Review
Cell Biology
Adam E. Sundby, Ruxandra Molnar, Julie M. Claycomb
Summary: Germ granules, composed of RNA and proteins, are non-membrane bound organelles present only within the germ cells of animals. They play critical roles in specifying the germ lineage, inheritance of epigenetic information, and gene regulation, with a significant proportion of proteins involved in RNA metabolism and sRNA pathways. This review synthesizes current knowledge of germ granules in the C. elegans germline, focusing on their functions in sRNA pathways, transgenerational inheritance, and fertility.
TRENDS IN CELL BIOLOGY
(2021)
Review
Biochemistry & Molecular Biology
Malgorzata Kurkowiak, Lukasz Arcimowicz, Elzbieta Chrusciel, Zuzanna Urban-Wojciuk, Ines Papak, Liam Keegan, Mary O'Connell, Jacek Kowalski, Ted Hupp, Natalia Marek-Trzonkowska
Summary: RNA editing is a prevalent form of post-transcriptional RNA modification that can be aberrant in diseases like cancer. Enzymes belonging to the ADAR family catalyze the deamination of adenosine to inosine, impacting mRNA and protein production and function. Studying in vivo RNA editing events can help identify pathological signaling mechanisms relevant to human cancer physiology.
Article
Multidisciplinary Sciences
Dongdong Li, Yufan Liu, Peishan Yi, Zhiwen Zhu, Wei Li, Qiangfeng Cliff Zhang, Jin Billy Li, Guangshuo Ou
Summary: This study revealed a mechanism in Caenorhabditis elegans where RNA editing regulates hyperactive kinases, suggesting a widespread mechanism for kinase regulation.
Article
Multidisciplinary Sciences
Keita Yoshida, Yuji Suehiro, Katsufumi Dejima, Sawako Yoshina, Shohei Mitani
Summary: This study identifies two novel systemic RNAi-related factors, REXD-1 and TBC-3, that work together with SID-5 to promote the systemic spreading of dsRNA. The findings reveal specific pathways that regulate the export of dsRNA and imply the importance of spreading RNA molecules for intercellular communication.
Article
Genetics & Heredity
Han Ting Chou, Francisco Valencia, Jacqueline C. Alexander, Avery Davis Bell, Diptodip Deb, Daniel A. Pollard, Annalise B. Paaby
Summary: The discovery of the ability of experimental dsRNA delivery to induce gene silencing has revolutionized genetics research. However, the efficacy of this RNA interference (RNAi) varies within the natural population of Caenorhabditis elegans, raising questions about the understanding of RNAi in the lab compared to its activity in nature. This study investigates why some wild strains of C. elegans do not mount a strong RNAi response to germline targets. The results demonstrate functional diversification in the small RNA pathways in C. elegans, suggesting that RNAi processes are rapidly evolving in nature.
Article
Multidisciplinary Sciences
Haoqing Shen, Omer An, Xi Ren, Yangyang Song, Sze Jing Tang, Xin-Yu Ke, Jian Han, Daryl Jin Tai Tay, Vanessa Hui En Ng, Fernando Bellido Molias, Priyankaa Pitcheshwar, Ka Wai Leong, Ker-Kan Tan, Henry Yang, Leilei Chen
Summary: This study demonstrates that ADARs play a significant role in regulating the circular transcriptome. ADARs can stabilize or destabilize circRNA secondary structures through editing, and also enhance the binding of RNA-binding proteins. These ADARs-regulated circRNAs are widely expressed in various cancers and have functional relevance to tumorigenesis.
NATURE COMMUNICATIONS
(2022)
Article
Multidisciplinary Sciences
J. Brucker Nourse, Shannon N. Russell, Nathan A. Moniz, Kylie Peter, Lena M. Seyfarth, Madison Scott, Han-A Park, Kim A. Caldwell, Guy A. Caldwell
Summary: This study investigates the TNK2 gene variants in Parkinson's disease (PD) patients and their potential impact on dopaminergic neurodegeneration. The findings suggest that TNK2 dysfunction may contribute to PD, possibly through sustained or aberrant activity. The study also highlights the importance of TNK2 and its ortholog SID-3 in coordinating dopaminergic and epigenetic signaling. Experimental results using Caenorhabditis elegans and rat primary neurons demonstrate the neuroprotective effects of TNK2 inhibition and NEDD4 activation.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2023)
Article
Multidisciplinary Sciences
Phillip A. Frankino, Talha F. Siddiqi, Theodore Bolas, Raz Bar-Ziv, Holly K. Gildea, Hanlin Zhang, Ryo Higuchi-Sanabria, Andrew Dillin
Summary: The transcription factor SKN-1/NRF2 can sense and respond to changes in metabolic state. Knockdown of the amidohydrolase T12A2.1/amdh-1 activates a unique subset of SKN-1 regulated genes, independent of P38-MAPK signaling components. Histidine catabolism genes are required for this activation, possibly through accumulation of a specific catabolite. Activating SKN-1 results in increased oxidative stress resistance but decreased survival to heat stress.
Article
Multidisciplinary Sciences
Dandan Qian, Ye Cong, Runhao Wang, Quan Chen, Chuangye Yan, Deshun Gong
Summary: This study presents the cryo-electron microscopy structures of human SIDT2, which forms a dimer and acts as a transporter rather than a channel. Additionally, it exhibits ceramidase activity. These findings enhance our understanding of the structure-function relationships in the SID1 family proteins.
NATURE COMMUNICATIONS
(2023)
Article
Biology
Yucen Hu, Jingxiu Xu, Erqing Gao, Xueyuan Fan, Jieli Wei, Bingcheng Ye, Suhong Xu, Weirui Ma
Summary: Imaging endogenous mRNAs in live animals is achieved using the MS2-based signal amplification with the Suntag system. This technique has high temporal resolution and utilizes 8xMS2 stem-loops, eliminating the need to insert a 1300 nt 24xMS2 into the genome for imaging endogenous mRNAs. By utilizing this tool, gene expression activation and dynamics of endogenous mRNAs in live C. elegans epidermis can be imaged.
Review
Genetics & Heredity
Katerina K. Yamamoto, Cathy Savage-Dunn
Summary: This article summarizes the roles of transforming growth factor-beta (TGF-beta) signaling in aging and immunity, highlighting the significance of using Caenorhabditis elegans as a research model.
FRONTIERS IN GENETICS
(2023)
Article
Gastroenterology & Hepatology
Yangyang Song, Omer An, Xi Ren, Tim Hon Man Chan, Daryl Jin Tai Tay, Sze Jing Tang, Jian Han, HuiQi Hong, Vanessa Hui En Ng, Xinyu Ke, Haoqing Shen, Priyankaa Pitcheshwar, Jaymie Siqi Lin, Ka Wai Leong, Fernando Bellido Molias, Henry Yang, Dennis Kappei, Leilei Chen
Summary: RNA editing lowers the level of edited COPA gene in tumor samples, leading to the transformation of COPA protein from a cancer-promoting form to a cancer-suppressive form. The loss of edited COPA promotes the development of liver cancer.
JOURNAL OF HEPATOLOGY
(2021)
Article
Multidisciplinary Sciences
Hayao Ohno, Zhirong Bao
Summary: This study reveals that Caenorhabditis elegans undergoes alternative embryogenesis in response to maternal gut microbes, resulting in changes in cell divisions, morphology, and reproduction. The miR-35 microRNA family transmits intergenerational information to regulate embryonic development. These findings challenge the assumption of an invariant cell lineage in C. elegans and provide insights into how organisms adapt to environmental changes through epigenetic control.
Article
Cell Biology
Jonathan J. Froehlich, Bora Uyar, Margareta Herzog, Kathrin Theil, Petar Glazar, Altuna Akalin, Nikolaus Rajewsky
Summary: Understanding how regulatory sequences control gene expression is crucial for explaining phenotypes in health and disease. This study used inducible Cas9 and multiplexed guide RNAs to create mutations in enhancers/promoters and 3'UTRs of multiple genes in C. elegans, showing the impact on expression and fitness. The approach enabled parallel analysis of regulatory sequences directly in animals, providing insights into how specific binding sites can independently regulate gene expression.
Article
Multidisciplinary Sciences
Joan Carles Puchalt, Antonio-Jose Sanchez-Salmeron, Eugenio Ivorra, Silvia Llopis, Roberto Martinez, Patricia Martorell
Summary: A new monitoring machine, SiViS, was developed for analyzing C. elegans cultures seeded with E. coli using standard Petri plates. The system utilizes active vision illumination and image-processing pipelines for motion detection, demonstrating consistent replicates in lifespan experiments and no significant differences compared to manual assays. The flexibility of SiViS allows adaptation to other C. elegans studies beyond longevity assays.
SCIENTIFIC REPORTS
(2021)
Article
Neurosciences
Camron D. Bryant, Deniz Bagdas, Lisa R. Goldberg, Tala Khalefa, Eric R. Reed, Stacey L. Kirkpatrick, Julia C. Kelliher, Melanie M. Chen, William E. Johnson, Megan K. Mulligan, M. Imad Damaj
Article
Biochemistry & Molecular Biology
Maura E. Walker, Nirupa R. Matthan, Gloria Solano-Aguilar, Saebyeol Jang, Sukla Lakshman, Aleksey Molokin, Tyler Faits, Joseph F. Urban, W. Evan Johnson, Stefania Lamon-Fava, Alice H. Lichtenstein
JOURNAL OF NUTRITIONAL BIOCHEMISTRY
(2019)
Article
Immunology
Yukari C. Manabe, Bruno B. Andrade, Nikhil Gupte, Samantha Leong, Manisha Kintali, Mitch Matoga, Cynthia Riviere, Wadzanai Samaneka, Javier R. Lama, Kogieleum Naidoo, Yue Zhao, W. Evan Johnson, Jerrold J. Ellner, Mina C. Hosseinipour, Gregory P. Bisson, Padmini Salgame, Amita Gupta
CLINICAL INFECTIOUS DISEASES
(2020)
Article
Biochemistry & Molecular Biology
Seiko Ikezu, Hana Yeh, Jean-Christophe Delpech, Maya E. Woodbury, Alicia A. Van Enoo, Zhi Ruan, Sudhir Sivakumaran, Yang You, Carl Holland, Teresa Guillamon-Vivancos, Asuka Yoshii-Kitahara, Mina B. Botros, Charlotte Madore, Pin-Hao Chao, Ankita Desani, Solaiappan Manimaran, Srinidhi Venkatesan Kalavai, W. Evan Johnson, Oleg Butovsky, Maria Medalla, Jennifer Luebke, Tsuneya Ikezu
Summary: The study reveals that maternal immune activation affects microglial cells and neuronal functions in the prefrontal cortex of mice, leading to behavioral abnormalities and neuronal dysfunction. Treatment with colony stimulating factor 1 receptor inhibitors corrects the microglial, synaptic, and neurobehavioral dysfunctions associated with MIA.
MOLECULAR PSYCHIATRY
(2021)
Article
Immunology
Samantha Leong, Yue Zhao, Rodrigo Ribeiro-Rodrigues, Edward C. Jones-Lopez, Carlos Acuna-Villaorduna, Patricia Marques Rodrigues, Moises Palaci, David Alland, Reynaldo Dietze, Jerrold J. Ellner, W. Evan Johnson, Padmini Salgame
Article
Behavioral Sciences
Richard K. Babbs, Jacob A. Beierle, Emily J. Yao, Julia C. Kelliher, Arthurine R. Medeiros, Jeya Anandakumar, Anyaa A. Shah, Melanie M. Chen, William E. Johnson, Camron D. Bryant
Article
Biochemical Research Methods
Yuqing Zhang, Prasad Patil, W. Evan Johnson, Giovanni Parmigiani
Summary: This study compares two strategies for handling batch effects in genomic data, showing that an ensemble learning strategy offers more robust performance, especially in cases of high severity of batch effects. The results provide practical guidelines for the development and evaluation of genomic classifiers.
Article
Infectious Diseases
W. Evan Johnson, Aubrey Odom, Chelsie Cintron, Mutharaj Muthaiah, Selby Knudsen, Noyal Joseph, Senbagavalli Babu, Subitha Lakshminarayanan, David F. Jenkins, Yue Zhao, Ethel Nankya, C. Robert Horsburgh, Gautam Roy, Jerrold Ellner, Sonali Sarkar, Padmini Salgame, Natasha S. Hochberg
Summary: The study developed a computational profiling platform to analyze TB signature gene sets and found that existing gene sets for TB performed well in malnourished individuals, showing significant discriminatory power between TB and LTBI with a high area under the curve. This highlights the importance of considering comorbidities like malnutrition in the interpretation of gene expression signatures for TB.
BMC INFECTIOUS DISEASES
(2021)
Article
Microbiology
Molly R. Braun, Sarah L. Noton, Emmeline L. Blanchard, Afzaal Shareef, Philip J. Santangelo, W. Evan Johnson, Rachel Fearns
Summary: Respiratory syncytial virus (RSV) is a significant cause of respiratory disease in infants and the elderly, with no vaccines or effective antiviral treatments available. The M2-1 protein in RSV plays a key role in viral transcription, binding to specific RSV RNA sequences and possibly having an additional role in cellular RNA interactions. This study aimed to elucidate the function of M2-1 in RSV mRNA transcription, revealing its involvement in viral RNA generation and its binding to specific cellular mRNAs, suggesting a potential dual role in infection.
Article
Microbiology
Yue Zhao, Anthony Federico, Tyler Faits, Solaiappan Manimaran, Daniel Segre, Stefano Monti, W. Evan Johnson
Summary: Animalcules is an interactive microbiome analysis toolkit that supports various types of microbiome data analysis, including 16S rRNA sequencing data, shotgun DNA metagenomics data, and RNA-sequencing based metatranscriptomics datasets. It combines traditional and novel analytics, visualization methods, and provides rich analysis features, allowing users to explore and discover insights from their data through command-line functions or an interactive interface.
Article
Cell Biology
Jean-Christophe Delpech, Dhruba Pathak, Merina Varghese, Srinidhi Venkatesan Kalavai, Emma C. Hays, Patrick R. Hof, W. Evan Johnson, Seiko Ikezu, Maria Medalla, Jennifer Luebke, Tsuneya Ikezu
Summary: The study shows that in early stages of Alzheimer's disease, Wfs1(+) neurons in the ECII region are associated with abnormally phosphorylated tau, leading to the spread of tau and potential functional abnormalities in CA1 pyramidal neurons.
SCIENCE TRANSLATIONAL MEDICINE
(2021)
Article
Biochemical Research Methods
Dakota Y. Hawkins, Daniel T. Zuch, James Huth, Nahomie Rodriguez-Sastre, Kelley R. McCutcheon, Abigail Glick, Alexandra T. Lion, Christopher F. Thomas, Abigail E. Descoteaux, William Evan Johnson, Cynthia A. Bradham
Summary: In this study, a novel unsupervised algorithm called ICAT is proposed, which can accurately identify and resolve cell states in single-cell RNA sequencing experiments, especially in perturbation experiments, where cell states need to be matched and population substructure needs to be removed. Through validation using simulated and real datasets, it is shown that ICAT outperforms current integration workflows and is robust to various conditions. Empirical validation in a developmental model demonstrates that only ICAT can identify perturbation-unique cellular responses.
Article
Biotechnology & Applied Microbiology
Shiyi Yang, Sean E. Corbett, Yusuke Koga, Zhe Wang, W. Evan Johnson, Masanao Yajima, Joshua D. Campbell
Article
Nutrition & Dietetics
Maura E. Walker, Nirupa R. Matthan, Stefania Lamon-Fava, Gloria Solano-Aguilar, Saebyeol Jang, Sukla Lakshman, Aleksey Molokin, Joseph F. Urban, Tyler Faits, W. Evan Johnson, Alice H. Lichtenstein
CURRENT DEVELOPMENTS IN NUTRITION
(2019)
Review
Oncology
Joao B. Xavier, Vincent B. Young, Joseph Skufca, Fiona Ginty, Traci Testerman, Alexander T. Pearson, Paul Macklin, Amir Mitchell, Ilya Shmulevich, Lei Xie, J. Gregory Caporaso, Keith A. Crandall, Nicole L. Simone, Filipa Godoy-Vitorino, Timothy J. Griffin, Katrine L. Whiteson, Heather H. Gustafson, Daniel J. Slade, Thomas M. Schmidt, Marina R. S. Walther-Antonio, Tal Korem, Bobbie-Jo M. Webb-Robertson, Mark P. Styczynski, W. Evan Johnson, Christian Jobin, Jason M. Ridlon, Andrew Y. Koh, Michael Yu, Libusha Kelly, Jennifer A. Wargo