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Xu S, Dai Q, Zheng Y. Male spiny frogs enter the underwater battlefield with loose skin exhibiting enhanced penetration of capillaries into the epidermis. ZOOLOGICAL LETTERS 2023; 9:19. [PMID: 37803369 PMCID: PMC10557191 DOI: 10.1186/s40851-023-00219-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/13/2023] [Accepted: 08/23/2023] [Indexed: 10/08/2023]
Abstract
The skin has multiple functions, and capillaries can penetrate the epidermis to shorten the diffusion path while allowing maintenance of overall epidermal thickness for nonrespiratory roles. However, a method for quantifying the capillary penetration extent is lacking. Such a method may facilitate making comparisons and detecting associations, potentially making the extent a useful variable in biological studies. We quantified the extent as the ratio of the average minimum thickness of epidermis overlying each capillary to the average epidermal thickness along a skin section and then explored its performance in the Emei mustache toad, Leptobrachium boringii, a species in which breeding males with loose skin call and fight each other with maxillary spines underwater. The ratio showed informative associations with other variables, such as perfused capillary density. It displayed small intragroup variation and could be more sensitive than other variables in revealing structural differences in the skin. The ratio estimates were lowest and were correlated with epidermal and stratum compactum thicknesses in breeding males, i.e., a covariation but not reinforcement against stabbing, constituting early evidence consistent with the increased extensibility of loose skin conferring a defensive advantage during combat in amphibians. In addition, our results lead to the hypothesis that high hemoglobin density along subepidermal capillaries favors the maintenance of low blood partial oxygen pressure and hence increases cutaneous oxygen uptake. We also provide evidence supporting the new idea that the cooccurrence of loose skin and underwater calling found in some frogs can be explained by the latter benefiting from a large functional respiratory surface area. Awareness of the usefulness of the ratio may promote its application and the quantification of the penetration. Regarding exchange surface design, these findings for L. boringii imply a case in which looseness increases surface area as well as prevents damage.
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Affiliation(s)
- Shuang Xu
- Chengdu Institute of Biology, Chinese Academy of Sciences, #9 of Section 4, Ren-Min-Nan Road, Wuhou District, Chengdu, 610041, Sichuan Province, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Qiang Dai
- Chengdu Institute of Biology, Chinese Academy of Sciences, #9 of Section 4, Ren-Min-Nan Road, Wuhou District, Chengdu, 610041, Sichuan Province, China
| | - Yuchi Zheng
- Chengdu Institute of Biology, Chinese Academy of Sciences, #9 of Section 4, Ren-Min-Nan Road, Wuhou District, Chengdu, 610041, Sichuan Province, China.
- Key Laboratory of Southwest China Wildlife Resources Conservation (Ministry of Education), China West Normal University, Nanchong, 637009, Sichuan, China.
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2
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Desyatirkina IA, Makarova AA, Pang S, Xu CS, Hess H, Polilov AA. Multiscale head anatomy of Megaphragma (Hymenoptera: Trichogrammatidae). ARTHROPOD STRUCTURE & DEVELOPMENT 2023; 76:101299. [PMID: 37666087 DOI: 10.1016/j.asd.2023.101299] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Revised: 08/10/2023] [Accepted: 08/15/2023] [Indexed: 09/06/2023]
Abstract
Methods of three-dimensional electron microscopy have been actively developed recently and open up great opportunities for morphological work. This approach is especially useful for studying microinsects, since it is possible to obtain complete series of high-resolution sections of a whole insect. Studies on the genus Megaphragma are especially important, since the unique phenomenon of lysis of most of the neuron nuclei was discovered in species of this genus. In this study we reveal the anatomical structure of the head of Megaphragma viggianii at all levels from organs to subcellular structures. Despite the miniature size of the body, most of the organ systems of M. viggianii retain the structural plan and complexity of organization at all levels. The set of muscles and the well-developed stomatogastric nervous system of this species correspond to those of larger insects, and there is also a well-developed tracheal system in the head of this species. Reconstructions of the head of M. viggianii at the cellular and subcellular levels were obtained, and of volumetric data were analyzed. A total of 689 nucleated cells of the head were reconstructed. The ultrastructure of M. viggianii is surprisingly complex, and the evolutionary benefits of such complexity are probably among the factors limiting the further miniaturization of parasitoid wasps.
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Affiliation(s)
- Inna A Desyatirkina
- Department of Entomology, Faculty of Biology, Lomonosov Moscow State University, Moscow, Russia.
| | - Anastasia A Makarova
- Department of Entomology, Faculty of Biology, Lomonosov Moscow State University, Moscow, Russia
| | - Song Pang
- Janelia Research Campus of the Howard Hughes Medical Institute, Ashburn, USA; Yale School of Medicine, New Haven, CT, USA
| | - C Shan Xu
- Janelia Research Campus of the Howard Hughes Medical Institute, Ashburn, USA; Department of Cellular and Molecular Physiology, Yale School of Medicine, New Haven, CT, USA
| | - Harald Hess
- Janelia Research Campus of the Howard Hughes Medical Institute, Ashburn, USA
| | - Alexey A Polilov
- Department of Entomology, Faculty of Biology, Lomonosov Moscow State University, Moscow, Russia
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3
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Bury S, Kratochvíl L, Starostová Z. Scaling of erythrocyte shape and nucleus size among squamate reptiles: reanalysis points to constrained, proportional rather than adaptive changes. ROYAL SOCIETY OPEN SCIENCE 2023; 10:221513. [PMID: 37122952 PMCID: PMC10130710 DOI: 10.1098/rsos.221513] [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: 11/25/2022] [Accepted: 04/04/2023] [Indexed: 05/03/2023]
Abstract
Small erythrocytes might be beneficial for blood rheology, as they contribute less to blood viscosity than large erythrocytes. We predicted that rheological disadvantages of larger erythrocytes could be alleviated by relatively smaller nucleus size in larger cells allowing higher flexibility and by more elongated shape. Across squamate reptiles, we found that species with larger erythrocytes tend to have smaller ratio of nucleus size to cell size (N : C ratio), but that larger erythrocytes tend to be rounder, not more elongated. Nevertheless, we document that in fact nucleus area changes with erythrocyte area more or less linearly, which is also true for the relationship between cell length and cell width. These linear relationships suggest that nucleus size and cell size, and cell width and cell length, might be constrained to largely proportional mutual changes. The shifts in widely used N : C ratio and elongation ratio (cell length/cell width) with cell size might be misleading, as they do not reflect adaptive or maladaptive changes of erythrocytes, but rather mathematically trivial scaling of the ratios of two variables with a linear relationship with non-zero intercepts. We warn that ratio scaling without analyses of underlying patterns of evolutionary changes can lead to misinterpretation of evolutionary processes.
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Affiliation(s)
- Stanisław Bury
- Department of Comparative Anatomy, Institute of Zoology and Biomedical Research, Jagiellonian University, Gronostajowa 9, 30-387 Kraków, Poland
| | - Lukáš Kratochvíl
- Department of Ecology, Faculty of Science, Charles University, Viničná 7, 12844 Prague, Czech Republic
| | - Zuzana Starostová
- Department of Zoology, Faculty of Science, Charles University, Viničná 7, 12844 Prague, Czech Republic
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4
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Soliman SA, Abd-Elhafeez HH, Mohamed NE, Alrashdi BM, Alghamdi AAA, Elmansi A, Salah AS, El-Gendy SAA, Rutland CS, Massoud D. Morphological and cytochemical characteristics of Varanus niloticus (Squamata, Varanidae) blood cells. Microsc Res Tech 2023; 86:600-613. [PMID: 36722417 DOI: 10.1002/jemt.24298] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2022] [Revised: 12/21/2022] [Accepted: 01/13/2023] [Indexed: 02/02/2023]
Abstract
Varanus niloticus is a lizard residing within the Varanidae family. To date no studies detailing its blood morphology and characteristics have been conducted. This study used histologically stained blood and bone marrow samples to visualize the cells and their characteristics. The erythrocytes were nucleated, these nuclei were located in the middle of the elliptical cells. Hemoglobin filled the erythrocyte cytoplasm. Eosinophils were large cells with lobed nuclei and spherical acidophilic granules. Large granulocytes called heterophils were present and characterized by their fusiform/pleomorphic cytoplasmic granules. Small spherical granulocytes, known as basophils, presented with round, deeply stained metachromatic granules that gave the cytoplasm a dusty or cobblestoned appearance which was able to cover the nucleus, which in turn had an unusual shape. Thrombocytes ranged in shape from ellipsoidal to fusiform. They featured an elliptical, centrally located nucleus and a pale cytoplasm, with small vacuoles, and fine acidophilic granulation. The smallest variety of non-granular leukocytes was the lymphocytes. Their cytoplasm was sparse, finely granular, light blue, had tiny cytoplasmic projections, featuring a high nucleus: cytoplasm ratio. Larger and smaller sized populations of lymphocytes were distinguished, with the larger cells similar in size to azurophils. In general, the pleomorphic monocytes were the biggest mononuclear leucocytes, displaying cytoplasmic projections. Their nuclei were ovoid, kidney- or bean-shaped, with vacuolated and granular cytoplasms. Round cells were common among the monocytic azurophils, and they had a granular cytoplasm, and their nuclei were typically eccentric. The present research identifies the cell types and morphologies within the Varanus niloticus. HIGHLIGHTS: H&E, PAS, toluidine blue, methylene blue, and Safranin O stains provided morphological and morphometric descriptions of Varanus niloticus blood cells from blood smears and bone marrow. The Varanus niloticus had nucleated erythrocytes and white blood cells, mostly granulocytes (heterophils, eosinophils, and basophils) and mononuclear cells (azurophils, lymphocytes, and monocytes). Aquatic vertebrate Varanus niloticus had larger erythrocytes than terrestrial counterparts. Blood cell morphological and cytochemical features were similar to other reptilian species, with some species-specific differences, which likely accommodate differing environmental conditions. These results may help clinical researchers track the pathological conditions and support conservation of these wild animals.
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Affiliation(s)
- Soha A Soliman
- Department of Histology, Faculty of Veterinary Medicine, South Valley University, Qena, Egypt
| | - Hanan H Abd-Elhafeez
- Department of Cell and Tissues, Faculty of Veterinary Medicine, Assiut University, Assiut, Egypt
| | - Nor-Elhoda Mohamed
- Faculty of Science, Biomedicine Branch, University of Science & Technology in Zewail City, Cairo, Egypt
| | - Barakat M Alrashdi
- Biology Department, College of Science, Jouf University, Sakaka, Saudi Arabia
| | - Abdullah A A Alghamdi
- Department of Biology, Faculty of Science, Al-Baha University, Al-Baha, Saudi Arabia
| | - Ahmed Elmansi
- Biology Department, Faculty of Science, King Khalid University, Abha, Saudi Arabia.,Zoology Department, Faculty of Science, Mansoura University, Mansoura, Egypt
| | - Abdallah S Salah
- Department of Aquaculture, Faculty of Aquatic and Fisheries Sciences, Kafrelsheikh University, Kafrelsheikh, Egypt.,Institute of Aquaculture, University of Stirling, Stirling, UK
| | - Samir A A El-Gendy
- Department of Anatomy and Embryology, Faculty of Veterinary Medicine, Alexandria University, Alexandria, Egypt
| | - Catrin S Rutland
- School of Veterinary Medicine and Science, Faculty of Medicine and Health Science, University of Nottingham, Nottingham, UK
| | - Diaa Massoud
- Biology Department, College of Science, Jouf University, Sakaka, Saudi Arabia.,Department of Zoology, Faculty of Science, Fayoum University, Fayoum, Egypt
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Pincheira‐Donoso D, Harvey LP, Johnson JV, Hudson D, Finn C, Goodyear LEB, Guirguis J, Hyland EM, Hodgson DJ. Genome size does not influence extinction risk in the world's amphibians. Funct Ecol 2022. [DOI: 10.1111/1365-2435.14247] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Affiliation(s)
| | - Lilly P. Harvey
- School of Science and Technology Nottingham Trent University Nottingham UK
| | - Jack V. Johnson
- School of Biological Sciences Queen's University Belfast Belfast UK
| | - Dave Hudson
- Centre for Ecology and Conservation, College of Life and Environmental Sciences University of Exeter Penryn UK
| | - Catherine Finn
- School of Biological Sciences Queen's University Belfast Belfast UK
| | | | - Jacinta Guirguis
- School of Biological Sciences Queen's University Belfast Belfast UK
| | - Edel M. Hyland
- School of Biological Sciences Queen's University Belfast Belfast UK
| | - Dave J. Hodgson
- Centre for Ecology and Conservation, College of Life and Environmental Sciences University of Exeter Penryn UK
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6
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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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7
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Makarova AA, Veko EN, Polilov AA. Metamorphosis and denucleation of the brain in the miniature wasp Megaphragma viggianii (Hymenoptera: Trichogrammatidae). ARTHROPOD STRUCTURE & DEVELOPMENT 2022; 70:101200. [PMID: 35961234 DOI: 10.1016/j.asd.2022.101200] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Revised: 07/08/2022] [Accepted: 07/11/2022] [Indexed: 06/15/2023]
Abstract
Holometabolan brains undergo structural and allometric changes and complex reorganizations during metamorphosis. In minute egg parasitoids, brain formation is shifted to the late larva and young pupa, due to extreme de-embryonization. The brains of Megaphragma wasps undergo denucleation, the details of which remained unknown. We describe the morphological and volumetric changes in the brain of Megaphragma viggianii (Trichogrammatidae) during pupal development with emphasis on the lysis of nuclei and show that the absolute and relative volume of the brain decrease by a factor of 5 from prepupa to adult at the expense of the cell body rind. The first foci of lysis appear during early pupal development, but most nuclei (up to 97%) are lost between pharate adult and adult. The first signs of lysis (destruction of the nuclear envelopes) occur in pupae with red eyes. The number of lysis foci (organelle destruction and increasing number of lysosomes and degree of chromatin compaction) strongly increases in pupae with black eyes. The cell body rind volume strongly decreases during pupal development (in larger insects it increases slightly or remains unchanged). Elucidation of the lysis of nuclei in neurons and of the functioning of an anucleate brain is an important objective for neuroscience.
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Affiliation(s)
| | - Egor N Veko
- Faculty of Biology, Lomonosov Moscow State University, Moscow, Russia
| | - Alexey A Polilov
- Faculty of Biology, Lomonosov Moscow State University, Moscow, Russia
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8
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Itgen MW, Natalie GR, Siegel DS, Sessions SK, Mueller RL. Genome size drives morphological evolution in organ-specific ways. Evolution 2022; 76:1453-1468. [PMID: 35657770 PMCID: PMC9545640 DOI: 10.1111/evo.14519] [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: 08/19/2021] [Revised: 03/23/2022] [Accepted: 04/11/2022] [Indexed: 01/22/2023]
Abstract
Morphogenesis is an emergent property of biochemical and cellular interactions during development. Genome size and the correlated trait of cell size can influence these interactions through effects on developmental rate and tissue geometry, ultimately driving the evolution of morphology. We tested whether variation in genome and body size is related to morphological variation in the heart and liver using nine species of the salamander genus Plethodon (genome sizes 29-67 gigabases). Our results show that overall organ size is a function of body size, whereas tissue structure changes dramatically with evolutionary increases in genome size. In the heart, increased genome size is correlated with a reduction of myocardia in the ventricle, yielding proportionally less force-producing mass and greater intertrabecular space. In the liver, increased genome size is correlated with fewer and larger vascular structures, positioning hepatocytes farther from the circulatory vessels that transport key metabolites. Although these structural changes should have obvious impacts on organ function, their effects on organismal performance and fitness may be negligible because low metabolic rates in salamanders relax selective pressure on function of key metabolic organs. Overall, this study suggests large genome and cell size influence the developmental systems involved in heart and liver morphogenesis.
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Affiliation(s)
- Michael W. Itgen
- Department of BiologyColorado State UniversityFort CollinsColorado80523USA
| | | | - Dustin S. Siegel
- Department of BiologySoutheast Missouri State UniversityCape GirardeauMissouri63701USA
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9
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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] [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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10
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Penman Z, Deeming DC, Soulsbury CD. Ecological and life-history correlates of erythrocyte size and shape in Lepidosauria. J Evol Biol 2022; 35:708-718. [PMID: 35384114 PMCID: PMC9322653 DOI: 10.1111/jeb.14004] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2021] [Revised: 12/20/2021] [Accepted: 03/04/2022] [Indexed: 11/05/2022]
Abstract
Blood oxygen‐carrying capacity is shaped both by the ambient oxygen availability as well as species‐specific oxygen demand. Erythrocytes are a critical part of oxygen transport and both their size and shape can change in relation to species‐specific life‐history, behavioural or ecological conditions. Here, we test whether components of the environment (altitude), life history (reproductive mode, body temperature) and behaviour (diving, foraging mode) drive erythrocyte size variation in the Lepidosauria (lizards, snakes and rhynchocephalians). We collected data on erythrocyte size (area) and shape (L/W: elongation ratio) from Lepidosauria across the globe (N = 235 species). Our analyses show the importance of oxygen requirements as a driver of erythrocyte size. Smaller erythrocytes were associated with the need for faster delivery (active foragers, high‐altitude species, warmer body temperatures), whereas species with greater oxygen demands (diving species, viviparous species) had larger erythrocytes. Erythrocyte size shows considerable cross‐species variation, with a range of factors linked to the oxygen delivery requirements being major drivers of these differences. A key future aspect for study would include within‐individual plasticity and how changing states, for example, pregnancy, perhaps alter the size and shape of erythrocytes in Lepidosaurs.
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Affiliation(s)
- Zachary Penman
- School of Life Sciences and Environmental Sciences, University of Lincoln, Lincoln, UK
| | - D Charles Deeming
- School of Life Sciences and Environmental Sciences, University of Lincoln, Lincoln, UK
| | - Carl D Soulsbury
- School of Life Sciences and Environmental Sciences, University of Lincoln, Lincoln, UK
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11
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Makarova AA, Polilov AA. Structure of the Brain of the Smallest Coleoptera. DOKL BIOCHEM BIOPHYS 2022; 505:166-169. [PMID: 36038683 PMCID: PMC9613543 DOI: 10.1134/s1607672922040068] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2022] [Revised: 05/09/2022] [Accepted: 05/09/2022] [Indexed: 11/23/2022]
Abstract
The structure of the brain of the smallest coleopteran, Scydosella musawasensis Hall, 1999, is described for the first time. As in other extremely small beetles, the brain of S. musawasensis displays signs of miniaturization: displacement to the thorax, compactization, and a small number and size of the neurons. The body size of the studied smallest beetle is similar to that of the minute hymenopteran Megaphragma, which has a nearly anucleate nervous system. However, the structure of the brain of the studied smallest beetle is similar to that of large representatives of the order and is characterized by a high number of nuclei in the brain and a significant volume of the cell body rind. The neuropil of S. musawasensis occupies 60% of the brain volume, confirming the neuropilar constant rule.
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12
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Yap KN, Zhang Y. Revisiting the question of nucleated versus enucleated erythrocytes in birds and mammals. Am J Physiol Regul Integr Comp Physiol 2021; 321:R547-R557. [PMID: 34378417 DOI: 10.1152/ajpregu.00276.2020] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Erythrocyte enucleation is thought to have evolved in mammals to support their energetic cost of high metabolic activities. However, birds face similar selection pressure yet possess nucleated erythrocytes. Current hypotheses on the mammalian erythrocyte enucleation claim that the absence of cell organelles allows erythrocytes to 1) pack more hemoglobin into the cells to increase oxygen carrying capacity and 2) decrease erythrocyte size for increased surface area-to-volume ratio, and improved ability to traverse small capillaries. In this article, we first empirically tested current hypotheses using both conventional and phylogenetically informed analysis comparing literature values of mean cell hemoglobin concentration (MCHC) and mean cell volume (MCV) between 181 avian and 194 mammalian species. We found no difference in MCHC levels between birds and mammals using both conventional and phylogenetically corrected analysis. MCV was higher in birds than mammals according to conventional analysis, but the difference was lost when we controlled for phylogeny. These results suggested that avian and mammalian erythrocytes may employ different strategies to solve a common problem. To further investigate existing hypotheses or develop new hypothesis, we need to understand the functions of various organelles in avian erythrocytes. Consequently, we covered potential physiological functions of various cell organelles in avian erythrocytes based on current knowledge, while making explicit comparisons to their mammalian counterparts. Finally, we proposed by taking an integrative and comparative approach, using tools from molecular biology to evolutionary biology, would allow us to better understand the fundamental physiological functions of various components of avian and mammalian erythrocytes.
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Affiliation(s)
- Kang Nian Yap
- Department of Biological Sciences, Auburn University, Auburn, AL, United States
| | - Yufeng Zhang
- School of Health Studies, University of Memphis, Memphis, TN, United States
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13
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Lamichhaney S, Catullo R, Keogh JS, Clulow S, Edwards SV, Ezaz T. A bird-like genome from a frog: Mechanisms of genome size reduction in the ornate burrowing frog, Platyplectrum ornatum. Proc Natl Acad Sci U S A 2021; 118:e2011649118. [PMID: 33836564 PMCID: PMC7980411 DOI: 10.1073/pnas.2011649118] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
The diversity of genome sizes across the tree of life is of key interest in evolutionary biology. Various correlates of variation in genome size, such as accumulation of transposable elements (TEs) or rate of DNA gain and loss, are well known, but the underlying molecular mechanisms driving or constraining genome size are poorly understood. Here, we study one of the smallest genomes among frogs characterized thus far, that of the ornate burrowing frog (Platyplectrum ornatum) from Australia, and compare it to other published frog and vertebrate genomes to examine the forces driving reduction in genome size. At ∼1.06 gigabases (Gb), the P. ornatum genome is like that of birds, revealing four major mechanisms underlying TE dynamics: reduced abundance of all major classes of TEs; increased net deletion bias in TEs; drastic reduction in intron lengths; and expansion via gene duplication of the repertoire of TE-suppressing Piwi genes, accompanied by increased expression of Piwi-interacting RNA (piRNA)-based TE-silencing pathway genes in germline cells. Transcriptomes from multiple tissues in both sexes corroborate these results and provide insight into sex-differentiation pathways in Platyplectrum Genome skimming of two closely related frog species (Lechriodus fletcheri and Limnodynastes fletcheri) confirms a reduction in TEs as a major driver of genome reduction in Platyplectrum and supports a macroevolutionary scenario of small genome size in frogs driven by convergence in life history, especially rapid tadpole development and tadpole diet. The P. ornatum genome offers a model for future comparative studies on mechanisms of genome size reduction in amphibians and vertebrates generally.
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Affiliation(s)
- Sangeet Lamichhaney
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138
- Museum of Comparative Zoology, Harvard University, Cambridge, MA 02138
| | - Renee Catullo
- Division of Ecology and Evolution, Research School of Biology, Australian National University, Acton, ACT, Australia 2601
- Australian National Insect Collection and Future Science Platform Environomics, Commonwealth Scientific and Industrial Research Organization, Acton, ACT, Australia 2601
| | - J Scott Keogh
- Division of Ecology and Evolution, Research School of Biology, Australian National University, Acton, ACT, Australia 2601
| | - Simon Clulow
- Department of Biological Sciences, Macquarie University, Sydney, NSW, Australia 2109
| | - Scott V Edwards
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138;
- Museum of Comparative Zoology, Harvard University, Cambridge, MA 02138
| | - Tariq Ezaz
- Institute for Applied Ecology, Faculty of Science and Technology, University of Canberra, Canberra, ACT, Australia 2617
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14
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Abstract
The size of the intracellular structure that encloses genomic DNA - known as the nucleus in eukaryotes and nucleoid in prokaryotes - is believed to scale according to cell size and genomic content inside them across the tree of life. However, an actual scaling relationship remains largely unexplored across eukaryotic species. Here, I collected a large dataset of nuclear and cell volumes in diverse species across different phyla, including some prokaryotes, from the published literature and assessed the scaling relationship. Although entire inter-species data showed that nuclear volume correlates with cell volume, the quantitative scaling property exhibited differences among prokaryotes, unicellular eukaryotes and multicellular eukaryotes. Additionally, the nuclear volume correlates with genomic content inside the nucleus of multicellular eukaryotes but not of prokaryotes and unicellular eukaryotes. In this Hypothesis, I, thus, propose that the basic concept of nuclear-size scaling is conserved across eukaryotes; however, structural and mechanical properties of nuclear membranes and chromatin can result in different scaling relationships of nuclear volume to cell volume and genomic content among species. In particular, eukaryote-specific properties of the nuclear membrane may contribute to the extreme flexibility of nuclear size with regard to DNA density inside the nucleus.
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Affiliation(s)
- Yuki Hara
- Evolutionary Cell Biology Laboratory, Faculty of Science, Yamaguchi University, Yoshida 1677-1, Yamaguchi city 753-8512, Japan
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15
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Wesley CC, Mishra S, Levy DL. Organelle size scaling over embryonic development. WILEY INTERDISCIPLINARY REVIEWS-DEVELOPMENTAL BIOLOGY 2020; 9:e376. [PMID: 32003549 DOI: 10.1002/wdev.376] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/26/2019] [Revised: 12/19/2019] [Accepted: 01/08/2020] [Indexed: 12/13/2022]
Abstract
Cell division without growth results in progressive cell size reductions during early embryonic development. How do the sizes of intracellular structures and organelles scale with cell size and what are the functional implications of such scaling relationships? Model organisms, in particular Caenorhabditis elegans worms, Drosophila melanogaster flies, Xenopus laevis frogs, and Mus musculus mice, have provided insights into developmental size scaling of the nucleus, mitotic spindle, and chromosomes. Nuclear size is regulated by nucleocytoplasmic transport, nuclear envelope proteins, and the cytoskeleton. Regulators of microtubule dynamics and chromatin compaction modulate spindle and mitotic chromosome size scaling, respectively. Developmental scaling relationships for membrane-bound organelles, like the endoplasmic reticulum, Golgi, mitochondria, and lysosomes, have been less studied, although new imaging approaches promise to rectify this deficiency. While models that invoke limiting components and dynamic regulation of assembly and disassembly can account for some size scaling relationships in early embryos, it will be exciting to investigate the contribution of newer concepts in cell biology such as phase separation and interorganellar contacts. With a growing understanding of the underlying mechanisms of organelle size scaling, future studies promise to uncover the significance of proper scaling for cell function and embryonic development, as well as how aberrant scaling contributes to disease. This article is categorized under: Establishment of Spatial and Temporal Patterns > Regulation of Size, Proportion, and Timing Early Embryonic Development > Fertilization to Gastrulation Comparative Development and Evolution > Model Systems.
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Affiliation(s)
- Chase C Wesley
- Department of Molecular Biology, University of Wyoming, Laramie, Wyoming
| | - Sampada Mishra
- Department of Molecular Biology, University of Wyoming, Laramie, Wyoming
| | - Daniel L Levy
- Department of Molecular Biology, University of Wyoming, Laramie, Wyoming
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16
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Li JL, Zarbock A, Hidalgo A. Platelets as autonomous drones for hemostatic and immune surveillance. J Exp Med 2020; 214:2193-2204. [PMID: 28720569 PMCID: PMC5551582 DOI: 10.1084/jem.20170879] [Citation(s) in RCA: 54] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2017] [Revised: 06/26/2017] [Accepted: 07/06/2017] [Indexed: 12/13/2022] Open
Abstract
Platelets participate in many important physiological processes, including hemostasis and immunity. However, despite their broad participation in these evolutionarily critical roles, the anucleate platelet is uniquely mammalian. In contrast with the large nucleated equivalents in lower vertebrates, we find that the design template for the evolutionary specialization of platelets shares remarkable similarities with human-engineered unmanned aerial vehicles in terms of overall autonomy, maneuverability, and expendability. Here, we review evidence illustrating how platelets are uniquely suited for surveillance and the manner in which they consequently provide various types of support to other cell types.
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Affiliation(s)
- Jackson LiangYao Li
- Area of Developmental and Cell Biology, Centro Nacional de Investigaciones Cardiovasculares Carlos III, Madrid, Spain.,Singapore Immunology Network, Agency for Science, Technology and Research, Singapore, Singapore
| | - Alexander Zarbock
- Department of Anesthesiology, Intensive Care, and Pain Medicine, University of Münster, Münster, Germany
| | - Andrés Hidalgo
- Area of Developmental and Cell Biology, Centro Nacional de Investigaciones Cardiovasculares Carlos III, Madrid, Spain.,Institute for Cardiovascular Prevention, Ludwig-Maximillians-University, Munich, Germany
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17
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Soslau G. The role of the red blood cell and platelet in the evolution of mammalian and avian endothermy. JOURNAL OF EXPERIMENTAL ZOOLOGY PART B-MOLECULAR AND DEVELOPMENTAL EVOLUTION 2019; 334:113-127. [DOI: 10.1002/jez.b.22922] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/06/2019] [Revised: 10/04/2019] [Accepted: 11/09/2019] [Indexed: 12/12/2022]
Affiliation(s)
- Gerald Soslau
- Department of Biochemistry and Molecular BiologyDrexel University College of MedicinePhiladelphia Pennsylvania
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18
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Womack MC, Metz MJ, Hoke KL. Larger Genomes Linked to Slower Development and Loss of Late-Developing Traits. Am Nat 2019; 194:854-864. [PMID: 31738099 DOI: 10.1086/705897] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Abstract
Genome size varies widely among organisms and is known to affect vertebrate development, morphology, and physiology. In amphibians, genome size is hypothesized to contribute to loss of late-forming structures, although this hypothesis has mainly been discussed in salamanders. Here we estimated genome size for 22 anuran species and combined this novel data set with existing genome size data for an additional 234 anuran species to determine whether larger genome size is associated with loss of a late-forming anuran sensory structure, the tympanic middle ear. We established that genome size is negatively correlated with development rate across 90 anuran species and found that genome size evolution is correlated with evolutionary loss of the middle ear bone (columella) among 241 species (224 eared and 17 earless). We further tested whether the development of the tympanic middle ear could be constrained by large cell sizes and small body sizes during key stages of tympanic middle ear development (metamorphosis). Together, our evidence suggests that larger genomes, slower development rate, and smaller body sizes at metamorphosis may contribute to the loss of the anuran tympanic middle ear. We conclude that increases in anuran genome size, although less drastic than those in salamanders, may affect development of late-forming traits.
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19
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Itgen MW, Prša P, Janža R, Skubic L, Townsend JH, Kladnik A, Mali LB, Sessions SK. Genome Size Diversification in Central American Bolitoglossine Salamanders (Caudata; Plethodontidae). COPEIA 2019. [DOI: 10.1643/ch-18-156] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Affiliation(s)
- Michael W. Itgen
- Department of Biology, Colorado State University, 200 West Lake Street, 1878 Campus Delivery, Fort Collins, Colorado 80523; . Send reprint requests to this address
| | - Patrik Prša
- Institute of Pathophysiology, Faculty of Medicine, University of Ljubljana, Zaloška 4, Ljubljana, 1000, Slovenia;
| | - Rok Janža
- Department of Organisms and Ecosystems Research, National Institute of Biology, Večna pot 111, Ljubljana, 1000, Slovenia;
| | - Lucijan Skubic
- Institute of Microbiology and Immunology, Faculty of Medicine, University of Ljubljana, Zaloška 4, Ljubljana, 1000, Slovenia;
| | - Josiah H. Townsend
- Department of Biology, Indiana University of Pennsylvania, 975 Oakland Avenue, Indiana, Pennsylvania 15701;
| | - Aleš Kladnik
- Department of Biology, Biotechnical faculty, University of Ljubljana, Slovenia; Mailing address: Jamnikarjeva 101, Ljubljana, 1000, Slovenia; (AK) ; and (LBM)
| | - Lilijana Bizjak Mali
- Department of Biology, Biotechnical faculty, University of Ljubljana, Slovenia; Mailing address: Jamnikarjeva 101, Ljubljana, 1000, Slovenia; (AK) ; and (LBM)
| | - Stanley K. Sessions
- Department of Biology, Hartwick College, 1 Hartwick Drive, Oneonta, New York 13820;
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20
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Lertzman-Lepofsky G, Mooers AØ, Greenberg DA. Ecological constraints associated with genome size across salamander lineages. Proc Biol Sci 2019; 286:20191780. [PMID: 31530144 DOI: 10.1098/rspb.2019.1780] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Salamanders have some of the largest, and most variable, genome sizes among the vertebrates. Larger genomes have been associated with larger cell sizes, lower metabolic rates, and longer embryonic and larval durations in many different taxonomic groups. These life-history traits are often important for dictating fitness under different environmental conditions, suggesting that a species' genome size may have the potential to constrain its ecological distribution. We test how genome size varies with the ephemerality of larval habitat across the salamanders, predicting that species with larger genomes will be constrained to more permanent habitats that permit slower development, while species with smaller genomes will be more broadly distributed across the gradient of habitat ephemerality. We found that salamanders with larger genomes are almost exclusively associated with permanent aquatic habitats. In addition, the evolutionary transition rate between permanent and ephemeral larval habitats is much higher in salamander lineages with smaller genome sizes. These patterns suggest that genome size may act as an evolutionary constraint on the ecological habitats of salamanders, restricting those species with large genomes and slower development to habitats with permanent sources of water.
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Affiliation(s)
- Gavia Lertzman-Lepofsky
- Department of Biological Sciences, Simon Fraser University, Burnaby, British Columbia, Canada V5A 1S6
| | - Arne Ø Mooers
- Department of Biological Sciences, Simon Fraser University, Burnaby, British Columbia, Canada V5A 1S6
| | - Dan A Greenberg
- Department of Biological Sciences, Simon Fraser University, Burnaby, British Columbia, Canada V5A 1S6
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21
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Hoffman JF. Reflections on the crooked timber of red blood cell physiology. Blood Cells Mol Dis 2019; 79:102354. [PMID: 31449971 DOI: 10.1016/j.bcmd.2019.102354] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2019] [Accepted: 08/16/2019] [Indexed: 01/07/2023]
Affiliation(s)
- Joseph F Hoffman
- Department of Cellular and Molecular Physiology, Yale University School of Medicine, New Haven, CT 06520, United States.
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22
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Anderson HL, Brodsky IE, Mangalmurti NS. The Evolving Erythrocyte: Red Blood Cells as Modulators of Innate Immunity. THE JOURNAL OF IMMUNOLOGY 2019; 201:1343-1351. [PMID: 30127064 DOI: 10.4049/jimmunol.1800565] [Citation(s) in RCA: 115] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/20/2018] [Accepted: 05/16/2018] [Indexed: 12/23/2022]
Abstract
The field of red cell biology is undergoing a quiet revolution. Long assumed to be inert oxygen carriers, RBCs are emerging as important modulators of the innate immune response. Erythrocytes bind and scavenge chemokines, nucleic acids, and pathogens in circulation. Depending on the conditions of the microenvironment, erythrocytes may either promote immune activation or maintain immune quiescence. We examine erythrocyte immune function through a comparative and evolutionary lens, as this framework may offer perspective into newly recognized roles of human RBCs. Next, we review the known immune roles of human RBCs and discuss their activity in the context of sepsis where erythrocyte function may prove important to disease pathogenesis. Given the limited success of immunomodulatory therapies in treating inflammatory diseases, we propose that the immunologic function of RBCs provides an understudied and potentially rich area of research that may yield novel insights into mechanisms of immune regulation.
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Affiliation(s)
- H Luke Anderson
- Department of Biology, University of Pennsylvania, Philadelphia, PA 19104
| | - Igor E Brodsky
- Department of Pathobiology, University of Pennsylvania School of Veterinary Medicine, Philadelphia, PA 19104.,Institute for Immunology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104
| | - Nilam S Mangalmurti
- Institute for Immunology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104; .,Pulmonary, Allergy and Critical Care Division, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104; and.,Penn Center for Pulmonary Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104
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23
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Bury S, Bury A, Sadowska ET, Cichoń M, Bauchinger U. More than just the numbers-contrasting response of snake erythrocytes to thermal acclimation. Naturwissenschaften 2019; 106:24. [PMID: 31069520 DOI: 10.1007/s00114-019-1617-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2018] [Revised: 01/29/2019] [Accepted: 04/11/2019] [Indexed: 11/29/2022]
Abstract
Acclimation to lower temperatures decreases energy expenditure in ectotherms but increases oxygen consumption in most endotherms, when dropped below thermoneutrality. Such differences should be met by adjustments in oxygen transport through blood. Changes in hematological variables in correspondence to that in metabolic rates are, however, not fully understood, particularly in non-avian reptiles. We investigated the effect of thermal acclimation on a snake model, the grass snakes (Natrix natrix). After 6 months of acclimation to either 18 °C or 32 °C hematocrit, hemoglobin concentration, erythrocyte number, and size were assessed. All variables revealed significantly lower values under warm compared to cold ambient temperature. Our data suggest that non-avian reptiles, similarly as birds, reduce erythrocyte fraction under energy-demanding temperatures. Due to low deformability of nucleated erythrocytes in sauropsids, such reduced fraction may be important in decreasing blood viscosity to optimize blood flow. Novel findings on flexible erythrocyte size provide an important contribution to this optimization process.
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Affiliation(s)
- Stanisław Bury
- Institute of Environmental Sciences, Jagiellonian University, Gronostajowa 7, 30-387, Cracow, Poland.
| | - Agata Bury
- Institute of Environmental Sciences, Jagiellonian University, Gronostajowa 7, 30-387, Cracow, Poland
| | - Edyta T Sadowska
- Institute of Environmental Sciences, Jagiellonian University, Gronostajowa 7, 30-387, Cracow, Poland
| | - Mariusz Cichoń
- Institute of Environmental Sciences, Jagiellonian University, Gronostajowa 7, 30-387, Cracow, Poland
| | - Ulf Bauchinger
- Institute of Environmental Sciences, Jagiellonian University, Gronostajowa 7, 30-387, Cracow, Poland
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24
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Red blood cells, compasses and snap shots. Blood Cells Mol Dis 2018; 71:67-70. [PMID: 29599084 DOI: 10.1016/j.bcmd.2018.03.003] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2018] [Accepted: 03/20/2018] [Indexed: 12/11/2022]
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25
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Bozler J, Kacsoh BZ, Bosco G. Nematocytes: Discovery and characterization of a novel anculeate hemocyte in Drosophila falleni and Drosophila phalerata. PLoS One 2017; 12:e0188133. [PMID: 29141015 PMCID: PMC5687758 DOI: 10.1371/journal.pone.0188133] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2017] [Accepted: 11/01/2017] [Indexed: 12/27/2022] Open
Abstract
Immune challenges, such as parasitism, can be so pervasive and deleterious that they constitute an existential threat to a species' survival. In response to these ecological pressures, organisms have developed a wide array of novel behavioral, cellular, and molecular adaptations. Research into these immune defenses in model systems has resulted in a revolutionary understanding of evolution and functional biology. As the field has expanded beyond the limited number of model organisms our appreciation of evolutionary innovation and unique biology has widened as well. With this in mind, we have surveyed the hemolymph of several non-model species of Drosophila. Here we identify and describe a novel hemocyte, type-II nematocytes, found in larval stages of numerous Drosophila species. Examined in detail in Drosophila falleni and Drosophila phalerata, we find that these remarkable cells are distinct from previously described hemocytes due to their anucleate state (lacking a nucleus) and unusual morphology. Type-II nematocytes are long, narrow cells with spindle-like projections extending from a cell body with high densities of mitochondria and microtubules, and exhibit the ability to synthesize proteins. These properties are unexpected for enucleated cells, and together with our additional characterization, we demonstrate that these type-II nematocytes represent a biological novelty. Surprisingly, despite the absence of a nucleus, we observe through live cell imaging that these cells remain motile with a highly dynamic cellular shape. Furthermore, these cells demonstrate the ability to form multicellular structures, which we suggest may be a component of the innate immune response to macro-parasites. In addition, live cell imaging points to a large nucleated hemocyte, type-I nematocyte, as the progenitor cell, leading to enucleation through a budding or asymmetrical division process rather than nuclear ejection: This study is the first to report such a process of enucleation. Here we describe these cells in detail for the first time and examine their evolutionary history in Drosophila.
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Affiliation(s)
- Julianna Bozler
- Department of Molecular and Systems Biology, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire, United States of America
| | - Balint Z. Kacsoh
- Department of Molecular and Systems Biology, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire, United States of America
| | - Giovanni Bosco
- Department of Molecular and Systems Biology, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire, United States of America
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26
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Beaulieu M, Benoit L, Abaga S, Kappeler PM, Charpentier MJE. Mind the cell: Seasonal variation in telomere length mirrors changes in leucocyte profile. Mol Ecol 2017; 26:5603-5613. [DOI: 10.1111/mec.14329] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2017] [Revised: 06/30/2017] [Accepted: 08/07/2017] [Indexed: 12/30/2022]
Affiliation(s)
- Michaël Beaulieu
- Zoological Institute and Museum; University of Greifswald; Greifswald Germany
| | | | | | - Peter M. Kappeler
- Behavioral Ecology and Sociobiology Unit; German Primate Center (DPZ); Göttingen Germany
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27
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Newman CE, Gregory TR, Austin CC. The dynamic evolutionary history of genome size in North American woodland salamanders. Genome 2017; 60:285-292. [DOI: 10.1139/gen-2016-0166] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The genus Plethodon is the most species-rich salamander genus in North America, and nearly half of its species face an uncertain future. It is also one of the most diverse families in terms of genome sizes, which range from 1C = 18.2 to 69.3 pg, or 5–20 times larger than the human genome. Large genome size in salamanders results in part from accumulation of transposable elements and is associated with various developmental and physiological traits. However, genome sizes have been reported for only 25% of the species of Plethodon (14 of 55). We collected genome size data for Plethodon serratus to supplement an ongoing phylogeographic study, reconstructed the evolutionary history of genome size in Plethodontidae, and inferred probable genome sizes for the 41 species missing empirical data. Results revealed multiple genome size changes in Plethodon: genomes of western Plethodon increased, whereas genomes of eastern Plethodon decreased, followed by additional decreases or subsequent increases. The estimated genome size of P. serratus was 21 pg. New understanding of variation in genome size evolution, along with genome size inferences for previously unstudied taxa, provide a foundation for future studies on the biology of plethodontid salamanders.
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Affiliation(s)
- Catherine E. Newman
- Museum of Natural Science, Louisiana State University, 119 Foster Hall, Baton Rouge, LA 70803, USA
- Department of Biological Sciences, Louisiana State University, Baton Rouge, LA, USA
| | - T. Ryan Gregory
- Department of Integrative Biology, University of Guelph, Guelph, ON, Canada
| | - Christopher C. Austin
- Museum of Natural Science, Louisiana State University, 119 Foster Hall, Baton Rouge, LA 70803, USA
- Department of Biological Sciences, Louisiana State University, Baton Rouge, LA, USA
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28
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Newman CE, Austin CC. Sequence capture and next‐generation sequencing of ultraconserved elements in a large‐genome salamander. Mol Ecol 2016; 25:6162-6174. [DOI: 10.1111/mec.13909] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2016] [Revised: 10/26/2016] [Accepted: 11/01/2016] [Indexed: 12/24/2022]
Affiliation(s)
- Catherine E. Newman
- Museum of Natural Science Louisiana State University 119 Foster Hall Baton Rouge LA 70803 USA
- Department of Biological Sciences Louisiana State University 202 Life Sciences Building Baton Rouge LA 70803 USA
| | - Christopher C. Austin
- Museum of Natural Science Louisiana State University 119 Foster Hall Baton Rouge LA 70803 USA
- Department of Biological Sciences Louisiana State University 202 Life Sciences Building Baton Rouge LA 70803 USA
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29
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Small RNAs from a Big Genome: The piRNA Pathway and Transposable Elements in the Salamander Species Desmognathus fuscus. J Mol Evol 2016; 83:126-136. [PMID: 27743003 DOI: 10.1007/s00239-016-9759-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2016] [Accepted: 10/06/2016] [Indexed: 01/26/2023]
Abstract
Most of the largest vertebrate genomes are found in salamanders, a clade of amphibians that includes 686 species. Salamander genomes range in size from 14 to 120 Gb, reflecting the accumulation of large numbers of transposable element (TE) sequences from all three TE classes. Although DNA loss rates are slow in salamanders relative to other vertebrates, high levels of TE insertion are also likely required to explain such high TE loads. Across the Tree of Life, novel TE insertions are suppressed by several pathways involving small RNA molecules. In most known animals, TE activity in the germline is primarily regulated by the Piwi-interacting RNA (piRNA) pathway. In this study, we test the hypothesis that salamanders' unusually high TE loads reflect the loss of the ancestral piRNA-mediated TE-silencing machinery. We characterized the small RNA pool in the female and male adult gonads, testing for the presence of small RNA molecules that bear the characteristics of TE-targeting piRNAs. We also analyzed the amino acid sequences of piRNA pathway proteins from salamanders and other vertebrates, testing whether the overall patterns of sequence divergence are consistent with conserved pathway function across the vertebrate clade. Our results do not support the hypothesis of piRNA pathway loss; instead, they suggest that the piRNA pathway is expressed in salamanders. Given these results, we propose hypotheses to explain how the extraordinary TE loads in salamander genomes could have accumulated, despite the expression of TE-silencing machinery.
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30
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Canapa A, Barucca M, Biscotti MA, Forconi M, Olmo E. Transposons, Genome Size, and Evolutionary Insights in Animals. Cytogenet Genome Res 2016; 147:217-39. [PMID: 26967166 DOI: 10.1159/000444429] [Citation(s) in RCA: 83] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/03/2015] [Indexed: 11/19/2022] Open
Abstract
The relationship between genome size and the percentage of transposons in 161 animal species evidenced that variations in genome size are linked to the amplification or the contraction of transposable elements. The activity of transposable elements could represent a response to environmental stressors. Indeed, although with different trends in protostomes and deuterostomes, comprehensive changes in genome size were recorded in concomitance with particular periods of evolutionary history or adaptations to specific environments. During evolution, genome size and the presence of transposable elements have influenced structural and functional parameters of genomes and cells. Changes of these parameters have had an impact on morphological and functional characteristics of the organism on which natural selection directly acts. Therefore, the current situation represents a balance between insertion and amplification of transposons and the mechanisms responsible for their deletion or for decreasing their activity. Among the latter, methylation and the silencing action of small RNAs likely represent the most frequent mechanisms.
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Affiliation(s)
- Adriana Canapa
- Dipartimento di Scienze della Vita e dell'Ambiente, Universitx00E0; Politecnica delle Marche, Ancona, Italy
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31
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Phylogenetic and Ontogenetic View of Erythroblastic Islands. BIOMED RESEARCH INTERNATIONAL 2015; 2015:873628. [PMID: 26557707 PMCID: PMC4628717 DOI: 10.1155/2015/873628] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/02/2015] [Accepted: 07/08/2015] [Indexed: 12/27/2022]
Abstract
Erythroblastic islands are a hallmark of mammalian erythropoiesis consisting of a central macrophage surrounded by and interacting closely with the maturing erythroblasts. The macrophages are thought to serve many functions such as supporting erythroblast proliferation, supplying iron for hemoglobin, promoting enucleation, and clearing the nuclear debris; moreover, inhibition of erythroblastic island formation is often detrimental to erythropoiesis. There is still much not understood about the role that macrophages and microenvironment play in erythropoiesis and insights may be gleaned from a comparative analysis with erythropoietic niches in nonmammalian vertebrates which, unlike mammals, have erythrocytes that retain their nucleus. The phylogenetic development of erythroblastic islands in mammals in which the erythrocytes are anucleate underlines the importance of the macrophage in erythroblast enucleation.
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32
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Levy DL, Heald R. Biological Scaling Problems and Solutions in Amphibians. Cold Spring Harb Perspect Biol 2015; 8:a019166. [PMID: 26261280 DOI: 10.1101/cshperspect.a019166] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Size is a primary feature of biological systems that varies at many levels, from the organism to its constituent cells and subcellular structures. Amphibians populate some of the extremes in biological size and have provided insight into scaling mechanisms, upper and lower size limits, and their physiological significance. Body size variation is a widespread evolutionary tactic among amphibians, with miniaturization frequently correlating with direct development that occurs without a tadpole stage. The large genomes of salamanders lead to large cell sizes that necessitate developmental modification and morphological simplification. Amphibian extremes at the cellular level have provided insight into mechanisms that accommodate cell-size differences. Finally, how organelles scale to cell size between species and during development has been investigated at the molecular level, because subcellular scaling can be recapitulated using Xenopus in vitro systems.
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Affiliation(s)
- Daniel L Levy
- Department of Molecular Biology, University of Wyoming, Laramie, Wyoming 82071
| | - Rebecca Heald
- Department of Molecular and Cell Biology, University of California, Berkeley, California 94720
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33
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Teltser C, Greenwald KR. Survivorship of Ploidy-variable UnisexualAmbystomaSalamanders Across Developmental Stages. HERPETOLOGICA 2015. [DOI: 10.1655/herpetologica-d-14-00007] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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Sun C, Mueller RL. Hellbender genome sequences shed light on genomic expansion at the base of crown salamanders. Genome Biol Evol 2015; 6:1818-29. [PMID: 25115007 PMCID: PMC4122941 DOI: 10.1093/gbe/evu143] [Citation(s) in RCA: 48] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Among animals, genome sizes range from 20 Mb to 130 Gb, with 380-fold variation across vertebrates. Most of the largest vertebrate genomes are found in salamanders, an amphibian clade of 660 species. Thus, salamanders are an important system for studying causes and consequences of genomic gigantism. Previously, we showed that plethodontid salamander genomes accumulate higher levels of long terminal repeat (LTR) retrotransposons than do other vertebrates, although the evolutionary origins of such sequences remained unexplored. We also showed that some salamanders in the family Plethodontidae have relatively slow rates of DNA loss through small insertions and deletions. Here, we present new data from Cryptobranchus alleganiensis, the hellbender. Cryptobranchus and Plethodontidae span the basal phylogenetic split within salamanders; thus, analyses incorporating these taxa can shed light on the genome of the ancestral crown salamander lineage, which underwent expansion. We show that high levels of LTR retrotransposons likely characterize all crown salamanders, suggesting that disproportionate expansion of this transposable element (TE) class contributed to genomic expansion. Phylogenetic and age distribution analyses of salamander LTR retrotransposons indicate that salamanders' high TE levels reflect persistence and diversification of ancestral TEs rather than horizontal transfer events. Finally, we show that relatively slow DNA loss rates through small indels likely characterize all crown salamanders, suggesting that a decreased DNA loss rate contributed to genomic expansion at the clade's base. Our identification of shared genomic features across phylogenetically distant salamanders is a first step toward identifying the evolutionary processes underlying accumulation and persistence of high levels of repetitive sequence in salamander genomes.
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Arenas CM, Gómez-Molina A, Delgado JP. Maintaining plethodontid salamanders in the laboratory for regeneration studies. Methods Mol Biol 2015; 1290:71-8. [PMID: 25740477 DOI: 10.1007/978-1-4939-2495-0_5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/22/2023]
Abstract
Limb regeneration studies have been extensively carried out in species of Ambystomatidae and Salamandridae families. So far limited research has been conducted in species belonging to the Plethodontidae family, where some of the species differs from other salamander families due to their direct development, thus absence of a larval life. Here, we describe a protocol to maintain the plethodontid salamanders of genus Bolitoglossa species under laboratory conditions to perform regeneration studies.
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Affiliation(s)
- Claudia Marcela Arenas
- Grupo Genética, Regeneración y Cáncer, Instituto de Biología, Universidad de Antioquia, Calle 67 NO. 53-108, Medellín, Colombia
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Abstract
Regeneration is studied in a few model species of salamanders, but the ten families of salamanders show considerable variation, and this has implications for our understanding of salamander biology. The most recent classification of the families identifies the cryptobranchoidea as the basal group which diverged in the early Jurassic. Variation in the sizes of genomes is particularly obvious, and reflects a major contribution from transposable elements which is already present in the basal group.Limb development has been a focus for evodevo studies, in part because of the variable property of pre-axial dominance which distinguishes salamanders from other tetrapods. This is thought to reflect the selective pressures that operate on a free-living aquatic larva, and might also be relevant for the evolution of limb regeneration. Recent fossil evidence suggests that both pre-axial dominance and limb regeneration were present 300 million years ago in larval temnospondyl amphibians that lived in mountain lakes. A satisfying account of regeneration in salamanders may need to address all these different aspects in the future.
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Jockusch EL, Martínez-Solano I, Timpe EK. The Effects of Inference Method, Population Sampling, and Gene Sampling on Species Tree Inferences: An Empirical Study in Slender Salamanders (Plethodontidae: Batrachoseps). Syst Biol 2014; 64:66-83. [DOI: 10.1093/sysbio/syu078] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Elizabeth L. Jockusch
- Department of Ecology and Evolutionary Biology, University of Connecticut, 75 N. Eagleville Road, U-3043, Storrs, CT 06269-3043, USA; and 2CIBIO-InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Campus Agrário de Vairão, Universidade do Porto, 4485-661 Vairão, Portugal
| | - Iñigo Martínez-Solano
- Department of Ecology and Evolutionary Biology, University of Connecticut, 75 N. Eagleville Road, U-3043, Storrs, CT 06269-3043, USA; and 2CIBIO-InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Campus Agrário de Vairão, Universidade do Porto, 4485-661 Vairão, Portugal
- Department of Ecology and Evolutionary Biology, University of Connecticut, 75 N. Eagleville Road, U-3043, Storrs, CT 06269-3043, USA; and 2CIBIO-InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Campus Agrário de Vairão, Universidade do Porto, 4485-661 Vairão, Portugal
| | - Elizabeth K. Timpe
- Department of Ecology and Evolutionary Biology, University of Connecticut, 75 N. Eagleville Road, U-3043, Storrs, CT 06269-3043, USA; and 2CIBIO-InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Campus Agrário de Vairão, Universidade do Porto, 4485-661 Vairão, Portugal
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Thom CS, Traxler EA, Khandros E, Nickas JM, Zhou OY, Lazarus JE, Silva APG, Prabhu D, Yao Y, Aribeana C, Fuchs SY, Mackay JP, Holzbaur ELF, Weiss MJ. Trim58 degrades Dynein and regulates terminal erythropoiesis. Dev Cell 2014; 30:688-700. [PMID: 25241935 DOI: 10.1016/j.devcel.2014.07.021] [Citation(s) in RCA: 65] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2013] [Revised: 04/24/2014] [Accepted: 07/28/2014] [Indexed: 01/23/2023]
Abstract
TRIM58 is an E3 ubiquitin ligase superfamily member implicated by genome-wide association studies to regulate human erythrocyte traits. Here, we show that Trim58 expression is induced during late erythropoiesis and that its depletion by small hairpin RNAs (shRNAs) inhibits the maturation of late-stage nucleated erythroblasts to anucleate reticulocytes. Imaging flow cytometry studies demonstrate that Trim58 regulates polarization and/or extrusion of erythroblast nuclei. In vitro, Trim58 directly binds and ubiquitinates the intermediate chain of the microtubule motor dynein. In cells, Trim58 stimulates proteasome-dependent degradation of the dynein holoprotein complex. During erythropoiesis, Trim58 expression, dynein loss, and enucleation occur concomitantly, and all are inhibited by Trim58 shRNAs. Dynein regulates nuclear positioning and microtubule organization, both of which undergo dramatic changes during erythroblast enucleation. Thus, we propose that Trim58 promotes this process by eliminating dynein. Our findings identify an erythroid-specific regulator of enucleation and elucidate a previously unrecognized mechanism for controlling dynein activity.
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Affiliation(s)
- Christopher S Thom
- Division of Hematology, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA; Cell and Molecular Biology Graduate Group, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Elizabeth A Traxler
- Division of Hematology, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA; Cell and Molecular Biology Graduate Group, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Eugene Khandros
- Division of Hematology, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA; Cell and Molecular Biology Graduate Group, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Jenna M Nickas
- Division of Hematology, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Olivia Y Zhou
- Division of Hematology, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Jacob E Lazarus
- Cell and Molecular Biology Graduate Group, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Department of Physiology and Pennsylvania Muscle Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Ana P G Silva
- School of Molecular Bioscience, The University of Sydney, Sydney NSW 2006, Australia
| | - Dolly Prabhu
- Division of Hematology, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Yu Yao
- Division of Hematology, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Chiaka Aribeana
- Division of Hematology, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Serge Y Fuchs
- Department of Animal Biology and Mari Lowe Comparative Oncology Center, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Joel P Mackay
- School of Molecular Bioscience, The University of Sydney, Sydney NSW 2006, Australia
| | - Erika L F Holzbaur
- Department of Physiology and Pennsylvania Muscle Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Mitchell J Weiss
- Division of Hematology, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA.
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Ellis LL, Huang W, Quinn AM, Ahuja A, Alfrejd B, Gomez FE, Hjelmen CE, Moore KL, Mackay TFC, Johnston JS, Tarone AM. Intrapopulation genome size variation in D. melanogaster reflects life history variation and plasticity. PLoS Genet 2014; 10:e1004522. [PMID: 25057905 PMCID: PMC4109859 DOI: 10.1371/journal.pgen.1004522] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2013] [Accepted: 04/24/2014] [Indexed: 12/01/2022] Open
Abstract
We determined female genome sizes using flow cytometry for 211 Drosophila melanogaster sequenced inbred strains from the Drosophila Genetic Reference Panel, and found significant conspecific and intrapopulation variation in genome size. We also compared several life history traits for 25 lines with large and 25 lines with small genomes in three thermal environments, and found that genome size as well as genome size by temperature interactions significantly correlated with survival to pupation and adulthood, time to pupation, female pupal mass, and female eclosion rates. Genome size accounted for up to 23% of the variation in developmental phenotypes, but the contribution of genome size to variation in life history traits was plastic and varied according to the thermal environment. Expression data implicate differences in metabolism that correspond to genome size variation. These results indicate that significant genome size variation exists within D. melanogaster and this variation may impact the evolutionary ecology of the species. Genome size variation accounts for a significant portion of life history variation in an environmentally dependent manner, suggesting that potential fitness effects associated with genome size variation also depend on environmental conditions. Genome size evolution is ubiquitous, and–even after decades of research–mysterious. There are two major classes of hypotheses regarding genome size evolution, those that attribute its causes to evolutionarily neutral processes and those that suggest a role for selection. Numerous correlations between genome size and fitness-related phenotypes have been documented, suggesting selection could play a role in genome size evolution. Unfortunately, many of the effects in those studies are confounded with factors that could provide alternative explanations. Here, we show that 211 inbred strains of Drosophila melanogaster exhibit abundant variation in genome size, which correlates with life history traits in a temperature-dependent manner. Gene expression analyses suggest a role for differences in metabolism between strains with large and small genomes. Thus, there is genetic variation in genome size within D. melanogaster, and this variation is connected to variation in environmentally dependent life history traits. These observations indicate that selection is indeed a potential mechanism by which genome size can evolve. Our results also suggest that higher levels of genetic architecture may explain some of the genetic contribution to biologically important complex traits and raise the possibility that nucleotide quantity can contribute to phenotype in addition to quality.
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Affiliation(s)
- Lisa L. Ellis
- Department of Entomology, Texas A&M University, College Station, Texas, United States of America
| | - Wen Huang
- Department of Biological Sciences, North Carolina State University, Raleigh, North Carolina, United States of America
| | - Andrew M. Quinn
- Department of Entomology, Texas A&M University, College Station, Texas, United States of America
- University of Texas Health Science Center, Houston, Texas, United States of America
| | - Astha Ahuja
- Baylor Human Genome Sequencing Center, Houston, Texas, United States of America
| | - Ben Alfrejd
- Department of Entomology, Texas A&M University, College Station, Texas, United States of America
| | - Francisco E. Gomez
- Department of Soil and Crop Science, Texas A&M University, College Station, Texas, United States of America
| | - Carl E. Hjelmen
- Department of Entomology, Texas A&M University, College Station, Texas, United States of America
| | - Kristi L. Moore
- Department of Entomology, Texas A&M University, College Station, Texas, United States of America
| | - Trudy F. C. Mackay
- Department of Biological Sciences, North Carolina State University, Raleigh, North Carolina, United States of America
| | - J. Spencer Johnston
- Department of Entomology, Texas A&M University, College Station, Texas, United States of America
| | - Aaron M. Tarone
- Department of Entomology, Texas A&M University, College Station, Texas, United States of America
- * E-mail:
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Hermaniuk A, Pruvost NBM, Kierzkowski P, Ogielska M. Genetic and Cytogenetic Characteristics of Pentaploidy in Water Frogs. HERPETOLOGICA 2013. [DOI: 10.1655/herpetologica-d-12-00037] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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41
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Sun C, Shepard DB, Chong RA, López Arriaza J, Hall K, Castoe TA, Feschotte C, Pollock DD, Mueller RL. LTR retrotransposons contribute to genomic gigantism in plethodontid salamanders. Genome Biol Evol 2011; 4:168-83. [PMID: 22200636 PMCID: PMC3318908 DOI: 10.1093/gbe/evr139] [Citation(s) in RCA: 130] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/22/2011] [Indexed: 01/20/2023] Open
Abstract
Among vertebrates, most of the largest genomes are found within the salamanders, a clade of amphibians that includes 613 species. Salamander genome sizes range from ~14 to ~120 Gb. Because genome size is correlated with nucleus and cell sizes, as well as other traits, morphological evolution in salamanders has been profoundly affected by genomic gigantism. However, the molecular mechanisms driving genomic expansion in this clade remain largely unknown. Here, we present the first comparative analysis of transposable element (TE) content in salamanders. Using high-throughput sequencing, we generated genomic shotgun data for six species from the Plethodontidae, the largest family of salamanders. We then developed a pipeline to mine TE sequences from shotgun data in taxa with limited genomic resources, such as salamanders. Our summaries of overall TE abundance and diversity for each species demonstrate that TEs make up a substantial portion of salamander genomes, and that all of the major known types of TEs are represented in salamanders. The most abundant TE superfamilies found in the genomes of our six focal species are similar, despite substantial variation in genome size. However, our results demonstrate a major difference between salamanders and other vertebrates: salamander genomes contain much larger amounts of long terminal repeat (LTR) retrotransposons, primarily Ty3/gypsy elements. Thus, the extreme increase in genome size that occurred in salamanders was likely accompanied by a shift in TE landscape. These results suggest that increased proliferation of LTR retrotransposons was a major molecular mechanism contributing to genomic expansion in salamanders.
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Affiliation(s)
- Cheng Sun
- Department of Biology, Colorado State University
| | - Donald B. Shepard
- Department of Biology, Colorado State University
- Current address: Department of Fisheries, Wildlife and Conservation Biology; University of Minnesota
| | | | | | - Kathryn Hall
- Department of Biochemistry and Molecular Genetics, University of Colorado School of Medicine
| | - Todd A. Castoe
- Department of Biochemistry and Molecular Genetics, University of Colorado School of Medicine
| | | | - David D. Pollock
- Department of Biochemistry and Molecular Genetics, University of Colorado School of Medicine
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Rundell RJ, Leander BS. Masters of miniaturization: Convergent evolution among interstitial eukaryotes. Bioessays 2010; 32:430-7. [DOI: 10.1002/bies.200900116] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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43
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Wake DB. What Salamanders Have Taught Us About Evolution. ANNUAL REVIEW OF ECOLOGY EVOLUTION AND SYSTEMATICS 2009. [DOI: 10.1146/annurev.ecolsys.39.110707.173552] [Citation(s) in RCA: 96] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- David B. Wake
- Department of Integrative Biology and Museum of Vertebrate Zoology, University of California, Berkeley, California 94720-3160;
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