Article
Multidisciplinary Sciences
Marta Losa, Iros Barozzi, Marco Osterwalder, Viviana Hermosilla-Aguayo, Angela Morabito, Brandon H. Chacon, Peyman Zarrineh, Ausra Girdziusaite, Jean Denis Benazet, Jianjian Zhu, Susan Mackem, Terence D. Capellini, Diane Dickel, Nicoletta Bobola, Aimee Zuniga, Axel Visel, Rolf Zeller, Licia Selleri
Summary: This study investigates how transcription factors with widespread distribution in vertebrate embryos can perform tissue-specific functions. The researchers demonstrate that PBX TALE homeoproteins interact with the transcriptional regulator HAND2 to regulate a gene regulatory network (GRN) in subsets of hindlimb mesenchymal cells, revealing principles of cooperation between promiscuous and tissue-specific regulators in developmental programs.
NATURE COMMUNICATIONS
(2023)
Article
Cell Biology
Aubrey G. A. Howard, Aaron C. Nguyen, Joshua Tworig, Priya Ravisankar, Eileen W. Singleton, Can Li, Grayson Kotzur, Joshua S. Waxman, Rosa A. Uribe
Summary: Neural crest cells (NCCs) are migratory and multipotent stem cells essential to vertebrate embryonic development. This study identifies the gene Hoxb5b as a regulator of NCC development, demonstrating that elevated Hoxb5b levels promote expansion of zebrafish NCCs and specifically expand expression domains of vagal NCC markers. The study also shows that early increase in vagal NCCs leads to supernumerary enteric neural progenitors, but these fail to properly expand into enterically fated neurons in the gut tissue.
FRONTIERS IN CELL AND DEVELOPMENTAL BIOLOGY
(2022)
Article
Biology
Humberto G. Ferron, Philip C. J. Donoghue
Summary: The study analyzes the evolution of swimming speed in early vertebrates based on fin morphology and challenges the hypothesis of a trend towards more active lifestyles in the lineage leading to jawed groups.
COMMUNICATIONS BIOLOGY
(2022)
Article
Developmental Biology
Makoto Abe, Timothy C. Cox, Anthony B. Firulli, Stanley M. Kanai, Jacob Dahlka, Kim-Chew Lim, James Douglas Engel, David E. Clouthier
Summary: Neural crest cells in the mandibular and maxillary prominences initially respond to signals from both regions, with GATA3 playing a crucial role in separating the upper and lower jaw domains during development by influencing BMP4 and FGF8 gene regulatory networks.
Review
Biotechnology & Applied Microbiology
Hiba Asrar, Abigail S. Tucker
Summary: Major organs and tissues require close association with the vasculature during development and for later function. Recent research has revealed novel roles for endothelial cells in tissue morphogenesis and differentiation, highlighting the importance of providing a vasculature when constructing tissues and organs for tissue engineering. Important signaling pathways regulating the cross talk between endothelial cells and their environment have been identified in various organ systems.
FRONTIERS IN BIOENGINEERING AND BIOTECHNOLOGY
(2022)
Article
Dentistry, Oral Surgery & Medicine
X. Wang, Y. Liang, Z. Zhu, W. Li, B. Shi, Y. Deng, C. Li, O. Sha
Summary: This study demonstrates that fibronectin 1 (Fn1) synthesized by neural crest cells (NCCs) plays a crucial role in regulating the patterning of the third pharyngeal pouch and the morphogenesis of the thymus/parathyroid.
JOURNAL OF DENTAL RESEARCH
(2022)
Article
Cell Biology
Aubrey G. A. Howard, Rosa A. Uribe
Summary: This review discusses the process of neural crest epithelial-to-mesenchymal transition (EMT) and the roles of extracellular matrix (ECM) and cellular effector proteins in the migration of neural crest cells. It also introduces the regulation of EMT and ECM remodeling during neural crest cell ontogenesis by Hox transcription factors.
Article
Multidisciplinary Sciences
Ahmadreza Azizi, Michel Pleimling
Summary: The study investigates the performance of machine learning algorithms trained with configurations from Monte Carlo simulations of the two-dimensional Ising model. Convolutional neural networks are effective in locating the phase transition point accurately and displaying finite-size scaling with Ising critical exponent. However, restricted Boltzmann machines generate configurations with magnetizations and energies not allowed in the original system, leading to incorrect weight distributions and spatial correlations. Shortcomings are also observed when training RBM with configurations from the non-conserved Ising model.
SCIENTIFIC REPORTS
(2021)
Article
Multidisciplinary Sciences
Michael A. Sackville, Christopher B. Cameron, J. Andrew Gillis, Colin J. Brauner
Summary: Gas exchange and ion regulation are crucial in the evolution of vertebrates. Gills are involved in gas exchange and become the dominant site for larger or more active vertebrates, while all three taxa exhibit ion regulation in their gills. Ammocoete gills are responsible for all ion flux, indicating an earlier origin of ion regulation at gills than gas exchange in vertebrates.
Article
Biochemistry & Molecular Biology
Alberto Pezzotta, James Briscoe
Summary: This article describes the mechanism of morphogen-driven cell fate decisions in developing tissues. An alternative framework using optimal control theory is developed to tackle the problem of morphogen patterning. This approach recovers experimentally observed properties of patterning strategies and offers insight into design principles that produce timely, precise, and reproducible morphogen patterning.
Article
Plant Sciences
Yan Zhu, John Schiefelbein
Summary: By studying the wild plants Rhodiola rosea, Boehmeria nivea, and Cucumis sativus, it was found that R. rosea and B. nivea belong to the Type III root hair cell distribution pattern, while C. sativus belongs to the Type I pattern. There are significant similarities in the structure, expression, and function of Arabidopsis patterning gene homologs in R. rosea and B. nivea, while major changes were observed in C. sativus. It is proposed that different Type III species in superrosids inherited the patterning gene regulatory network from a common ancestor, while Type I species arose through mutations in multiple lineages.
Article
Genetics & Heredity
Gokul Gopinathan, Xinmin Zhang, Xianghong Luan, Thomas G. H. Diekwisch
Summary: In this study, the epigenetic events that limit HOX gene expression in craniofacial tissues were investigated. High levels of repressive H3K27me3 marks were found on the HOX gene promoters in undifferentiated neural crest cells, while the ratio of K4/K27 marks was less repressive in differentiated odontogenic progenitors and other craniofacial tissues. The elevated levels of HOX genes, especially those from the HOXA and HOXB clusters, were found in alveolar bone cells. The induction of HOX expression in craniofacial neural crest cells resulted in decreased mineralization markers and promoting HOX gene expression in developing teeth led to increased patterning events and gene expression.
Article
Microbiology
Fan Xiong, Sijia Chen, Ivan Jakovlic, Wenxiang Li, Ming Li, Hong Zou, Guitang Wang, Shangong Wu
Summary: This study found that the bile acid profile, especially secondary bile acids, underwent significant changes when grass carp and mice were fed with Citrobacter freundii. Additionally, lipid metabolism was significantly affected by C. freundii. Analysis of liver transcriptome sequencing data revealed that the CYP7A1 gene was significantly up-regulated in both grass carp and mice. Overexpression of HNF4B in grass carp resulted in a significant increase in the expression level of CYP7A1. These findings suggest that intestinal microbiota play a conserved role in bile acid metabolism in vertebrates, and HNF4B may be an important regulator of bile acid metabolism in fish.
FRONTIERS IN MICROBIOLOGY
(2022)
Article
Developmental Biology
Emily V. W. Setton, Prashant P. Sharma
Summary: The study showed that Wnt signaling might not be essential for maintaining Wnt8 expression across Arthropoda, as knockdown of arr resulted in varying degrees of posterior truncations in insects. Severe loss of arr expression disrupted the Wnt pathway systemically, yet interestingly did not abolish Wnt8 expression in all three species, indicating the complexity of the regulatory mechanisms involved.
DEVELOPMENTAL BIOLOGY
(2021)
Article
Biology
Antigoni Gogolou, Celine Souilhol, Ilaria Granata, Filip J. Wymeersch, Ichcha Manipur, Matthew Wind, Thomas J. R. Frith, Maria Guarini, Alessandro Bertero, Christoph Bock, Florian Halbritter, Minoru Takasato, Mario R. Guarracino, Anestis Tsakiridis
Summary: The neural crest (NC) is an important cell population in embryonic development, and understanding its regionalization is crucial. This study investigates the acquisition of posterior axial identity in NC cells derived from neuromesodermal progenitors (NMPs) through the regulation of transcription factors and signaling pathways. The findings reveal a previously unknown role of TBXT in influencing posterior NC fate and highlight the existence of cell type-dependent modes of posterior axial identity control.
Article
Cell Biology
Bianca A. Ulloa, Samima S. Habbsa, Kathryn S. Potts, Alana Lewis, Mia McKinstry, Sara G. Payne, Julio C. Flores, Anastasia Nizhnik, Maria Feliz Norberto, Christian Mosimann, Teresa Bowman
Summary: By using single-cell transcriptomics and lineage-tracing approaches, it was found that nascent HSCs have self-renewal capabilities but display differentiation latency, while HSC-independent embryonic progenitors can sustain hematopoiesis during development.
Article
Anatomy & Morphology
Robert L. Lalonde, Cassie L. Kemmler, Frederike W. Riemslagh, Andrew J. Aman, Jelena Kresoja-Rakic, Hannah R. Moran, Susan Nieuwenhuize, David M. Parichy, Alexa Burger, Christian Mosimann
Summary: This study compares the recombination efficiency and reporter expression pattern of commonly used Switch reporter lines, and finds that ubi:Switch and hsp70l:Switch show better recombination efficiency in specific tissues during early zebrafish development.
DEVELOPMENTAL DYNAMICS
(2022)
Article
Multidisciplinary Sciences
Vasileios Papadogiannis, Alessandro Pennati, Hugo J. Parker, Ute Rothbacher, Cedric Patthey, Marianne E. Bronner, Sebastian M. Shimeld
Summary: This study investigates the role of the Hmx gene in the development of sensory ganglia in vertebrates. The results demonstrate the conservation of regulatory and functional properties of Hmx between Ciona and vertebrates, and suggest that bipolar tail neurons might be homologous to cranial sensory ganglia.
Article
Multidisciplinary Sciences
Karin D. Prummel, Helena L. Crowell, Susan Nieuwenhuize, Eline C. Brombacher, Stephan Daetwyler, Charlotte Soneson, Jelena Kresoja-Rakic, Manuel Ronner, Agnese Kocere, Alexander Ernst, Zahra Labbaf, David E. Clouthier, Anthony B. Firulli, Hector Sanchez-Iranzo, Sundar R. Naganathan, Rebecca O'Rourke, Erez Raz, Nadia Mercader, Alexa Burger, Emanuela Felley-Bosco, Jan Huisken, Mark D. Robinson, Christian Mosimann
Summary: This study uncovers the early origins of mesothelium progenitor cells in zebrafish, linking the function of the Hand2 gene to mesothelium formation and the re-activation of mesothelioma tumors.
NATURE COMMUNICATIONS
(2022)
Article
Biology
Fatma Mansour, Christian Hinze, Narasimha Swamy Telugu, Jelena Kresoja, Iman B. Shaheed, Christian Mosimann, Sebastian Diecke, Kai M. Schmidt-Ott
Summary: CEP83 plays a crucial role in the differentiation of human-induced pluripotent stem cells (hiPSCs) towards intermediate mesoderm (IM). Inactivating deletions of CEP83 in hiPSCs disrupted the differentiation into IM progenitor cells and resulted in abnormal induction of lateral plate mesoderm (LPM) markers. This study highlights the importance of CEP83 in regulating the balance between IM and LPM formation from hiPSCs.
Article
Multidisciplinary Sciences
Kenny Mattonet, Frederike W. Riemslagh, Stefan Guenther, Karin D. Prummel, Gokul Kesavan, Stefan Hans, Ingo Ebersberger, Michael Brand, Alexa Burger, Sven Reischauer, Christian Mosimann, Didier Y. R. Stainier
Summary: This study reveals that Npas4l/Tal1/Lmo2 play a role in the fate decision between the endothelial and pronephron lineages. Npas4l induces the expression of the transcription factor genes etsrp, tall, and Imo2, which are crucial for endothelial specification.
Article
Developmental Biology
Zainab Afzal, Jeffrey J. Lange, Christof Nolte, Sean McKinney, Christopher Wood, Ariel Paulson, Bony De Kumar, Jay Unruh, Brian D. Slaughter, Robb Krumlauf
Summary: Signaling pathways regulate the patterns of Hox gene expression in axial identity specification. Little is known about the properties of cis-regulatory elements and transcriptional mechanisms that control Hox expression through graded signaling inputs. This study optimized a single molecule fluorescent in situ hybridization (smFISH) technique to evaluate the role of three retinoic acid response element (RARE)-dependent enhancers in regulating nascent transcription patterns of Hoxb genes. The results suggest that these enhancers have differential impacts on global and local patterns of transcription, and their competitive interactions are important for maintaining proper levels and patterns of Hoxb transcription.
Review
Cell Biology
Agnese Kocere, Robert L. Lalonde, Christian Mosimann, Alexa Burger
Summary: Syndromic birth defects are rare diseases that can present with multiple organ defects. The developmental plasticity of lateral plate mesoderm (LPM) may explain the seemingly unrelated defects in these diseases. Integrating patient genome-sequencing data with model organism studies provides insights into complex LPM-associated birth defects. Understanding the common LPM origin of congenital phenotypes allows us to discover developmental mechanisms and anticipate comorbidities in congenital diseases affecting the cardiovascular system and beyond.
DISEASE MODELS & MECHANISMS
(2022)
Article
Multidisciplinary Sciences
Keh-Weei Tzung, Robert L. Lalonde, Karin D. Prummel, Harsha Mahabaleshwar, Hannah R. Moran, Jan Stundl, Amanda N. Cass, Yao Le, Robert Lea, Karel Dorey, Monika J. Tomecka, Changqing Zhang, Eline C. Brombacher, William T. White, Henry H. Roehl, Frank J. Tulenko, Christoph Winkler, Peter D. Currie, Enrique Amaya, Marcus C. Davis, Marianne E. Bronner, Christian Mosimann, Tom J. Carney
Summary: The development of paired appendages was a key innovation during vertebrate evolution. This study identifies the larval zebrafish unpaired pre-anal fin fold (PAFF) as a developmental intermediate between median and paired fins. The study also demonstrates that increasing bone morphogenetic protein signaling can bifurcate the PAFF into paired fin folds. This work provides evidence for the existence of lateral fin folds as embryonic anlage for the elaboration to paired fins.
Article
Multidisciplinary Sciences
Cassie L. Kemmler, Jana Smolikova, Hannah R. Moran, Brandon J. Mannion, Dunja Knapp, Fabian Lim, Anna Czarkwiani, Viviana Hermosilla Aguayo, Vincent Rapp, Olivia E. Fitch, Seraina Boetschi, Licia Selleri, Emma Farley, Ingo Braasch, Maximina Yun, Axel Visel, Marco Osterwalder, Christian Mosimann, Zbynek Kozmik, Alexa Burger
Summary: In this study, researchers identified the enhancers responsible for the specific expression of Brachyury/T/TBXT in the notochord of mammals. These enhancers act as auto-regulatory shadow enhancers, controlling the development of the notochord.
NATURE COMMUNICATIONS
(2023)
Article
Developmental Biology
Zainab Afzal, Robb Krumlauf
Summary: Hox genes are crucial for the development of animals, as they regulate the regional identity of cells and tissues. Understanding the mechanisms behind the precise regulation of Hox gene expression is important for tissue development. Recent findings have shed light on the dynamics and molecular mechanisms of transcriptional regulation, leading to increased interest in understanding how these mechanisms contribute to the regulation of Hox gene expression.
JOURNAL OF DEVELOPMENTAL BIOLOGY
(2022)
Article
Cardiac & Cardiovascular Systems
Catherine Pfefferli, Hannah R. Moran, Anastasia Felker, Christian Mosimann, Anna Jazwinska
Summary: The study reveals the presence of myocardial cells derived from FHF in both developing and adult zebrafish hearts, predominantly located in the outer curvature and right side of the ventricle in embryonic stages. These lineage-labeled cells persist in adulthood, positioned in a region opposite to the atrium and encompassing the apex, indicating a cell-based compartmentalization of the adult zebrafish ventricle.
JOURNAL OF CARDIOVASCULAR DEVELOPMENT AND DISEASE
(2021)
Review
Cardiac & Cardiovascular Systems
Cassie L. Kemmler, Frederike W. Riemslagh, Hannah R. Moran, Christian Mosimann
Summary: The zebrafish model allows for studying early heart morphogenesis and mechanisms of congenital disease; despite having only two heart chambers, the zebrafish heart integrates key processes central to cardiac development across vertebrates; the combination of transgenic reporters and CRISPR-Cas9 for genome engineering enables functional testing of candidate genes associated with congenital heart defects.
JOURNAL OF CARDIOVASCULAR DEVELOPMENT AND DISEASE
(2021)
