Maternal Wnt11b regulates cortical rotation during Xenopus axis formation: analysis of maternal-effect wnt11b mutants Houston, Douglas W.; Elliott, Karen L.; Coppenrath, Kelsey; Wlizla, Marcin; Horb, Marko E. Asymmetric signalling centres in the early embryo are essential for axis formation in vertebrates. These regions (e.g. amphibian dorsal morula, mammalian anterior visceral endoderm) require stabilised nuclear β-catenin, but the role of localised Wnt ligand signalling activity in their establishment remains unclear. In Xenopus, dorsal β-catenin is initiated by vegetal microtubule-mediated symmetry breaking in the fertilised egg, known as ‘cortical rotation’. Localised wnt11b mRNA and ligand-independent activators of β-catenin have been implicated in dorsal β-catenin activation, but the extent to which each contributes to axis formation in this paradigm remains unclear. Here, we describe a CRISPR-mediated maternal-effect mutation in Xenopus laevis wnt11b.L. We find that wnt11b is maternally required for robust dorsal axis formation and for timely gastrulation, and zygotically for left-right asymmetry. Importantly, we show that vegetal microtubule assembly and cortical rotation are reduced in wnt11b mutant eggs. In addition, we show that activated Wnt coreceptor Lrp6 and Dishevelled lack behaviour consistent with roles in early β-catenin stabilisation, and that neither is regulated by Wnt11b. This work thus implicates Wnt11b in the distribution of putative dorsal determinants rather than in comprising the determinants themselves. © The Author(s), 2022. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Houston, D. W., Elliott, K. L., Coppenrath, K., Wlizla, M., & Horb, M. E. Maternal Wnt11b regulates cortical rotation during Xenopus axis formation: analysis of maternal-effect wnt11b mutants. Development, 149(17), (2022): dev.200552, https://doi.org/10.1242/dev.200552.

Normal table of Xenopus development: a new graphical resource Zahn, Natalya; James-Zorn, Christina; Ponferrada, Virgilio G.; Adams, Dany S.; Grzymkowski, Julia; Buchholz, Daniel R.; Nascone-Yoder, Nanette M.; Horb, Marko E.; Moody, Sally A.; Vize, Peter D.; Zorn, Aaron M. Normal tables of development are essential for studies of embryogenesis, serving as an important resource for model organisms, including the frog Xenopus laevis. Xenopus has long been used to study developmental and cell biology, and is an increasingly important model for human birth defects and disease, genomics, proteomics and toxicology. Scientists utilize Nieuwkoop and Faber's classic ‘Normal Table of Xenopus laevis (Daudin)’ and accompanying illustrations to enable experimental reproducibility and reuse the illustrations in new publications and teaching. However, it is no longer possible to obtain permission for these copyrighted illustrations. We present 133 new, high-quality illustrations of X. laevis development from fertilization to metamorphosis, with additional views that were not available in the original collection. All the images are available on Xenbase, the Xenopus knowledgebase (http://www.xenbase.org/entry/zahn.do), for download and reuse under an attributable, non-commercial creative commons license. Additionally, we have compiled a ‘Landmarks Table’ of key morphological features and marker gene expression that can be used to distinguish stages quickly and reliably (https://www.xenbase.org/entry/landmarks-table.do). This new open-access resource will facilitate Xenopus research and teaching in the decades to come. © The Author(s), 2022. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Zahn, N., James-Zorn, C., Ponferrada, V. G., Adams, D. S., Grzymkowski, J., Buchholz, D. R., Nascone-Yoder, N. M., Horb, M., Moody, S. A., Vize, P. D., & Zorn, A. M. Normal table of Xenopus development: a new graphical resource. Development, 149(14), (2022): dev200356, https://doi.org/10.1242/dev.200356.

The evolution of synaptic and cognitive capacity: insights from the nervous system transcriptome of Aplysia Orvis, Joshua; Albertin, Carolin B.; Shrestha, Pragya; Chen, Shuangshuang; Zheng, Melanie; Rodriguez, Cheyenne J.; Tallon, Luke J.; Mahurkar, Anup; Zimin, Aleksey V.; Kim, Michelle; Liu, Kelvin; Kandel, Eric R.; Fraser, Claire M.; Sossin, Wayne; Abrams, Thomas W. The gastropod mollusk Aplysia is an important model for cellular and molecular neurobiological studies, particularly for investigations of molecular mechanisms of learning and memory. We developed an optimized assembly pipeline to generate an improved Aplysia nervous system transcriptome. This improved transcriptome enabled us to explore the evolution of cognitive capacity at the molecular level. Were there evolutionary expansions of neuronal genes between this relatively simple gastropod Aplysia (20,000 neurons) and Octopus (500 million neurons), the invertebrate with the most elaborate neuronal circuitry and greatest behavioral complexity? Are the tremendous advances in cognitive power in vertebrates explained by expansion of the synaptic proteome that resulted from multiple rounds of whole genome duplication in this clade? Overall, the complement of genes linked to neuronal function is similar between Octopus and Aplysia. As expected, a number of synaptic scaffold proteins have more isoforms in humans than in Aplysia or Octopus. However, several scaffold families present in mollusks and other protostomes are absent in vertebrates, including the Fifes, Lev10s, SOLs, and a NETO family. Thus, whereas vertebrates have more scaffold isoforms from select families, invertebrates have additional scaffold protein families not found in vertebrates. This analysis provides insights into the evolution of the synaptic proteome. Both synaptic proteins and synaptic plasticity evolved gradually, yet the last deuterostome-protostome common ancestor already possessed an elaborate suite of genes associated with synaptic function, and critical for synaptic plasticity. © The Author(s), 2022. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Orvis, J., Albertin, C., Shrestha, P., Chen, S., Zheng, M., Rodriguez, C., Tallon, L., Mahurkar, A., Zimin, A., Kim, M., Liu, K., Kandel, E., Fraser, C., Sossin, W., & Abrams, T. The evolution of synaptic and cognitive capacity: insights from the nervous system transcriptome of Aplysia. Proceedings of the National Academy of Sciences of the United States of America, 119(28), (2022): e2122301119, https://doi.org/10.1073/pnas.2122301119.

Developing immortal cell lines from Xenopus embryos, four novel cell lines derived from Xenopus tropicalis Gorbsky, Gary J.; Daum, John R.; Sapkota, Hem; Summala, Katja; Yoshida, Hitoshi; Georgescu, Constantin; Wren, Jonathan D.; Peshkin, Leonid; Horb, Marko E. The diploid anuran Xenopus tropicalis has emerged as a key research model in cell and developmental biology. To enhance the usefulness of this species, we developed methods for generating immortal cell lines from Nigerian strain (NXR_1018, RRID:SCR_013731) X. tropicalis embryos. We generated 14 cell lines that were propagated for several months. We selected four morphologically distinct lines, XTN-6, XTN-8, XTN-10 and XTN-12 for further characterization. Karyotype analysis revealed that three of the lines, XTN-8, XTN-10 and XTN-12 were primarily diploid. XTN-6 cultures showed a consistent mixed population of diploid cells, cells with chromosome 8 trisomy, and cells containing a tetraploid content of chromosomes. The lines were propagated using conventional culture methods as adherent cultures at 30°C in a simple, diluted L-15 medium containing fetal bovine serum without use of a high CO2 incubator. Transcriptome analysis indicated that the four lines were distinct lineages. These methods will be useful in the generation of cell lines from normal and mutant strains of X. tropicalis as well as other species of Xenopus. © The Author(s), 2022. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Gorbsky, G. J., Daum, J. R., Sapkota, H., Summala, K., Yoshida, H., Georgescu, C., Wren, J. D., Peshkin, L., & Horb, M. E. Developing immortal cell lines from Xenopus embryos, four novel cell lines derived from Xenopus tropicalis. Open Biology, 12(7), (2022): 220089, https://doi.org/10.1098/rsob.220089.

Deletion in chromosome 6 spanning alpha-synuclein and multimerin1 loci in the Rab27a/b double knockout mouse Pattanayak, Rudradip; Underwood, Rachel; Crowley, Michael R.; Crossman, David K.; Morgan, Jennifer R.; Yacoubian, Talene A. We report an incidental 358.5 kb deletion spanning the region encoding for alpha-synuclein (αsyn) and multimerin1 (Mmrn1) in the Rab27a/Rab27b double knockout (DKO) mouse line previously developed by Tolmachova and colleagues in 2007. Western blot and RT-PCR studies revealed lack of αsyn expression at either the mRNA or protein level in Rab27a/b DKO mice. PCR of genomic DNA from Rab27a/b DKO mice demonstrated at least partial deletion of the Snca locus using primers targeted to exon 4 and exon 6. Most genes located in proximity to the Snca locus, including Atoh1, Atoh2, Gm5570, Gm4410, Gm43894, and Grid2, were shown not to be deleted by PCR except for Mmrn1. Using whole genomic sequencing, the complete deletion was mapped to chromosome 6 (60,678,870–61,037,354), a slightly smaller deletion region than that previously reported in the C57BL/6J substrain maintained by Envigo. Electron microscopy of cortex from these mice demonstrates abnormally enlarged synaptic terminals with reduced synaptic vesicle density, suggesting potential interplay between Rab27 isoforms and αsyn, which are all highly expressed at the synaptic terminal. Given this deletion involving several genes, the Rab27a/b DKO mouse line should be used with caution or with appropriate back-crossing to other C57BL/6J mouse substrain lines without this deletion. © The Author(s), 2022. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Pattanayak, R., Underwood, R., Crowley, M. R., Crossman, D. K., Morgan, J. R., & Yacoubian, T. A. Deletion in chromosome 6 spanning alpha-synuclein and multimerin1 loci in the Rab27a/b double knockout mouse. Scientific Reports, 12(1), (2022): 9837, https://doi.org/10.1038/s41598-022-13557-8.

An experimental method for evoking and characterizing dynamic color patterning of cuttlefish during prey capture Kim, Danbee; Buresch, Kendra C.; Hanlon, Roger T.; Kampff, Adam R. Cuttlefish are active carnivores that possess a wide repertoire of body patterns that can be changed within milliseconds for many types of camouflage and communication. The forms and functions of many body patterns are well known from ethological studies in the field and laboratory. Yet one aspect has not been reported in detail: the category of rapid, brief and high-contrast changes in body coloration (“Tentacle Shot Patterns” or TSPs) that always occur with the ejection of two ballistic tentacles to strike live moving prey (“Tentacles Go Ballistic” or TGB moment). We designed and tested a mechanical device that presented prey in a controlled manner, taking advantage of a key stimulus for feeding: motion of the prey. High-speed video recordings show a rapid transition into TSPs starting 114 ms before TGB (N = 114). TSPs are then suppressed as early as 470–500 ms after TGB (P < 0.05) in unsuccessful hunts, while persisting for at least 3 s after TGB in successful hunts. A granularity analysis revealed significant differences in the large-scale high-contrast body patterning present in TSPs compared to the camouflage body pattern deployed beforehand. TSPs best fit the category of secondary defense called deimatic displaying, meant to briefly startle predators and interrupt their attack sequence while cuttlefish are distracted by striking prey. We characterize TSPs as a pattern category for which the main distinguishing feature is a high-contrast signaling pattern with aspects of Acute Conflict Mottle or Acute Disruptive Pattern. The data and methodology presented here open opportunities for quantifying the rapid neural responses in this visual sensorimotor set of behaviors. © The Author(s), 2022. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Kim, D., Buresch, K. C., Hanlon, R. T., & Kampff, A. R. An experimental method for evoking and characterizing dynamic color patterning of cuttlefish during prey capture. Journal of Biological Methods, 9(2), (2022): e161, https://doi.org/10.14440/jbm.2022.386.

Point spread function of the polarized light field microscope Tran, Mai Thi; Oldenbourg, Rudolf We examined the point spread function of the polarized light field microscope and established a computational framework to solve the forward problem in polarized light field imaging, for the purpose of furthering its use as a quantitative tool for measuring three-dimensional maps of the birefringence of transparent objects. We recorded experimental polarized light field images of small calcite crystals and of larger birefringent objects and compared our experimental results to numerical simulations based on polarized light ray tracing. We find good agreement between all our experiments and simulations, which leads us to propose polarized light ray tracing as one solution to the forward problem for the complex, nonlinear imaging mode of the polarized light field microscope. Solutions to the ill-posed inverse problem might be found in analytical methods and/or deep learning approaches that are based on training data generated by the forward solution presented here. Author Posting. © Optical Society of America, 2022. This article is posted here by permission of Optical Society of America for personal use. Users may use, reuse, and build upon the article, or use the article for text or data mining, so long as such uses are for non-commercial purposes and appropriate attribution is maintained. The definitive version was published in Journal of the Optical Society of America A 39(6), (2022): 1095–1103, https://doi.org/10.1364/JOSAA.458034.

Spinal cord regeneration—the origins of progenitor cells for functional rebuilding Walker, Sarah E.; Echeverri, Karen The spinal cord is one of the most important structures for all vertebrate animals as it connects almost all parts of the body to the brain. Injury to the mammalian spinal cord has devastating consequences, resulting in paralysis with little to no hope of recovery. In contrast, other vertebrate animals have been known for centuries to be capable of functionally regenerating large lesions in the spinal cord. Here, we will review the current knowledge of spinal cord regeneration and recent work in different proregenerative animals that has begun to shed light on the cellular and molecular mechanisms these animals use to direct cells to rebuild a complex, functional spinal cord. © The Author(s), 2022. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Walker, S. E., & Echeverri, K. Spinal cord regeneration—the origins of progenitor cells for functional rebuilding. Current Opinion in Genetics & Development, 75, (2022):101917, https://doi.org/10.1016/j.gde.2022.101917.

Identification of LINE retrotransposons and long non-coding RNAs expressed in the octopus brain Petrosino, Giuseppe; Ponte, Giovanna; Volpe, Massimiliano; Zarrella, Ilaria; Ansaloni, Federico; Langella, Concetta; Di Cristina, Giulia; Finaurini, Sara; Russo, Monia T.; Basu, Swaraj; Musacchia, Francesco; Ristoratore, Filomena; Pavlinic, Dinko; Benes, Vladimir; Ferrante, Maria I.; Albertin, Carolin B.; Simakov, Oleg; Gustincich, Stefano; Sanges, Remo Background Transposable elements (TEs) widely contribute to the evolution of genomes allowing genomic innovations, generating germinal and somatic heterogeneity, and giving birth to long non-coding RNAs (lncRNAs). These features have been associated to the evolution, functioning, and complexity of the nervous system at such a level that somatic retrotransposition of long interspersed element (LINE) L1 has been proposed to be associated to human cognition. Among invertebrates, octopuses are fascinating animals whose nervous system reaches a high level of complexity achieving sophisticated cognitive abilities. The sequencing of the genome of the Octopus bimaculoides revealed a striking expansion of TEs which were proposed to have contributed to the evolution of its complex nervous system. We recently found a similar expansion also in the genome of Octopus vulgaris. However, a specific search for the existence and the transcription of full-length transpositionally competent TEs has not been performed in this genus. Results Here, we report the identification of LINE elements competent for retrotransposition in Octopus vulgaris and Octopus bimaculoides and show evidence suggesting that they might be transcribed and determine germline and somatic polymorphisms especially in the brain. Transcription and translation measured for one of these elements resulted in specific signals in neurons belonging to areas associated with behavioral plasticity. We also report the transcription of thousands of lncRNAs and the pervasive inclusion of TE fragments in the transcriptomes of both Octopus species, further testifying the crucial activity of TEs in the evolution of the octopus genomes. Conclusions The neural transcriptome of the octopus shows the transcription of thousands of putative lncRNAs and of a full-length LINE element belonging to the RTE class. We speculate that a convergent evolutionary process involving retrotransposons activity in the brain has been important for the evolution of sophisticated cognitive abilities in this genus. © The Author(s), 2022. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Petrosino, G., Ponte, G., Volpe, M., Zarrella, I., Ansaloni, F., Langella, C., Di Cristina, G., Finaurini, S., Russo, M., Basu, S., Musacchia, F., Ristoratore, F., Pavlinic, D., Benes, V., Ferrante, M., Albertin, C., Simakov, O., Gustincich, S., Fiorito, G., & Sanges, R. Identification of LINE retrotransposons and long non-coding RNAs expressed in the octopus brain. BMC Biology, 20(1) (2022): 116, https://doi.org/10.1186/s12915-022-01303-5.

Endogenous retroviruses augment amphibian (Xenopus laevis) tadpole antiviral protection Kalia, Namarta; Hauser, Kelsey A.; Burton, Sarah; Hossainey, Muhammad Riadul Haque; Zelle, Mira; Horb, Marko E.; Grayfer, Leon The global amphibian declines are compounded by infections with members of the Ranavirus genus such as Frog Virus 3 (FV3). Premetamorphic anuran amphibians are believed to be significantly more susceptible to FV3 while this pathogen targets the kidneys of both pre- and postmetamorphic animals. Paradoxically, FV3-challenged Xenopus laevis tadpoles exhibit lower kidney viral loads than adult frogs. Presently, we demonstrate that X. laevis tadpoles are intrinsically more resistant to FV3 kidney infections than cohort-matched metamorphic and postmetamorphic froglets and that this resistance appears to be epigenetically conferred by endogenous retroviruses (ERVs). Using a X. laevis kidney-derived cell line, we show that enhancing ERV gene expression activates cellular double-stranded RNA-sensing pathways, resulting in elevated mRNA levels of antiviral interferon (IFN) cytokines and thus greater anti-FV3 protection. Finally, our results indicate that large esterase-positive myeloid-lineage cells, rather than renal cells, are responsible for the elevated ERV/IFN axis seen in the tadpole kidneys. This conclusion is supported by our observation that CRISPR-Cas9 ablation of colony-stimulating factor-3 results in abolished homing of these myeloid cells to tadpole kidneys, concurrent with significantly abolished tadpole kidney expression of both ERVs and IFNs. We believe that the manuscript marks an important step forward in understanding the mechanisms controlling amphibian antiviral defenses and thus susceptibility and resistance to pathogens like FV3. Author Posting. © American Society for Microbiology , 2022. This article is posted here by permission of American Society for Microbiology for personal use, not for redistribution. The definitive version was published in Kalia, N., Hauser, K., Burton, S., Hossainey, M., Zelle, M., Horb, M., & Grayfer, L. Endogenous retroviruses augment amphibian (Xenopus laevis) tadpole antiviral protection. Journal of Virology, 96(11), (2022): e00634-22, https://doi.org/10.1128/jvi.00634-22.

Genome and transcriptome mechanisms driving cephalopod evolution Albertin, Carolin B.; Medina-Ruiz, Sofia; Mitros, Therese; Schmidbaur, Hannah; Sanchez, Gustavo; Wang, Z. Yan; Grimwood, Jane; Rosenthal, Joshua J. C.; Ragsdale, Clifton W.; Simakov, Oleg; Rokhsar, Daniel S. Cephalopods are known for their large nervous systems, complex behaviors and morphological innovations. To investigate the genomic underpinnings of these features, we assembled the chromosomes of the Boston market squid, Doryteuthis (Loligo) pealeii, and the California two-spot octopus, Octopus bimaculoides, and compared them with those of the Hawaiian bobtail squid, Euprymna scolopes. The genomes of the soft-bodied (coleoid) cephalopods are highly rearranged relative to other extant molluscs, indicating an intense, early burst of genome restructuring. The coleoid genomes feature multi-megabase, tandem arrays of genes associated with brain development and cephalopod-specific innovations. We find that a known coleoid hallmark, extensive A-to-I mRNA editing, displays two fundamentally distinct patterns: one exclusive to the nervous system and concentrated in genic sequences, the other widespread and directed toward repetitive elements. We conclude that coleoid novelty is mediated in part by substantial genome reorganization, gene family expansion, and tissue-dependent mRNA editing. © The Author(s), 2022. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Albertin, C. B., Medina-Ruiz, S., Mitros, T., Schmidbaur, H., Sanchez, G., Wang, Z. Y., Grimwood, J., Rosenthal, J. J. C., Ragsdale, C. W., Simakov, O., & Rokhsar, D. S. Genome and transcriptome mechanisms driving cephalopod evolution. Nature Communications, 13(1), (2022): 2427, https://doi.org/10.1038/s41467-022-29748-w.

Emergence of novel cephalopod gene regulation and expression through large-scale genome reorganization Schmidbaur, Hannah; Kawaguchi, Akane; Clarence, Tereza; Fu, Xiao; Hoang, Oi Pui; Zimmermann, Bob; Ritschard, Elena A.; Weissenbacher, Anton; Foster, Jamie S.; Nyholm, Spencer V.; Bates, Paul A.; Albertin, Carolin B.; Tanaka, Elly; Simakov, Oleg Coleoid cephalopods (squid, cuttlefish, octopus) have the largest nervous system among invertebrates that together with many lineage-specific morphological traits enables complex behaviors. The genomic basis underlying these innovations remains unknown. Using comparative and functional genomics in the model squid Euprymna scolopes, we reveal the unique genomic, topological, and regulatory organization of cephalopod genomes. We show that coleoid cephalopod genomes have been extensively restructured compared to other animals, leading to the emergence of hundreds of tightly linked and evolutionary unique gene clusters (microsyntenies). Such novel microsyntenies correspond to topological compartments with a distinct regulatory structure and contribute to complex expression patterns. In particular, we identify a set of microsyntenies associated with cephalopod innovations (MACIs) broadly enriched in cephalopod nervous system expression. We posit that the emergence of MACIs was instrumental to cephalopod nervous system evolution and propose that microsyntenic profiling will be central to understanding cephalopod innovations. © The Author(s), 2022. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Schmidbaur, H., Kawaguchi, A., Clarence, T., Fu, X., Hoang, O. P., Zimmermann, B., Ritschard, E. A., Weissenbacher, A., Foster, J. S., Nyholm, S., Bates, P. A., Albertin, C. B., Tanaka, E., & Simakov, O. Emergence of novel cephalopod gene regulation and expression through large-scale genome reorganization. Nature Communications, 13(1), (2022): 2172, https://doi.org/10.1038/s41467-022-29694-7.

Advances in genome editing tools Horb, Marko E.; Abu-Daya, Anita; Wlizla, Marcin; Noble, Anna; Guille, Matthew This book focuses on the amphibian, Xenopus, one of the most commonly used model animals in the biological sciences. Over the past 50 years, the use of Xenopus has made possible many fundamental contributions to our knowledge in cell biology, developmental biology, molecular biology, and neurobiology. In recent years, with the completion of the genome sequence of the main two species and the application of genome editing techniques, Xenopus has emerged as a powerful system to study fundamental disease mechanisms and test treatment possibilities. Xenopus has proven an essential vertebrate model system for understanding fundamental cell and developmental biological mechanisms, for applying fundamental knowledge to pathological processes, for deciphering the function of human disease genes, and for understanding genome evolution. Key Features Provides historical context of the contributions of the model system Includes contributions from an international team of leading scholars Presents topics spanning cell biology, developmental biology, genomics, and disease model Describes recent experimental advances Incorporates richly illustrated diagrams and color images © The Author(s), 2022. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Horb, M., Abu-Daya, A., Wlizla, M., Noble, A., & Guille, M. “Advances in genome editing tools.” In Xenopus, edited by Abraham Fainsod, Sally A. Moody, 207–221. Boca Raton: CRC Press, 2022, https://doi.org/10.1201/9781003050230-16.

Activating transcription factor 3 (ATF3) is a highly conserved pro-regenerative transcription factor in the vertebrate nervous system Katz, Hilary R.; Arcese, Anthony A.; Bloom, Ona E.; Morgan, Jennifer R. The vertebrate nervous system exhibits dramatic variability in regenerative capacity across species and neuronal populations. For example, while the mammalian central nervous system (CNS) is limited in its regenerative capacity, the CNS of many other vertebrates readily regenerates after injury, as does the peripheral nervous system (PNS) of mammals. Comparing molecular responses across species and tissues can therefore provide valuable insights into both conserved and distinct mechanisms of successful regeneration. One gene that is emerging as a conserved pro-regenerative factor across vertebrates is activating transcription factor 3 (ATF3), which has long been associated with tissue trauma. A growing number of studies indicate that ATF3 may actively promote neuronal axon regrowth and regeneration in species ranging from lampreys to mammals. Here, we review data on the structural and functional conservation of ATF3 protein across species. Comparing RNA expression data across species that exhibit different abilities to regenerate their nervous system following traumatic nerve injury reveals that ATF3 is consistently induced in neurons within the first few days after injury. Genetic deletion or knockdown of ATF3 expression has been shown in mouse and zebrafish, respectively, to reduce axon regeneration, while inducing ATF3 promotes axon sprouting, regrowth, or regeneration. Thus, we propose that ATF3 may be an evolutionarily conserved regulator of neuronal regeneration. Identifying downstream effectors of ATF3 will be a critical next step in understanding the molecular basis of vertebrate CNS regeneration. © The Author(s), 2022. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Katz, H. R., Arcese, A. A., Bloom, O., & Morgan, J. R. Activating transcription factor 3 (ATF3) is a highly conserved pro-regenerative transcription factor in the vertebrate nervous system. Frontiers in Cell and Developmental Biology, 10, (2022): 824036, https://doi.org/10.3389/fcell.2022.824036.

Modulation of G(q)/PLC-mediated signaling by acute lithium exposure Sánchez Triviño, Cesar Adolfo; Landinez, Maria Paula; Duran, Sara; Gomez, Maria del Pilar; Nasi, Enrico Although lithium has long been one of the most widely used pharmacological agents in psychiatry, its mechanisms of action at the cellular and molecular levels remain poorly understood. One of the targets of Li+ is the phosphoinositide pathway, but whereas the impact of Li+ on inositol lipid metabolism is well documented, information on physiological effects at the cellular level is lacking. We examined in two mammalian cell lines the effect of acute Li+ exposure on the mobilization of internal Ca2+ and phospholipase C (PLC)-dependent membrane conductances. We first corroborated by Western blots and immunofluorescence in HEK293 cells the presence of key signaling elements of a muscarinic PLC pathway (M1AchR, Gq, PLC-β1, and IP3Rs). Stimulation with carbachol evoked a dose-dependent mobilization of Ca, as determined with fluorescent indicators. This was due to release from internal stores and proved susceptible to the PLC antagonist U73122. Li+ exposure reproducibly potentiated the Ca response in a concentration-dependent manner extending to the low millimolar range. To broaden those observations to a neuronal context and probe potential Li modulation of electrical signaling, we next examined the cell line SHsy5y. We replicated the potentiating effects of Li on the mobilization of internal Ca, and, after characterizing the basic properties of the electrical response to cholinergic stimulation, we also demonstrated an equally robust upregulation of muscarinic membrane currents. Finally, by directly stimulating the signaling pathway at different links downstream of the receptor, the site of action of the observed Li effects could be narrowed down to the G protein and its interaction with PLC-β. These observations document a modulation of Gq/PLC/IP3-mediated signaling by acute exposure to lithium, reflected in distinct physiological changes in cellular responses. © The Author(s), 2022. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Sanchez Trivino, C. A., Landinez, M. P., Duran, S., Gomez, M. del P., & Nasi, E. Modulation of G(q)/PLC-mediated signaling by acute lithium exposure. Frontiers in Cellular Neuroscience, 16, (2022): 838939, https://doi.org/10.3389/fncel.2022.838939.

Regulation of stem cell identity by miR-200a during spinal cord regeneration Walker, Sarah E.; Sabin, Keith Z.; Gearhart, Micah D.; Yamamoto, Kenta Axolotls are an important model organism for multiple types of regeneration, including functional spinal cord regeneration. Remarkably, axolotls can repair their spinal cord after a small lesion injury and can also regenerate their entire tail following amputation. Several classical signaling pathways that are used during development are reactivated during regeneration, but how this is regulated remains a mystery. We have previously identified miR-200a as a key factor that promotes successful spinal cord regeneration. Here, using RNA-seq analysis, we discovered that the inhibition of miR-200a results in an upregulation of the classical mesodermal marker brachyury in spinal cord cells after injury. However, these cells still express the neural stem cell marker sox2. In vivo cell tracking allowed us to determine that these cells can give rise to cells of both the neural and mesoderm lineage. Additionally, we found that miR-200a can directly regulate brachyury via a seed sequence in the 3′UTR of the gene. Our data indicate that miR-200a represses mesodermal cell fate after a small lesion injury in the spinal cord when only glial cells and neurons need to be replaced. © The Author(s), 2022. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Walker, S. E., Sabin, K. Z., Gearhart, M. D., Yamamoto, K., & Echeverri, K. Regulation of stem cell identity by miR-200a during spinal cord regeneration. Development, 149(3), (2022): dev200033, https://doi.org/10.1242/dev.200033.

Pupil dilation and constriction in the skate Leucoraja erinacea in a simulated natural light field Mäthger, Lydia M.; Bok, Michael J.; Liebich, Jan; Sicius, Lucia; Nilsson, Dan-Eric The skate Leucoraja erinacea has an elaborately shaped pupil, whose characteristics and functions have received little attention. The goal of our study was to investigate the pupil response in relation to natural ambient light intensities. First, we took a recently developed sensory–ecological approach, which gave us a tool for creating a controlled light environment for behavioural work: during a field survey, we collected a series of calibrated natural habitat images from the perspective of the skates' eyes. From these images, we derived a vertical illumination profile using custom-written software for quantification of the environmental light field (ELF). After collecting and analysing these natural light field data, we created an illumination set-up in the laboratory, which closely simulated the natural vertical light gradient that skates experience in the wild and tested the light responsiveness – in particular the extent of dilation – of the skate pupil to controlled changes in this simulated light field. Additionally, we measured pupillary dilation and constriction speeds. Our results confirm that the skate pupil changes from nearly circular under low light to a series of small triangular apertures under bright light. A linear regression analysis showed a trend towards smaller skates having a smaller dynamic range of pupil area (dilation versus constriction ratio around 4-fold), and larger skates showing larger ranges (around 10- to 20-fold). Dilation took longer than constriction (between 30 and 45 min for dilation; less than 20 min for constriction), and there was considerable individual variation in dilation/constriction time. We discuss our findings in terms of the visual ecology of L. erinacea and consider the importance of accurately simulating natural light fields in the laboratory. Author Posting. © Company of Biologists, 2022. This article is posted here by permission of Company of Biologists for personal use, not for redistribution. The definitive version was published in Journal of Experimental Biology 225(4), (2022): jeb243221, https://doi.org/10.1242/jeb.243221.

Ramisyllis kingghidorahi n. Sp., a new branching annelid from Japan Aguado, M. Teresa; Ponz-Segrelles, Guillermo; Glasby, Christopher J.; Ribeiro, Rannyele P.; Nakamura, Mayuko; Oguchi, Kohei; Omori, Akihito; Kohtsuka, Hisanori; Fischer, Christian; Ise, Yuji; Jimi, Naoto; Miura, Toru Among over 20,000 species of Annelida, only two branching species with a highly modified body-pattern are known until now: the Syllidae Syllis ramosa McIntosh, 1879, and Ramisyllis multicaudata Glasby et al. (Zoological Journal of the Linnean Society, 164, 481–497, 2012). Both have unusual ramified bodies with one head and multiple branches and live inside the canals of host sponges. Using an integrative approach (combining morphology, internal anatomy, ecology, phylogeny, genetic divergence, and the complete mitochondrial genome), we describe a new branching species from Japan, Ramisyllis kingghidorahi n. sp., inhabiting an undescribed species of Petrosia (Porifera: Demospongiae) from shallow waters. We compare the new species with its closest relative, R. multicaudata; emend the diagnosis of Ramisyllis; and discuss previous reports of S. ramosa. This study suggests a much higher diversity of branching syllids than currently known. Finally, we discuss possible explanations for the feeding behaviour in the new species in relation to its highly ciliated wall of the digestive tubes (especially at the distal branches and anus), and provide a hypothesis for the evolution of branching body patterns as the result of an adaptation to the host sponge labyrinthic canal system. © The Author(s), 2022. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Aguado, M. T., Ponz-Segrelles, G., Glasby, C. J., Ribeiro, R. P., Nakamura, M., Oguchi, K., Omori, A., Kohtsuka, H., Fisher, C., Ise, Y., Jimi, N., & Miura, T. Ramisyllis kingghidorahi n. Sp., a new branching annelid from Japan. Organisms Diversity & Evolution. (2022), https://doi.org/10.1007/s13127-021-00538-4.

Uncovering the effects of symbiosis and temperature on coral calcification Dellaert, Zoe; Vargas, Phillip A.; La Riviere, Patrick J.; Roberson, Loretta M. We tested the impact of temperature and symbiont state on calcification in corals, using the facultatively symbiotic coral Astrangia poculata as a model system. Symbiotic and aposymbiotic colonies of A. poculata were reared in 15, 20, and 27 °C conditions. We used scanning electron microscopy to quantify how these physiological and environmental conditions impact skeletal structure. Buoyant weight data over time revealed that temperature significantly affects calcification rates. Scanning electron microscopy of A. poculata skeletons showed that aposymbiotic colonies appear to have a lower density of calcium carbonate in actively growing septal spines. We describe a novel approach to analyze the roughness and texture of scanning electron microscopy images. Quantitative analysis of the roughness of septal spines revealed that aposymbiotic colonies have a rougher surface than symbiotic colonies in tropical conditions (27 °C). This trend reversed at 15 °C, a temperature at which the symbionts of A. poculata may exhibit parasitic properties. Analysis of surface texture patterns showed that temperature impacts the spatial variance of crystals on the spine surface. Few published studies have examined the skeleton of A. poculata by using scanning electron microscopy. Our approach provides a way to study detailed changes in skeletal microstructure in response to environmental parameters and can serve as a proxy for more expensive and time-consuming analyses. Utilizing a facultatively symbiotic coral that is native to both temperate and tropical regions provides new insights into the impact of both symbiosis and temperature on calcification in corals. Author Posting. © University of Chicago, 2022. This article is posted here by permission of University of Chicago for personal use, not for redistribution. The definitive version was published in Biological Bulletin 242(1), (2022): 62-73, https://doi.org/10.1086/716711.

Common environmental pollutants negatively affect development and regeneration in the sea anemone Nematostella vectensis holobiont Klein, Sylvia; Frazier, Victoria; Readdean, Timothy; Lucas, Emily; Diaz-Jimenez, Erica P.; Sogin, Mitchell L.; Ruff, S. Emil; Echeverri, Karen The anthozoan sea anemone Nematostella vectensis belongs to the phylum of cnidarians which also includes jellyfish and corals. Nematostella are native to United States East Coast marsh lands, where they constantly adapt to changes in salinity, temperature, oxygen concentration and pH. Its natural ability to continually acclimate to changing environments coupled with its genetic tractability render Nematostella a powerful model organism in which to study the effects of common pollutants on the natural development of these animals. Potassium nitrate, commonly used in fertilizers, and Phthalates, a component of plastics are frequent environmental stressors found in coastal and marsh waters. Here we present data showing how early exposure to these pollutants lead to dramatic defects in development of the embryos and eventual mortality possibly due to defects in feeding ability. Additionally, we examined the microbiome of the animals and identified shifts in the microbial community that correlated with the type of water that was used to grow the animals, and with their exposure to pollutants. © The Author(s), 2021. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Klein, S., Frazier, V., Readdean, T., Lucas, E., Diaz-Jimenez, E. P., Sogin, M., Ruff, E. S., & Echeverri, K. Common environmental pollutants negatively affect development and regeneration in the sea anemone Nematostella vectensis holobiont. Frontiers in Ecology and Evolution, 9, (2021): 786037, https://doi.org/10.3389/fevo.2021.786037.