Article
Developmental Biology
Vasileios Papadogiannis, Dorit Hockman, Silvia Mercurio, Claire Ramsay, Mark Hintze, Cedric Patthey, Andrea Streit, Sebastian M. Shimeld
Summary: The Estrogen Related Receptor (ERR) nuclear hormone receptor genes play diverse roles in vertebrate development. In embryos, ERR genes are expressed in various tissues, particularly the nervous system. Most jawed vertebrates and lampreys have four ERR paralogues, which are ancestrally linked to Estrogen Receptor genes. Conserved non-coding sequences in ERR introns are found to be regulatory and drive gene expression in the nervous system.
DEVELOPMENTAL BIOLOGY
(2023)
Article
Plant Sciences
Yingying Wen, Ying Qin, Bingyi Shao, Jianwu Li, Chongbo Ma, Yan Liu, Boyun Yang, Xiaohua Jin
Summary: The plastomes of Gastrodieae, a mycoheterotrophic clade of the Orchidaceae family, are characterized by reduced structure and gene content, low GC content, rrn block formation, lineage-specific reconfiguration, and positive selection. They serve as an excellent model for studying plastome evolution and provide insights into plastome evolution in parasitic plants.
Review
Ecology
Madeleine E. Aase-Remedios, David E. K. Ferrier
Summary: Comparative approaches in studying chordate genomes have revealed the significance of gene duplications, including whole genome duplications, in the evolution of gene families. Duplicated genes are key in developmental biology and play a role in major evolutionary transitions, with mechanisms such as retention, subfunctionalization, neofunctionalization, and specialization. Understanding the impact of gene duplication on chordate evolution, including the retention and loss patterns of duplicated genes, remains a complex topic that requires further exploration with the help of sequencing projects and genomic resources.
FRONTIERS IN ECOLOGY AND EVOLUTION
(2021)
Article
Neurosciences
Giacomo Gattoni, Toby G. R. Andrews, Elia Benito-Gutierrez
Summary: Despite the highly regionalized molecular structure of the amphioxus neural tube, little is known about the morphogenetic mechanisms regulating the emergence of specific cell types at distinct sites in the nervous system. Proliferation plays a crucial role in shaping and regionalizing the amphioxus neural axis during development, with specific regions depending on proliferation at precise time-points for their maturation. This study highlights the importance of tightly controlled proliferation in establishing the cell type repertoire and influencing tissue geometry in amphioxus embryos.
FRONTIERS IN NEUROSCIENCE
(2022)
Article
Multidisciplinary Sciences
Takashi Goto, Takashi Soyano, Meng Liu, Tomoko Mori, Masayoshi Kawaguchi
Summary: Nodule development requires spatiotemporal coordination between root epidermis and root cortex. In this study, we found that IAA carboxyl methyltransferase 1 (IAMT1) is transiently induced in wild-type roots at early stages of infection, but shows different expression dynamics in the mutant daphne. Knockdown of one of the IAMT1s, IAMT1a, inhibits nodule development in the root cortex. We also observed an increase in root MeIAA levels with rhizobial infection, and application of MeIAA induces expression of the symbiotic gene NIN in the absence of infection.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Article
Biochemistry & Molecular Biology
Akira Noga, Mao Horii, Yumi Goto, Kiminori Toyooka, Takashi Ishikawa, Masafumi Hirono
Summary: The study reveals the importance of centriolar protein Bld10p in the formation of centriole structural symmetry, particularly in the cartwheel-independent mechanism. Bld10p plays a role in determining the inter-triplet distance and regulating the centriole structure in the absence of the cartwheel.
Article
Biology
William R. Jeffery, Bo Li, Mandy Ng, Lianwei Li, Spela Goricki, Li Ma
Summary: In Ciona intestinalis, while adult stem cells in the branchial sac vasculature proliferate and progenitor cells migrate to the site of distal injury, regeneration only occurs in the proximal fragments. By analyzing the transcriptome of regenerating animals, we found that the chaperone system genes hsp70, dnaJb4, and bag3 are significantly upregulated in the branchial sac vasculature following distal injury. The upregulation of these heat shock protein genes is crucial for regeneration.
Article
Microbiology
Diana Cortes-Selva, Lisa Gibbs, J. Alan Maschek, Marcia Nascimento, Tyler Van Ry, James E. Cox, Eyal Amiel, Keke C. Fairfax
Summary: The study reveals that bone marrow derived macrophages from male mice infected with Schistosoma mansoni have long-lasting increases in lipid metabolism and this metabolic reprogramming can be transferred to uninfected hosts through bone marrow transplantation. Furthermore, the polarization of type-2 cytokines is not enough to replicate the infection-induced metabolic changes, indicating a unique and long-lasting reprogramming of macrophage metabolic signature induced by helminth infection.
Article
Biochemistry & Molecular Biology
Eun-Ah Christine Song, Monika Che, Jason Osinski, Kirsten Smalley, Erich Horeth, Satrajit Sinha, Rose-Anne Romano
Summary: ANp63 is crucial in maintaining and renewing myoepithelial cells in the salivary glands. These cells function as bipotent progenitor cells during homeostasis and contribute to the differentiation of ductal and acinar cells. However, their contribution to regeneration following severe injury is independent of delta Np63.
CELL DEATH AND DIFFERENTIATION
(2023)
Review
Neurosciences
Megan L. Martik, Marianne E. Bronner
Summary: The paper discusses the importance of the neural crest and cranial placodes in vertebrate evolution, as well as recent findings on the gradual evolution of neural crest cells in the course of deuterostome evolution. The results suggest a progressive addition of cell types to the repertoire of neural crest derivatives throughout vertebrate evolution.
NATURE REVIEWS NEUROSCIENCE
(2021)
Article
Cell Biology
Enrico Berrino, Umberto Miglio, Sara Erika Bellomo, Carla Debernardi, Alberto Bragoni, Annalisa Petrelli, Eliano Cascardi, Silvia Giordano, Filippo Montemurro, Caterina Marchio, Tiziana Venesio, Anna Sapino
Summary: L1 reactivation is associated with aggressive features of breast cancer and worse clinical outcomes.
Article
Oncology
Jiaqian Liang, Liyang Wang, Larysa Poluben, Mannan Nouri, Seiji Arai, Lisha Xie, Olga S. Voznesensky, Laura Cato, Xin Yuan, Joshua W. Russo, Henry W. Long, Myles Brown, Shaoyong Chen, Steven P. Balk
Summary: In castration-resistant prostate cancer (CRPC), the splice variant ARv7 can function independently of the full length ARfl, with both contributing independently to overall AR activity.
Article
Infectious Diseases
Libin Chen, Weiwei Jiang, Wanyan Wu, Siyuan Zhang, Juncheng Cai, Ting Lv, Bin Xiang, Qiuyan Lin, Ming Liao, Chan Ding, Tao Ren
Summary: This study identified the prevalence of GI-19 and GI-7 subtypes of infectious bronchitis virus (IBV) in China and investigated the evolution and transmission dynamics of the GI-7 subtype. The results suggested that the GI-7 subtype originated from Taiwan and spread mainly in South China, with low codon usage bias in the S1 gene. The findings provide valuable insights for the prevention and control of viral infection.
TRANSBOUNDARY AND EMERGING DISEASES
(2023)
Article
Cell Biology
Simona Machacova, Zbynek Kozmik, Iryna Kozmikova
Summary: The study analyzed the cis-regulatory sequence of amphioxus Chordin and identified an enhancer that is dependent on Nodal signaling for the formation of the chordate dorsal organizer. This finding provides insights into the evolution of organizer-specific gene regulation in chordates.
DEVELOPMENT GENES AND EVOLUTION
(2022)
Article
Ecology
Jesse Jorna, Jackson B. Linde, Peter C. Searle, Abigail C. Jackson, Mary-Elise Nielsen, Madeleine S. Nate, Natalie A. Saxton, Felix Grewe, Maria de los Angeles Herrera-Campos, Richard W. Spjut, Huini Wu, Brian Ho, H. Thorsten Lumbsch, Steven D. Leavitt
Summary: Species delimitation among closely related species remains challenging due to discrepancies between traditional phenotype-based approaches and natural groupings. High-throughput sequencing has made it more cost-effective to acquire genome-scale data, allowing for the resolution of ambiguous species boundaries. Despite the development of various species delimitation analyses, such as BPP and SNAPP+BFD, empirical molecular approaches may still be biased by confounding factors, leading to inconsistent results. Cross-validating results between different datasets and controlling for genetic divergence at the population level can improve the reliability of species delimitation.
ECOLOGY AND EVOLUTION
(2021)
Article
Anatomy & Morphology
Nicholas D. Holland, Ildiko M. L. Somorjai
Summary: The epidermis of a cephalochordate undergoes changes in cell arrangement and structure after tail amputation, with cells initially dispersing before returning to a close hexagonal grid pattern. Additionally, there is a temporary formation of intercellular gaps near the regenerating tail, which eventually closes up and reverts back to the original close association between cells.
Review
Fisheries
Morag Clinton, David E. K. Ferrier, Samuel A. M. Martin, Andrew S. Brierley
Summary: This review summarizes the impact of gelatinous plankton on finfish aquaculture, focusing on the effects of cnidarians on fish health. Current monitoring and mitigation strategies are presented, along with identified critical knowledge gaps.
ICES JOURNAL OF MARINE SCIENCE
(2021)
Review
Ecology
Madeleine E. Aase-Remedios, David E. K. Ferrier
Summary: Comparative approaches in studying chordate genomes have revealed the significance of gene duplications, including whole genome duplications, in the evolution of gene families. Duplicated genes are key in developmental biology and play a role in major evolutionary transitions, with mechanisms such as retention, subfunctionalization, neofunctionalization, and specialization. Understanding the impact of gene duplication on chordate evolution, including the retention and loss patterns of duplicated genes, remains a complex topic that requires further exploration with the help of sequencing projects and genomic resources.
FRONTIERS IN ECOLOGY AND EVOLUTION
(2021)
Article
Biology
Baruch Rinkevich, Loriano Ballarin, Pedro Martinez, Ildiko Somorjai, Oshrat Ben-Hamo, Ilya Borisenko, Eugene Berezikov, Alexander Ereskovsky, Eve Gazave, Denis Khnykin, Lucia Manni, Olga Petukhova, Amalia Rosner, Eric Rottinger, Antonietta Spagnuolo, Michela Sugni, Stefano Tiozzo, Bert Hobmayer
Summary: Adult stem cells in various animals exhibit diverse activities and phenotypes, with some being rare, morphologically undifferentiated, and undergoing asymmetric cell division. They play roles in maintaining tissue homeostasis, repair, and regeneration, potentially making up a substantial portion of animal cells.
BIOLOGICAL REVIEWS
(2022)
Article
Biotechnology & Applied Microbiology
Madeleine E. Aase-Remedios, Clara Coll-Llado, David E. K. Ferrier
Summary: Research on muscle responses to feeding-fasting-refeeding experiments reveals the genetic mechanisms involved in muscle degradation and maintenance, providing insight into the regulatory pathways of muscle nutrient response.
Article
Microbiology
Morag Clinton, Adam J. Wyness, Samuel A. M. Martin, Andrew S. Brierley, David E. K. Ferrier
Summary: This study compared the microbial assemblages obtained from Atlantic salmon gills using swabbing and biopsy excision, revealing clear divergence in microbial communities obtained through different sampling strategies. Swabbing consistently isolated a more diverse microbial consortia, while biopsy extraction hinted at potential for more cryptic localization of some community members. Overall, the study highlights the importance of considering different sampling methods when studying fish microbiomes.
Article
Cell Biology
Nuria P. Torres-Aguila, Marika Salonna, Stefan Hoppler, David E. K. Ferrier
Summary: Wnt signaling is essential for animal development, regeneration and also plays a role in diseases. TCF/LEF proteins mediate Wnt/beta-catenin-regulated gene expression. Vertebrates possess a high diversity of TCF/LEF family genes compared to invertebrates, suggesting changes in Wnt signaling during vertebrate evolution. This study clarifies the relationships within the TCF/LEF gene family in chordates through comparative analysis of gene structure, molecular phylogeny, and gene synteny. The results suggest that the four TCF/LEF paralog subfamilies in jawed vertebrates evolved through two rounds of whole-genome duplications. The TCF gene structure in jawless vertebrates resembles the ancestral vertebrate structure.
DEVELOPMENT GROWTH & DIFFERENTIATION
(2022)
Review
Evolutionary Biology
B. Duygu Ozpolat, Nadine Randel, Elizabeth A. Williams, Luis Alberto Bezares-Calderon, Gabriele Andreatta, Guillaume Balavoine, Paola Y. Bertucci, David E. K. Ferrier, Maria Cristina Gambi, Eve Gazave, Mette Handberg-Thorsager, Jorg Hardege, Cameron Hird, Yu-Wen Hsieh, Jerome Hui, Kevin Nzumbi Mutemi, Stephan Q. Schneider, Oleg Simakov, Hernando M. Vergara, Michel Vervoort, Gaspar Jekely, Kristin Tessmar-Raible, Florian Raible, Detlev Arendt
Summary: Nereid Platynereis dumerilii is a marine annelid used as a model for research in genetics, regeneration, reproduction biology, neurobiology, and other fields. Its unique features make it an important species in scientific exploration.
Article
Immunology
Morag Clinton, Elzbieta Krol, Dagoberto Sepulveda, Nikolaj R. Andersen, Andrew S. Brierley, David E. K. Ferrier, Per Juel Hansen, Niels Lorenzen, Samuel A. M. Martin
Summary: The gill of teleost fish serves as a multifunctional organ involved in protection against pathogens and environmental antigens, but its molecular response to harmful algal blooms remains largely unknown. Studies on juvenile rainbow trout exposed to toxin-producing algae revealed potential inflammatory responses and gill disorders induced by the blooms, suggesting the importance of monitoring and mitigating toxicity of harmful algal blooms.
FRONTIERS IN IMMUNOLOGY
(2021)
Article
Cell Biology
Ildiko M. L. Somorjai, Matthias T. Ehebauer, Hector Escriva, Jordi Garcia-Fernandez
Summary: The study demonstrates that pharmacological inhibition of JNK signaling in cephalochordate embryos results in morphological abnormalities such as notochord elongation defects, cell delamination, and altered gene expression. This suggests a conserved role of JNK signaling in regulating cellular behavior and tissue differentiation during cephalochordate morphogenesis.
FRONTIERS IN CELL AND DEVELOPMENTAL BIOLOGY
(2021)
Article
Anatomy & Morphology
Nicholas D. Holland, Linda Z. Holland, Ildiko M. L. Somorjai
Summary: This study describes the three-dimensional distribution and fine structure of fibroblasts in the adult cephalochordate Asymmetron lucayanum using serial block-face scanning electron microscopy. The fibroblasts in the tail region were sparsely distributed, resembling vertebrate telocytes. They were involved in the production of nonfibrous components of the extracellular matrix through the release of dense material and secretion of granular material.
JOURNAL OF MORPHOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Marc Ramos-Llorens, Francisco Hontoria, Juan C. Navarro, David E. K. Ferrier, Oscar Monroig
Summary: Aquatic single-cell organisms have long been thought to be the only primary producers of omega-3 long-chain polyunsaturated fatty acids (LC-PUFA). However, it has now been discovered that multiple invertebrates, including annelids, possess methyl-end desaturases that contribute to the production of LC-PUFA in the ocean. In this study, the front-end desaturase gene repertoire in annelids was examined, revealing at least two front-end desaturases with ω-5 and ω-6 ω-8 desaturase activities.
BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR AND CELL BIOLOGY OF LIPIDS
(2023)
Article
Biology
Sean Tsz Sum Law, Yifei Yu, Wenyan Nong, Wai Lok So, Yiqian Li, Thomas Swale, David E. K. Ferrier, Jianwen Qiu, Peiyuan Qian, Jerome Ho Lam Hui
Summary: This study reports the first chromosome-level deep-sea cnidarian genome from an Actinernus sp. anemone, revealing molecular adaptations to extreme environments such as a mega-array of homeobox genes and cnidarian-specific microRNA complements. Additionally, the loss of circadian rhythm genes suggests an adaptation to the dark deep-sea environment.
PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES
(2023)
Article
Biology
Wenyan Nong, Yifei Yu, Madeleine E. Aase-Remedios, Yichun Xie, Wai Lok So, Yiqian Li, Cheuk Fung Wong, Toby Baril, Sean T. S. Law, Sheung Yee Lai, Jasmine Haimovitz, Thomas Swale, Shan-Shan Chen, Zhen-Peng Kai, Xi Sun, Zhongdao Wu, Alexander Hayward, David E. K. Ferrier, Jerome H. L. Hui
Summary: This study presents the first genome assembly for the snail B. straminea, offering new insights into phenomena related to schistosomiasis vector snails and evolutionary genomics questions regarding molluscs. The research identified developmental homeobox genes, hormonal genes, and stress-response genes in the genome, as well as syntenic conservation and evolutionary changes in gene clusters in comparison with other mollusc genomes. The presence of sesquiterpenoid and cholesterol metabolic pathway genes in Gastropoda was also revealed, along with a sesquiterpenoid hormone responsive system in B. straminea.
Article
Anatomy & Morphology
Nicholas D. Holland, Ildiko M. L. Somorjai
Summary: Lancelets in the subphylum Cephalochordata, such as Asymmetron lucayanum, display rapid tail regeneration with distinct morphological changes over a 14-day period, including differentiation of cells and formation of new tissues resembling those originally lost. Serial blockface scanning electron microscopy did not reveal blastema-like cell aggregation in the regenerate, providing important insights for future studies on cephalochordate regeneration.
JOURNAL OF MORPHOLOGY
(2021)
