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  • Article
    Lampreys and spinal cord regeneration: "a very special claim on the interest of zoologists," 1830s-present
    (Frontiers Media, 2023-05-09) Maxson Jones, Kathryn ; Morgan, Jennifer R.
    Employing history of science methods, including analyses of the scientific literature, archival documents, and interviews with scientists, this paper presents a history of lampreys in neurobiology from the 1830s to the present. We emphasize the lamprey's roles in helping to elucidate spinal cord regeneration mechanisms. Two attributes have long perpetuated studies of lampreys in neurobiology. First, they possess large neurons, including multiple classes of stereotypically located, 'identified' giant neurons in the brain, which project their large axons into the spinal cord. These giant neurons and their axonal fibers have facilitated electrophysiological recordings and imaging across biological scales, ranging from molecular to circuit-level analyses of nervous system structures and functions and including their roles in behavioral output. Second, lampreys have long been considered amongst the most basal extant vertebrates on the planet, so they have facilitated comparative studies pointing to conserved and derived characteristics of vertebrate nervous systems. These features attracted neurologists and zoologists to studies of lampreys between the 1830s and 1930s. But, the same two attributes also facilitated the rise of the lamprey in neural regeneration research after 1959, when biologists first wrote about the spontaneous, robust regeneration of some identified CNS axons in larvae after spinal cord injuries, coupled with recovery of normal swimming. Not only did large neurons promote fresh insights in the field, enabling studies incorporating multiple scales with existing and new technologies. But investigators also were able to attach a broad scope of relevance to their studies, interpreting them as suggesting conserved features of successful, and sometimes even unsuccessful, CNS regeneration. Lamprey research demonstrated that functional recovery takes place without the reformation of the original neuronal connections, for instance, by way of imperfect axonal regrowth and compensatory plasticity. Moreover, research performed in the lamprey model revealed that factors intrinsic to neurons are integral in promoting or hindering regeneration. As this work has helped illuminate why basal vertebrates accomplish CNS regeneration so well, whereas mammals do it so poorly, this history presents a case study in how biological and medical value have been, and could continue to be, gleaned from a non-traditional model organism for which molecular tools have been developed only relatively recently.
  • Article
    Age-associated DNA methylation changes in Xenopus frogs
    (Taylor and Francis Group, 2023-04-06) Morselli, Marco ; Bennett, Ronan ; Shaidani, Nikko-Ideen ; Horb, Marko ; Peshkin, Leonid ; Pellegrini, Matteo
    Age-associated changes in DNA methylation have been characterized across various animals, but not yet in amphibians, which are of particular interest because they include widely studied model organisms. In this study, we present clear evidence that the aquatic vertebrate speciesdisplays patterns of age-associated changes in DNA methylation. We have generated whole-genome bisulfite sequencing (WGBS) profiles from skin samples of nine frogs representing young, mature, and old adults and characterized the gene- and chromosome-scale DNA methylation changes with age. Many of the methylation features and changes we observe are consistent with what is known in mammalian species, suggesting that the mechanism of age-related changes is conserved. Moreover, we selected a few thousand age-associated CpG sites to build an assay based on targeted DNA methylation analysis (TBSseq) to expand our findings in future studies involving larger cohorts of individuals. Preliminary results of a pilot TBSeq experiment recapitulate the findings obtained with WGBS setting the basis for the development of an epigenetic clock assay. The results of this study will allow us to leverage the unique resources available forto study how DNA methylation relates to other hallmarks of ageing.
  • Article
    Hsc70 rescues the synaptic vesicle trafficking defects caused by α-synuclein dimers
    (Caltech Library, 2023-03-01) Brady, Emily B ; McQuillan, Molly ; Medeiros, Audrey T ; Bubacco, Luigi ; Sousa, Rui ; Lafer, Eileen M ; Morgan, Jennifer R
    Aberrant buildup of α-synuclein is associated with Parkinson's disease (PD) and other neurodegenerative disorders. At synapses, α-synuclein accumulation leads to severe synaptic vesicle trafficking defects. We previously demonstrated that different molecular species of α-synuclein produce distinct effects on synaptic vesicle recycling, and that the synaptic phenotypes caused by monomeric α-synuclein were ameliorated by Hsc70. Here, we tested whether Hsc70 could also correct synaptic deficits induced by α-synuclein dimers. Indeed, co-injection of Hsc70 with α-synuclein dimers completely reversed the synaptic deficits, resulting in synapses with normal appearance. This work lends additional support for pursuing chaperone-based strategies to treat PD and other synucleinopathies.
  • Article
    Identification of exceptionally potent adenosine deaminases RNA editors from high body temperature organisms
    (Public Library of Science, 2023-03-06) Avram-Shperling, Adi ; Kopel, Eli ; Twersky, Itamar ; Gabay, Orshay ; Ben-David, Amit ; Karako-Lampert, Sarit ; Rosenthal, Joshua J C ; Levanon, Erez Y ; Eisenberg, Eli ; Ben-Aroya, Shay
    The most abundant form of RNA editing in metazoa is the deamination of adenosines into inosines (A-to-I), catalyzed by ADAR enzymes. Inosines are read as guanosines by the translation machinery, and thus A-to-I may lead to protein recoding. The ability of ADARs to recode at the mRNA level makes them attractive therapeutic tools. Several approaches for Site-Directed RNA Editing (SDRE) are currently under development. A major challenge in this field is achieving high on-target editing efficiency, and thus it is of much interest to identify highly potent ADARs. To address this, we used the baker yeast Saccharomyces cerevisiae as an editing-naïve system. We exogenously expressed a range of heterologous ADARs and identified the hummingbird and primarily mallard-duck ADARs, which evolved at 40-42°C, as two exceptionally potent editors. ADARs bind to double-stranded RNA structures (dsRNAs), which in turn are temperature sensitive. Our results indicate that species evolved to live with higher core body temperatures have developed ADAR enzymes that target weaker dsRNA structures and would therefore be more effective than other ADARs. Further studies may use this approach to isolate additional ADARs with an editing profile of choice to meet specific requirements, thus broadening the applicability of SDRE.
  • Article
    A small noncoding RNA links ribosome recovery and translation control to dedifferentiation during salamander limb regeneration
    (Elsevier, 2023-03-08) Subramanian, Elaiyaraja ; Elewa, Ahmed ; Brito, Gonçalo ; Kumar, Anoop ; Segerstolpe, Åsa ; Karampelias, Christos ; Björklund, Åsa ; Sandberg, Rickard ; Echeverri, Karen ; Lui, Weng-Onn ; Andersson, Olov ; Simon, András
    Building a blastema from the stump is a key step of salamander limb regeneration. Stump-derived cells temporarily suspend their identity as they contribute to the blastema by a process generally referred to as dedifferentiation. Here, we provide evidence for a mechanism that involves an active inhibition of protein synthesis during blastema formation and growth. Relieving this inhibition results in a higher number of cycling cells and enhances the pace of limb regeneration. By small RNA profiling and fate mapping of skeletal muscle progeny as a cellular model for dedifferentiation, we find that the downregulation of miR-10b-5p is critical for rebooting the translation machinery. miR-10b-5p targets ribosomal mRNAs, and its artificial upregulation causes decreased blastema cell proliferation, reduction in transcripts that encode ribosomal subunits, diminished nascent protein synthesis, and retardation of limb regeneration. Taken together, our data identify a link between miRNA regulation, ribosome biogenesis, and protein synthesis during newt limb regeneration.
  • Article
    Proprioceptive feedback amplification restores effective locomotion in a neuromechanical model of lampreys with spinal injuries
    (National Academy of Sciences, 2023-03-10) Hamlet, Christina ; Fauci, Lisa ; Morgan, Jennifer R. ; Tytell, Eric D
    Spinal injuries in many vertebrates can result in partial or complete loss of locomotor ability. While mammals often experience permanent loss, some nonmammals, such as lampreys, can regain swimming function, though the exact mechanism is not well understood. One hypothesis is that amplified proprioceptive (body-sensing) feedback can allow an injured lamprey to regain functional swimming even if the descending signal is lost. This study employs a multiscale, integrative, computational model of an anguilliform swimmer fully coupled to a viscous, incompressible fluid and examines the effects of amplified feedback on swimming behavior. This represents a model that analyzes spinal injury recovery by combining a closed-loop neuromechanical model with sensory feedback coupled to a full Navier-Stokes model. Our results show that in some cases, feedback amplification below a spinal lesion is sufficient to partially or entirely restore effective swimming behavior.
  • Article
    Kirkegaardia Blake, 2016 (Annelida: Cirratulidae) from Southeastern Brazil with description of nine new species
    (Public Library of Science, 2022-05-10) Freitas, Roberta ; Ribeiro, Rannyele Passos ; Ruta, Christine
    This is the first taxonomic study of cirratulid polychaetes of the genus Kirkegaardia Blake, 2016 from Brazil. Nine new species of the genus are described from the Southern Brazilian coast (50-3000 m deep). The genus Kirkegaardia is generally subdivided into three distinct groups of species (Kirkegaardia dorsobranchialis-heterochaeta, Kirkegaardia baptisteae-tesselata and Kirkegaardia luticastella) and several out-group species for which relationships remains to be defined. In this study, new species were included in the Kirkegaardia dorsobranchialis-heterochaeta and Kirkegaardia baptisteae-tesselata groups. Kirkegaardia dorsobranchialis-heterochaeta is characterized by thoracic parapodia elevated producing a channel between the notopodia, elongate pre-setigerous region that is either entirely smooth or modified with a dorsal ridge and/or rings, and noto- and neurosetae capillaries denticulated. As belonging to this group, K. blakei sp. nov., K. brisae sp. nov., K. goytaca sp. nov., K. jongo sp. nov. and K. papaveroi sp. nov. are described here. Kirkegaardia baptisteae-tesselata includes species that lack thoracic parapodia elevated and mid-dorsal thoracic groove, although a dorsal ridge is sometimes developed. In the pre-setigerous region dorsal ridges and rings are present or absent. Most species in this group have neurosetae denticulated, and notosetae capillaries of other types. This study adds K. helenae sp. nov., K. medusa sp. nov., K. nupem sp. nov. and K. zafirae sp. nov. to the latter species group. In addition, two new records are provided for K. hampsoni. A key to cirratulid polychaete species reported from Brazilian waters is provided.
  • Article
    Semi-supervised visual tracking of marine animals using autonomous underwater vehicles
    (Springer, 2023-03-01) Cai, Levi ; McGuire, Nathan E. ; Hanlon, Roger ; T Aran Mooney ; Girdhar, Yogesh
    In-situ visual observations of marine organisms is crucial to developing behavioural understandings and their relations to their surrounding ecosystem. Typically, these observations are collected via divers, tags, and remotely-operated or human-piloted vehicles. Recently, however, autonomous underwater vehicles equipped with cameras and embedded computers with GPU capabilities are being developed for a variety of applications, and in particular, can be used to supplement these existing data collection mechanisms where human operation or tags are more difficult. Existing approaches have focused on using fully-supervised tracking methods, but labelled data for many underwater species are severely lacking. Semi-supervised trackers may offer alternative tracking solutions because they require less data than fully-supervised counterparts. However, because there are not existing realistic underwater tracking datasets, the performance of semi-supervised tracking algorithms in the marine domain is not well understood. To better evaluate their performance and utility, in this paper we provide (1) a novel dataset specific to marine animals located at http://warp.whoi.edu/vmat/, (2) an evaluation of state-of-the-art semi-supervised algorithms in the context of underwater animal tracking, and (3) an evaluation of real-world performance through demonstrations using a semi-supervised algorithm on-board an autonomous underwater vehicle to track marine animals in the wild.
  • Article
    Extensive recoding of the neural proteome in cephalopods by RNA editing
    (Annual Reviews, 2023-02) Rosenthal, Joshua J.C. ; Eisenberg, Eli
    The coleoid cephalopods have the largest brains, and display the most complex behaviors, of all invertebrates. The molecular and cellular mechanisms that underlie these remarkable advancements remain largely unexplored. Early molecular cloning studies of squid ion channel transcripts uncovered an unusually large number of A?I RNA editing sites that recoded codons. Further cloning of other neural transcripts showed a similar pattern. The advent of deep-sequencing technologies and the associated bioinformatics allowed the mapping of RNA editing events across the entire neural transcriptomes of various cephalopods. The results were remarkable: They contained orders of magnitude more recoding editing sites than any other taxon. Although RNA editing sites are abundant in most multicellular metazoans, they rarely recode. In cephalopods, the majority of neural transcripts are recoded. Recent studies have focused on whether these events are adaptive, as well as other noncanonical aspects of cephalopod RNA editing.
  • Article
    Development of a selection assay for small guide RNAs that drive efficient site-directed RNA editing
    (Oxford University Press, 2023-02-25) Diaz Quiroz, Juan Felipe ; Ojha, Namrata ; Shayhidin, Elnur E. ; De Silva, Dasuni ; Dabney, Jesse ; Lancaster, Amy ; Coull, James ; Milstein, Stuart ; Fraley, Andrew W. ; Brown, Christopher R. ; Rosenthal, Joshua J. C.
    A major challenge confronting the clinical application of site-directed RNA editing (SDRE) is the design of small guide RNAs (gRNAs) that can drive efficient editing. Although many gRNA designs have effectively recruited endogenous Adenosine Deaminases that Act on RNA (ADARs), most of them exceed the size of currently FDA-approved antisense oligos. We developed an unbiased in vitro selection assay to identify short gRNAs that promote superior RNA editing of a premature termination codon. The selection assay relies on hairpin substrates in which the target sequence is linked to partially randomized gRNAs in the same molecule, so that gRNA sequences that promote editing can be identified by sequencing. These RNA substrates were incubated in vitro with ADAR2 and the edited products were selected using amplification refractory mutation system PCR and used to regenerate the substrates for a new round of selection. After nine repetitions, hairpins which drove superior editing were identified. When gRNAs of these hairpins were delivered in trans, eight of the top ten short gRNAs drove superior editing both in vitro and in cellula. These results show that efficient small gRNAs can be selected using our approach, an important advancement for the clinical application of SDRE.
  • Article
    The common morphospecies Cypridopsis vidua (O.F. MÜLLER, 1776) (Crustacea, Ostracoda) is not an obligate parthenogen
    (Royal Belgian Zoology Society, 2023-01-19) Martens, Koen ; Shribak, Michael ; Arkhipova, Irina ; Schön, Isa
    The common non-marine ostracod Cypridopsis vidua (O.F. Müller, 1776) is used as a proxy in various biological disciplines, such as (palaeo-)ecology, evolutionary biology, ecotoxicology and parasitology. This morphospecies was considered to be an obligate parthenogen. We report on the discovery of the first population of C. vidua with males from Woods Hole (MA, USA) and determine that it is a population with mixed reproduction. We describe the morphology of the males and of the sexual and asexual females. We illustrate a copula of a male and a sexual female as well insemination in a sexual female, showing that males are functional. Therefore, Cypridopsis vidua is a morphospecies with mixed reproduction, not a full apomictic parthenogen. We use, for the first time, polychromatic polarization microscope technology to illustrate soft parts of ostracods. In addition, we compare the sexual species C. bisexualis, C. okeechobei, C. howei and C. schwartzi and conclude that these species, especially the latter three, are morphologically very close to C. vidua.
  • Article
    Site-directed A→I RNA editing as a therapeutic tool: moving beyond genetic mutations
    (Cold Spring Harbor Laboratory Press, 2023-01-23) Quiroz, Juan F. Diaz ; Siskel, Louise D. ; Rosenthal, Joshua J. C.
    Adenosine deamination by the ADAR family of enzymes is a natural process that edits genetic information as it passes through messenger RNA. Adenosine is converted to inosine in mRNAs, and this base is interpreted as guanosine during translation. Realizing the potential of this activity for therapeutics, a number of researchers have developed systems that redirect ADAR activity to new targets, ones that are not normally edited. These site-directed RNA editing (SDRE) systems can be broadly classified into two categories: ones that deliver an antisense RNA oligonucleotide to bind opposite a target adenosine, creating an editable structure that endogenously expressed ADARs recognize, and ones that tether the catalytic domain of recombinant ADAR to an antisense RNA oligonucleotide that serves as a targeting mechanism, much like with CRISPR-Cas or RNAi. To date, SDRE has been used mostly to try and correct genetic mutations. Here we argue that these applications are not ideal SDRE, mostly because RNA edits are transient and genetic mutations are not. Instead, we suggest that SDRE could be used to tune cell physiology to achieve temporary outcomes that are therapeutically advantageous, particularly in the nervous system. These include manipulating excitability in nociceptive neural circuits, abolishing specific phosphorylation events to reduce protein aggregation related to neurodegeneration or reduce the glial scarring that inhibits nerve regeneration, or enhancing G protein-coupled receptor signaling to increase nerve proliferation for the treatment of sensory disorders like blindness and deafness.
  • Article
    Cuttlefish conservation: a global review of methods to ameliorate unwanted fishing mortality and other anthropogenic threats to sustainability
    (Oxford University Press, 2022-11-24) Barrett, C. J. ; Bensbai, J. ; Broadhurst, M. K. ; Bustamante, P. ; Clark, R. ; Cooke, G. M. ; Di Cosmo, A. ; Drerup, C. ; Escolar, O. ; Fernández-Álvarez, F. A. ; Ganias, K. ; Hall, K. C. ; Hanlon, R. T. ; Hernández-Urcera, J. ; Hua, Q. Q. H. ; Lacoue-Labarthe, T. ; Lewis, J. ; Lishchenko, F. ; Maselli, V. ; Moustahfid, H. ; Nakajima, R. ; O’Brien, C. E. ; Parkhouse, L. ; Pengelly, S. ; Pierce, G. J. ; Ramírez, J. G. ; Robin, J-P. ; Sajikumar, K. K. ; Sasikumar, G. ; Smith, C. L. ; Villanueva, R. ; Yến, D. T. H.
    Cuttlefish are an important global fisheries resource, and their demand is placing increasing pressure on populations in many areas, necessitating conservation measures. We reviewed evidence from case studies spanning Europe, Africa, Asia, and Australia encompassing diverse intervention methods (fisheries closures, protected areas, habitat restoration, fishing-gear modifications, promoting egg survival, and restocking), and we also discuss the effects of pollution on cuttlefish. We conclude: (1) spatio-temporal closures need to encompass substantial portions of a species’ range and protect at least one major part of their life cycle; (2) fishing-gear modifications have the potential to reduce unwanted cuttlefish capture, but more comprehensive trials are needed; (3) egg survival can be improved by diverting and salvaging from traps; (4) existing lab rearing and restocking may not produce financially viable results; and (5) fisheries management policies should be regularly reviewed in light of rapid changes in cuttlefish stock status. Further, citizen science can provide data to reduce uncertainty in empirical assessments. The information synthesized in this review will guide managers and stakeholders to implement regulations and conservation initiatives that increase the productivity and sustainability of fisheries interacting with cuttlefish, and highlights gaps in knowledge that need to be addressed.
  • Article
    Estimating production cost for large-scale seaweed farms
    (Taylor and Francis, 2022-11-11) Kite-Powell, Hauke L. ; Ask, Erick ; Augyte, Simona ; Bailey, David ; Decker, Julie ; Goudey, Clifford A. ; Grebe, Gretchen ; Li, Yaoguang ; Lindell, Scott ; Manganelli, Domenic ; Marty-Rivera, Michael ; Ng, Crystal ; Roberson, Loretta ; Stekoll, Michael ; Umanzor, Schery ; Yarish, Charles
    Seaweed farming has the potential to produce feedstocks for many applications, including food, feeds, fertilizers, biostimulants, and biofuels. Seaweeds have advantages over land-based biomass in that they require no freshwater inputs and no allocation of arable land. To date, seaweed farming has not been practiced at scales relevant to meaningful biofuel production. Here we describe a techno-economic model of large-scale seaweed farms and its application to the cultivation of the cool temperate species Saccharina latissima (sugar kelp) and the tropical seaweed Eucheumatopsis isiformis. At farm scales of 1000 ha or more, our model suggests that farm gate production costs in waters up to 200 km from the onshore support base are likely to range between $200 and $300 per dry tonne. The model also suggests that production costs below $100 per dry tonne may be achievable in some settings, which would make these seaweeds economically competitive with land-based biofuel feedstocks. While encouraging, these model results and some assumptions on which they are based require further field validation.
  • Article
    Rapamycin treatment during development extends life span and health span of male mice and Daphnia magna
    (American Association for the Advancement of Science, 2022-09-16) Shindyapina, Anastasia V ; Cho, Yongmin ; Kaya, Alaattin ; Tyshkovskiy, Alexander ; Castro, José P ; Deik, Amy ; Gordevicius, Juozas ; Poganik, Jesse R ; Clish, Clary B ; Horvath, Steve ; Peshkin, Leonid ; Gladyshev, Vadim N
    Development is tightly connected to aging, but whether pharmacologically targeting development can extend life remains unknown. Here, we subjected genetically diverse UMHET3 mice to rapamycin for the first 45 days of life. The mice grew slower and remained smaller than controls for their entire lives. Their reproductive age was delayed without affecting offspring numbers. The treatment was sufficient to extend the median life span by 10%, with the strongest effect in males, and helped to preserve health as measured by frailty index scores, gait speed, and glucose and insulin tolerance tests. Mechanistically, the liver transcriptome and epigenome of treated mice were younger at the completion of treatment. Analogous to mice, rapamycin exposure during development robustly extended the life span of and reduced its body size. Overall, the results demonstrate that short-term rapamycin treatment during development is a novel longevity intervention that acts by slowing down development and aging, suggesting that aging may be targeted already early in life.
  • Article
    Maternal Wnt11b regulates cortical rotation during Xenopus axis formation: analysis of maternal-effect wnt11b mutants
    (The Company of Biologists, 2022-09-08) 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.
  • Article
    The evolution of synaptic and cognitive capacity: insights from the nervous system transcriptome of Aplysia
    (National Academy of Sciences, 2022-07-08) 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.
  • Article
    Normal table of Xenopus development: a new graphical resource
    (The Company of Biologists, 2022-07-14) 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.
  • Article
    Developing immortal cell lines from Xenopus embryos, four novel cell lines derived from Xenopus tropicalis
    (The Royal Society, 2022-07-06) 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.
  • Article
    Point spread function of the polarized light field microscope
    (Optica, 2022-05-26) 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.