, injection sites, and optic fiber/Neuropixels probe tracts) from different species including mice, rats, and zebrafish into reference spaces. |
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| Neural barcoding representing cortical spatiotemporal dynamics based on continuous-time Markov chains |
| Jordan M. Culp, Donovan M. Ashby, Antis G. George, G. Campbell Teskey, Wilten Nicola, Alexander McGirr |
| Culp et al. develop the Markovian neural barcode technique, a formal computational model of cortical brain dynamics that compactly encodes normative brain function and subsequent deviations due to experimental manipulations. The neural barcoding technique is designed as a contemporary lens to study the spatiotemporal statistics of cortical imaging data. |
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| A multicellular analysis calcium imaging toolbox for ImageJ |
| John Hageter, Audrey DelGaudio, Maegan Leathery, Braxton Johnson, Tegan Raupp, James Holcomb, Axel Faz Treviño, Julius Jonaitis, Morgan S. Bridi, Andrew Dacks, Eric J. Horstick |
| Hageter et al. developed an open-source toolkit (MCA) that works within the widely used imaging software, ImageJ. They provide an overview of the main functions MCA uses to analyze data from imaging datasets. They apply their software to a variety of model organisms and stimulus types to highlight the versatility of their software. |
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| Predictive modeling of molecular activity underlying physical cell-cell interactions |
| Tamjeed Azad, Sarah K. Walker, Gabriel D. Victora, Yuri Pritykin |
| Azad et al. introduce Gloss, a computational framework that links intracellular gene programs measured with scRNA-seq to physical cell-cell interactions measured by LIPSTIC. Using a group lasso approach, Gloss robustly identifies the molecular drivers of immune communication in models of cancer and viral infection. |
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| An orthogonal CRISPR/Cpf1 platform for precise spatiotemporal gene regulation and osteoporotic fracture repair |
| Jie Zhao, Zengliang Wang, Lina Lu, Guoyun Bu, Zukang Miao, Yang Zhang, Yue Guo, Zhao Yang, Jianxiong Ma, Jun Jiao, Xinlong Ma |
| Zhao et al. developed OREC, an orthogonal CRISPR/Cpf1 platform combining chemical and light control for simultaneous regulation of multiple genes with spatiotemporal precision. The system successfully enhanced osteoporotic fracture repair in mice by activating bone formation while suppressing inhibitory signals, demonstrating therapeutic potential for complex gene therapy applications. |
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| Evaluation of statistical differential analysis methods for identification of senescent cells using single-cell transcriptomics |
| Dongmei Li, Pinxin Liu, Irfan Rahman, Martin Zand, Gloria Pryhuber, Timothy Dye, Maciej Goniewicz, Aditi Uday Gurkar, Melanie Königshoff, Oliver Eickelberg, Ana Mora, Mauricio Rojas, Qin Ma, Jose Lugo-Martinez, Ziv Bar-Joseph, Serafina Lanna, Toren Finkel, Zidian Xie |
| In a benchmarking study with both simulated and real single-cell RNA sequencing datasets, Li et al. evaluate 10 differential gene expression (DGE) methods implemented in the Seurat package. The DESeq2 method outperforms the others, leading the authors to recommend it for DGE analyses in the Seurat package. |
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| Multi-omic analysis of guided and unguided forebrain organoids reveals differences in cellular composition and metabolic profiles |
| Marie Sejberg Øhlenschlæger, Pia Jensen, Jesper Foged Havelund, Sissel Ida Schmidt, Fadumo Abdullahi Mohamed, Magdalena Sutcliffe, Sofie Blomberg Elmkvist, Lucrezia Criscuolo, Steven W. Wingett, Ilaria Chiaradia, Elif Bayram, Jeppe Allen Abildsten Nicolaisen, Lene Andrup Jakobsen, Jonathan Brewer, Michael Eriksen Benros, Kristine Freude, Nils Joakim Færgeman, Madeline A. Lancaster, Martin Røssel Larsen, Helle Bogetofte |
| Øhlenschlæger et al. perform a multi-omic analysis of forebrain organoids generated by two key methods, guided and unguided differentiation. They document significant differences in the cell type composition and metabolic profiles of the two forebrain organoid types, providing a resource and methodological guide for the neural organoid field. |
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