Article
Multidisciplinary Sciences
Andrew R. Burns, Rachel J. Baker, Megan Kitner, Jessica Knox, Brittany Cooke, Jonathan R. Volpatti, Aditya S. Vaidya, Emily Puumala, Bruna M. Palmeira, Elizabeth M. Redman, Jamie Snider, Sagar Marwah, Sai W. Chung, Margaret H. MacDonald, Jens Tiefenbach, Chun Hu, Qi Xiao, Constance A. M. Finney, Henry M. Krause, Sonya A. MacParland, Igor Stagljar, John S. Gilleard, Leah E. Cowen, Susan L. F. Meyer, Sean R. Cutler, James J. Dowling, Mark Lautens, Inga Zasada, Peter J. Roy
Summary: Parasitic nematodes pose a major threat to global food security, especially as the world population is set to reach 10 billion. Traditional nematicides have been banned due to their poor selectivity, leaving farmers with limited means of pest control. This study identifies a family of selective imidazothiazole nematicides, called selectivins, which undergo cytochrome P450-mediated bioactivation in nematodes.
Article
Biology
Xinwei Yu, Matthew S. Creamer, Francesco Randi, Anuj K. Sharma, Scott W. Linderman, Andrew M. Leifer
Summary: A method called fDNC, based on the transformer network architecture, is proposed for automated tracking and identifying neurons in C. elegans. This method predicts neural correspondence quickly without requiring straightening or transforming the animal into a canonical coordinate system, making it suitable for future real-time applications.
Article
Neurosciences
Stephanie N. Bowles, Casonya M. Johnson
Summary: The research found that in C. elegans, astrocyte-like cephalic glia (CEPglia) and the glia-specific bHLH transcription factor HLH-17 influence mating behavior and the defecation motor program (DMP) through different mechanisms. CEPglia mediate complex behaviors by signaling to the GABAergic DVB neuron, while HLH-17 activity influences discrete steps within those behaviors.
JOURNAL OF NEUROSCIENCE RESEARCH
(2021)
Editorial Material
Biochemistry & Molecular Biology
Jeremy J. Grubbs, David M. Raizen
Summary: Fatigue and sleepiness are common responses to tissue injury, and a new study shows how the innate immune system mediates injury-induced sleep.
Article
Biochemistry & Molecular Biology
Ramesh K. Narayanan, Megan H. Brewer, Gonzalo Perez-Siles, Melina Ellis, Carolyn Ly, Andrew Burgess, Brent Neumann, Garth A. Nicholson, Steve Vucic, Marina L. Kennerson
Summary: CMT is a common neurodegenerative disorder caused by mutations in over 90 genes, with the p.R158H mutation in the PDK3 gene being responsible for CMTX6. In vivo models of CMTX6 in C. elegans have successfully replicated synaptic transmission deficits and locomotion defects seen in patients, providing insight into cellular function and metabolic pathways affected by the mutation.
HUMAN MOLECULAR GENETICS
(2022)
Article
Food Science & Technology
Yanan Wang, Jiachen Shi, Kun Liu, Yu Wang, Yongjiang Xu, Yuanfa Liu
Summary: This study investigated the effects of different edible oils on the aging process and lifespan of Caenorhabditis elegans. The results showed that teaseed oil (TO) could prolong lifespan and slow down aging by regulating lipid metabolism. Furthermore, there were significant differences in gene expression levels and metabolites between the control group and the TO group.
FOOD SCIENCE AND HUMAN WELLNESS
(2023)
Article
Biochemical Research Methods
Edward D. Lee, Xiaowen Chen, Bryan C. Daniels
Summary: The relationship between biological circuitry and behavior is complex and difficult to study experimentally. This study develops a theoretical framework that simplifies the problem by using minimal perturbations to the system. It is found that even with small perturbations, the system behavior remains close to normal and the range of perturbations is greatly reduced. By applying this protocol to a minimal model of neural activity in C. elegans, it is demonstrated that a few pivotal neurons strongly affect the statistics of synchronous activity, highlighting their importance in neural control of behavior.
PLOS COMPUTATIONAL BIOLOGY
(2022)
Article
Cell Biology
Nicola Facchinello, Claudio Laquatra, Lisa Locatello, Giorgia Beffagna, Raquel Branas Casas, Chiara Fornetto, Alberto Dinarello, Laura Martorano, Andrea Vettori, Giovanni Risato, Rudy Celeghin, Giacomo Meneghetti, Massimo Mattia Santoro, Agnes Delahodde, Francesco Vanzi, Andrea Rasola, Luisa Dalla Valle, Maria Berica Rasotto, Tiziana Lodi, Enrico Baruffini, Francesco Argenton, Natascia Tiso
Summary: The study successfully generated zebrafish Polg models to faithfully mimic multiple defects detected in POLG disorders, providing a valuable platform for therapeutic research on the disease.
CELL DEATH & DISEASE
(2021)
Article
Multidisciplinary Sciences
James J. Doyle, Claudia Maios, Celine Vrancx, Sarah Duhaime, Babykumari Chitramuthu, Hugh P. J. Bennett, Andrew Bateman, J. Alex Parker
Summary: The article discusses the link between GRN mutations and frontotemporal dementia (FTD) discovered in 2006 and highlights the need for advancing genetic and small-molecule therapeutics for GRN-related FTD. Research using the nematode model, Caenorhabditis elegans, shows that loss of nematode GRN ortholog results in behavioral and molecular defects, and implicates the sphingolipid metabolic pathway in regulating these defects. High-throughput drug screening using nematodes has identified two small molecules with potential therapeutic applications against GRN/pgrn-1 deficiency, offering avenues for mechanistic and therapeutic research into GRN-related neurodegeneration.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2021)
Article
Biochemical Research Methods
Shigekazu Oda, Emi Sato-Ebine, Akinobu Nakamura, Koutarou D. Kimura, Kazuhiro Aoki
Summary: Optogenetic techniques responsive to red/near-infrared light were successfully implemented in C. elegans, allowing manipulation of cell signaling and induction of defecation motor program. These tools will greatly contribute to elucidating the molecular mechanisms underlying C. elegans behaviors.
ACS SYNTHETIC BIOLOGY
(2023)
Review
Cell Biology
Wan Jun Gan, Fumio Motegi
Summary: Cell polarity involves the asymmetric arrangement of cellular components along specific axes, achieved by breaking symmetry with mechanochemical modulation of the actin cytoskeleton. In Caenorhabditis elegans zygote, polarity is initiated by the centrosome, which controls the mechanics of the cell cortex to establish advective flow of cortical proteins including actin and PAR proteins. The chemical signaling from the centrosome through the Aurora A kinase-mediated cascade converts the organization of the contractile actomyosin network from apolar to polar state.
FRONTIERS IN CELL AND DEVELOPMENTAL BIOLOGY
(2021)
Article
Chemistry, Inorganic & Nuclear
Hui Chong, Chuan Tan, Siyu Fang, Xichen Chen, Qi Tao, Xiaohui Yuan, Jinzhi Li, Cunhui Zhai, Chengxin Fei, Di Yang, Hongying Fan, Hongxia Shao, Aijian Qin, Guoxiu Wang, Zhonghua Shi, Ting Z'hang, Hang Yao, Hualing Li, Chengyin Wang
Summary: Two novel BODIPY-bearing complexes with pyridine and pyrimidine motifs showed stronger interactions with DNA compared to cisplatin. They exhibited improved anti-chemoresistance capabilities and significantly decreased lifespan and body length in a cisplatin-resistant model. Upregulation of certain genes related to chemoresistance was observed upon exposure to cisplatin, but not to the synthesized Pt(II) complexes.
INORGANIC CHEMISTRY
(2021)
Article
Chemistry, Analytical
Seleipiri Charles, Guillaume Aubry, Han-Ting Chou, Annalise B. Paaby, Hang Lu
Summary: The article introduces a method for large-scale smFISH imaging using microfluidics to reduce labor intensity. By designing embryo traps and developing a protocol that allows for efficient chemical exchange of hundreds of C. elegans embryos simultaneously, the bottleneck of performing efficient reagent exchange on chip for large numbers of embryos is addressed. Additionally, the device design optimizes imaging throughput and allows for high-temporal-resolution studies, benefiting large-scale RNAi and drug screens beyond C. elegans embryos.
ANALYTICAL CHEMISTRY
(2021)
Article
Biochemical Research Methods
Khaled Youssef, Daphne Archonta, Terrance J. Kubiseski, Anurag Tandon, Pouya Rezai
Summary: This paper reveals the novel effect of electric field on adult C. elegans egg-laying behavior, showing that the electric egg-laying rate is significantly influenced by EF strength, direction, and exposure duration, as well as worm aging. The involvement and sensitivity of specific neurons and muscles to the EF are demonstrated, and the assay can be used for cellular screening and mapping of the neural basis of electrosensation.
Article
Genetics & Heredity
Erik Rosenhahn, Thomas J. O'Brien, Maha S. Zaki, Ina Sorge, Dagmar Wieczorek, Kevin Rostasy, Antonio Vitobello, Sophie Nambot, Fowzan S. Alkuraya, Mais O. Hashem, Amal Alhashem, Brahim Tabarki, Abdullah S. Alamri, Ayat H. Al Safar, Dalal K. Bubshait, Nada F. Alahmady, Joseph G. Gleeson, Mohamed S. Abdel-Hamid, Nicole Lesko, Sofia Ygberg, Sandrina P. Correia, Anna Wredenberg, Shahryar Alavi, Seyed M. Seyedhassani, Mahya Ebrahimi Nasab, Haytham Hussien, Tarek E. Omar, Ines Harzallah, Renaud Touraine, Homa Tajsharghi, Heba Morsy, Henry Houlden, Mohammad Shahrooei, Maryam Ghavideldarestani, Ghada M. H. Abdel-Salam, Annalaura Torella, Mariateresa Zanobio, Gaetano Terrone, Nicola Brunetti-Pierri, Abdolmajid Omrani, Julia Hentschel, Johannes R. Lemke, Heinrich Sticht, Rami Abou Jamra, Andre E. X. Brown, Reza Maroofian, Konrad Platzer
Summary: This study identifies bi-allelic loss-of-function variants in the PPFIBP1 gene as a cause of severe neurodevelopmental disorder, characterized by early-onset epilepsy, microcephaly, and periventricular calcifications.
AMERICAN JOURNAL OF HUMAN GENETICS
(2022)
Article
Biochemical Research Methods
Charlotte Soneson, Avi Srivastava, Rob Patro, Michael B. Stadler
Summary: RNA velocity analysis estimates the rate of change of gene expression levels in single cells, enabling prediction of future gene expression profiles and developmental relationships. This study compares five widely used quantification tools in five experimental datasets, highlighting differences in estimates and their impact on downstream analysis, emphasizing the importance of careful consideration of genomic features and quantification algorithms in RNA velocity analysis workflow.
PLOS COMPUTATIONAL BIOLOGY
(2021)
Article
Hematology
Shuang Song, Chun Cao, Mohamed-Amin Choukrallah, Fengyuan Tang, Gerhard Christofori, Hubertus Kohler, Fabian Wu, Barna D. Fodor, Mathias Frederiksen, Simon N. Willis, Jacob T. Jackson, Stephen L. Nutt, Stefan Dirnhofer, Michael B. Stadler, Patrick Matthias
Summary: The study demonstrates that OBF1, OCT2, and OCT1 play crucial roles in B-cell specificity and GC formation, as they extensively colocalize on the promoters or enhancers of genes involved in GC formation. They regulate each other and are essential for proliferation of lymphoma cell lines derived from GC, indicating OBF1 controls a key regulatory node in GC differentiation.
Article
Medicine, Research & Experimental
Federica Zilli, Pedro Marques Ramos, Priska Auf Der Maur, Charly Jehanno, Atul Sethi, Marie-May Coissieux, Tobias Eichlisberger, Loic Sauteur, Adelin Rouchon, Laura Bonapace, Joana Pinto Couto, Roland Rad, Michael Rugaard Jensen, Andrea Banfi, Michael B. Stadler, Mohamed Bentires-Alj
Summary: NFIB is a transcription factor that plays a crucial role in promoting primary mammary tumor growth and lung metastatic colonization by increasing the expression of ERO1A. Its high expression is associated with poor prognosis in basal-like breast cancer patients.
EMBO MOLECULAR MEDICINE
(2021)
Article
Genetics & Heredity
Taro Kitazawa, Dania Machlab, Onkar Joshi, Nicola Maiorano, Hubertus Kohler, Sebastien Ducret, Sandra Kessler, Henrik Gezelius, Charlotte Soneson, Panagiotis Papasaikas, Guillermina Lopez-Bendito, Michael B. Stadler, Filippo M. Rijli
Summary: This study reveals a developmental epigenetic mechanism involving a unique bipartite Polycomb chromatin signature that regulates the rapidity and amplitude of transcriptional responses to relevant stimuli, while preventing inappropriate activation of stimulus-response genes. The bipartite signature includes active H3K27ac on promoters but repressive Ezh2-dependent H3K27me3 on gene bodies, allowing for fast stimulus-dependent mark removal and gene induction.
Article
Genetics & Heredity
Mario Iurlaro, Michael B. Stadler, Francesca Masoni, Zainab Jagani, Giorgio G. Galli, Dirk Schubeler
Summary: Chromatin accessibility, which involves transcription factor binding and nucleosomal reorganization, relies on the continuous activity of nucleosome remodelers. Inhibition of the remodeler complex leads to decreased accessibility and TF binding within minutes. The restoration of accessibility, nucleosome depletion, and gene expression upon inhibitor removal suggests that accessible chromatin is continuously regenerated in a cell-autonomous manner.
Article
Biochemistry & Molecular Biology
Daniel Olivieri, Eleonora Castelli, Yumiko K. Kawamura, Panagiotis Papasaikas, Ilya Lukonin, Melanie Rittirsch, Daniel Hess, Sebastien A. Smallwood, Michael B. Stadler, Antoine H. F. M. Peters, Joerg Betschinger
Summary: Mouse embryonic stem cells are biased towards producing embryonic endoderm rather than extraembryonic endoderm, which is regulated by transcriptional repressors Hdac3 and Dax1. Pluripotency factors Nr5a2 and Esrrb promote cell type conversion, and perturbation of the barrier extends mESC potency. This study shows that transcriptional repressors stabilize pluripotency by biasing the equilibrium between embryonic and extraembryonic lineages in mESCs.
Review
Andrology
Faruk Hadziselimovic, Gilvydas Verkauskas, Michael B. Stadler
Summary: This study analyzed gene expression levels in testicular and neural tissues, as well as hormone levels and RNA data of pre-pubertal cryptorchidism patients, showing that GnRHa treatment can improve gene expression levels and restore fertility in patients.
BASIC AND CLINICAL ANDROLOGY
(2021)
Article
Cell Biology
Stephen P. Methot, Jan Padeken, Giovanna Brancati, Peter Zeller, Colin E. Delaney, Dimos Gaidatzis, Hubertus Kohler, Alexander van Oudenaarden, Helge Grosshans, Susan M. Gasser
Summary: The deposition of H3K9me2 and H3K9me3 can repress lineage-specific and germline genes in terminally differentiated Caenorhabditis elegans tissues by restricting the activity of specific transcription factors. Changes in H3K9me during development affect gene regulation and the maintenance of cellular functions.
NATURE CELL BIOLOGY
(2021)
Article
Biochemical Research Methods
Dania Machlab, Lukas Burger, Charlotte Soneson, Filippo M. Rijli, Dirk Schuebeler, Michael B. Stadler
Summary: Proteins binding to specific nucleotide sequences, such as transcription factors, have significant roles in regulating gene expression. The monaLisa package, an R/Bioconductor package, provides methods to identify relevant transcription factors from experimental data. It allows seamless motif analyses without relying on software outside of R.
Article
Multidisciplinary Sciences
Klement Stojanovski, Helge Grosshans, Benjamin D. Towbin
Summary: Animals need to reach the correct size during development, but stochastic differences in growth rate can lead to variations in size. This study shows that the nematode C. elegans uses an oscillatory timer to couple growth and development, buffering fluctuations in growth to ensure the correct size.
NATURE COMMUNICATIONS
(2022)
Article
Biochemistry & Molecular Biology
Milou W. M. Meeuse, Yannick P. Hauser, Smita Nahar, A. Alexander T. Smith, Kathrin Braun, Chiara Azzi, Markus Rempfler, Helge Grosshans
Summary: Development of C. elegans involves four larval stages terminated by molts, which are regulated by rhythmic transcription. Transcription factors GRH-1, BLMP-1, NHR-23, NHR-25, MYRF-1, and BED-3 were identified as components of the gene regulatory networks responsible for progression through larval stages. Depletion of GRH-1, a Grainyhead/LSF transcription factor, resulted in extended molt durations, impaired cuticle shedding, and larval death. GRH-1 is required for each molt and preferentially binds to promoters of genes expressed during this phase, suggesting it is part of a core molting-clock gene regulatory network. The findings may have implications beyond nematodes, as mammalian orthologues of GRH-1, BLMP-1, and NHR-23 are involved in rhythmic skin regeneration in mice.
Article
Genetics & Heredity
Sebastian Kaluscha, Silvia Domcke, Christiane Wirbelauer, Michael B. Stadler, Sevi Durdu, Lukas Burger, Dirk Schuebeler
Summary: Cytosine methylation efficiently silences CpG-rich regulatory regions of genes and repeats in mammalian genomes by directly inhibiting the binding of transcription factors rather than indirectly inhibiting via recruitment of methyl-CpG-binding domain proteins.
Article
Cell & Tissue Engineering
Simon Suppinger, Marietta Zinner, Nadim Aizarani, Ilya Lukonin, Raphael Ortiz, Chiara Azzi, Michael B. Stadler, Stefano Vianello, Giovanni Palla, Hubertus Kohler, Alexandre Mayran, Matthias P. Lutolf, Prisca Liberali
Summary: In this study, gastruloids were generated from pluripotent stem cells and single-cell genomic analysis was used to map cell states and types during their development. The researchers also identified an early spatial variability in pluripotency that determined the response to Wnt activation. A compound screen was performed on thousands of gastruloids to derive a phenotypic landscape and infer genetic interactions. This study provides important insights into the development and generation of complex patterns in gastruloids.
Article
Cell Biology
Priska Auf der Maur, Marcel P. Trefny, Zora Baumann, Milica Vulin, Ana Luisa Correia, Maren Diepenbruck, Nicolas Kramer, Katrin Volkmann, Bogdan-Tiberius Preca, Pedro Ramos, Cedric Leroy, Tobias Eichlisberger, Katarzyna Buczak, Federica Zilli, Ryoko Okamoto, Roland Rad, Michael Rugaard Jensen, Christine Fritsch, Alfred Zippelius, Michael B. Stadler, Mohamed Bentires-Alj
Summary: A genome-wide screen and resistance screen identified NF1 loss in mammary tumors resistant to a PI3Ka inhibitor. NF1 loss reduces sensitivity to PI3Ka inhibition and is associated with enhanced glycolysis and lower levels of ROS. NAC supplementation sensitizes NF1 knockout cells to PI3Ka inhibition and enhances the inhibitory effect on mTOR signaling.
CELL REPORTS MEDICINE
(2023)
Article
Biochemistry & Molecular Biology
Ilkin Aygun, Alicja Rzepczak, Takashi S. Miki
Summary: XRN2 is a 5'-to-3' exoribonuclease that degrades or trims various types of RNA in the nucleus. Through investigating its role in the detoxification of deoxyribose nucleic acid, we identified relevant molecular pathways that are important for germline development. These findings provide insights into the essential role of XRN-2 in germline development.
GENETICS AND MOLECULAR BIOLOGY
(2023)