Article
Biochemistry & Molecular Biology
Lance C. Novak, Juihsuan Chou, Medina Colic, Christopher A. Bristow, Traver Hart
Summary: PICKLES is an updated web interface for accessing a database of genome-scale CRISPR knockout fitness screens in human cell lines. It allows researchers to explore gene knockout fitness phenotypes across different cell lines and tissue types, and compare them with fitness, expression, or mutation profiles of other genes.
NUCLEIC ACIDS RESEARCH
(2023)
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.
Review
Genetics & Heredity
Daniel Schraivogel, Lars M. Steinmetz, Leopold Parts
Summary: Assigning functions to genes and controlling their expression are crucial in cell biology and therapeutic development. Genetic screening, especially single-cell CRISPR screening, has become an efficient and unbiased method. It has the potential to revolutionize biomedical research in the coming decades.
ANNUAL REVIEW OF GENETICS
(2023)
Article
Multidisciplinary Sciences
Chong Li, Jonas Simon Fleck, Catarina Martins-Costa, Thomas R. Burkard, Jan Themann, Marlene Stuempflen, Angela Maria Peer, Abel Vertesy, Jamie B. Littleboy, Christopher Esk, Ulrich Elling, Gregor Kasprian, Nina S. Corsini, Barbara Treutlein, Juergen A. Knoblich
Summary: The study develops a high-throughput CRISPR screening system in cerebral organoids to identify vulnerable cell types and gene regulatory networks associated with autism spectrum disorder. The researchers found that perturbing members of the chromatin remodelling complex can affect cell fate determination in progenitor cells.
Article
Biochemical Research Methods
Tanaz Abid, Amy B. Goodale, Zohra Kalani, Meghan Wyatt, Elizabeth M. Gonzalez, Kevin Ning Zhou, Kenin Qian, Dana Novikov, Alexandra-Larisa Condurat, Pratiti Bandopadhayay, Federica Piccioni, Nicole S. Persky, David E. Root
Summary: Spheroid culture systems have revolutionized cell propagation and modeling of tumor growth in vitro. Genome-wide CRISPR screening has proven valuable in understanding cancer cell lines, and similar screening methods for three-dimensional spheroid cultures will be crucial for future biological discovery.
Article
Biochemical Research Methods
Veronica Gheorghe, Traver Hart
Summary: This study systematically investigates the best practices for generating coessentiality networks from CRISPR knockout data and proposes a partial correlation-based approach for exploring context-dependent interactions.
BMC BIOINFORMATICS
(2022)
Review
Oncology
Raquel Ancos-Pintado, Irene Bragado-Garcia, Maria Luz Morales, Roberto Garcia-Vicente, Andres Arroyo-Barea, Alba Rodriguez-Garcia, Joaquin Martinez-Lopez, Maria Linares, Maria Hernandez-Sanchez
Summary: High-throughput CRISPR screening is an unbiased method for studying hematological malignancies, allowing for the identification of modulator genes, therapeutic targets, biomarkers, and genetic determinants. This review summarizes the most relevant CRISPR screening studies in hematology, discussing libraries, algorithms, and databases used in the analysis of CRISPR screens. The review focuses on identifying drug resistance genes, therapeutic targets, synthetic lethal interactions, and biomarkers of malignant transformations and immune evasion mechanisms. The future directions of CRISPR screening approaches are also discussed, emphasizing the importance of gene validation and data integration.
Article
Biotechnology & Applied Microbiology
Alessandro Vinceti, Emre Karakoc, Clare Pacini, Umberto Perron, Riccardo Roberto De Lucia, Mathew J. Garnett, Francesco Iorio
Summary: CRISPR-Cas9 genome-wide screens are crucial for exploring cancer dependencies, with identifying core-fitness genes being essential for assessing therapeutic target safety and understanding tissue-specific genetic diseases. CoRe, an R package, outperforms other tools in identifying reliable and biologically relevant core-fitness genes, aiding in the prioritization of therapeutic targets.
Article
Biology
Baolong Xia, Raghuvir Viswanatha, Yanhui Hu, Stephanie E. Mohr, Norbert Perrimon
Summary: This study establishes a CRISPR activation screening platform in Drosophila cells and identifies three novel rapamycin resistance genes. Mechanistic studies reveal that one of the genes enhances resistance by activating the RTK-Akt-mTOR signaling pathway, which requires cholesterol and clathrin-coated pits at the cell membrane. This research provides a novel platform for functional genetic studies in Drosophila cells.
Article
Engineering, Biomedical
Liqun Zhou, Luojia Yang, Yanzhi Feng, Sidi Chen
Summary: Pooled screening technology creates a pool of cells with genetic variants to examine changes in behavior or function. It enables scientists to systematically investigate gene function by inducing mutations or perturbing expression. With the advancements in gene editing tools and computational capabilities, this technology offers opportunities to understand biological processes and identify therapeutic targets in humans, animals, and plants.
CURRENT OPINION IN BIOMEDICAL ENGINEERING
(2023)
Article
Cell Biology
Yulong Tang, Simeng Liao, Guang Liu, Xia Xiong, Hongnan Liu, Fengna Li, Zhiliang Tan, Xiangfeng Kong, Yulong Yin, Bie Tan
Summary: DoNick-seq is an advanced method that can simultaneously evaluate multiple gene interactions and the effects of amino acid depletion, efficiently identifying gene targets, cell numbers, and cellular profiles. This method facilitates high-throughput functional dissection of complex cellular responses at the single-cell level and increases the accuracy of CRISPR single-cell transcriptomics.
CELL BIOLOGY AND TOXICOLOGY
(2022)
Review
Pharmacology & Pharmacy
Natasha Salame, Katharine Fooks, Nehme El-Hachem, Jean-Pierre Bikorimana, Francois E. Mercier, Moutih Rafei
Summary: This article introduces the importance of multi-omic approaches in cancer research, including phenotype-based high-throughput drug screening and computational approaches that link transcriptomic profiling with existing pharmaceutical compounds. In addition, it also discusses the application of CRISPR genome editing technology in studying drug resistance and sensitization mechanisms.
FRONTIERS IN PHARMACOLOGY
(2022)
Article
Infectious Diseases
Simon X. M. Dong, Frederick S. Vizeacoumar, Kalpana K. Bhanumathy, Nezeka Alli, Cristina Gonzalez-Lopez, Niranjala Gajanayaka, Ramon Caballero, Hamza Ali, Andrew Freywald, Edana Cassol, Jonathan B. Angel, Franco J. Vizeacoumar, Ashok Kumar
Summary: This study identified novel gene targets that induce apoptosis in HIV-infected macrophages, highlighting the potential of these targets for eliminating HIV-infected macrophages and reservoirs. The results suggest that targeting respiratory chain complex II and IV genes may selectively induce apoptosis of HIV-infected macrophages through enhanced ROS production, providing a potential strategy for HIV cure.
BMC INFECTIOUS DISEASES
(2021)
Article
Oncology
Ryne C. Ramaker, Andrew A. Hardigan, Emily R. Gordon, Carter A. Wright, Richard M. Myers, Sara J. Cooper
Summary: The study identified that cellular resistance in PDAC patients to multiple chemotherapies is primarily mediated by the activation of ABCG2 and genes in transcriptional co-repressor complexes, with HDAC1 being a key player. Activation of HDAC1 leads to changes in cell phenotype and is associated with decreased survival rates in PDAC patients. The development of the analysis tool PancDS allows for predicting drug sensitivity in PDAC tumors and cell lines.
Article
Biology
Ludovica Proietti, Gabriele Manhart, Elizabeth Heyes, Selina Troester, Florian Grebien
Summary: CRISPR/Cas9 screening is a revolutionary method in functional genomics that has been widely used to identify genetic dependencies in cancer cells. This article presents an efficient protocol for cloning guide RNAs into lentiviral vectors, producing lentiviral supernatants, and transducing target cells in a 96-well format. The authors also describe a competitive cell proliferation assay using flow cytometry, which allows for the simultaneous screening of multiple genes in a fast and reproducible manner. This protocol can be extended to measure other parameters accessible to flow-based measurements.
Article
Ecology
Nathaly R. Guerrero-Ramirez, Liesje Mommer, Gregoire T. Freschet, Colleen M. Iversen, M. Luke McCormack, Jens Kattge, Hendrik Poorter, Fons van Der Plas, Joana Bergmann, Thom W. Kuyper, Larry M. York, Helge Bruelheide, Daniel C. Laughlin, Ina C. Meier, Catherine Roumet, Marina Semchenko, Christopher J. Sweeney, Jasper van Ruijven, Oscar J. Valverde-Barrantes, Isabelle Aubin, Jane A. Catford, Peter Manning, Adam Martin, Ruben Milla, Vanessa Minden, Juli G. Pausas, Stuart W. Smith, Nadejda A. Soudzilovskaia, Christian Ammer, Bradley Butterfield, Joseph Craine, Johannes H. C. Cornelissen, Franciska T. de Vries, Marney E. Isaac, Koen Kramer, Christian Koenig, Eric G. Lamb, Vladimir G. Onipchenko, Josep Penuelas, Peter B. Reich, Matthias C. Rillig, Lawren Sack, Bill Shipley, Leho Tedersoo, Fernando Valladares, Peter van Bodegom, Patrick Weigelt, Justin P. Wright, Alexandra Weigelt
Summary: Root trait data are essential for understanding plant form and function, yet they are often overlooked in large-scale studies and global models. The Global Root Trait (GRooT) Database was created to address this gap and provide readily available data for the integration of root trait data into large-scale analyses.
GLOBAL ECOLOGY AND BIOGEOGRAPHY
(2021)
Article
Plant Sciences
Ian R. McGregor, Ryan Helcoski, Norbert Kunert, Alan J. Tepley, Erika B. Gonzalez-Akre, Valentine Herrmann, Joseph Zailaa, Atticus E. L. Stovall, Norman A. Bourg, William J. McShea, Neil Pederson, Lawren Sack, Kristina J. Anderson-Teixeira
Summary: The study found that tree height was negatively correlated with drought tolerance, with taller trees being more vulnerable to drought due to exposure to higher solar radiation and evaporative demand. Additionally, species with leaves that lost less water and shrinkage upon desiccation showed greater drought tolerance under dry conditions.
Article
Biodiversity Conservation
Stuart J. Davies, Iveren Abiem, Kamariah Abu Salim, Salomon Aguilar, David Allen, Alfonso Alonso, Kristina Anderson-Teixeira, Ana Andrade, Gabriel Arellano, Peter S. Ashton, Patrick J. Baker, Matthew E. Baker, Jennifer L. Baltzer, Yves Basset, Pulcherie Bissiengou, Stephanie Bohlman, Norman A. Bourg, Warren Y. Brockelman, Sarayudh Bunyavejchewin, David F. R. P. Burslem, Min Cao, Dairon Cardenas, Li-Wan Chang, Chia-Hao Chang-Yang, Kuo-Jung Chao, Wei-Chun Chao, Hazel Chapman, Yu-Yun Chen, Ryan A. Chisholm, Chengjin Chu, George Chuyong, Keith Clay, Liza S. Comita, Richard Condit, Susan Cordell, Handanakere S. Dattaraja, Alexandre Adalardo de Oliveira, Jan den Ouden, Matteo Detto, Christopher Dick, Xiaojun Du, Alvaro Duque, Sisira Ediriweera, Erle C. Ellis, Nestor Laurier Engone Obiang, Shameema Esufali, Corneille E. N. Ewango, Edwino S. Fernando, Jonah Filip, Gunter A. Fischer, Robin Foster, Thomas Giambelluca, Christian Giardina, Gregory S. Gilbert, Erika Gonzalez-Akre, I. A. U. N. Gunatilleke, C. V. S. Gunatilleke, Zhanqing Hao, Billy C. H. Hau, Fangliang He, Hongwei Ni, Robert W. Howe, Stephen P. Hubbell, Andreas Huth, Faith Inman-Narahari, Akira Itoh, David Janik, Patrick A. Jansen, Mingxi Jiang, Daniel J. Johnson, F. Andrew Jones, Mamoru Kanzaki, David Kenfack, Somboon Kiratiprayoon, Kamil Kral, Lauren Krizel, Suzanne Lao, Andrew J. Larson, Yide Li, Xiankun Li, Creighton M. Litton, Yu Liu, Shirong Liu, Shawn K. Y. Lum, Matthew S. Luskin, James A. Lutz, Hong Truong Luu, Keping Ma, Jean-Remy Makana, Yadvinder Malhi, Adam Martin, Caly McCarthy, Sean M. McMahon, William J. McShea, Herve Memiaghe, Xiangcheng Mi, David Mitre, Mohizah Mohamad, Logan Monks, Helene C. Muller-Landau, Paul M. Musili, Jonathan A. Myers, Anuttara Nathalang, Kang Min Ngo, Natalia Norden, Vojtech Novotny, Michael J. O'Brien, David Orwig, Rebecca Ostertag, Konstantinos Papathanassiou, Geoffrey G. Parker, Rolando Perez, Ivette Perfecto, Richard P. Phillips, Nantachai Pongpattananurak, Hans Pretzsch, Haibo Ren, Glen Reynolds, Lillian J. Rodriguez, Sabrina E. Russo, Lawren Sack, Weiguo Sang, Jessica Shue, Anudeep Singh, Guo-Zhang M. Song, Raman Sukumar, I-Fang Sun, Hebbalalu S. Suresh, Nathan G. Swenson, Sylvester Tan, Sean C. Thomas, Duncan Thomas, Jill Thompson, Benjamin L. Turner, Amanda Uowolo, Maria Uriarte, Renato Valencia, John Vandermeer, Alberto Vicentini, Marco Visser, Tomas Vrska, Xugao Wang, Xihua Wang, George D. Weiblen, Timothy J. S. Whitfeld, Y. Wolf, S. Joseph Wright, Han Xu, Tze Leong Yao, Sandra L. Yap, Wanhui Ye, Mingjian Yu, Minhua Zhang, Daoguang Zhu, Li Zhu, Jess K. Zimmerman, Daniel Zuleta
Summary: ForestGEO is a network of scientists and long-term forest dynamics plots that aims to advance understanding of forest diversity and dynamics, as well as strengthen global capacity for forest science research. With large-scale plot dimensions, comprehensive censusing, and investigation of various biotic and abiotic drivers, ForestGEO provides a holistic view of forest functioning. Through extensive research, ForestGEO has made significant contributions in areas such as species coexistence and diversity, and ecosystem functioning, while also highlighting the need for further research to predict the impacts of climate change and other stressors on forest diversity and function.
BIOLOGICAL CONSERVATION
(2021)
Article
Plant Sciences
Norbert Kunert, Joseph Zailaa, Valentine Herrmann, Helene C. Muller-Landau, S. Joseph Wright, Rolando Perez, Sean M. McMahon, Richard C. Condit, Steven P. Hubbell, Lawren Sack, Stuart J. Davies, Kristina J. Anderson-Teixeira
Summary: The study found that leaf water potential is an effective indicator to explain habitat preferences among tropical tree species in response to drought. Evergreen tree species with lower leaf water potential were associated with drier habitats, while this trait did not predict habitat associations among deciduous species. Leaf water potential holds the potential to predict vegetation responses to climate change.
Article
Geosciences, Multidisciplinary
Daniel Sousa, Joshua B. Fisher, Fernando Romero Galvan, Ryan P. Pavlick, Susan Cordell, Thomas W. Giambelluca, Christian P. Giardina, Gregory S. Gilbert, Faith Imran-Narahari, Creighton M. Litton, James A. Lutz, Malcolm P. North, David A. Orwig, Rebecca Ostertag, Lawren Sack, Richard P. Phillips
Summary: Imaging spectroscopy technology can improve maps of tree-mycorrhizal associations by capturing accurate ground truth observations through forest canopy signals. This approach could greatly enhance the spatial precision of mycorrhizal distributions globally and facilitate the incorporation of dynamic shifts in forest composition into Earth system models.
GEOPHYSICAL RESEARCH LETTERS
(2021)
Article
Multidisciplinary Sciences
Alec S. Baird, Samuel H. Taylor, Jessica Pasquet-Kok, Christine Vuong, Yu Zhang, Teera Watcharamongkol, Christine Scoffoni, Erika J. Edwards, Pascal-Antoine Christin, Colin P. Osborne, Lawren Sack
Summary: Grasses globally demonstrate shorter and narrower leaves under colder and drier climates, with thermal advantages and unique vein development compared to eudicotyledonous plants. This distribution showcases convergence in adaptation to climate across major plant lineages, emphasizing the importance of leaf size and venation architecture for grass performance in various ecosystems.
Article
Plant Sciences
Rutuja Chitra-Tarak, Chonggang Xu, Salomon Aguilar, Kristina J. Anderson-Teixeira, Jeff Chambers, Matteo Detto, Boris Faybishenko, Rosie A. Fisher, Ryan G. Knox, Charles D. Koven, Lara M. Kueppers, Nobert Kunert, Stefan J. Kupers, Nate G. McDowell, Brent D. Newman, Steven R. Paton, Rolando Perez, Laurent Ruiz, Lawren Sack, Jeffrey M. Warren, Brett T. Wolfe, Cynthia Wright, S. Joseph Wright, Joseph Zailaa, Sean M. McMahon
Summary: Deep-water access is an important mechanism for plants to survive drought, delaying dehydration and reducing mortality rates. Research shows that the extent of deep-water access in tree species is related to root depth, dehydration risk, and can help reduce mortality risk caused by drought.
Article
Plant Sciences
Leila R. Fletcher, Christine Scoffoni, Colin Farrell, Thomas N. Buckley, Matteo Pellegrini, Lawren Sack
Summary: Research has found that there is a decoupling between relative growth rate and adaptation to cold or dry climates in Arabidopsis ecotypes. This decoupling is consistent with the presence of multiple stress resistance and avoidance mechanisms, contributing to the wide geographic range and resilience of the species.
Article
Plant Sciences
Priera H. Panescu, Marvin Browne, Kathleen K. Chen, Lawren Sack, Heather D. Maynard
Summary: This study found that the polyacrylate-based hydrogel improved the function of tomato plants under drought conditions, while the trehalose hydrogel was ineffective. This research is important for evaluating hydrogels that can prevent water wastage in agriculture and improve crop health under drought conditions.
Review
Plant Sciences
Nidhi Vinod, Martijn Slot, Ian R. McGregor, Elsa M. Ordway, Marielle N. Smith, Tyeen C. Taylor, Lawren Sack, Thomas N. Buckley, Kristina J. Anderson-Teixeira
Summary: Rising temperatures affect forests at different scales, with significant vertical variation across forest strata. This study evaluates the vertical variation in microclimate, leaf temperatures, traits, and gas exchange in forests, and discusses the implications for tree and ecosystem ecology. Integrating these patterns and mechanisms into models is critical for predicting forest-climate feedback as the climate continues to change.
Article
Biodiversity Conservation
Jeffrey D. D. Wood, Lianhong Gu, Paul J. J. Hanson, Christian Frankenberg, Lawren Sack
Summary: Soil and atmospheric droughts pose increasing threats to plant survival and productivity worldwide. However, there are conceptual gaps that limit our ability to predict the impacts of drought on ecosystems under climate change. This study introduces the concept of the ecosystem wilting point (psi(EWP)), which integrates the drought response of a plant community across the soil-plant-atmosphere continuum. The findings show that psi(EWP) serves as a threshold defining significant shifts in ecosystem functional state.
GLOBAL CHANGE BIOLOGY
(2023)
Article
Plant Sciences
Holly A. A. Beckett, Teresa Neeman, Tomas I. Fuenzalida, Callum Bryant, Sara Chica Latorre, Leuwin I. Ovington, Lawren Sack, Patrick Meir, Marilyn C. Ball
Summary: The incidence and severity of global mangrove mortality due to drought is increasing. Yet, little is understood of the capacity of mangroves to show long-term acclimation of leaf water relations to severe drought. Our study found that the legacy of severe drought enhanced salinity tolerance in the subsequent dry season through coordinated adjustments that reduced leaf water potential and increased cell wall rigidity. These adjustments enable greater leaf function with minimal adjustments, contributing fundamentally to mangrove function under varying salinity regimes.
PLANT CELL AND ENVIRONMENT
(2023)
Review
Plant Sciences
Christine Scoffoni, Caetano Albuquerque, Thomas N. N. Buckley, Lawren Sack
Summary: A surge of papers have reported low leaf vulnerability to xylem embolism during drought. Here, we focus on the less studied, and more sensitive, outside-xylem leaf hydraulic responses to multiple internal and external conditions. Detailed experiments suggest these dynamic responses arise at least in part from strong control of radial water movement across the vein bundle sheath. While leaf xylem vulnerability may influence leaf and plant survival during extreme drought, outside-xylem dynamic responses are important for the control and resilience of water transport and leaf water status for gas exchange and growth.
Article
Plant Sciences
Marvin Browne, Megan K. Bartlett, Christian Henry, Mona Jarrahi, Grace John, Christine Scoffoni, Nezih Tolga Yardimci, Lawren Sack
Summary: Intra-specific trait variation (ITV) is important in various processes, but it is rarely quantified for ecophysiological traits such as PV curve parameters. This study found low ITV for PV parameters compared to other morphological traits and strong intraspecific relationships among PV traits, using a conservative sampling design.
PHYSIOLOGIA PLANTARUM
(2023)
Article
Multidisciplinary Sciences
Congcong Liu, Lawren Sack, Ying Li, Jiahui Zhang, Kailiang Yu, Qiongyu Zhang, Nianpeng He, Guirui Yu
Summary: The relationship between stomatal traits and environmental drivers across plant communities is important for understanding ecosystem fluxes. This study explores the community-scale stomatal trait-environment relationships and finds a trade-off between stomatal density and size. Stomatal density is mainly associated with precipitation, while stomatal size is mainly associated with temperature. The study also reveals that stomatal traits vary with climatic seasonality and extreme conditions. These findings have implications for predicting future water and carbon cycles.
NATURE COMMUNICATIONS
(2023)