1
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Toli EA, Kemppainen P, Bounas A, Sotiropoulos K. Genetic insight into a polygenic trait using a novel genome-wide association approach in a wild amphibian population. Mol Ecol 2024; 33:e17344. [PMID: 38597332 DOI: 10.1111/mec.17344] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2023] [Revised: 03/20/2024] [Accepted: 03/25/2024] [Indexed: 04/11/2024]
Abstract
Body size variation is central in the evolution of life-history traits in amphibians, but the underlying genetic architecture of this complex trait is still largely unknown. Herein, we studied the genetic basis of body size and fecundity of the alternative morphotypes in a wild population of the Greek smooth newt (Lissotriton graecus). By combining a genome-wide association approach with linkage disequilibrium network analysis, we were able to identify clusters of highly correlated loci thus maximizing sequence data for downstream analysis. The putatively associated variants explained 12.8% to 44.5% of the total phenotypic variation in body size and were mapped to genes with functional roles in the regulation of gene expression and cell cycle processes. Our study is the first to provide insights into the genetic basis of complex traits in newts and provides a useful tool to identify loci potentially involved in fitness-related traits in small data sets from natural populations in non-model species.
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Affiliation(s)
- Elisavet-Aspasia Toli
- Molecular Ecology & Conservation Genetics Lab, Department of Biological Applications & Technology, University of Ioannina, Ioannina, Greece
| | - Petri Kemppainen
- Area of Ecology and Biodiversity, School of Biological Sciences, University of Hong Kong, Hong Kong City, Hong Kong SAR
- Ecological Genetics Research Unit, Organismal and Evolutionary Biology Programme, University of Helsinki, Helsinki, Finland
| | - Anastasios Bounas
- Molecular Ecology & Conservation Genetics Lab, Department of Biological Applications & Technology, University of Ioannina, Ioannina, Greece
| | - Konstantinos Sotiropoulos
- Molecular Ecology & Conservation Genetics Lab, Department of Biological Applications & Technology, University of Ioannina, Ioannina, Greece
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2
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Hawley L, Smalling KL, Glaberman S. Critical review of the phytohemagglutinin assay for assessing amphibian immunity. CONSERVATION PHYSIOLOGY 2023; 11:coad090. [PMID: 38090122 PMCID: PMC10714196 DOI: 10.1093/conphys/coad090] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Revised: 09/15/2023] [Accepted: 10/26/2023] [Indexed: 04/26/2024]
Abstract
Infectious diseases are a major driver of the global amphibian decline. In addition, many factors, including genetics, stress, pollution, and climate change can influence the response to pathogens. Therefore, it is important to be able to evaluate amphibian immunity in the laboratory and in the field. The phytohemagglutinin (PHA) assay is an inexpensive and relatively non-invasive tool that has been used extensively to assess immunocompetence, especially in birds, and more recently in amphibians. However, there is substantial variation in experimental methodology among amphibian PHA studies in terms of species and life stages, PHA doses and injection sites, and use of experimental controls. Here, we compile and compare all known PHA studies in amphibians to identify knowledge gaps and develop best practices for future work. We found that research has only been conducted on a limited number of species, which may not reflect the diversity of amphibians. There is also a lack of validation studies in most species, so that doses and timing of PHA injection and subsequent swelling measurements may not effectively evaluate immunocompetence. Based on these and other findings, we put forward a set of recommendations to make future PHA studies more consistent and improve the ability to utilize this assay in wild populations, where immune surveillance is greatly needed.
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Affiliation(s)
- Lauren Hawley
- Department of Environmental Science and Policy, George Mason University, Fairfax, VA, USA
| | - Kelly L Smalling
- New Jersey Water Science Center, U.S. Geological Survey, Lawrenceville, NJ, USA
| | - Scott Glaberman
- Department of Environmental Science and Policy, George Mason University, Fairfax, VA, USA
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3
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Cachoux VML, Balakireva M, Gracia M, Bosveld F, López-Gay JM, Maugarny A, Gaugué I, di Pietro F, Rigaud SU, Noiret L, Guirao B, Bellaïche Y. Epithelial apoptotic pattern emerges from global and local regulation by cell apical area. Curr Biol 2023; 33:4807-4826.e6. [PMID: 37827152 PMCID: PMC10681125 DOI: 10.1016/j.cub.2023.09.049] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Revised: 08/07/2023] [Accepted: 09/20/2023] [Indexed: 10/14/2023]
Abstract
Geometry is a fundamental attribute of biological systems, and it underlies cell and tissue dynamics. Cell geometry controls cell-cycle progression and mitosis and thus modulates tissue development and homeostasis. In sharp contrast and despite the extensive characterization of the genetic mechanisms of caspase activation, we know little about whether and how cell geometry controls apoptosis commitment in developing tissues. Here, we combined multiscale time-lapse microscopy of developing Drosophila epithelium, quantitative characterization of cell behaviors, and genetic and mechanical perturbations to determine how apoptosis is controlled during epithelial tissue development. We found that early in cell lives and well before extrusion, apoptosis commitment is linked to two distinct geometric features: a small apical area compared with other cells within the tissue and a small relative apical area with respect to the immediate neighboring cells. We showed that these global and local geometric characteristics are sufficient to recapitulate the tissue-scale apoptotic pattern. Furthermore, we established that the coupling between these two geometric features and apoptotic cells is dependent on the Hippo/YAP and Notch pathways. Overall, by exploring the links between cell geometry and apoptosis commitment, our work provides important insights into the spatial regulation of cell death in tissues and improves our understanding of the mechanisms that control cell number and tissue size.
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Affiliation(s)
- Victoire M L Cachoux
- Institut Curie, Université PSL, Sorbonne Université, CNRS UMR3215, INSERM U934, Genetics and Developmental Biology, 75005 Paris, France
| | - Maria Balakireva
- Institut Curie, Université PSL, Sorbonne Université, CNRS UMR3215, INSERM U934, Genetics and Developmental Biology, 75005 Paris, France
| | - Mélanie Gracia
- Institut Curie, Université PSL, Sorbonne Université, CNRS UMR3215, INSERM U934, Genetics and Developmental Biology, 75005 Paris, France
| | - Floris Bosveld
- Institut Curie, Université PSL, Sorbonne Université, CNRS UMR3215, INSERM U934, Genetics and Developmental Biology, 75005 Paris, France
| | - Jesús M López-Gay
- Institut Curie, Université PSL, Sorbonne Université, CNRS UMR3215, INSERM U934, Genetics and Developmental Biology, 75005 Paris, France
| | - Aude Maugarny
- Institut Curie, Université PSL, Sorbonne Université, CNRS UMR3215, INSERM U934, Genetics and Developmental Biology, 75005 Paris, France
| | - Isabelle Gaugué
- Institut Curie, Université PSL, Sorbonne Université, CNRS UMR3215, INSERM U934, Genetics and Developmental Biology, 75005 Paris, France
| | - Florencia di Pietro
- Institut Curie, Université PSL, Sorbonne Université, CNRS UMR3215, INSERM U934, Genetics and Developmental Biology, 75005 Paris, France
| | - Stéphane U Rigaud
- Institut Curie, Université PSL, Sorbonne Université, CNRS UMR3215, INSERM U934, Genetics and Developmental Biology, 75005 Paris, France
| | - Lorette Noiret
- Institut Curie, Université PSL, Sorbonne Université, CNRS UMR3215, INSERM U934, Genetics and Developmental Biology, 75005 Paris, France
| | - Boris Guirao
- Institut Curie, Université PSL, Sorbonne Université, CNRS UMR3215, INSERM U934, Genetics and Developmental Biology, 75005 Paris, France.
| | - Yohanns Bellaïche
- Institut Curie, Université PSL, Sorbonne Université, CNRS UMR3215, INSERM U934, Genetics and Developmental Biology, 75005 Paris, France.
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4
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Zhou CY, Dekker B, Liu Z, Cabrera H, Ryan J, Dekker J, Heald R. Mitotic chromosomes scale to nuclear-cytoplasmic ratio and cell size in Xenopus. eLife 2023; 12:e84360. [PMID: 37096661 PMCID: PMC10260010 DOI: 10.7554/elife.84360] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2022] [Accepted: 04/21/2023] [Indexed: 04/26/2023] Open
Abstract
During the rapid and reductive cleavage divisions of early embryogenesis, subcellular structures such as the nucleus and mitotic spindle scale to decreasing cell size. Mitotic chromosomes also decrease in size during development, presumably to scale coordinately with mitotic spindles, but the underlying mechanisms are unclear. Here we combine in vivo and in vitro approaches using eggs and embryos from the frog Xenopus laevis to show that mitotic chromosome scaling is mechanistically distinct from other forms of subcellular scaling. We found that mitotic chromosomes scale continuously with cell, spindle, and nuclear size in vivo. However, unlike for spindles and nuclei, mitotic chromosome size cannot be reset by cytoplasmic factors from earlier developmental stages. In vitro, increasing nuclear-cytoplasmic (N/C) ratio is sufficient to recapitulate mitotic chromosome scaling, but not nuclear or spindle scaling, through differential loading of maternal factors during interphase. An additional pathway involving importin α scales mitotic chromosomes to cell surface area/volume ratio (SA/V) during metaphase. Finally, single-chromosome immunofluorescence and Hi-C data suggest that mitotic chromosomes shrink during embryogenesis through decreased recruitment of condensin I, resulting in major rearrangements of DNA loop architecture to accommodate the same amount of DNA on a shorter chromosome axis. Together, our findings demonstrate how mitotic chromosome size is set by spatially and temporally distinct developmental cues in the early embryo.
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Affiliation(s)
- Coral Y Zhou
- Department of Molecular and Cell Biology, University of California, BerkeleyBerkeleyUnited States
| | - Bastiaan Dekker
- Department of Systems Biology, University of Massachusetts Medical SchoolWorcesterUnited States
| | - Ziyuan Liu
- Department of Molecular and Cell Biology, University of California, BerkeleyBerkeleyUnited States
| | - Hilda Cabrera
- Department of Molecular and Cell Biology, University of California, BerkeleyBerkeleyUnited States
| | - Joel Ryan
- Advanced BioImaging Facility, McGill UniversityMontrealCanada
| | - Job Dekker
- Department of Systems Biology, University of Massachusetts Medical SchoolWorcesterUnited States
- Howard Hughes Medical InstituteChevy ChaseUnited States
| | - Rebecca Heald
- Department of Molecular and Cell Biology, University of California, BerkeleyBerkeleyUnited States
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5
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Balachandra S, Sarkar S, Amodeo AA. The Nuclear-to-Cytoplasmic Ratio: Coupling DNA Content to Cell Size, Cell Cycle, and Biosynthetic Capacity. Annu Rev Genet 2022; 56:165-185. [PMID: 35977407 PMCID: PMC10165727 DOI: 10.1146/annurev-genet-080320-030537] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Though cell size varies between different cells and across species, the nuclear-to-cytoplasmic (N/C) ratio is largely maintained across species and within cell types. A cell maintains a relatively constant N/C ratio by coupling DNA content, nuclear size, and cell size. We explore how cells couple cell division and growth to DNA content. In some cases, cells use DNA as a molecular yardstick to control the availability of cell cycle regulators. In other cases, DNA sets a limit for biosynthetic capacity. Developmentally programmed variations in the N/C ratio for a given cell type suggest that a specific N/C ratio is required to respond to given physiological demands. Recent observations connecting decreased N/C ratios with cellular senescence indicate that maintaining the proper N/C ratio is essential for proper cellular functioning. Together, these findings suggest a causative, not simply correlative, role for the N/C ratio in regulating cell growth and cell cycle progression.
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Affiliation(s)
- Shruthi Balachandra
- Department of Biological Sciences, Dartmouth College, Hanover, New Hampshire, USA; ,
| | - Sharanya Sarkar
- Department of Microbiology and Immunology, Dartmouth College, Hanover, New Hampshire, USA;
| | - Amanda A Amodeo
- Department of Biological Sciences, Dartmouth College, Hanover, New Hampshire, USA; ,
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6
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Acevedo AA, Palma RE, Olalla-Tárraga MÁ. Ecological and evolutionary trends of body size in Pristimantis frogs, the world's most diverse vertebrate genus. Sci Rep 2022; 12:18106. [PMID: 36302809 PMCID: PMC9613995 DOI: 10.1038/s41598-022-22181-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2022] [Accepted: 10/11/2022] [Indexed: 12/30/2022] Open
Abstract
Body size is a key organismal trait. However, the environmental and evolutionary factors that drive body size patterns at the interspecific level remain unclear. Here, we explored these relationships between phenotype-environment using neotropical frogs of Pristimantis, the world's most diverse vertebrate genus. We analyzed: (a) whether this group follows the Rensch's rule, a trend of sexual size dimorphism (SSD) to increase with size when males are the larger sex; (b) whether environmental constraints have influenced body size variation; and (c) how the rates of body size evolution have varied over time. Analyses were based on two information sources, the first one including body sizes of ~ 85% (495 species) of known species in the genus, and a second one incorporating molecular phylogenetic information for 257 species. Our results showed that all Pristimantis species exhibited marked SSD but did not follow Rensch's rule. We found that the models that best explained body size in males, females, and SSD contained environmental variations in temperature, precipitation, and elevation as predictors. In turn, body size has evolved toward an optimum, with a decelerating rate of evolution differentiated between the large Pristimantis clades.
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Affiliation(s)
- Aldemar A. Acevedo
- grid.7870.80000 0001 2157 0406Laboratory of Evolutionary Biology, Department of Ecology, Faculty of Biological Sciences, Pontificia Universidad Católica de Chile, Santiago, Chile ,grid.443909.30000 0004 0385 4466Laboratory of Genetics and Evolution, Department of Ecological Sciences, Faculty of Sciences, Universidad de Chile, Santiago, Chile ,grid.441950.d0000 0001 2107 1033Grupo de Investigación en Ecología y Biogeografía, Universidad de Pamplona, Pamplona, Colombia
| | - R. Eduardo Palma
- grid.7870.80000 0001 2157 0406Laboratory of Evolutionary Biology, Department of Ecology, Faculty of Biological Sciences, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Miguel Ángel Olalla-Tárraga
- grid.28479.300000 0001 2206 5938Department of Biology and Geology, Physics & Inorganic Chemistry, Universidad Rey Juan Carlos, Móstoles, Spain
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7
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Abstract
Cells adopt a size that is optimal for their function, and pushing them beyond this limit can cause cell aging and death by senescence or reduce proliferative potential. However, by increasing their genome copy number (ploidy), cells can increase their size dramatically and homeostatically maintain physiological properties such as biosynthesis rate. Recent studies investigating the relationship between cell size and rates of biosynthesis and metabolism under normal, polyploid, and pathological conditions are revealing new insights into how cells attain the best function or fitness for their size by tuning processes including transcription, translation, and mitochondrial respiration. A new frontier is to connect single-cell scaling relationships with tissue and whole-organism physiology, which promises to reveal molecular and evolutionary principles underlying the astonishing diversity of size observed across the tree of life.
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Affiliation(s)
- Clotilde Cadart
- Molecular and Cell Biology Department, University of California, Berkeley, Berkeley, CA 94720-3200
| | - Rebecca Heald
- Molecular and Cell Biology Department, University of California, Berkeley, Berkeley, CA 94720-3200
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8
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Essner RL, Pereira REE, Blackburn DC, Singh AL, Stanley EL, Moura MO, Confetti AE, Pie MR. Semicircular canal size constrains vestibular function in miniaturized frogs. SCIENCE ADVANCES 2022; 8:eabn1104. [PMID: 35704574 PMCID: PMC9200278 DOI: 10.1126/sciadv.abn1104] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/03/2021] [Accepted: 05/04/2022] [Indexed: 06/15/2023]
Abstract
Miniaturization has evolved repeatedly in frogs in the moist leaf litter environments of rainforests worldwide. Miniaturized frogs are among the world's smallest vertebrates and exhibit an array of enigmatic features. One area where miniaturization has predictable consequences is the vestibular system, which acts as a gyroscope, providing sensory information about movement and orientation. We investigated the vestibular system of pumpkin toadlets, Brachycephalus (Anura: Brachycephalidae), a clade of miniaturized frogs from Brazil. The semicircular canals of miniaturized frogs are the smallest recorded for adult vertebrates, resulting in low sensitivity to angular acceleration due to insufficient displacement of endolymph. This translates into a lack of postural control during jumping in Brachycephalus and represents a physical constraint resulting from Poiseuille's law, which governs movement of fluids within tubes.
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Affiliation(s)
- Richard L. Essner
- Department of Biological Sciences, Southern Illinois University Edwardsville , Edwardsville, IL, USA
| | - Rudá E. E. Pereira
- Programa de Pós-Graduação em Zoologia, Universidade Federal do Paraná, Curitiba, Paraná, Brazil
| | - David C. Blackburn
- Florida Museum of Natural History, University of Florida, , Gainesville, FL, USA
| | - Amber L. Singh
- Florida Museum of Natural History, University of Florida, , Gainesville, FL, USA
| | - Edward L. Stanley
- Florida Museum of Natural History, University of Florida, , Gainesville, FL, USA
| | - Mauricio O. Moura
- Departamento de Zoologia, Universidade Federal do Paraná, Curitiba, Paraná, Brazil
- Mater Natura—Instituto de Estudos Ambientais, Curitiba, Paraná, Brazil
| | - André E. Confetti
- Programa de Pós-Graduação em Zoologia, Universidade Federal do Paraná, Curitiba, Paraná, Brazil
| | - Marcio R. Pie
- Department of Biology, Edge Hill University, Ormskirk, Lancashire, UK
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9
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Martins RA, Greenspan SE, Medina D, Buttimer S, Marshall VM, Neely WJ, Siomko S, Lyra ML, Haddad CFB, São-Pedro V, Becker CG. Signatures of functional bacteriome structure in a tropical direct-developing amphibian species. Anim Microbiome 2022; 4:40. [PMID: 35672870 PMCID: PMC9172097 DOI: 10.1186/s42523-022-00188-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Accepted: 05/17/2022] [Indexed: 11/10/2022] Open
Abstract
Abstract
Background
Host microbiomes may differ under the same environmental conditions and these differences may influence susceptibility to infection. Amphibians are ideal for comparing microbiomes in the context of disease defense because hundreds of species face infection with the skin-invading microbe Batrachochytrium dendrobatidis (Bd), and species richness of host communities, including their skin bacteria (bacteriome), may be exceptionally high. We conducted a landscape-scale Bd survey of six co-occurring amphibian species in Brazil’s Atlantic Forest. To test the bacteriome as a driver of differential Bd prevalence, we compared bacteriome composition and co-occurrence network structure among the six focal host species.
Results
Intensive sampling yielded divergent Bd prevalence in two ecologically similar terrestrial-breeding species, a group with historically low Bd resistance. Specifically, we detected the highest Bd prevalence in Ischnocnema henselii but no Bd detections in Haddadus binotatus. Haddadus binotatus carried the highest bacteriome alpha and common core diversity, and a modular network partitioned by negative co-occurrences, characteristics associated with community stability and competitive interactions that could inhibit Bd colonization.
Conclusions
Our findings suggest that community structure of the bacteriome might drive Bd resistance in H. binotatus, which could guide microbiome manipulation as a conservation strategy to protect diverse radiations of direct-developing species from Bd-induced population collapses.
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10
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Niide T, Asari S, Kawabata K, Hara Y. Specificity of Nuclear Size Scaling in Frog Erythrocytes. Front Cell Dev Biol 2022; 10:857862. [PMID: 35663388 PMCID: PMC9159806 DOI: 10.3389/fcell.2022.857862] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2022] [Accepted: 04/21/2022] [Indexed: 11/29/2022] Open
Abstract
In eukaryotes, the cell has the ability to modulate the size of the nucleus depending on the surrounding environment, to enable nuclear functions such as DNA replication and transcription. From previous analyses of nuclear size scaling in various cell types and species, it has been found that eukaryotic cells have a conserved scaling rule, in which the nuclear size correlates with both cell size and genomic content. However, there are few studies that have focused on a certain cell type and systematically analyzed the size scaling properties in individual species (intra-species) and among species (inter-species), and thus, the difference in the scaling rules among cell types and species is not well understood. In the present study, we analyzed the size scaling relationship among three parameters, nuclear size, cell size, and genomic content, in our measured datasets of terminally differentiated erythrocytes of five Anura frogs and collected datasets of different species classes from published papers. In the datasets of isolated erythrocytes from individual frogs, we found a very weak correlation between the measured nuclear and cell cross-sectional areas. Within the erythrocytes of individual species, the correlation of the nuclear area with the cell area showed a very low hypoallometric relationship, in which the relative nuclear size decreased when the cell size increased. These scaling trends in intra-species erythrocytes are not comparable to the known general correlation in other cell types. When comparing parameters across species, the nuclear areas correlated with both cell areas and genomic contents among the five frogs and the collected datasets in each species class. However, the contribution of genomic content to nuclear size determination was smaller than that of the cell area in all species classes. In particular, the estimated degree of the contribution of genomic content was greater in the amphibian class than in other classes. Together with our imaging analysis of structural components in nuclear membranes, we hypothesized that the observed specific features in nuclear size scaling are achieved by the weak interaction of the chromatin with the nuclear membrane seen in frog erythrocytes.
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Affiliation(s)
| | | | | | - Yuki Hara
- Evolutionary Cell Biology Laboratory, Faculty of Science, Yamaguchi University, Yamaguchi, Japan
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11
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Proximate Composition, Predictive Analysis and Allometric Relationships, of the Edible Water Frog (Pelophylax epeiroticus) in Lake Pamvotida (Northwest Greece). SUSTAINABILITY 2022. [DOI: 10.3390/su14063150] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
The edible water frog Pelophylax epeiroticus, distributed mainly in Northwest Greece and utilized commercially as food, was investigated in lake Pamvotida (Ioannina). The objective was to assess aspects of population structure (sex ratio, morphometric characteristics, allometric relationships) and proximate composition of the Epirus water frog (Pelophylax epeiroticus). Commercial samples (31 females and 54 males) were obtained and sex ratio, morphometric characteristics, allometric relationships and proximate composition were assessed. A significantly lower abundance of females was indicated (31 females and 54 males). Body length range was higher in females (females 3.4 mm, males 2.6 mm), whereas total weight range was higher in males (females 45.08 gr, males 48.35 gr). Differences in allometric relationships were indicated between sexes. The high protein (15.93 ± 3.32) and low lipid (0.25 ± 0.13) contents indicated that P. epeiroticus is an excellent food source of high nutritional value. A tree classification algorithm indicated that the principal contributing component for sex classification was dry matter, followed by a proportion of edible flesh and protein content. A predicted future increase in demand for wild-caught individuals requires the use of a suitable management plan, coupled with the development of farming practices aiming to assure the sustainable exploitation of this important resource and alleviate the pressure on its populations.
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12
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Labisko J, Bunbury N, Griffiths RA, Groombridge JJ, Chong-Seng L, Bradfield KS, Streicher JW. Survival of climate warming through niche shifts: Evidence from frogs on tropical islands. GLOBAL CHANGE BIOLOGY 2022; 28:1268-1286. [PMID: 34874078 DOI: 10.1111/gcb.15997] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Revised: 10/07/2021] [Accepted: 11/12/2021] [Indexed: 06/13/2023]
Abstract
How will organisms cope when forced into warmer-than-preferred thermal environments? This is a key question facing our ability to monitor and manage biota as average annual temperatures increase, and is of particular concern for range-limited terrestrial species unable to track their preferred climatic envelope. Being ectothermic, desiccation prone, and often spatially restricted, island-inhabiting tropical amphibians exemplify this scenario. Pre-Anthropocene case studies of how insular amphibian populations responded to the enforced occupation of warmer-than-ancestral habitats may add a valuable, but currently lacking, perspective. We studied a population of frogs from the Seychelles endemic family Sooglossidae which, due to historic sea-level rise, have been forced to occupy a significantly warmer island (Praslin) than their ancestors and close living relatives. Evidence from thermal activity patterns, bioacoustics, body size distributions, and ancestral state estimations suggest that this population shifted its thermal niche in response to restricted opportunities for elevational dispersal. Relative to conspecifics, Praslin sooglossids also have divergent nuclear genotypes and call characters, a finding consistent with adaptation causing speciation in a novel thermal environment. Using an evolutionary perspective, our study reveals that some tropical amphibians have survived episodes of historic warming without the aid of dispersal and therefore may have the capacity to adapt to the currently warming climate. However, two otherwise co-distributed sooglossid species are absent from Praslin, and the deep evolutionary divergence between the frogs on Praslin and their closest extant relatives (~8 million years) may have allowed for gradual thermal adaptation and speciation. Thus, local extinction is still a likely outcome for tropical frogs experiencing warming climates in the absence of dispersal corridors to thermal refugia.
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Affiliation(s)
- Jim Labisko
- Durrell Institute of Conservation and Ecology, School of Anthropology and Conservation, University of Kent, Canterbury, Kent, UK
- Island Biodiversity and Conservation centre, University of Seychelles, Victoria, Seychelles
- Centre for Biodiversity and Environment Research, Department of Genetics, Evolution and Environment, University College London, London, UK
| | - Nancy Bunbury
- Seychelles Islands Foundation, Victoria, Mahé, Seychelles
- Centre for Ecology and Conservation, University of Exeter, Cornwall Campus, Penryn, UK
| | - Richard A Griffiths
- Durrell Institute of Conservation and Ecology, School of Anthropology and Conservation, University of Kent, Canterbury, Kent, UK
| | - Jim J Groombridge
- Durrell Institute of Conservation and Ecology, School of Anthropology and Conservation, University of Kent, Canterbury, Kent, UK
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13
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Cordero GA. Disentangling the correlated evolution of body size, life history, and ontogeny in miniaturized chelydroid turtles. Evol Dev 2021; 23:439-458. [PMID: 34037309 DOI: 10.1111/ede.12386] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2021] [Revised: 04/27/2021] [Accepted: 05/03/2021] [Indexed: 12/21/2022]
Abstract
Organismal miniaturization is defined by a reduction in body size relative to a large ancestor. In vertebrate animals, miniaturization is achieved by suppressing the energetics of growth. However, this might interfere with reproductive strategies in egg-laying species with limited energy budgets for embryo growth and differentiation. In general, the extent to which miniaturization coincides with alterations in animal development remains obscure. To address the interplay among body size, life history, and ontogeny, miniaturization in chelydroid turtles was examined. The analyses corroborated that miniaturization in the Chelydroidea clade is underlain by a dampening of the ancestral growth trajectory. There were no associated shifts in the early sequence of developmental transformations, though the relative duration of organogenesis was shortened in miniaturized embryos. The size of eggs, hatchlings, and adults was positively correlated within Chelydroidea. A phylogenetically broader exploration revealed an alternative miniaturization mode wherein exceptionally large hatchlings grow minimally and thus attain diminutive adult sizes. Lastly, it is shown that miniaturized Chelydroidea turtles undergo accelerated ossification coupled with a ~10% reduction in shell bones. As in other vertebrates, the effects of miniaturization were not systemic, possibly owing to opposing functional demands and tissue geometric constraints. This underscores the integrated and hierarchical nature of developmental systems.
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Affiliation(s)
- Gerardo A Cordero
- Department of Geosciences, University of Tübingen, Tübingen, Germany
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14
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Bonett RM, Ledbetter NM, Hess AJ, Herrboldt MA, Denoël M. Repeated ecological and life cycle transitions make salamanders an ideal model for evolution and development. Dev Dyn 2021; 251:957-972. [PMID: 33991029 DOI: 10.1002/dvdy.373] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Revised: 04/16/2021] [Accepted: 05/10/2021] [Indexed: 11/11/2022] Open
Abstract
Observations on the ontogeny and diversity of salamanders provided some of the earliest evidence that shifts in developmental trajectories have made a substantial contribution to the evolution of animal forms. Since the dawn of evo-devo there have been major advances in understanding developmental mechanisms, phylogenetic relationships, evolutionary models, and an appreciation for the impact of ecology on patterns of development (eco-evo-devo). Molecular phylogenetic analyses have converged on strong support for the majority of branches in the Salamander Tree of Life, which includes 764 described species. Ancestral reconstructions reveal repeated transitions between life cycle modes and ecologies. The salamander fossil record is scant, but key Mesozoic species support the antiquity of life cycle transitions in some families. Colonization of diverse habitats has promoted phenotypic diversification and sometimes convergence when similar environments have been independently invaded. However, unrelated lineages may follow different developmental pathways to arrive at convergent phenotypes. This article summarizes ecological and endocrine-based causes of life cycle transitions in salamanders, as well as consequences to body size, genome size, and skeletal structure. Salamanders offer a rich source of comparisons for understanding how the evolution of developmental patterns has led to phenotypic diversification following shifts to new adaptive zones.
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Affiliation(s)
- Ronald M Bonett
- Department of Biological Science, The University of Tulsa, Tulsa, Oklahoma, USA
| | | | - Alexander J Hess
- Department of Biological Science, The University of Tulsa, Tulsa, Oklahoma, USA
| | - Madison A Herrboldt
- Department of Biological Science, The University of Tulsa, Tulsa, Oklahoma, USA
| | - Mathieu Denoël
- Laboratory of Ecology and Conservation of Amphibians (LECA), Freshwater and Oceanic science Unit of reSearch (FOCUS), University of Liège, Liège, Belgium
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15
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Flynn RW, Hoskins TD, Iacchetta M, de Perre C, Lee LS, Hoverman JT, Sepulveda MS. Dietary exposure and accumulation of per- and polyfluoroalkyl substances alters growth and reduces body condition of post-metamorphic salamanders. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 765:142730. [PMID: 33077234 DOI: 10.1016/j.scitotenv.2020.142730] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/23/2020] [Revised: 09/11/2020] [Accepted: 09/24/2020] [Indexed: 06/11/2023]
Abstract
Per- and polyfluoroalkyl substances (PFAS) are contaminants of concern due to their persistence, potential to bioaccumulate, and toxicity. While dietary exposure is the primary route of exposure for terrestrial species, data on dietary PFAS uptake and adverse effects are largely restricted to mammals. As such, substantial data gaps exist that hinder ecological risk assessment, including environmentally relevant exposure levels and taxa. Using a 30-d laboratory experiment, we examined the effects of dietary PFAS-exposure on post-metamorphic tiger salamanders (Ambystoma tigrinum). We fed salamanders crickets exposed to perfluorooctanoic acid (PFOA), perfluorooctane sulfonate (PFOS), perfluorohexane sulfonate (PFHxS), or 6:2 fluorotelomer sulfonate (6:2 FTS) at low (<1.0), medium (2-5), or high (16-62) ng PFAS/g/d (wet weight) dose rates. We found that only PFOS resulted in substantial biomagnification. Despite limited evidence for biomagnification, PFAS altered growth and generally reduced body condition. Salamanders with the highest burdens of PFOS grew less and had lower body conditions, while burdens of PFHxS and PFOA were only associated with reduced growth. There was no evidence that environmentally relevant doses of PFAS increase liver size in salamanders. Our results demonstrate that dietary exposure and accumulation of PFAS can impact fitness-related traits in amphibians and contribute to trophic transfer in terrestrial food webs.
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Affiliation(s)
- R Wesley Flynn
- Department of Forestry and Natural Resources, Purdue University, 715 West State Street, West Lafayette, IN 47907, United States of America.
| | - Tyler D Hoskins
- Department of Forestry and Natural Resources, Purdue University, 715 West State Street, West Lafayette, IN 47907, United States of America
| | - Michael Iacchetta
- Department of Forestry and Natural Resources, Purdue University, 715 West State Street, West Lafayette, IN 47907, United States of America
| | - Chloe de Perre
- Department of Agronomy, Purdue University, 915 West State Street, West Lafayette, IN 47907, United States of America
| | - Linda S Lee
- Department of Agronomy, Purdue University, 915 West State Street, West Lafayette, IN 47907, United States of America
| | - Jason T Hoverman
- Department of Forestry and Natural Resources, Purdue University, 715 West State Street, West Lafayette, IN 47907, United States of America
| | - Maria S Sepulveda
- Department of Forestry and Natural Resources, Purdue University, 715 West State Street, West Lafayette, IN 47907, United States of America
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16
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Castro KMSA, Amado TF, Olalla-Tárraga MÁ, Gouveia SF, Navas CA, Martinez PA. Water constraints drive allometric patterns in the body shape of tree frogs. Sci Rep 2021; 11:1218. [PMID: 33441858 PMCID: PMC7806824 DOI: 10.1038/s41598-020-80456-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2020] [Accepted: 12/16/2020] [Indexed: 01/29/2023] Open
Abstract
The origin of morphological diversity is a critical question in evolutionary biology. Interactions between the environment and developmental processes have determining roles in morphological diversity, creating patterns through space and over time. Also, the shape of organisms tends to vary with increasing size as a result of those developmental processes, known as allometry. Several studies have demonstrated that the body sizes of anurans are associated with hydric conditions in their environments and that localities with high water stress tend to select for larger individuals. However, how environmental conditions alter those patterns of covariance between size and shape is still elusive. We used 3D geometric morphometric analyses, associated with phylogenetic comparative methods, to determine if the morphological variations and allometric patterns found in Arboranae (Anura) is linked to water conservation mechanisms. We found effects of the hydric stress on the shape of Arboranae species, favouring globular shapes. Also, the allometric patterns varied in intensity according to the water stress gradient, being particularly relevant for smaller frogs, and more intense in environments with higher water deficits. Our study provides empirical evidence that more spherical body shapes, especially among smaller species, reflect an important adaptation of anurans to water conservation in water-constrained environments.
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Affiliation(s)
- Kathleen M S A Castro
- Programa de Pós-Graduação em Ecologia e Conservação, Universidade Federal de Sergipe, São Cristóvão, Sergipe, 49.000-100, Brazil.
- PIBi Lab - Laboratório de Pesquisas Integrativas em Biodiversidade, Universidade Federal de Sergipe, São Cristóvão, Sergipe, 49100-000, Brazil.
| | - Talita F Amado
- Departamento de Biología, Geología, Física y Química Inorgánica, Universidad Rey Juan Carlos, Tulipán s/n, Móstoles, 28933, Madrid, Spain
- PIBi Lab - Laboratório de Pesquisas Integrativas em Biodiversidade, Universidade Federal de Sergipe, São Cristóvão, Sergipe, 49100-000, Brazil
| | - Miguel Á Olalla-Tárraga
- Departamento de Biología, Geología, Física y Química Inorgánica, Universidad Rey Juan Carlos, Tulipán s/n, Móstoles, 28933, Madrid, Spain
| | - Sidney F Gouveia
- Departamento de Ecologia, Universidade Federal de Sergipe, São Cristóvão, Sergipe, Brazil
- PIBi Lab - Laboratório de Pesquisas Integrativas em Biodiversidade, Universidade Federal de Sergipe, São Cristóvão, Sergipe, 49100-000, Brazil
| | - Carlos A Navas
- Departamento de Fisiologia Geral, Instituto de Biociência, Universidade de São Paulo, São Paulo, Brazil
| | - Pablo A Martinez
- Departamento de Biologia, Universidade Federal de Sergipe, São Cristóvão, Sergipe, Brazil
- PIBi Lab - Laboratório de Pesquisas Integrativas em Biodiversidade, Universidade Federal de Sergipe, São Cristóvão, Sergipe, 49100-000, Brazil
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17
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Dynamic optima in cell sizes during early development enable normal gastrulation in zebrafish embryos. Dev Biol 2020; 468:26-40. [DOI: 10.1016/j.ydbio.2020.09.002] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Accepted: 09/01/2020] [Indexed: 11/21/2022]
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18
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Heijo H, Shimogama S, Nakano S, Miyata A, Iwao Y, Hara Y. DNA content contributes to nuclear size control in Xenopus laevis. Mol Biol Cell 2020; 31:2703-2717. [PMID: 32997613 PMCID: PMC7927187 DOI: 10.1091/mbc.e20-02-0113] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2020] [Revised: 08/28/2020] [Accepted: 09/25/2020] [Indexed: 12/17/2022] Open
Abstract
Cells adapt to drastic changes in genome quantity during evolution and cell division by adjusting the nuclear size to exert genomic functions. However, the mechanism by which DNA content within the nucleus contributes to controlling the nuclear size remains unclear. Here, we experimentally evaluated the effects of DNA content by utilizing cell-free Xenopus egg extracts and imaging of in vivo embryos. Upon manipulation of DNA content while maintaining cytoplasmic effects constant, both plateau size and expansion speed of the nucleus correlated highly with DNA content. We also found that nuclear expansion dynamics was altered when chromatin interaction with the nuclear envelope or chromatin condensation was manipulated while maintaining DNA content constant. Furthermore, excess membrane accumulated on the nuclear surface when the DNA content was low. These results clearly demonstrate that nuclear expansion is determined not only by cytoplasmic membrane supply but also by the physical properties of chromatin, including DNA quantity and chromatin structure within the nucleus, rather than the coding sequences themselves. In controlling the dynamics of nuclear expansion, we propose that chromatin interaction with the nuclear envelope plays a role in transmitting chromatin repulsion forces to the nuclear membrane.
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Affiliation(s)
- Hiroko Heijo
- Evolutionary Cell Biology Laboratory, Faculty of Science, Yamaguchi University, Yoshida 1677-1, Yamaguchi City, 753-8512, Japan
| | - Sora Shimogama
- Evolutionary Cell Biology Laboratory, Faculty of Science, Yamaguchi University, Yoshida 1677-1, Yamaguchi City, 753-8512, Japan
| | - Shuichi Nakano
- Evolutionary Cell Biology Laboratory, Faculty of Science, Yamaguchi University, Yoshida 1677-1, Yamaguchi City, 753-8512, Japan
| | - Anna Miyata
- Evolutionary Cell Biology Laboratory, Faculty of Science, Yamaguchi University, Yoshida 1677-1, Yamaguchi City, 753-8512, Japan
| | - Yasuhiro Iwao
- Laboratory of Molecular Developmental Biology, Department of Biology, Graduate School of Sciences and Technology for Innovation, Yamaguchi University, Yoshida 1677-1, Yamaguchi City, 753-8512, Japan
| | - Yuki Hara
- Evolutionary Cell Biology Laboratory, Faculty of Science, Yamaguchi University, Yoshida 1677-1, Yamaguchi City, 753-8512, Japan
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19
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Daza JD, Stanley EL, Bolet A, Bauer AM, Arias JS, Čerňanský A, Bevitt JJ, Wagner P, Evans SE. Enigmatic amphibians in mid-Cretaceous amber were chameleon-like ballistic feeders. Science 2020; 370:687-691. [DOI: 10.1126/science.abb6005] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2020] [Accepted: 09/08/2020] [Indexed: 12/20/2022]
Affiliation(s)
- Juan D. Daza
- Department of Biological Sciences, Sam Houston State University, Huntsville, TX, USA
| | - Edward L. Stanley
- Department of Herpetology, Florida Museum of Natural History, Gainesville, FL, USA
| | - Arnau Bolet
- Institut Català de Paleontologia Miquel Crusafont, Universitat Autònoma de Barcelona, Cerdanyola del Vallès, Spain
- School of Earth Sciences, University of Bristol, Bristol, UK
| | - Aaron M. Bauer
- Department of Biology and Center for Biodiversity and Ecosystem Stewardship, Villanova University, Villanova, PA, USA
| | - J. Salvador Arias
- Unidad Ejecutora Lillo, CONICET - FML, San Miguel de Tucumán, Argentina
| | - Andrej Čerňanský
- Department of Ecology, Laboratory of Evolutionary Biology, Faculty of Natural Sciences, Comenius University in Bratislava, Bratislava, Slovakia
| | - Joseph J. Bevitt
- Australian Centre for Neutron Scattering, Australian Nuclear Science and Technology Organisation, Sydney, NSW, Australia
| | - Philipp Wagner
- Department of Research and Conservation, Allwetterzoo Münster, Münster, Germany
| | - Susan E. Evans
- Department of Cell and Developmental Biology, University College London, London, UK
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20
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Decena-Segarra LP, Bizjak-Mali L, Kladnik A, Sessions SK, Rovito SM. Miniaturization, Genome Size, and Biological Size in a Diverse Clade of Salamanders. Am Nat 2020; 196:634-648. [PMID: 33064588 DOI: 10.1086/711019] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
AbstractGenome size (C-value) can affect organismal traits across levels of biological organization from tissue complexity to metabolism. Neotropical salamanders show wide variation in genome and body sizes, including several clades with miniature species. Because miniaturization imposes strong constraints on morphology and development and because genome size is strongly correlated with cell size, we hypothesize that body size has played an important role in the evolution of genome size in bolitoglossine salamanders. If this hypothesis is correct, then genome size and body size should be correlated in this group. Using Feulgen image analysis densitometry, we estimated genome sizes for 60 species of Neotropical salamanders. We also estimated the "biological size" of species by comparing genome size and physical body sizes in a phylogenetic context. We found a significant correlation between C-value and physical body size using optimal regression with an Ornstein-Uhlenbeck model and report the smallest salamander genome found to date. Our index of biological size showed that some salamanders with large physical body size have smaller biological body size than some miniature species and that several clades demonstrate patterns of increased or decreased biological size compared with their physical size. Our results suggest a causal relationship between physical body size and genome size and show the importance of considering the impact of both on the biological size of organisms. Indeed, biological size may be a more appropriate measure than physical size when considering phenotypic consequences of genome size evolution in many groups.
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21
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Cell Biology: Social Distancing of Microtubule Ends Increases Their Assembly Rates. Curr Biol 2020; 30:R888-R890. [PMID: 32750351 DOI: 10.1016/j.cub.2020.06.014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Microtubules assembled from artificial centrosomes in microfluidic chambers of defined size are amenable to high resolution live imaging of their dynamics and space-filling properties. By using this experimental regime in conjunction with cytoplasmic extract, a new study finds that microtubule end density negatively influences their assembly rates.
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22
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Condez TH, Haddad CFB, Zamudio KR. Historical biogeography and multi-trait evolution in miniature toadlets of the genus Brachycephalus (Anura: Brachycephalidae). Biol J Linn Soc Lond 2020. [DOI: 10.1093/biolinnean/blz200] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
Abstract
Evolutionary changes towards a miniaturized body plan may directly affect other important phenotypic traits related to the physiology, behaviour and ecology of organisms. The frog genus Brachycephalus is an outstanding example of a radiation of miniaturized species endemic to the Brazilian Atlantic Forest. We inferred ancestral states and historical changes in body size, body colour and hyperossification to test hypotheses about diversification and selective environmental mechanisms leading to the evolution of these specialized traits. The ancestral distribution was associated with high-elevation regions in the northern Serra do Mar mountain range, and diversification in the genus was coincident with important geological and climatic events during the history of the Atlantic Forest. The dynamic historical changes provided an opportunity for multiple lowland lineages and for speciation via dispersal and vicariance in multiple invasions of the highlands. The ancestral Brachycephalus was reconstructed as miniaturized and dull coloured, without hyperossification in the skin, skull or postcranial skeleton. A parallel evolution of phenotypic traits has occurred in northern and southern Atlantic Forest lineages, beginning in the Miocene. Shifts in body size are not related to elevation range or latitude. However, we found a significant correlation between the evolution of hyperossification and aposematism with increasing body size.
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Affiliation(s)
- Thais H Condez
- Instituto Nacional da Mata Atlântica (INMA), Avenida José Ruschi, Santa Teresa, Espírito Santo, Brazil
| | - Célio F B Haddad
- Departamento de Zoologia e Centro de Aquicultura (CAUNESP), Instituto de Biociências, Universidade Estadual Paulista Júlio de Mesquita Filho, Rio Claro, São Paulo, Brazil
| | - Kelly R Zamudio
- Ecology and Evolutionary Biology (EEB), Cornell University, Corson Hall, Ithaca, New York, United States
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23
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Abstract
The genetic control of the characteristic cell sizes of different species and tissues is a long-standing enigma. Plants are convenient for studying this question in a multicellular context, as their cells do not move and are easily tracked and measured from organ initiation in the meristems to subsequent morphogenesis and differentiation. In this article, we discuss cell size control in plants compared with other organisms. As seen from yeast cells to mammalian cells, size homeostasis is maintained cell autonomously in the shoot meristem. In developing organs, vacuolization contributes to cell size heterogeneity and may resolve conflicts between growth control at the cellular and organ levels. Molecular mechanisms for cell size control have implications for how cell size responds to changes in ploidy, which are particularly important in plant development and evolution. We also discuss comparatively the functional consequences of cell size and their potential repercussions at higher scales, including genome evolution.
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Affiliation(s)
- Marco D'Ario
- Department of Cell and Developmental Biology, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, United Kingdom
| | - Robert Sablowski
- Department of Cell and Developmental Biology, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, United Kingdom
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24
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Berenson DF, Zatulovskiy E, Xie S, Skotheim JM. Constitutive expression of a fluorescent protein reports the size of live human cells. Mol Biol Cell 2019; 30:2985-2995. [PMID: 31599704 PMCID: PMC6857566 DOI: 10.1091/mbc.e19-03-0171] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2019] [Revised: 09/20/2019] [Accepted: 10/01/2019] [Indexed: 11/11/2022] Open
Abstract
Cell size is important for cell physiology because it sets the geometric scale of organelles and biosynthesis. A number of methods exist to measure different aspects of cell size, but each has significant drawbacks. Here, we present an alternative method to measure the size of single human cells using a nuclear localized fluorescent protein expressed from a constitutive promoter. We validate this method by comparing it to several established cell size measurement strategies, including flow cytometry optical scatter, total protein dyes, and quantitative phase microscopy. We directly compare our fluorescent protein measurement with the commonly used measurement of nuclear volume and show that our measurements are more robust and less dependent on image segmentation. We apply our method to examine how cell size impacts the cell division cycle and reaffirm that there is a negative correlation between size at cell birth and G1 duration. Importantly, combining our size reporter with fluorescent labeling of a different protein in a different color channel allows measurement of concentration dynamics using simple wide-field fluorescence imaging. Thus, we expect our method will be of use to researchers interested in how dynamically changing protein concentrations control cell fates.
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Affiliation(s)
| | | | - Shicong Xie
- Department of Biology, Stanford University, Stanford, CA 94305
| | - Jan M. Skotheim
- Department of Biology, Stanford University, Stanford, CA 94305
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25
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French BT, Straight AF. The Power of Xenopus Egg Extract for Reconstitution of Centromere and Kinetochore Function. PROGRESS IN MOLECULAR AND SUBCELLULAR BIOLOGY 2019; 56:59-84. [PMID: 28840233 DOI: 10.1007/978-3-319-58592-5_3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Faithful transmission of genetic information during cell division requires attachment of chromosomes to the mitotic spindle via the kinetochore. In vitro reconstitution studies are beginning to uncover how the kinetochore is assembled upon the underlying centromere, how the kinetochore couples chromosome movement to microtubule dynamics, and how cells ensure the site of kinetochore assembly is maintained from one generation to the next. Here we give special emphasis to advances made in Xenopus egg extract, which provides a unique, biochemically tractable in vitro system that affords the complexity of cytoplasm and nucleoplasm to permit reconstitution of the dynamic, cell cycle-regulated functions of the centromere and kinetochore.
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Affiliation(s)
- Bradley T French
- Department of Biochemistry, Stanford University, 279 Campus Drive, Beckman 409, Stanford, CA, 94305, USA
| | - Aaron F Straight
- Department of Biochemistry, Stanford University, 279 Campus Drive, Beckman 409, Stanford, CA, 94305, USA.
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26
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Bredeweg EM, Urbina J, Morzillo AT, Garcia TS. Starting on the Right Foot: Carryover Effects of Larval Hydroperiod and Terrain Moisture on Post-metamorphic Frog Movement Behavior. Front Ecol Evol 2019. [DOI: 10.3389/fevo.2019.00097] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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27
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Kitaoka M, Heald R, Gibeaux R. Spindle assembly in egg extracts of the Marsabit clawed frog, Xenopus borealis. Cytoskeleton (Hoboken) 2018; 75:244-257. [PMID: 29573195 DOI: 10.1002/cm.21444] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2018] [Revised: 03/16/2018] [Accepted: 03/19/2018] [Indexed: 11/05/2022]
Abstract
Egg extracts of the African clawed frog Xenopus laevis have provided a cell-free system instrumental in elucidating events of the cell cycle, including mechanisms of spindle assembly. Comparison with extracts from the diploid Western clawed frog, Xenopus tropicalis, which is smaller at the organism, cellular and subcellular levels, has enabled the identification of spindle size scaling factors. We set out to characterize the Marsabit clawed frog, Xenopus borealis, which is intermediate in size between the two species, but more recently diverged in evolution from X. laevis than X. tropicalis. X. borealis eggs were slightly smaller than those of X. laevis, and slightly smaller spindles were assembled in egg extracts. Interestingly, microtubule distribution across the length of the X. borealis spindles differed from both X. laevis and X. tropicalis. Extract mixing experiments revealed common scaling phenomena among Xenopus species, while characterization of spindle factors katanin, TPX2, and Ran indicate that X. borealis spindles possess both X. laevis and X. tropicalis features. Thus, X. borealis egg extract provides a third in vitro system to investigate interspecies scaling and spindle morphometric variation.
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Affiliation(s)
- Maiko Kitaoka
- Department of Molecular and Cell Biology, University of California, Berkeley, California 94720
| | - Rebecca Heald
- Department of Molecular and Cell Biology, University of California, Berkeley, California 94720
| | - Romain Gibeaux
- Department of Molecular and Cell Biology, University of California, Berkeley, California 94720
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28
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Haupt A, Minc N. How cells sense their own shape - mechanisms to probe cell geometry and their implications in cellular organization and function. J Cell Sci 2018; 131:131/6/jcs214015. [PMID: 29581183 DOI: 10.1242/jcs.214015] [Citation(s) in RCA: 48] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Cells come in a variety of shapes that most often underlie their functions. Regulation of cell morphogenesis implies that there are mechanisms for shape sensing that still remain poorly appreciated. Global and local cell geometry features, such as aspect ratio, size or membrane curvature, may be probed by intracellular modules, such as the cytoskeleton, reaction-diffusion systems or molecular complexes. In multicellular tissues, cell shape emerges as an important means to transduce tissue-inherent chemical and mechanical cues into intracellular organization. One emergent paradigm is that cell-shape sensing is most often based upon mechanisms of self-organization, rather than determinism. Here, we review relevant work that has elucidated some of the core principles of how cellular geometry may be conveyed into spatial information to guide processes, such as polarity, signaling, morphogenesis and division-plane positioning.
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Affiliation(s)
- Armin Haupt
- Institut Jacques Monod, CNRS UMR7592 and Université Paris Diderot, 15 rue Hélène Brion, 75205 Paris Cedex 13, France
| | - Nicolas Minc
- Institut Jacques Monod, CNRS UMR7592 and Université Paris Diderot, 15 rue Hélène Brion, 75205 Paris Cedex 13, France
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29
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Clarke EK, Rivera Gomez KA, Mustachi Z, Murph MC, Schvarzstein M. Manipulation of Ploidy in Caenorhabditis elegans. J Vis Exp 2018. [PMID: 29608173 PMCID: PMC5931776 DOI: 10.3791/57296] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Mechanisms that involve whole genome polyploidy play important roles in development and evolution; also, an abnormal generation of tetraploid cells has been associated with both the progression of cancer and the development of drug resistance. Until now, it has not been feasible to easily manipulate the ploidy of a multicellular animal without generating mostly sterile progeny. Presented here is a simple and rapid protocol for generating tetraploid Caenorhabditis elegans animals from any diploid strain. This method allows the user to create a bias in chromosome segregation during meiosis, ultimately increasing ploidy in C. elegans. This strategy relies on the transient reduction of expression of the rec-8 gene to generate diploid gametes. A rec-8 mutant produces diploid gametes that can potentially produce tetraploids upon fertilization. This tractable scheme has been used to generate tetraploid strains carrying mutations and chromosome rearrangements to gain insight into chromosomal dynamics and interactions during pairing and synapsis in meiosis. This method is efficient for generating stable tetraploid strains without genetic markers, can be applied to any diploid strain, and can be used to derive triploid C. elegans. This straightforward method is useful for investigating other fundamental biological questions relevant to genome instability, gene dosage, biological scaling, extracellular signaling, adaptation to stress, development of resistance to drugs, and mechanisms of speciation.
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Affiliation(s)
- Erlyana K Clarke
- Brooklyn College, Biology Department, City University of New York
| | - Katherine A Rivera Gomez
- Brooklyn College, Biology Department, City University of New York; The Graduate Center, Biology Department, City University of New York
| | - Zaki Mustachi
- Brooklyn College, Biology Department, City University of New York
| | - Mikaela C Murph
- Brooklyn College, Biology Department, City University of New York; Advanced Science Research Center, City University of New York
| | - Mara Schvarzstein
- Brooklyn College, Biology Department, City University of New York; The Graduate Center, Biology Department, City University of New York; Advanced Science Research Center, City University of New York;
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30
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Takagi J, Shimamoto Y. High-quality frozen extracts of Xenopus laevis eggs reveal size-dependent control of metaphase spindle micromechanics. Mol Biol Cell 2017; 28:2170-2177. [PMID: 28592634 PMCID: PMC5531733 DOI: 10.1091/mbc.e17-03-0174] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2017] [Revised: 05/30/2017] [Accepted: 05/31/2017] [Indexed: 11/15/2022] Open
Abstract
Cell-free extracts from unfertilized Xenopus laevis eggs offer the opportunity for a variety of biochemical and biophysical assays for analyzing essential cell cycle events such as metaphase spindle assembly. However, the extracts often exhibit substantial variation in quality and have low storage stability, factors that hamper their experimental utility. Here we report a simple two-step method for preparing frozen egg extracts that retain spindle assembly activity levels similar to those of freshly prepared extracts. Extract degradation associated with the freeze-thaw process can be substantially reduced by using centrifugal filter-based dehydration and slow sample cooling. Large amounts of frozen extract stocks from single-batch preparations allowed us to collect extensive data in micromanipulation experiments, which are often low-throughput, and thus enabled the clarification of correlations between metaphase spindle size and stiffness. Our method provides an assay platform with minimized biological variability and improves the accessibility of egg extracts for research.
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Affiliation(s)
- Jun Takagi
- Quantitative Mechanobiology Laboratory, Center for Frontier Research, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan
| | - Yuta Shimamoto
- Quantitative Mechanobiology Laboratory, Center for Frontier Research, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan
- Department of Genetics, School of Life Science, SOKENDAI, Mishima, Shizuoka 411-8540, Japan
- PRIME, Japan Agency for Medical Research and Development, Tokyo 100-0004, Japan
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Spencer AK, Schaumberg AJ, Zallen JA. Scaling of cytoskeletal organization with cell size in Drosophila. Mol Biol Cell 2017; 28:1519-1529. [PMID: 28404752 PMCID: PMC5449150 DOI: 10.1091/mbc.e16-10-0691] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2016] [Revised: 03/31/2017] [Accepted: 04/05/2017] [Indexed: 11/11/2022] Open
Abstract
Actin-rich denticle precursors are regularly distributed in the Drosophila embryo. Cytoskeletal scaling occurs through changes in denticle number and spacing. Denticle spacing scales with cell length over a 10-fold range. Accurate denticle positioning requires the microtubule cytoskeleton. Spatially organized macromolecular complexes are essential for cell and tissue function, but the mechanisms that organize micron-scale structures within cells are not well understood. Microtubule-based structures such as mitotic spindles scale with cell size, but less is known about the scaling of actin structures within cells. Actin-rich denticle precursors cover the ventral surface of the Drosophila embryo and larva and provide templates for cuticular structures involved in larval locomotion. Using quantitative imaging and statistical modeling, we demonstrate that denticle number and spacing scale with cell length over a wide range of cell sizes in embryos and larvae. Denticle number and spacing are reduced under space-limited conditions, and both features robustly scale over a 10-fold increase in cell length during larval growth. We show that the relationship between cell length and denticle spacing can be recapitulated by specific mathematical equations in embryos and larvae and that accurate denticle spacing requires an intact microtubule network and the microtubule minus end–binding protein, Patronin. These results identify a novel mechanism of microtubule-dependent actin scaling that maintains precise patterns of actin organization during tissue growth.
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Affiliation(s)
- Alison K Spencer
- Gerstner Sloan Kettering Graduate School of Biomedical Sciences.,Howard Hughes Medical Institute and Developmental Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065
| | - Andrew J Schaumberg
- Weill Cornell Graduate School of Medical Sciences and the Tri-Institutional PhD Program in Computational Biology and Medicine, Memorial Sloan Kettering Cancer Center, New York, NY 10065
| | - Jennifer A Zallen
- Howard Hughes Medical Institute and Developmental Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065
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Edens LJ, Levy DL. A Cell-Free Assay Using Xenopus laevis Embryo Extracts to Study Mechanisms of Nuclear Size Regulation. J Vis Exp 2016. [PMID: 27584618 DOI: 10.3791/54173] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
A fundamental question in cell biology is how cell and organelle sizes are regulated. It has long been recognized that the size of the nucleus generally scales with the size of the cell, notably during embryogenesis when dramatic reductions in both cell and nuclear sizes occur. Mechanisms of nuclear size regulation are largely unknown and may be relevant to cancer where altered nuclear size is a key diagnostic and prognostic parameter. In vivo approaches to identifying nuclear size regulators are complicated by the essential and complex nature of nuclear function. The in vitro approach described here to study nuclear size control takes advantage of the normal reductions in nuclear size that occur during Xenopus laevis development. First, nuclei are assembled in X. laevis egg extract. Then, these nuclei are isolated and resuspended in cytoplasm from late stage embryos. After a 30 - 90 min incubation period, nuclear surface area decreases by 20 - 60%, providing a useful assay to identify cytoplasmic components present in late stage embryos that contribute to developmental nuclear size scaling. A major advantage of this approach is the relative facility with which the egg and embryo extracts can be biochemically manipulated, allowing for the identification of novel proteins and activities that regulate nuclear size. As with any in vitro approach, validation of results in an in vivo system is important, and microinjection of X. laevis embryos is particularly appropriate for these studies.
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Affiliation(s)
- Lisa J Edens
- Department of Molecular Biology, University of Wyoming
| | - Daniel L Levy
- Department of Molecular Biology, University of Wyoming;
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Vuković LD, Jevtić P, Zhang Z, Stohr BA, Levy DL. Nuclear size is sensitive to NTF2 protein levels in a manner dependent on Ran binding. J Cell Sci 2016; 129:1115-27. [PMID: 26823604 DOI: 10.1242/jcs.181263] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2015] [Accepted: 01/20/2016] [Indexed: 12/20/2022] Open
Abstract
Altered nuclear size is associated with many cancers, and determining whether cancer-associated changes in nuclear size contribute to carcinogenesis necessitates an understanding of mechanisms of nuclear size regulation. Although nuclear import rates generally positively correlate with nuclear size, NTF2 levels negatively affect nuclear size, despite the role of NTF2 (also known as NUTF2) in nuclear recycling of the import factor Ran. We show that binding of Ran to NTF2 is required for NTF2 to inhibit nuclear expansion and import of large cargo molecules in Xenopus laevis egg and embryo extracts, consistent with our observation that NTF2 reduces the diameter of the nuclear pore complex (NPC) in a Ran-binding-dependent manner. Furthermore, we demonstrate that ectopic NTF2 expression in Xenopus embryos and mammalian tissue culture cells alters nuclear size. Finally, we show that increases in nuclear size during melanoma progression correlate with reduced NTF2 expression, and increasing NTF2 levels in melanoma cells is sufficient to reduce nuclear size. These results show a conserved capacity for NTF2 to impact on nuclear size, and we propose that NTF2 might be a new cancer biomarker.
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Affiliation(s)
- Lidija D Vuković
- Department of Molecular Biology, University of Wyoming, Laramie, WY 82071, USA
| | - Predrag Jevtić
- Department of Molecular Biology, University of Wyoming, Laramie, WY 82071, USA
| | - Zhaojie Zhang
- Department of Zoology and Physiology, University of Wyoming, Laramie, WY 82071, USA
| | - Bradley A Stohr
- Department of Pathology, University of California, San Francisco, CA 94143, USA
| | - Daniel L Levy
- Department of Molecular Biology, University of Wyoming, Laramie, WY 82071, USA
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Abstract
Organelle function is often directly related to organelle size. However, it is not necessarily absolute size but the organelle-to-cell-size ratio that is critical. Larger cells generally have increased metabolic demands, must segregate DNA over larger distances, and require larger cytokinetic rings to divide. Thus, organelles often must scale to the size of the cell. The need for scaling is particularly acute during early development during which cell size can change rapidly. Here, we highlight scaling mechanisms for cellular structures as diverse as centrosomes, nuclei, and the mitotic spindle, and distinguish them from more general mechanisms of size control. In some cases, scaling is a consequence of the underlying mechanism of organelle size control. In others, size-control mechanisms are not obviously related to cell size, implying that scaling results indirectly from cell-size-dependent regulation of size-control mechanisms.
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Affiliation(s)
- Simone Reber
- Max Planck Institute of Molecular Genetics and Cell Biology, 01307 Dresden, Germany Integrative Research Institute (IRI) for the Life Sciences, Humboldt-Universität zu Berlin, 10115 Berlin, Germany
| | - Nathan W Goehring
- The Francis Crick Institute, WC2A 3LY London, United Kingdom MRC Laboratory of Molecular Cell Biology, University College London, WC1E 6BT London, United Kingdom
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