Article
Cell Biology
Arie Fridrich, Miguel Salinas-Saaverda, Itamar Kozlolvski, Joachim M. Surm, Eleni Chrysostomou, Abhinandan M. Tripathi, Uri Frank, Yehu Moran
Summary: The study reveals the importance of miR-2022 in initiating cell generation in Nematostella and its conservation across other cnidarian species.
Article
Multidisciplinary Sciences
Quentin I. B. Lemaitre, Natascha Bartsch, Ian U. Kouzel, Henriette Busengdal, Gemma Sian Richards, Patrick R. H. Steinmetz, Fabian Rentzsch
Summary: Endodermal neurogenesis is a rare phenomenon in animals. Researchers have identified a group of endoderm-specific neural progenitor cells in the cnidarian Nematostella vectensis, characterized by the expression of the transcription factor prdm14d. This study sheds light on the molecular regulation of non-ectodermal neurogenesis using Nematostella vectensis as a model, providing new insights into this poorly understood process.
NATURE COMMUNICATIONS
(2023)
Article
Biology
James M. Gahan, Lucas Leclere, Maria Hernandez-Valladares, Fabian Rentzsch
Summary: By analyzing the evolution of the CoREST-Lsd1-HDAC complex, researchers found that it is only present in choanoflagellates and animals. They identified a conserved CoREST complex in the sea anemone Nematostella vectensis. The expression pattern and mutant phenotypes of NvCoREST and NvLsd1 suggest that this complex is an ancient component of the animal developmental toolkit.
Article
Multidisciplinary Sciences
Leslie S. Babonis, Camille Enjolras, Joseph F. Ryan, Mark Q. Martindale
Summary: This study reveals the developmental mechanism of a truly novel cell type, cnidocytes. Cnidocytes develop by suppressing the neural fate of a subset of neurons expressing RFamide. A single regulatory gene, a C2H2-type zinc finger transcription factor (ZNF845), plays a crucial role in the development of cnidocytes and emerged through domain shuffling in the ancestor of cnidarians.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Article
Multidisciplinary Sciences
Shelly Reuven, Mieka Rinsky, Vera Brekhman, Assaf Malik, Oren Levy, Tamar Lotan
Summary: In cnidarians like Nematostella vectensis, long-term ecological success relies on sexual reproduction, with temperature and light being major inducers for spawning. Transcriptome analysis revealed upregulation of various processes like receptors and cytoskeleton during spawning induction, while downregulation of cell cycle and metabolism-related processes was observed. Our findings also suggest temperature change as a stronger inducer for spawning in Nematostella, expanding our understanding of sexual reproduction in cnidarians.
SCIENTIFIC REPORTS
(2021)
Article
Multidisciplinary Sciences
James M. Gahan, Ian U. Kouzel, Kamilla Ormevik Jansen, Pawel Burkhardt, Fabian Rentzsch
Summary: This study reveals the role of chromatin modifier Lsd1 in developmental regulation in cnidarians. The findings suggest that the integration of chromatin modifying proteins into developmental regulation predates the divergence of cnidarians and bilaterians, and is an ancient feature of animal development.
NATURE COMMUNICATIONS
(2022)
Article
Multidisciplinary Sciences
Layla Al-Shaer, Whitney Leach, Noor Baban, Mia Yagodich, Mathew C. C. Gibson, Michael J. J. Layden
Summary: We investigate factors influencing asexual reproduction in Nematostella vectensis, a burrowing sea anemone capable of transverse fission. Our study demonstrates that the presence of a burrowing substrate strongly promotes transverse fission and animal size does not affect fission rates. Gene expression analysis suggests that transcription factors and signaling pathways play vital roles in regulating transverse fission. Additionally, we find that the cell cycle is suppressed and cell adhesion and patterning mechanisms are downregulated during fission. This research provides insights into the reproductive biology of cnidarians.
ROYAL SOCIETY OPEN SCIENCE
(2023)
Article
Ecology
Shani Levy, Vera Brekhman, Anna Bakhman, Assaf Malik, Arnau Sebe-Pedros, Mickey Kosloff, Tamar Lotan
Summary: The study demonstrates that ectopic activation of GABA(B)R signaling affects neurogenic functions in the sea anemone Nematostella vectensis. The sustained activation of GABA(B)R signaling reversibly arrests the critical metamorphosis transition from planktonic larva to sessile polyp life stage. The findings point to an evolutionarily conserved function of GABA(B)R in neurogenesis regulation and shed light on early cnidarian development.
NATURE ECOLOGY & EVOLUTION
(2021)
Review
Physics, Multidisciplinary
Federico Bocci, Dongya Jia, Qing Nie, Mohit Kumar Jolly, Jose Onuchic
Summary: The last decade has seen a rise in theoretical and computational models used to describe complex gene regulatory networks and their dynamics, which can result in multistable and heterogeneous cell populations. The application of theoretical modeling in genetic and biochemical circuits has become more widespread, with theoreticians incorporating concepts from statistical physics, non-linear dynamics, and network theory. This review provides an overview of important methodologies in the field, discusses current and future challenges, offers hands-on tutorials for solving and simulating biological system models, and presents concrete examples for theoreticians interested in this fast-developing field.
REPORTS ON PROGRESS IN PHYSICS
(2023)
Article
Biochemistry & Molecular Biology
Ze-Tian Fang, Rajan Kapoor, Aniruddha Datta, Shuyu Liu, Matthew A. Stull, Paige G. Seitz, Charles D. Johnson, Sakiko Okumoto
Summary: The end-use quality of wheat flour is closely related to the amount and composition of storage proteins in the endosperm. TAM 111 and TAM 112 are two popular cultivars with significantly different protein content. Transcriptome data analysis revealed differences in starch metabolism and amino acid metabolism pathways between the two cultivars, as well as variations in the potential transcription factors regulating these pathways. These findings provide valuable insights for breeders and enhance our understanding of grain development mechanisms.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Biochemistry & Molecular Biology
Ying Guo, Tongli Wang, Fang-Fang Fu, Yousry A. El-Kassaby, Guibin Wang
Summary: The study revealed variations in photosynthetic capacity and related compounds in developing ginkgo leaves. A co-expression network was constructed to demonstrate the regulatory role of transcription factors in the photosynthetic light reaction pathway. This analysis identified candidate genes that could potentially improve photosynthetic capacity and yield in ginkgo trees.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Immunology
Jingwen Deng, Carlotta Schieler, Jose A. M. Borghans, Chuanjian Lu, Aridaman Pandit
Summary: This study used a machine learning approach to explore the gene regulatory networks of psoriasis and identified key regulators. Interferon signaling was found to play a crucial role in psoriatic inflammation.
FRONTIERS IN IMMUNOLOGY
(2022)
Article
Developmental Biology
Jacobo Solorzano, Enrique Carrillo-de Santa Pau, Teresa Laguna, Ana Busturia
Summary: By analyzing gene regulatory circuits between Polycomb/trithorax (PcG/trxG) proteins and microRNAs in the genome of Drosophila melanogaster, we have identified three classes of miRNA-PcG/trxG crosstalk interactions that define potential regulatory circuits, revealing a novel mechanism for the control of PcG/trxG and miRNA levels of expression in fruit flies.
DEVELOPMENTAL BIOLOGY
(2023)
Article
Geriatrics & Gerontology
Caterina Giovagnoni, Muhammad Ali, Lars M. T. Eijssen, Richard Maes, Kyonghwan Choe, Monique Mulder, Jos Kleinjans, Antonio del Sol, Enrico Glaab, Diego Mastroeni, Elaine Delvaux, Paul Coleman, Mario Losen, Ehsan Pishva, Pilar Martinez-Martinez, Daniel L. A. van den Hove
Summary: This study sheds light on the relationship between epigenetic and transcriptomic processes in regulating sphingolipid (SL) function in Alzheimer's disease (AD) patients. Transcriptomic and methylomic analysis revealed differentially expressed SL-related genes in AD patients and identified candidate genes that could potentially revert gene expression towards a healthy state. This approach may provide novel biomarkers and therapeutic alternatives for AD beyond traditional biological pathways.
NEUROBIOLOGY OF AGING
(2021)
Article
Computer Science, Information Systems
Ashis Pradhan, Mohan P. Pradhan, Ratika Pradhan
Summary: A river network is a natural geomorphological arrangement of stream segments, influenced by the terrain. Traditional digitization and attribute estimation methods are time-consuming and biased. This research proposes an efficient knowledge-based automated program that digitizes river networks accurately and generates desired stream attributes.
MULTIMEDIA TOOLS AND APPLICATIONS
(2023)
Article
Evolutionary Biology
Eve Gazave, Eric Rottinger
Summary: The ability of regeneration is common among animals, with different species showing varying levels of regenerative potential. Despite recent advances in regenerative studies, there is still a lack of comprehensive understanding of the evolution of animal regeneration.
JOURNAL OF EXPERIMENTAL ZOOLOGY PART B-MOLECULAR AND DEVELOPMENTAL EVOLUTION
(2021)
Article
Biochemistry & Molecular Biology
Barbara Porro, Thamilla Zamoum, Cedric Mallien, Benjamin C. C. Hume, Christian R. Voolstra, Eric Rottinger, Paola Furla, Didier Forcioli
Summary: This study investigated the flexibility of symbiont acquisition in the Mediterranean snakelocks sea anemone Anemonia viridis, revealing that the composition of within-host-symbiont populations is more dependent on geographical origin of the hosts rather than lineage. The similarities in host-symbiont communities were greater among different genets, suggesting a capacity for horizontal acquisition. The mixed-mode transmission strategy in A. viridis may explain the large phenotypic plasticity observed in this anemone.
Article
Clinical Neurology
Johann de Jong, Ioana Cutcutache, Matthew Page, Sami Elmoufti, Cynthia Dilley, Holger Froehlich, Martin Armstrong
Summary: This study successfully established a machine learning model that integrates clinical and genetic data to predict drug response in epilepsy patients, achieving significant results and providing a blueprint for the goals of precision medicine.
Review
Cell Biology
Eric Roettinger
Summary: Scientists have been intrigued by the ability of metazoans to regenerate lost or injured body parts, with whole body regeneration being a widespread phenomenon in aquatic/marine invertebrates. The sea anemone Nematostella vectensis has emerged as a key research model for understanding the cellular and molecular mechanisms underlying whole-body regeneration. Comparing embryonic development and regeneration in the same organism helps provide insight into specific elements of regeneration.
Article
Biochemistry & Molecular Biology
Robert E. Jinkerson, Joseph A. Russo, Casandra R. Newkirk, Andrea L. Kirk, Richard J. Chi, Mark Q. Martindale, Arthur R. Grossman, Masayuki Hatta, Tingting Xiang
Summary: Photosynthesis is not necessary for symbiosis establishment, but its impact depends on specific cnidarian-Symbiodiniaceae relationships. UV mutagenesis can generate photosynthetic mutants capable of infecting hosts in the absence of photosynthesis.
Article
Multidisciplinary Sciences
Allison Edgar, Jose Miguel Ponciano, Mark Q. Martindale
Summary: Research shows that ctenophores, specifically Mnemiopsis leidyi, do not have separate phases of early and adult reproduction. They start reproducing at a small body size and continue spawning under suitable environmental conditions. The constraints on reproductive capacity are similar in both small and large animals. These findings have significant implications for understanding resource partitioning and managing the species in its invaded range.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Article
Multidisciplinary Sciences
Leslie S. Babonis, Camille Enjolras, Joseph F. Ryan, Mark Q. Martindale
Summary: This study reveals the developmental mechanism of a truly novel cell type, cnidocytes. Cnidocytes develop by suppressing the neural fate of a subset of neurons expressing RFamide. A single regulatory gene, a C2H2-type zinc finger transcription factor (ZNF845), plays a crucial role in the development of cnidocytes and emerged through domain shuffling in the ancestor of cnidarians.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Article
Evolutionary Biology
Bailey M. Steinworth, Mark Q. Martindale, Joseph F. Ryan
Summary: Hox and ParaHox transcription factors play crucial roles in determining cell fates in animal development. In this study, researchers analyzed the complete set of Hox and ParaHox genes from various species of cnidarians, including all four medusozoan classes and both anthozoan classes. The results showed that the Hox genes involved in patterning anthozoan polyps are missing in the stem leading to Medusozoa. Additionally, the study provided new insights into the spatial and temporal expression patterns of Hox and ParaHox genes in a Scyphozoa jellyfish.
GENOME BIOLOGY AND EVOLUTION
(2023)
Article
Biochemistry & Molecular Biology
Jennifer Ortiz, Yuriy Bobkov, Melissa B. DeBiasse, Dorothy G. Mitchell, Allison Edgar, Mark Q. Martindale, Anthony G. Moss, Leslie S. Babonis, Joseph F. Ryan
Summary: This article investigates the innexin gene in four species of ctenophores and finds that these genes have evolved independently from those of other animals and were established early in the evolution of ctenophores. The study also shows that ctenophores have functional innexin hemichannels that are closely related to those of other animals. Overall, the results suggest that the last common ancestor of animals had channels capable of forming both gap junctions and innexin hemichannels, and that innexin genes have independently evolved in major lineages throughout Metazoa.
MOLECULAR BIOLOGY AND EVOLUTION
(2023)
Letter
Multidisciplinary Sciences
Allison Edgar, Jose Miguel Ponciano, Mark Q. Martindale
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2023)
Article
Biochemistry & Molecular Biology
Labib Rouhana, Allison Edgar, Fredrik Hugosson, Valeria Dountcheva, Mark Q. Martindale, Joseph F. Ryan
Summary: Differential regulation of gene expression is crucial for the astonishing diversity of life on Earth. Cytoplasmic polyadenylation, mediated by the CPEB family, regulates the translation of maternal transcripts and is present in animals but not non-animal lineages. Phylogenetic analyses reveal that CPEB1 and CPEB2 originated in the animal stem lineage. This study demonstrates the conservation of maternal expression and polyadenylation targets in cnidarians, ctenophores, and vertebrates, suggesting that cytoplasmic polyadenylation through CPEBs was a fundamental innovation in animal evolution.
MOLECULAR BIOLOGY AND EVOLUTION
(2023)
Article
Multidisciplinary Sciences
Leslie S. Babonis, Camille Enjolras, Abigail J. Reft, Brent M. Foster, Fredrik Hugosson, Joseph F. Ryan, Marymegan Daly, Mark Q. Martindale
Summary: Cnidocytes are explosive stinging cells unique to cnidarians, such as corals and jellyfish. Using CRISPR/Cas9-mediated genome editing, researchers have discovered that a single transcription factor, NvSox2, is responsible for determining two alternative fates of stinging cells in the sea anemone Nematostella vectensis. Knockout of NvSox2 transforms piercing cells into ensnaring cells, providing insights into the diversification of cell types.
NATURE COMMUNICATIONS
(2023)
Article
Cell Biology
Pei Zhang, Yuanzhen Zhu, Qunfei Guo, Ji Li, Xiaoyu Zhan, Hao Yu, Nianxia Xie, Huishuang Tan, Nina Lundholm, Lydia Garcia-Cuetos, Michael D. Martin, Meritxell Anto Subirats, Yi-Hsien Su, Inaki Ruiz-Trillo, Mark Q. Martindale, Jr-Kai Yu, M. Thomas P. Gilbert, Guojie Zhang, Qiye Li
Summary: By analyzing the RNA editomes of 22 Holozoa species, we provide substantial evidence that A-to-I mRNA editing is a regulatory innovation that originated in the last common ancestor of extant metazoans. This ancient biochemical process is preserved in most metazoans and primarily targets endogenous dsRNA formed by young repeats. We also find that intermolecular pairing of sense-antisense transcripts is an important mechanism for forming dsRNA substrates for A-to-I editing in some lineages. Recoding editing is rarely shared across lineages but preferentially targets genes involved in neural and cytoskeleton systems in bilaterians. We conclude that metazoan A-to-I editing initially emerged as a safeguard mechanism against repeat-derived dsRNA and was later co-opted into diverse biological processes due to its mutagenic nature.
Article
Chemistry, Physical
S. Tori Ellison, Senthilkumar Duraivel, Vignesh Subramaniam, Fredrik Hugosson, Bo Yu, Joseph J. Lebowitz, Habibeh Khoshbouei, Tanmay P. Lele, Mark Q. Martindale, Thomas E. Angelini
Summary: Cell type variation plays a crucial role in tissue physiology. To better understand the relationship between tissue structure and function, and to engineer accurate tissues, it is necessary to assemble 3D cellular structures with detailed precision. In this study, a method of 3D cell assembly with subcellular precision is introduced. The authors demonstrate the ability to create detailed cellular patterns and show functional characteristics after assembly.
Article
Engineering, Multidisciplinary
Jeremy Elias, Thomas Angelini, Mark Q. Martindale, Laurie Gower
Summary: Cellular strategies and regulation are crucial for the formation of biominerals. By studying the interaction between organic matrices and mineral precursors under different temperatures and seawater compositions, we identified suitable conditions for calcium carbonate infiltration. These findings are valuable for the development of novel biosynthetic materials.