1
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Anderson RP, Mughal S, Wedlake GO. Proterozoic microfossils continue to provide new insights into the rise of complex eukaryotic life. ROYAL SOCIETY OPEN SCIENCE 2024; 11:240154. [PMID: 39170929 PMCID: PMC11336685 DOI: 10.1098/rsos.240154] [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: 01/26/2024] [Revised: 07/11/2024] [Accepted: 07/12/2024] [Indexed: 08/23/2024]
Abstract
Eukaryotes have evolved to dominate the biosphere today, accounting for most documented living species and the vast majority of the Earth's biomass. Consequently, understanding how these biologically complex organisms initially diversified in the Proterozoic Eon over 539 million years ago is a foundational question in evolutionary biology. Over the last 70 years, palaeontologists have sought to document the rise of eukaryotes with fossil evidence. However, the delicate and microscopic nature of their sub-cellular features affords early eukaryotes diminished preservation potential. Chemical biomarker signatures of eukaryotes and the genetics of living eukaryotes have emerged as complementary tools for reconstructing eukaryote ancestry. In this review, we argue that exceptionally preserved Proterozoic microfossils are critical to interpreting these complementary tools, providing crucial calibrations to molecular clocks and testing hypotheses of palaeoecology. We highlight recent research on their preservation and biomolecular composition that offers new ways to enhance their utility.
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Affiliation(s)
- Ross P. Anderson
- Museum of Natural History, University of Oxford, OxfordOX1 3PW, UK
- All Souls College, University of Oxford, OxfordOX1 4AL, UK
| | - Sanaa Mughal
- Department of Earth and Atmospheric Sciences, University of Alberta, Edmonton, AlbertaT6G 2E3, Canada
| | - George O. Wedlake
- Department of Earth Sciences, University of Oxford, Oxford OX1 3AN, UK
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2
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Miao L, Yin Z, Knoll AH, Qu Y, Zhu M. 1.63-billion-year-old multicellular eukaryotes from the Chuanlinggou Formation in North China. SCIENCE ADVANCES 2024; 10:eadk3208. [PMID: 38266082 PMCID: PMC10807817 DOI: 10.1126/sciadv.adk3208] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/15/2023] [Accepted: 12/21/2023] [Indexed: 01/26/2024]
Abstract
Multicellularity is key to the functional and ecological success of the Eukarya, underpinning much of their modern diversity in both terrestrial and marine ecosystems. Despite the widespread occurrence of simple multicellular organisms among eukaryotes, when this innovation arose remains an open question. Here, we report cellularly preserved multicellular microfossils (Qingshania magnifica) from the ~1635-million-year-old Chuanlinggou Formation, North China. The fossils consist of large uniseriate, unbranched filaments with cell diameters up to 190 micrometers; spheroidal structures, possibly spores, occur within some cells. In combination with spectroscopic characteristics, the large size and morphological complexity of these fossils support their interpretation as eukaryotes, likely photosynthetic, based on comparisons with extant organisms. The occurrence of multicellular eukaryotes in Paleoproterozoic rocks not much younger than those containing the oldest unambiguous evidence of eukaryotes as a whole supports the hypothesis that simple multicellularity arose early in eukaryotic history, as much as a billion years before complex multicellular organisms diversified in the oceans.
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Affiliation(s)
- Lanyun Miao
- State Key Laboratory of Palaeobiology and Stratigraphy, Nanjing Institute of Geology and Palaeontology, Chinese Academy of Sciences, Nanjing 210008, China
| | - Zongjun Yin
- State Key Laboratory of Palaeobiology and Stratigraphy, Nanjing Institute of Geology and Palaeontology, Chinese Academy of Sciences, Nanjing 210008, China
| | - Andrew H. Knoll
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA
| | - Yuangao Qu
- Institute of Deep-sea Science and Engineering, Chinese Academy of Sciences, Sanya 572000, China
| | - Maoyan Zhu
- State Key Laboratory of Palaeobiology and Stratigraphy, Nanjing Institute of Geology and Palaeontology, Chinese Academy of Sciences, Nanjing 210008, China
- College of Earth and Planetary Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
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3
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Mohtasham Moein M, Rahmati K, Saradar A, Moon J, Karakouzian M. A Critical Review Examining the Characteristics of Modified Concretes with Different Nanomaterials. MATERIALS (BASEL, SWITZERLAND) 2024; 17:409. [PMID: 38255577 PMCID: PMC10817359 DOI: 10.3390/ma17020409] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/26/2023] [Revised: 01/03/2024] [Accepted: 01/09/2024] [Indexed: 01/24/2024]
Abstract
The movement of the construction industry towards sustainable development has drawn attention to the revision of concrete. In addition to reducing pollution, the use of nano-materials should lead to the provision of higher quality concrete in terms of regulatory items (workability, resistance characteristics, durability characteristics, microstructure). The present study investigates 15 key characteristics of concrete modified with nano-CaCO3, nano-clay, nano-TiO2, and nano-SiO2. The results of the study showed that nanomaterials significantly have a positive effect on the hydration mechanism and the production of more C-S-H gel. The evaluation of resistance characteristics also indicates the promising results of these valuable materials. The durability characteristics of nano-containing concrete showed significant improvement despite high dispersion. Concrete in coastal areas (such as bridges or platforms), concrete exposed to radiation (such as hospitals), concrete exposed to impact load (such as nuclear power plants), and concrete containing recycled aggregate (such as bricks, tiles, ceramics) can be effectively improved by using nanomaterials. It is hoped that the current review paper can provide an effective image and idea for future applied studies by other researchers.
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Affiliation(s)
| | - Komeil Rahmati
- Department of Civil Engineering, Somesara Branch, Islamic Azad University, Somesara 4361947496, Iran;
| | - Ashkan Saradar
- Department of Civil Engineering, University of Guilan, Rasht 419961377, Iran
| | - Jaeyun Moon
- Department of Mechanical Engineering, University of Nevada, 4505 S Maryland Pkwy, Las Vegas, NV 89154, USA;
| | - Moses Karakouzian
- Department of Civil and Environmental Engineering and Construction, University of Nevada, Las Vegas, NV 89154, USA
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4
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Barlow EV, House CH, Liu MC, Wetherington MT, Van Kranendonk MJ. Distinctive microfossil supports early Paleoproterozoic rise in complex cellular organisation. GEOBIOLOGY 2024; 22:e12576. [PMID: 37803496 DOI: 10.1111/gbi.12576] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/23/2022] [Revised: 08/14/2023] [Accepted: 09/07/2023] [Indexed: 10/08/2023]
Abstract
The great oxidation event (GOE), ~2.4 billion years ago, caused fundamental changes to the chemistry of Earth's surface environments. However, the effect of these changes on the biosphere is unknown, due to a worldwide lack of well-preserved fossils from this time. Here, we investigate exceptionally preserved, large spherical aggregate (SA) microfossils permineralised in chert from the c. 2.4 Ga Turee Creek Group in Western Australia. Field and petrographic observations, Raman spectroscopic mapping, and in situ carbon isotopic analyses uncover insights into the morphology, habitat, reproduction and metabolism of this unusual form, whose distinctive, SA morphology has no known counterpart in the fossil record. Comparative analysis with microfossils from before the GOE reveals the large SA microfossils represent a step-up in cellular organisation. Morphological comparison to extant micro-organisms indicates the SAs have more in common with coenobial algae than coccoidal bacteria, emphasising the complexity of this microfossil form. The remarkable preservation here provides a unique window into the biosphere, revealing an increase in the complexity of life coinciding with the GOE.
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Affiliation(s)
- Erica V Barlow
- Australian Centre for Astrobiology, School of Biological, Earth and Environmental Sciences, University of New South Wales, Kensington, New South Wales, Australia
- Australian Research Council Centre of Excellence for Core to Crust Fluid Systems (CCFS), Macquarie University, Sydney, New South Wales, Australia
- Department of Geosciences and the Earth and Environmental Systems Institute, Pennsylvania State University, University Park, Pennsylvania, USA
| | - Christopher H House
- Department of Geosciences and the Earth and Environmental Systems Institute, Pennsylvania State University, University Park, Pennsylvania, USA
| | - Ming-Chang Liu
- Department of Earth, Planetary, and Space Sciences, University of California at Los Angeles, Los Angeles, California, USA
- Lawrence Livermore National Laboratory, Livermore, California, USA
| | - Maxwell T Wetherington
- Materials Research Institute and Department of Materials Science & Engineering, Pennsylvania State University, University Park, Pennsylvania, USA
| | - Martin J Van Kranendonk
- Australian Centre for Astrobiology, School of Biological, Earth and Environmental Sciences, University of New South Wales, Kensington, New South Wales, Australia
- Australian Research Council Centre of Excellence for Core to Crust Fluid Systems (CCFS), Macquarie University, Sydney, New South Wales, Australia
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5
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Gauthier-Lafaye F, Gall B, Bentridi SE. The Oklo phenomenon, the discovery, first questions and first answers. RADIATION PROTECTION DOSIMETRY 2023; 199:2251-2257. [PMID: 37935004 DOI: 10.1093/rpd/ncad044] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/29/2022] [Accepted: 01/12/2023] [Indexed: 11/09/2023]
Abstract
The discovery in Nature of 16 reactions zones where sustained fission chain reaction occurred 1.95 b.y ago raised numerous questions in many scientific fields. Fifty years later, some of them are still unanswered. This article recalls the history of this discovery and the scientific facts before discussing the present-day understanding of this complex phenomenon.
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Affiliation(s)
- François Gauthier-Lafaye
- CNRS UMR7517, Laboratoire d'Hydrologie et de Géochimie de Strasbourg, Strasbourg F-67000, France
| | - Benoît Gall
- Université de Strasbourg, CNRS, IPHC UMR7178, Strasbourg F-67000, France
| | - Salah-Eddine Bentridi
- LESI, Faculty of Science and Technology, Khemis Miliana University, Khemis Miliana, Algeria
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6
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Nimal JC. Oklo: historic and lessons learned. RADIATION PROTECTION DOSIMETRY 2023; 199:2262-2268. [PMID: 37934999 DOI: 10.1093/rpd/ncad043] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Revised: 02/10/2023] [Accepted: 01/18/2023] [Indexed: 11/09/2023]
Abstract
Two outstanding phenomena have taken place in earlier geological era where Gabon is now located: the presence of natural nuclear reactors and the appearance of a very elaborated form of life for its age. Calculations performed to establish the sustained fission history of Oklo site are presented first. Second, possible correlations between these two anomalies are discussed. Could the presence of ionizing radiation be the cause of genetic mutations? Today's isotopic measurements allow us to improve our understanding of the irradiation suffered by organic matter over all times. The first objective is therefore to quantify the possible effects of such ionizing radiation. A second objective naturally appears: the storage of radioactive waste. Calculations issued from the first objective provide access to nuclear reactor waste formations and Oklo is the unique natural analogue of a long-term storage laboratory for nuclear waste. Returning to our primary objective, it is interesting to extend our reflections to other situations of naturally radioactive environments such as very old geological formations or lagoon.
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Affiliation(s)
- J C Nimal
- Commissariat à l'Énergie Atomique et aux Énergies Alternatives (CEA), Saclay, France
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7
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Abstract
The origin of modern eukaryotes is one of the key transitions in life's history, and also one of the least understood. Although the fossil record provides the most direct view of this process, interpreting the fossils of early eukaryotes and eukaryote-grade organisms is not straightforward. We present two end-member models for the evolution of modern (i.e., crown) eukaryotes-one in which modern eukaryotes evolved early, and another in which they evolved late-and interpret key fossils within these frameworks, including where they might fit in eukaryote phylogeny and what they may tell us about the evolution of eukaryotic cell biology and ecology. Each model has different implications for understanding the rise of complex life on Earth, including different roles of Earth surface oxygenation, and makes different predictions that future paleontological studies can test.
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Affiliation(s)
- Susannah M Porter
- Department of Earth Science, University of California at Santa Barbara, Santa Barbara, California, USA;
| | - Leigh Anne Riedman
- Department of Earth Science, University of California at Santa Barbara, Santa Barbara, California, USA;
- Earth Research Institute, University of California at Santa Barbara, Santa Barbara, California, USA;
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8
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Datta S, Ratcliff WC. Illuminating a new path to multicellularity. eLife 2022; 11:e83296. [PMID: 36217823 PMCID: PMC9553208 DOI: 10.7554/elife.83296] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
A new species of multicellular bacteria broadens our understanding of prokaryotic multicellularity and provides insight into how multicellular organisms arise.
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Affiliation(s)
- Sayantan Datta
- Interdisciplinary Graduate Program in Quantitative Biosciences, Georgia Institute of TechnologyAtlantaUnited States
- School of Biological Sciences, Georgia Institute of TechnologyAtlantaUnited States
| | - William C Ratcliff
- School of Biological Sciences, Georgia Institute of TechnologyAtlantaUnited States
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9
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González-Flores A, Jin J, Osinski G, Tsujita C. Acritarch-like Microorganisms from the 1.9 Ga Gunflint Chert, Canada. ASTROBIOLOGY 2022; 22:568-578. [PMID: 35442767 PMCID: PMC9125578 DOI: 10.1089/ast.2021.0081] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/09/2021] [Accepted: 03/12/2022] [Indexed: 06/14/2023]
Abstract
Fossil evidence of eukaryotic life older than 1.8 Ga has long been debated because known fossils of that age usually lack cellular micro- and ultra-structures that bear strong affinities to eukaryotes. These include fossils of the ∼1.9 Ga Gunflint Chert microbiota that, despite being exceptionally well preserved, have suffered from cellular degradation, which poses challenges to studying their delicate cellular structures. In this study, we use an extended-focal-depth imaging technique, in combination with scanning electron microscopy, to document multiple types of large (10-35 μm diameter), cyst-like bodies based on distinctive details such as (1) radially arranged internal strands similar to those in some acritarchs and dinoflagellates; (2) regularly spaced long tubular processes, stubby pustules, and/or robust podia on the cell surface; (3) reticulate cell-wall sculpturing such as scale-like tubercles, pits, and ridges; and (4) internal bodies that may represent membrane-bound organelles. These micro- and ultra-structures provide strong morphological evidence for the presence of protists in the late Paleoproterozoic.
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Affiliation(s)
- A.L. González-Flores
- Department of Earth Sciences, University of Western Ontario, London, Canada
- Institute for Earth and Space Exploration, University of Western Ontario, London, Canada
| | - J. Jin
- Department of Earth Sciences, University of Western Ontario, London, Canada
| | - G.R. Osinski
- Department of Earth Sciences, University of Western Ontario, London, Canada
- Institute for Earth and Space Exploration, University of Western Ontario, London, Canada
| | - C.J. Tsujita
- Department of Earth Sciences, University of Western Ontario, London, Canada
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10
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Auboeuf D. The Physics-Biology continuum challenges darwinism: Evolution is directed by the homeostasis-dependent bidirectional relation between genome and phenotype. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2021; 167:121-139. [PMID: 34097984 DOI: 10.1016/j.pbiomolbio.2021.05.008] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/19/2021] [Revised: 05/19/2021] [Accepted: 05/31/2021] [Indexed: 10/21/2022]
Abstract
The physics-biology continuum relies on the fact that life emerged from prebiotic molecules. Here, I argue that life emerged from the coupling between nucleic acid and protein synthesis during which proteins (or proto-phenotypes) maintained the physicochemical parameter equilibria (or proto-homeostasis) in the proximity of their encoding nucleic acids (or proto-genomes). This protected the proto-genome physicochemical integrity (i.e., atomic composition) from environmental physicochemical constraints, and therefore increased the probability of reproducing the proto-genome without variation. From there, genomes evolved depending on the biological activities they generated in response to environmental fluctuations. Thus, a genome maintaining homeostasis (i.e., internal physicochemical parameter equilibria), despite and in response to environmental fluctuations, maintains its physicochemical integrity and has therefore a higher probability to be reproduced without variation. Consequently, descendants have a higher probability to share the same phenotype than their parents. Otherwise, the genome is modified during replication as a consequence of the imbalance of the internal physicochemical parameters it generates, until new mutation-deriving biological activities maintain homeostasis in offspring. In summary, evolution depends on feedforward and feedback loops between genome and phenotype, as the internal physicochemical conditions that a genome generates ─ through its derived phenotype in response to environmental fluctuations ─ in turn either guarantee its stability or direct its variation. Evolution may not be explained by the Darwinism-derived, unidirectional principle (random mutations-phenotypes-natural selection) but rather by the bidirectional relationship between genome and phenotype, in which the phenotype in interaction with the environment directs the evolution of the genome it derives from.
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Affiliation(s)
- Didier Auboeuf
- ENS de Lyon, Univ Claude Bernard, CNRS UMR 5239, INSERM U1210, Laboratory of Biology and Modelling of the Cell, 46 Allée D'Italie, Site Jacques Monod, F-69007, Lyon, France.
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11
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Hao W, Mänd K, Li Y, Alessi DS, Somelar P, Moussavou M, Romashkin AE, Lepland A, Kirsimäe K, Planavsky NJ, Konhauser KO. The kaolinite shuttle links the Great Oxidation and Lomagundi events. Nat Commun 2021; 12:2944. [PMID: 34011941 PMCID: PMC8134571 DOI: 10.1038/s41467-021-23304-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2020] [Accepted: 04/19/2021] [Indexed: 02/03/2023] Open
Abstract
The ~2.22-2.06 Ga Lomagundi Event was the longest positive carbon isotope excursion in Earth's history and is commonly interpreted to reflect perturbations in continental weathering and the phosphorous cycle. Previous models have focused on mechanisms of increasing phosphorous solubilization during weathering without focusing on transport to the oceans and its dispersion in seawater. Building from new experimental results, here we report kaolinite readily absorbs phosphorous under acidic freshwater conditions, but quantitatively releases phosphorous under seawater conditions where it becomes bioavailable to phytoplankton. The strong likelihood of high weathering intensities and associated high kaolinite content in post-Great-Oxidation-Event paleosols suggests there would have been enhanced phosphorus shuttling from the continents into marine environments. A kaolinite phosphorous shuttle introduces the potential for nonlinearity in the fluxes of phosphorous to the oceans with increases in chemical weathering intensity.
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Affiliation(s)
- Weiduo Hao
- grid.17089.37Department of Earth and Atmospheric Sciences, University of Alberta, Edmonton, Canada
| | - Kaarel Mänd
- grid.17089.37Department of Earth and Atmospheric Sciences, University of Alberta, Edmonton, Canada ,grid.10939.320000 0001 0943 7661Department of Geology, University of Tartu, Tartu, Estonia
| | - Yuhao Li
- grid.17089.37Department of Earth and Atmospheric Sciences, University of Alberta, Edmonton, Canada
| | - Daniel S. Alessi
- grid.17089.37Department of Earth and Atmospheric Sciences, University of Alberta, Edmonton, Canada
| | - Peeter Somelar
- grid.10939.320000 0001 0943 7661Department of Geology, University of Tartu, Tartu, Estonia
| | - Mathieu Moussavou
- Department of Geology, University of Science and Technology of Masuku, Franceville, Gabon
| | - Alexander E. Romashkin
- grid.465343.30000 0004 0397 7466Institute of Geology, Karelian Science Centre, Petrozavodsk, Russia
| | - Aivo Lepland
- grid.10939.320000 0001 0943 7661Department of Geology, University of Tartu, Tartu, Estonia ,grid.10919.300000000122595234CAGE—Centre for Arctic Gas Hydrate, Environment and Climate, Department of Geosciences, UiT The Arctic University of Norway, Tromsø, Norway ,grid.438521.90000 0001 1034 0453Geological Survey of Norway (NGU), Trondheim, Norway
| | - Kalle Kirsimäe
- grid.10939.320000 0001 0943 7661Department of Geology, University of Tartu, Tartu, Estonia
| | - Noah J. Planavsky
- grid.47100.320000000419368710The Department of Earth and Planetary Sciences, Yale University, New Haven, CT USA
| | - Kurt O. Konhauser
- grid.17089.37Department of Earth and Atmospheric Sciences, University of Alberta, Edmonton, Canada
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12
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Kin K, Schaap P. Evolution of Multicellular Complexity in The Dictyostelid Social Amoebas. Genes (Basel) 2021; 12:487. [PMID: 33801615 PMCID: PMC8067170 DOI: 10.3390/genes12040487] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2021] [Revised: 03/17/2021] [Accepted: 03/20/2021] [Indexed: 12/14/2022] Open
Abstract
Multicellularity evolved repeatedly in the history of life, but how it unfolded varies greatly between different lineages. Dictyostelid social amoebas offer a good system to study the evolution of multicellular complexity, with a well-resolved phylogeny and molecular genetic tools being available. We compare the life cycles of the Dictyostelids with closely related amoebozoans to show that complex life cycles were already present in the unicellular common ancestor of Dictyostelids. We propose frost resistance as an early driver of multicellular evolution in Dictyostelids and show that the cell signalling pathways for differentiating spore and stalk cells evolved from that for encystation. The stalk cell differentiation program was further modified, possibly through gene duplication, to evolve a new cell type, cup cells, in Group 4 Dictyostelids. Studies in various multicellular organisms, including Dictyostelids, volvocine algae, and metazoans, suggest as a common principle in the evolution of multicellular complexity that unicellular regulatory programs for adapting to environmental change serve as "proto-cell types" for subsequent evolution of multicellular organisms. Later, new cell types could further evolve by duplicating and diversifying the "proto-cell type" gene regulatory networks.
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Affiliation(s)
- Koryu Kin
- School of Life Sciences, University of Dundee, Dundee DD1 5EH, UK;
- Institut de Biologia Evolutiva (CSIC-Universitat Pompeu Fabra), Passeig Marítim de la Barceloneta 37–49, 08003 Barcelona, Spain
| | - Pauline Schaap
- School of Life Sciences, University of Dundee, Dundee DD1 5EH, UK;
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13
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Bell PJ. Evidence supporting a viral origin of the eukaryotic nucleus. Virus Res 2020; 289:198168. [DOI: 10.1016/j.virusres.2020.198168] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2020] [Revised: 09/10/2020] [Accepted: 09/14/2020] [Indexed: 12/22/2022]
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14
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Vaccaro A, Kaplan Dor Y, Nambara K, Pollina EA, Lin C, Greenberg ME, Rogulja D. Sleep Loss Can Cause Death through Accumulation of Reactive Oxygen Species in the Gut. Cell 2020; 181:1307-1328.e15. [PMID: 32502393 DOI: 10.1016/j.cell.2020.04.049] [Citation(s) in RCA: 225] [Impact Index Per Article: 56.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2019] [Revised: 01/15/2020] [Accepted: 04/24/2020] [Indexed: 02/06/2023]
Abstract
The view that sleep is essential for survival is supported by the ubiquity of this behavior, the apparent existence of sleep-like states in the earliest animals, and the fact that severe sleep loss can be lethal. The cause of this lethality is unknown. Here we show, using flies and mice, that sleep deprivation leads to accumulation of reactive oxygen species (ROS) and consequent oxidative stress, specifically in the gut. ROS are not just correlates of sleep deprivation but drivers of death: their neutralization prevents oxidative stress and allows flies to have a normal lifespan with little to no sleep. The rescue can be achieved with oral antioxidant compounds or with gut-targeted transgenic expression of antioxidant enzymes. We conclude that death upon severe sleep restriction can be caused by oxidative stress, that the gut is central in this process, and that survival without sleep is possible when ROS accumulation is prevented. VIDEO ABSTRACT.
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Affiliation(s)
- Alexandra Vaccaro
- Department of Neurobiology, Harvard Medical School, Boston, MA 02115, USA
| | - Yosef Kaplan Dor
- Department of Neurobiology, Harvard Medical School, Boston, MA 02115, USA
| | - Keishi Nambara
- Department of Neurobiology, Harvard Medical School, Boston, MA 02115, USA
| | | | - Cindy Lin
- Department of Neurobiology, Harvard Medical School, Boston, MA 02115, USA
| | | | - Dragana Rogulja
- Department of Neurobiology, Harvard Medical School, Boston, MA 02115, USA.
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15
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Cavalier-Smith T, Chao EEY. Multidomain ribosomal protein trees and the planctobacterial origin of neomura (eukaryotes, archaebacteria). PROTOPLASMA 2020. [PMID: 31900730 DOI: 10.1007/s00709-019-01442] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 05/16/2023]
Abstract
Palaeontologically, eubacteria are > 3× older than neomura (eukaryotes, archaebacteria). Cell biology contrasts ancestral eubacterial murein peptidoglycan walls and derived neomuran N-linked glycoprotein coats/walls. Misinterpreting long stems connecting clade neomura to eubacteria on ribosomal sequence trees (plus misinterpreted protein paralogue trees) obscured this historical pattern. Universal multiprotein ribosomal protein (RP) trees, more accurate than rRNA trees, are taxonomically undersampled. To reduce contradictions with genically richer eukaryote trees and improve eubacterial phylogeny, we constructed site-heterogeneous and maximum-likelihood universal three-domain, two-domain, and single-domain trees for 143 eukaryotes (branching now congruent with 187-protein trees), 60 archaebacteria, and 151 taxonomically representative eubacteria, using 51 and 26 RPs. Site-heterogeneous trees greatly improve eubacterial phylogeny and higher classification, e.g. showing gracilicute monophyly, that many 'rDNA-phyla' belong in Proteobacteria, and reveal robust new phyla Synthermota and Aquithermota. Monoderm Posibacteria and Mollicutes (two separate wall losses) are both polyphyletic: multiple outer membrane losses in Endobacteria occurred separately from Actinobacteria; neither phylum is related to Chloroflexi, the most divergent prokaryotes, which originated photosynthesis (new model proposed). RP trees support an eozoan root for eukaryotes and are consistent with archaebacteria being their sisters and rooted between Filarchaeota (=Proteoarchaeota, including 'Asgardia') and Euryarchaeota sensu-lato (including ultrasimplified 'DPANN' whose long branches often distort trees). Two-domain trees group eukaryotes within Planctobacteria, and archaebacteria with Planctobacteria/Sphingobacteria. Integrated molecular/palaeontological evidence favours negibacterial ancestors for neomura and all life. Unique presence of key pre-neomuran characters favours Planctobacteria only as ancestral to neomura, which apparently arose by coevolutionary repercussions (explained here in detail, including RP replacement) of simultaneous outer membrane and murein loss. Planctobacterial C-1 methanotrophic enzymes are likely ancestral to archaebacterial methanogenesis and β-propeller-α-solenoid proteins to eukaryotic vesicle coats, nuclear-pore-complexes, and intraciliary transport. Planctobacterial chaperone-independent 4/5-protofilament microtubules and MamK actin-ancestors prepared for eukaryote intracellular motility, mitosis, cytokinesis, and phagocytosis. We refute numerous wrong ideas about the universal tree.
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Affiliation(s)
| | - Ema E-Yung Chao
- Department of Zoology, University of Oxford, South Parks Road, Oxford, OX1 3PS, UK
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16
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Cavalier-Smith T, Chao EEY. Multidomain ribosomal protein trees and the planctobacterial origin of neomura (eukaryotes, archaebacteria). PROTOPLASMA 2020; 257:621-753. [PMID: 31900730 PMCID: PMC7203096 DOI: 10.1007/s00709-019-01442-7] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/25/2019] [Accepted: 09/19/2019] [Indexed: 05/02/2023]
Abstract
Palaeontologically, eubacteria are > 3× older than neomura (eukaryotes, archaebacteria). Cell biology contrasts ancestral eubacterial murein peptidoglycan walls and derived neomuran N-linked glycoprotein coats/walls. Misinterpreting long stems connecting clade neomura to eubacteria on ribosomal sequence trees (plus misinterpreted protein paralogue trees) obscured this historical pattern. Universal multiprotein ribosomal protein (RP) trees, more accurate than rRNA trees, are taxonomically undersampled. To reduce contradictions with genically richer eukaryote trees and improve eubacterial phylogeny, we constructed site-heterogeneous and maximum-likelihood universal three-domain, two-domain, and single-domain trees for 143 eukaryotes (branching now congruent with 187-protein trees), 60 archaebacteria, and 151 taxonomically representative eubacteria, using 51 and 26 RPs. Site-heterogeneous trees greatly improve eubacterial phylogeny and higher classification, e.g. showing gracilicute monophyly, that many 'rDNA-phyla' belong in Proteobacteria, and reveal robust new phyla Synthermota and Aquithermota. Monoderm Posibacteria and Mollicutes (two separate wall losses) are both polyphyletic: multiple outer membrane losses in Endobacteria occurred separately from Actinobacteria; neither phylum is related to Chloroflexi, the most divergent prokaryotes, which originated photosynthesis (new model proposed). RP trees support an eozoan root for eukaryotes and are consistent with archaebacteria being their sisters and rooted between Filarchaeota (=Proteoarchaeota, including 'Asgardia') and Euryarchaeota sensu-lato (including ultrasimplified 'DPANN' whose long branches often distort trees). Two-domain trees group eukaryotes within Planctobacteria, and archaebacteria with Planctobacteria/Sphingobacteria. Integrated molecular/palaeontological evidence favours negibacterial ancestors for neomura and all life. Unique presence of key pre-neomuran characters favours Planctobacteria only as ancestral to neomura, which apparently arose by coevolutionary repercussions (explained here in detail, including RP replacement) of simultaneous outer membrane and murein loss. Planctobacterial C-1 methanotrophic enzymes are likely ancestral to archaebacterial methanogenesis and β-propeller-α-solenoid proteins to eukaryotic vesicle coats, nuclear-pore-complexes, and intraciliary transport. Planctobacterial chaperone-independent 4/5-protofilament microtubules and MamK actin-ancestors prepared for eukaryote intracellular motility, mitosis, cytokinesis, and phagocytosis. We refute numerous wrong ideas about the universal tree.
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Affiliation(s)
| | - Ema E-Yung Chao
- Department of Zoology, University of Oxford, South Parks Road, Oxford, OX1 3PS, UK
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17
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Affiliation(s)
- Jean‐François Lutz
- Université de Strasbourg, CNRSInstitut Charles Sadron, UPR22 23 rue du Loess 67034 Strasbourg Cedex 2 France
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18
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Aubineau J, El Albani A, Bekker A, Somogyi A, Bankole OM, Macchiarelli R, Meunier A, Riboulleau A, Reynaud JY, Konhauser KO. Microbially induced potassium enrichment in Paleoproterozoic shales and implications for reverse weathering on early Earth. Nat Commun 2019; 10:2670. [PMID: 31209248 PMCID: PMC6572813 DOI: 10.1038/s41467-019-10620-3] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2018] [Accepted: 05/20/2019] [Indexed: 01/12/2023] Open
Abstract
Illitisation requires potassium incorporation into a smectite precursor, a process akin to reverse weathering. However, it remains unclear whether microbes facilitate K+ uptake to the sediments and whether illitisation was important in the geological past. The 2.1 billion-year-old Francevillian Series of Gabon has been shown to host mat-related structures (MRS) and, in this regard, these rocks offer a unique opportunity to test whether ancient microbes induced illitisation. Here, we show high K content confined to illite particles that are abundant in the facies bearing MRS, but not in the host sandstone and black shale. This observation suggests that microbial biofilms trapped K+ from the seawater and released it into the pore-waters during respiration, resulting in illitisation. The K-rich illite developed exclusively in the fossilized MRS thus provides a new biosignature for metasediments derived from K-feldspar-depleted rocks that were abundant crustal components on ancient Earth.
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Affiliation(s)
- Jérémie Aubineau
- UMR 7285 CNRS IC2MP, University of Poitiers, Poitiers, 86073, France
| | | | - Andrey Bekker
- Department of Earth and Planetary Sciences, University of California, Riverside, CA, 92521, USA
| | - Andrea Somogyi
- Nanoscopium Beamline Synchrotron Soleil, BP 48, Saint-Aubin, Gif-sur-Yvette, 91192, France
| | - Olabode M Bankole
- UMR 7285 CNRS IC2MP, University of Poitiers, Poitiers, 86073, France
| | - Roberto Macchiarelli
- Department of Geosciences, University of Poitiers, Poitiers, 86073, France
- Department of Prehistory, UMR 7194 CNRS, National Museum of Natural History, Paris, 75005, France
| | - Alain Meunier
- UMR 7285 CNRS IC2MP, University of Poitiers, Poitiers, 86073, France
| | - Armelle Riboulleau
- UMR 8187 CNRS LOG, University of Lille, ULCO, Villeneuve d'Ascq, 59655, France
| | - Jean-Yves Reynaud
- UMR 8187 CNRS LOG, University of Lille, ULCO, Villeneuve d'Ascq, 59655, France
| | - Kurt O Konhauser
- Department of Earth and Atmospheric Sciences, University of Alberta, Edmonton, AB T6G 2E3, Canada
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19
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Organism motility in an oxygenated shallow-marine environment 2.1 billion years ago. Proc Natl Acad Sci U S A 2019; 116:3431-3436. [PMID: 30808737 DOI: 10.1073/pnas.1815721116] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Evidence for macroscopic life in the Paleoproterozoic Era comes from 1.8 billion-year-old (Ga) compression fossils [Han TM, Runnegar B (1992) Science 257:232-235; Knoll et al. (2006) Philos Trans R Soc Lond B 361:1023-1038], Stirling biota [Bengtson S et al. (2007) Paleobiology 33:351-381], and large colonial organisms exhibiting signs of coordinated growth from the 2.1-Ga Francevillian series, Gabon. Here we report on pyritized string-shaped structures from the Francevillian Basin. Combined microscopic, microtomographic, geochemical, and sedimentologic analyses provide evidence for biogenicity, and syngenicity and suggest that the structures underwent fossilization during early diagenesis close to the sediment-water interface. The string-shaped structures are up to 6 mm across and extend up to 170 mm through the strata. Morphological and 3D tomographic reconstructions suggest that the producer may have been a multicellular or syncytial organism able to migrate laterally and vertically to reach food resources. A possible modern analog is the aggregation of amoeboid cells into a migratory slug phase in cellular slime molds at times of starvation. This unique ecologic window established in an oxygenated, shallow-marine environment represents an exceptional record of the biosphere following the crucial changes that occurred in the atmosphere and ocean in the aftermath of the great oxidation event (GOE).
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20
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Aubineau J, El Albani A, Chi Fru E, Gingras M, Batonneau Y, Buatois LA, Geffroy C, Labanowski J, Laforest C, Lemée L, Mángano MG, Meunier A, Pierson-Wickmann AC, Recourt P, Riboulleau A, Trentesaux A, Konhauser KO. Unusual microbial mat-related structural diversity 2.1 billion years ago and implications for the Francevillian biota. GEOBIOLOGY 2018; 16:476-497. [PMID: 29923673 DOI: 10.1111/gbi.12296] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/15/2018] [Revised: 04/10/2018] [Accepted: 05/08/2018] [Indexed: 06/08/2023]
Abstract
The 2.1-billion-year-old (Ga) Francevillian series in Gabon hosts some of the oldest reported macroscopic fossils of various sizes and shapes, stimulating new debates on the origin, evolution and organization of early complex life. Here, we document ten representative types of exceptionally well-preserved mat-related structures, comprising "elephant-skin" textures, putative macro-tufted microbial mats, domal buildups, flat pyritized structures, discoidal microbial colonies, horizontal mat growth patterns, wrinkle structures, "kinneyia" structures, linear patterns and nodule-like structures. A combination of petrographic analyses, scanning electron microscopy, Raman spectroscopy and organic elemental analyses of carbon-rich laminae and microtexture, indicate a biological origin for these structures. The observed microtextures encompass oriented grains, floating silt-sized quartz grains, concentrated heavy minerals, randomly oriented clays, wavy-crinkly laminae and pyritized structures. Based on comparisons with modern analogues, as well as an average δ13 C organic matter (Corg ) composition of -32.94 ± 1.17‰ (1 standard deviation, SD) with an outlier of -41.26‰, we argue that the mat-related structures contain relicts of multiple carbon pathways including heterotrophic recycling of photosynthetically derived Corg . Moreover, the relatively close association of the macroscopic fossil assemblages to the microbial mats may imply that microbial communities acted as potential benthic O2 oases linked to oxyphototrophic cyanobacterial mats and grazing grounds. In addition, the mat's presence likely improved the preservation of the oldest large colonial organisms, as they are known to strongly biostabilize sediments. Our findings highlight the oldest community assemblage of microscopic and macroscopic biota in the aftermath of the "Great Oxidation Event," widening our understanding of biological organization during Earth's middle age.
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Affiliation(s)
| | | | - Ernest Chi Fru
- School of Earth and Ocean Sciences, Cardiff University, Cardiff, UK
| | - Murray Gingras
- Department of Earth and Atmospheric Sciences, University of Alberta, Edmonton, Alberta, Canada
| | - Yann Batonneau
- UMR CNRS IC2MP 7285, University of Poitiers, Poitiers, France
| | - Luis A Buatois
- Department of Geological Sciences, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
| | - Claude Geffroy
- UMR CNRS IC2MP 7285, University of Poitiers, Poitiers, France
| | | | - Claude Laforest
- UMR CNRS IC2MP 7285, University of Poitiers, Poitiers, France
| | - Laurent Lemée
- UMR CNRS IC2MP 7285, University of Poitiers, Poitiers, France
| | - Maria G Mángano
- Department of Geological Sciences, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
| | - Alain Meunier
- UMR CNRS IC2MP 7285, University of Poitiers, Poitiers, France
| | | | - Philippe Recourt
- UMR 8187 LOG CNRS, University of Lille, ULCO, Villeneuve d'Ascq, France
| | | | - Alain Trentesaux
- UMR 8187 LOG CNRS, University of Lille, ULCO, Villeneuve d'Ascq, France
| | - Kurt O Konhauser
- Department of Earth and Atmospheric Sciences, University of Alberta, Edmonton, Alberta, Canada
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21
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Zhou Z, Liu Y, Li M, Gu JD. Two or three domains: a new view of tree of life in the genomics era. Appl Microbiol Biotechnol 2018; 102:3049-3058. [PMID: 29484479 DOI: 10.1007/s00253-018-8831-x] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2017] [Revised: 01/30/2018] [Accepted: 02/01/2018] [Indexed: 12/26/2022]
Abstract
The deep phylogenetic topology of tree of life is in the center of a long-time dispute. The Woeseian three-domain tree theory, with the Eukarya evolving as a sister clade to Archaea, competes with the two-domain tree theory (the eocyte tree), with the Eukarya branched within Archaea. Revealed by the ongoing debate over the last three decades, sophisticated and proper phylogenetic methods should necessarily be paid with more emphasis, especially these are focusing on the compositional heterogeneity of sites and lineages, and the heterotachy issue. The newly emerging archaeal lineages with numerous eukaryotic-like features, such as membrane trafficking and cellular compartmentalization, are phylogenetically the closest to eukaryotes currently. These findings highlight the evolutionary history from an ancient archaeon to a more complex archaeon with protoeukaryotic-like features and complex cellular structures, thus providing clues to understand eukaryogenesis process. The increasing repertoire of precise genomic contents provides great advantages on understanding the deep phylogeny of tree of life and ancient evolutionary events on Eukarya branching process.
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Affiliation(s)
- Zhichao Zhou
- Institute for Advanced Study, Shenzhen University, Shenzhen, 518060, People's Republic of China.,Laboratory of Environmental Microbiology and Toxicology, School of Biological Sciences, The University of Hong Kong, Pokfulam Road, Hong Kong SAR, Hong Kong, People's Republic of China
| | - Yang Liu
- Institute for Advanced Study, Shenzhen University, Shenzhen, 518060, People's Republic of China.,Key Laboratory of Optoelectronic Devices and Systems of Ministry of Education and Guangdong Province, College of Optoelectronic Engineering, Shenzhen University, Shenzhen, 518060, People's Republic of China
| | - Meng Li
- Institute for Advanced Study, Shenzhen University, Shenzhen, 518060, People's Republic of China.
| | - Ji-Dong Gu
- Laboratory of Environmental Microbiology and Toxicology, School of Biological Sciences, The University of Hong Kong, Pokfulam Road, Hong Kong SAR, Hong Kong, People's Republic of China
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22
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Liang D. A Salutary Role of Reactive Oxygen Species in Intercellular Tunnel-Mediated Communication. Front Cell Dev Biol 2018; 6:2. [PMID: 29503816 PMCID: PMC5821100 DOI: 10.3389/fcell.2018.00002] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2017] [Accepted: 01/18/2018] [Indexed: 12/17/2022] Open
Abstract
The reactive oxygen species, generally labeled toxic due to high reactivity without target specificity, are gradually uncovered as signaling molecules involved in a myriad of biological processes. But one important feature of ROS roles in macromolecule movement has not caught attention until recent studies with technique advance and design elegance have shed lights on ROS signaling for intercellular and interorganelle communication. This review begins with the discussions of genetic and chemical studies on the regulation of symplastic dye movement through intercellular tunnels in plants (plasmodesmata), and focuses on the ROS regulatory mechanisms concerning macromolecule movement including small RNA-mediated gene silencing movement and protein shuttling between cells. Given the premise that intercellular tunnels (bridges) in mammalian cells are the key physical structures to sustain intercellular communication, movement of macromolecules and signals is efficiently facilitated by ROS-induced membrane protrusions formation, which is analogously applied to the interorganelle communication in plant cells. Although ROS regulatory differences between plant and mammalian cells exist, the basis for ROS-triggered conduit formation underlies a unifying conservative theme in multicellular organisms. These mechanisms may represent the evolutionary advances that have enabled multicellularity to gain the ability to generate and utilize ROS to govern material exchanges between individual cells in oxygenated environment.
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Affiliation(s)
- Dacheng Liang
- Hubei Collaborative Innovation Center for Grain Industry, School of Agriculture, Yangtze University, Jingzhou, China.,Engineering Research Center of Ecology and Agricultural Use of Wetland, Ministry of Education, Yangtze University, Jingzhou, China
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23
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Refined control of cell stemness allowed animal evolution in the oxic realm. Nat Ecol Evol 2018; 2:220-228. [DOI: 10.1038/s41559-017-0410-5] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2017] [Accepted: 11/10/2017] [Indexed: 12/26/2022]
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24
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Putzbach W, Gao QQ, Patel M, Haluck-Kangas A, Murmann AE, Peter ME. DISE: A Seed-Dependent RNAi Off-Target Effect That Kills Cancer Cells. Trends Cancer 2018; 4:10-19. [PMID: 29413418 DOI: 10.1016/j.trecan.2017.11.007] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2017] [Revised: 11/16/2017] [Accepted: 11/17/2017] [Indexed: 01/23/2023]
Abstract
Off-target effects (OTEs) represent a significant caveat for RNAi caused by substantial complementarity between siRNAs and unintended mRNAs. We now discuss the existence of three types of seed-dependent OTEs (sOTEs). Type I involves unintended targeting through the guide strand seed of an siRNA. Type II is caused by the activity of the seed on the designated siRNA passenger strand when loaded into the RNA-induced silencing complex (RISC). Both type I and II sOTEs will elicit unpredictable cellular responses. By contrast, in sOTE type III the guide strand seed preferentially targets essential survival genes resulting in death induced by survival gene elimination (DISE). In this Opinion article, we discuss DISE as a consequence of RNAi that may preferentially affect cancer cells.
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Affiliation(s)
- William Putzbach
- Department of Medicine, Division Hematology/Oncology, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Quan Q Gao
- Department of Medicine, Division Hematology/Oncology, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Monal Patel
- Department of Medicine, Division Hematology/Oncology, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Ashley Haluck-Kangas
- Department of Medicine, Division Hematology/Oncology, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Andrea E Murmann
- Department of Medicine, Division Hematology/Oncology, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Marcus E Peter
- Department of Medicine, Division Hematology/Oncology, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA; Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA.
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25
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Libby E, Conlin PL, Kerr B, Ratcliff WC. Stabilizing multicellularity through ratcheting. Philos Trans R Soc Lond B Biol Sci 2017; 371:rstb.2015.0444. [PMID: 27431522 PMCID: PMC4958938 DOI: 10.1098/rstb.2015.0444] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/09/2016] [Indexed: 12/19/2022] Open
Abstract
The evolutionary transition to multicellularity probably began with the formation of simple undifferentiated cellular groups. Such groups evolve readily in diverse lineages of extant unicellular taxa, suggesting that there are few genetic barriers to this first key step. This may act as a double-edged sword: labile transitions between unicellular and multicellular states may facilitate the evolution of simple multicellularity, but reversion to a unicellular state may inhibit the evolution of increased complexity. In this paper, we examine how multicellular adaptations can act as evolutionary ‘ratchets’, limiting the potential for reversion to unicellularity. We consider a nascent multicellular lineage growing in an environment that varies between favouring multicellularity and favouring unicellularity. The first type of ratcheting mutations increase cell-level fitness in a multicellular context but are costly in a single-celled context, reducing the fitness of revertants. The second type of ratcheting mutations directly decrease the probability that a mutation will result in reversion (either as a pleiotropic consequence or via direct modification of switch rates). We show that both types of ratcheting mutations act to stabilize the multicellular state. We also identify synergistic effects between the two types of ratcheting mutations in which the presence of one creates the selective conditions favouring the other. Ratcheting mutations may play a key role in diverse evolutionary transitions in individuality, sustaining selection on the new higher-level organism by constraining evolutionary reversion. This article is part of the themed issue ‘The major synthetic evolutionary transitions’.
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Affiliation(s)
- Eric Libby
- Santa Fe Institute, Santa Fe, NM 87501, USA
| | - Peter L Conlin
- Department of Biology and BEACON Center for the Study of Evolution in Action, University of Washington, Seattle, WA 98195, USA
| | - Ben Kerr
- Department of Biology and BEACON Center for the Study of Evolution in Action, University of Washington, Seattle, WA 98195, USA
| | - William C Ratcliff
- Department of Biology, Georgia Institute of Technology, Atlanta, GA 30332, USA
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26
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Foucher F, Hickman-Lewis K, Westall F, Brack A. A Statistical Approach to Illustrate the Challenge of Astrobiology for Public Outreach. Life (Basel) 2017; 7:life7040040. [PMID: 29072614 PMCID: PMC5745553 DOI: 10.3390/life7040040] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2017] [Revised: 10/24/2017] [Accepted: 10/25/2017] [Indexed: 01/08/2023] Open
Abstract
In this study, we attempt to illustrate the competition that constitutes the main challenge of astrobiology, namely the competition between the probability of extraterrestrial life and its detectability. To illustrate this fact, we propose a simple statistical approach based on our knowledge of the Universe and the Milky Way, the Solar System, and the evolution of life on Earth permitting us to obtain the order of magnitude of the distance between Earth and bodies inhabited by more or less evolved past or present life forms, and the consequences of this probability for the detection of associated biosignatures. We thus show that the probability of the existence of evolved extraterrestrial forms of life increases with distance from the Earth while, at the same time, the number of detectable biosignatures decreases due to technical and physical limitations. This approach allows us to easily explain to the general public why it is very improbable to detect a signal of extraterrestrial intelligence while it is justified to launch space probes dedicated to the search for microbial life in the Solar System.
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Affiliation(s)
- Frédéric Foucher
- CNRS, Centre de Biophysique Moléculaire, UPR 4301, Rue Charles Sadron, CS80054, 45071 Orléans CEDEX, France.
| | - Keyron Hickman-Lewis
- CNRS, Centre de Biophysique Moléculaire, UPR 4301, Rue Charles Sadron, CS80054, 45071 Orléans CEDEX, France.
| | - Frances Westall
- CNRS, Centre de Biophysique Moléculaire, UPR 4301, Rue Charles Sadron, CS80054, 45071 Orléans CEDEX, France.
| | - André Brack
- CNRS, Centre de Biophysique Moléculaire, UPR 4301, Rue Charles Sadron, CS80054, 45071 Orléans CEDEX, France.
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27
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Abstract
The first animals evolved from an unknown single-celled ancestor in the Precambrian period. Recently, the identification and characterization of the genomic and cellular traits of the protists most closely related to animals have shed light on the origin of animals. Comparisons of animals with these unicellular relatives allow us to reconstruct the first evolutionary steps towards animal multicellularity. Here, we review the results of these investigations and discuss their implications for understanding the earliest stages of animal evolution, including the origin of metazoan genes and genome function.
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28
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Abstract
AbstractVirtual paleontology is the study of fossils through three-dimensional digital visualizations; it represents a powerful and well-established set of tools for the analysis and dissemination of fossil data. Techniques are divisible into tomographic (i.e., slice-based) and surface-based types. Tomography has a long predigital history, but the recent explosion of virtual paleontology has resulted primarily from developments in X-ray computed tomography (CT), and of surface-based technologies (e.g., laser scanning). Destructive tomographic methods include forms of physical-optical tomography (e.g., serial grinding); these are powerful but problematic techniques. Focused Ion Beam (FIB) tomography is a modern alternative for microfossils; it is also destructive but is capable of extremely high resolutions. Nondestructive tomographic methods include the many forms of CT, which are the most widely used data-capture techniques at present, but are not universally applicable. Where CT is inappropriate, other nondestructive technologies (e.g., neutron tomography, magnetic resonance imaging, optical tomography) can prove suitable. Surface-based methods provide portable and convenient data capture for surface topography and texture, and might be appropriate when internal morphology is not of interest; technologies include laser scanning, photogrammetry, and mechanical digitization. Reconstruction methods that produce visualizations from raw data are many and various; selection of an appropriate workflow will depend on many factors, but is an important consideration that should be addressed prior to any study. The vast majority of three-dimensional fossils can now be studied using some form of virtual paleontology, and barriers to broader adaptation are being eroded. Technical issues regarding data sharing remain problematic. Technological developments continue; those promising tomographic recovery of compositional data are of particular relevance to paleontology.
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29
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Affiliation(s)
- Nicola McLoughlin
- Department of Geology and Albany Museum, Rhodes University, Grahamstown, 6140, South Africa
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30
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Three-dimensional preservation of cellular and subcellular structures suggests 1.6 billion-year-old crown-group red algae. PLoS Biol 2017; 15:e2000735. [PMID: 28291791 PMCID: PMC5349422 DOI: 10.1371/journal.pbio.2000735] [Citation(s) in RCA: 92] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2016] [Accepted: 02/07/2017] [Indexed: 01/10/2023] Open
Abstract
The ~1.6 Ga Tirohan Dolomite of the Lower Vindhyan in central India contains phosphatized stromatolitic microbialites. We report from there uniquely well-preserved fossils interpreted as probable crown-group rhodophytes (red algae). The filamentous form Rafatazmia chitrakootensis n. gen, n. sp. has uniserial rows of large cells and grows through diffusely distributed septation. Each cell has a centrally suspended, conspicuous rhomboidal disk interpreted as a pyrenoid. The septa between the cells have central structures that may represent pit connections and pit plugs. Another filamentous form, Denaricion mendax n. gen., n. sp., has coin-like cells reminiscent of those in large sulfur-oxidizing bacteria but much more recalcitrant than the liquid-vacuole-filled cells of the latter. There are also resemblances with oscillatoriacean cyanobacteria, although cell volumes in the latter are much smaller. The wider affinities of Denaricion are uncertain. Ramathallus lobatus n. gen., n. sp. is a lobate sessile alga with pseudoparenchymatous thallus, “cell fountains,” and apical growth, suggesting florideophycean affinity. If these inferences are correct, Rafatazmia and Ramathallus represent crown-group multicellular rhodophytes, antedating the oldest previously accepted red alga in the fossil record by about 400 million years. The last common ancestor of modern eukaryotes is generally believed to have lived during the Mesoproterozoic era, about 1.6 to 1 billion years ago, or possibly somewhat earlier. We studied exquisitely preserved fossil communities from ~1.6 billion-year-old sedimentary rocks in central India representing a shallow-water marine environment characterized by photosynthetic biomats. We discovered amidst extensive cyanobacterial mats a biota of filamentous and lobate organisms that share significant features with modern eukaryotic algae, more specifically red algae. The rocks mainly consist of calcium and magnesium carbonates, but the microbial mats and the fossils are preserved in calcium phosphate, letting us view the cellular and subcellular structures in three dimensions with the use of synchrotron-radiation X-ray tomographic microscopy. The most conspicuous internal objects in the cells of the filamentous forms are rhomboidal platelets that we interpret to be part of the photosynthetic machinery of red algae. The lobate forms grew as radiating globular or finger-like protrusions from a common centre. These fossils predate the previously earliest accepted red algae by about 400 million years, suggesting that eukaryotes may have a longer history than commonly assumed.
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31
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Selenium isotopes record extensive marine suboxia during the Great Oxidation Event. Proc Natl Acad Sci U S A 2017; 114:875-880. [PMID: 28096405 DOI: 10.1073/pnas.1615867114] [Citation(s) in RCA: 54] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
It has been proposed that an "oxygen overshoot" occurred during the early Paleoproterozoic Great Oxidation Event (GOE) in association with the extreme positive carbon isotopic excursion known as the Lomagundi Event. Moreover, it has also been suggested that environmental oxygen levels then crashed to very low levels during the subsequent extremely negative Shunga-Francevillian carbon isotopic anomaly. These redox fluctuations could have profoundly influenced the course of eukaryotic evolution, as eukaryotes have several metabolic processes that are obligately aerobic. Here we investigate the magnitude of these proposed oxygen perturbations using selenium (Se) geochemistry, which is sensitive to redox transitions across suboxic conditions. We find that δ82/78Se values in offshore shales show a positive excursion from 2.32 Ga until 2.1 Ga (mean +1.03 ± 0.67‰). Selenium abundances and Se/TOC (total organic carbon) ratios similarly show a peak during this interval. Together these data suggest that during the GOE there was pervasive suboxia in near-shore environments, allowing nonquantitative Se reduction to drive the residual Se oxyanions isotopically heavy. This implies O2 levels of >0.4 μM in these settings. Unlike in the late Neoproterozoic and Phanerozoic, when negative δ82/78Se values are observed in offshore environments, only a single formation, evidently the shallowest, shows evidence of negative δ82/78Se. This suggests that there was no upwelling of Se oxyanions from an oxic deep-ocean reservoir, which is consistent with previous estimates that the deep ocean remained anoxic throughout the GOE. The abrupt decline in δ82/78Se and Se/TOC values during the subsequent Shunga-Francevillian anomaly indicates a widespread decrease in surface oxygenation.
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Arguments Reinforcing the Three-Domain View of Diversified Cellular Life. ARCHAEA-AN INTERNATIONAL MICROBIOLOGICAL JOURNAL 2016; 2016:1851865. [PMID: 28050162 PMCID: PMC5165138 DOI: 10.1155/2016/1851865] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/16/2016] [Revised: 10/18/2016] [Accepted: 11/03/2016] [Indexed: 11/18/2022]
Abstract
The archaeal ancestor scenario (AAS) for the origin of eukaryotes implies the emergence of a new kind of organism from the fusion of ancestral archaeal and bacterial cells. Equipped with this “chimeric” molecular arsenal, the resulting cell would gradually accumulate unique genes and develop the complex molecular machineries and cellular compartments that are hallmarks of modern eukaryotes. In this regard, proteins related to phagocytosis and cell movement should be present in the archaeal ancestor, thus identifying the recently described candidate archaeal phylum “Lokiarchaeota” as resembling a possible candidate ancestor of eukaryotes. Despite its appeal, AAS seems incompatible with the genomic, molecular, and biochemical differences that exist between Archaea and Eukarya. In particular, the distribution of conserved protein domain structures in the proteomes of cellular organisms and viruses appears hard to reconcile with the AAS. In addition, concerns related to taxon and character sampling, presupposing bacterial outgroups in phylogenies, and nonuniform effects of protein domain structure rearrangement and gain/loss in concatenated alignments of protein sequences cast further doubt on AAS-supporting phylogenies. Here, we evaluate AAS against the traditional “three-domain” world of cellular organisms and propose that the discovery of Lokiarchaeota could be better reconciled under the latter view, especially in light of several additional biological and technical considerations.
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Höhn S, Hallmann A. Distinct shape-shifting regimes of bowl-shaped cell sheets - embryonic inversion in the multicellular green alga Pleodorina. BMC DEVELOPMENTAL BIOLOGY 2016; 16:35. [PMID: 27733125 PMCID: PMC5062935 DOI: 10.1186/s12861-016-0134-9] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/08/2016] [Accepted: 09/13/2016] [Indexed: 11/10/2022]
Abstract
BACKGROUND The multicellular volvocine alga Pleodorina is intermediate in organismal complexity between its unicellular relative, Chlamydomonas, and its multicellular relative, Volvox, which shows complete division of labor between different cell types. The volvocine green microalgae form a group of genera closely related to the genus Volvox within the order Volvocales (Chlorophyta). Embryos of multicellular volvocine algae consist of a cellular monolayer that, depending on the species, is either bowl-shaped or comprises a sphere. During embryogenesis, multicellular volvocine embryos turn their cellular monolayer right-side out to expose their flagella. This process is called 'inversion' and serves as simple model for epithelial folding in metazoa. While the development of spherical Volvox embryos has been the subject of detailed studies, the inversion process of bowl-shaped embryos is less well understood. Therefore, it has been unclear how the inversion of a sphere might have evolved from less complicated processes. RESULTS In this study we characterized the inversion of initially bowl-shaped embryos of the 64- to 128-celled volvocine species Pleodorina californica. We focused on the movement patterns of the cell sheet, cell shape changes and changes in the localization of cytoplasmic bridges (CBs) connecting the cells. The development of living embryos was recorded using time-lapse light microscopy. Moreover, fixed and sectioned embryos throughout inversion and at successive stages of development were analyzed by light and transmission electron microscopy. We generated three-dimensional models of the identified cell shapes including the localization of CBs. CONCLUSIONS In contrast to descriptions concerning volvocine embryos with lower cell numbers, the embryonic cells of P. californica undergo non-simultaneous and non-uniform cell shape changes. In P. californica, cell wedging in combination with a relocation of the CBs to the basal cell tips explains the curling of the cell sheet during inversion. In volvocine genera with lower organismal complexity, the cell shape changes and relocation of CBs are less pronounced in comparison to P. californica, while they are more pronounced in all members of the genus Volvox. This finding supports an increasing significance of the temporal and spatial regulation of cell shape changes and CB relocations with both increasing cell number and organismal complexity during evolution of differentiated multicellularity.
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Affiliation(s)
- Stephanie Höhn
- Department of Cellular and Developmental Biology of Plants, University of Bielefeld, Universitätsstr. 25, 33615, Bielefeld, Germany.,Present address: DAMTP, Biological Physics, University of Cambridge, Centre for Mathematical Sciences, Wilberforce Road, Cambridge, CB3 0WA, UK
| | - Armin Hallmann
- Department of Cellular and Developmental Biology of Plants, University of Bielefeld, Universitätsstr. 25, 33615, Bielefeld, Germany.
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Claverie JM, Abergel C. Giant viruses: The difficult breaking of multiple epistemological barriers. STUDIES IN HISTORY AND PHILOSOPHY OF BIOLOGICAL AND BIOMEDICAL SCIENCES 2016; 59:89-99. [PMID: 26972873 DOI: 10.1016/j.shpsc.2016.02.015] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/21/2016] [Accepted: 02/27/2016] [Indexed: 06/05/2023]
Abstract
The discovery of the first "giant virus", Mimivirus, in 2003 could solely have been that of an exceptional freak, a blind alley of evolution as occasionally encountered in biology, albeit without conceptual significance. On the contrary, once broken this epistemological barrier, additional unrelated families of giant viruses such as the Pandoraviruses, the Pithoviruses and most recently Mollivirus, were quickly unraveled, suggesting that an entire chapter of microbiology had been ignored since Pasteur and Ivanovski. In this article, we examine to what extent the giant viruses challenge previous definitions of viruses, the diversity of forms they could take, and how they might have evolved from extinct ancestral cellular lineages. Inspired by the epistemology of Gaston Bachelard, we will also suggest the reasons for which giant viruses laid hidden in plain sight for more than a century. Finally, we propose a new definition for "viruses" that paradoxically emphasize the fact that they do not encode a single universally shared macromolecule or biochemical function.
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Affiliation(s)
- Jean-Michel Claverie
- Structural and Genomic Information Laboratory, UMR 7256 (IMM FR 3479) CNRS Aix-Marseille Université, Luminy Campus, Marseille, France; Assistance Publique des Hôpitaux de Marseille, La Timone, 13005, Marseille, France.
| | - Chantal Abergel
- Structural and Genomic Information Laboratory, UMR 7256 (IMM FR 3479) CNRS Aix-Marseille Université, Luminy Campus, Marseille, France
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Abstract
Calcium carries messages to virtually all important functions of cells. Although it was already active in unicellular organisms, its role became universally important after the transition to multicellular life. In this Minireview, we explore how calcium ended up in this privileged position. Most likely its unique coordination chemistry was a decisive factor as it makes its binding by complex molecules particularly easy even in the presence of large excesses of other cations, e.g. magnesium. Its free concentration within cells can thus be maintained at the very low levels demanded by the signaling function. A large cadre of proteins has evolved to bind or transport calcium. They all contribute to buffer it within cells, but a number of them also decode its message for the benefit of the target. The most important of these "calcium sensors" are the EF-hand proteins. Calcium is an ambivalent messenger. Although essential to the correct functioning of cell processes, if not carefully controlled spatially and temporally within cells, it generates variously severe cell dysfunctions, and even cell death.
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Affiliation(s)
- Ernesto Carafoli
- From the Venetian Institute of Molecular Medicine, University of Padova, 35131 Padova, Italy and
| | - Joachim Krebs
- the Department of NMR Based Structural Biology, Max Planck Institute for Biophysical Chemistry, 37077 Goettingen, Germany
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Zhu S, Zhu M, Knoll AH, Yin Z, Zhao F, Sun S, Qu Y, Shi M, Liu H. Decimetre-scale multicellular eukaryotes from the 1.56-billion-year-old Gaoyuzhuang Formation in North China. Nat Commun 2016; 7:11500. [PMID: 27186667 PMCID: PMC4873660 DOI: 10.1038/ncomms11500] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2015] [Accepted: 04/04/2016] [Indexed: 11/23/2022] Open
Abstract
Fossils of macroscopic eukaryotes are rarely older than the Ediacaran Period (635–541 million years (Myr)), and their interpretation remains controversial. Here, we report the discovery of macroscopic fossils from the 1,560-Myr-old Gaoyuzhuang Formation, Yanshan area, North China, that exhibit both large size and regular morphology. Preserved as carbonaceous compressions, the Gaoyuzhuang fossils have statistically regular linear to lanceolate shapes up to 30 cm long and nearly 8 cm wide, suggesting that the Gaoyuzhuang fossils record benthic multicellular eukaryotes of unprecedentedly large size. Syngenetic fragments showing closely packed ∼10 μm cells arranged in a thick sheet further reinforce the interpretation. Comparisons with living thalloid organisms suggest that these organisms were photosynthetic, although their phylogenetic placement within the Eukarya remains uncertain. The new fossils provide the strongest evidence yet that multicellular eukaryotes with decimetric dimensions and a regular developmental program populated the marine biosphere at least a billion years before the Cambrian Explosion. Macroscopic organisms are rare in the fossil record until the Ediacaran Period, beginning 635 million years ago. Here, Zhu et al. report the discovery of 1.56-billion-year-old carbonaceous compression fossils that provide evidence of the evolution of macroscopic, multicellular eukaryotes long before the Ediacaran Period.
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Affiliation(s)
- Shixing Zhu
- Tianjin Institute of Geology and Mineral Resources, China Geological Survey, Tianjin 300170, China.,State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan 430074, China
| | - Maoyan Zhu
- State Key Laboratory of Palaeobiology and Stratigraphy, Nanjing Institute of Geology and Palaeontology, Chinese Academy of Sciences, Nanjing 210008, China
| | - Andrew H Knoll
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts 02138, USA
| | - Zongjun Yin
- State Key Laboratory of Palaeobiology and Stratigraphy, Nanjing Institute of Geology and Palaeontology, Chinese Academy of Sciences, Nanjing 210008, China
| | - Fangchen Zhao
- State Key Laboratory of Palaeobiology and Stratigraphy, Nanjing Institute of Geology and Palaeontology, Chinese Academy of Sciences, Nanjing 210008, China
| | - Shufen Sun
- Tianjin Institute of Geology and Mineral Resources, China Geological Survey, Tianjin 300170, China
| | - Yuangao Qu
- Centre for Geobiology, University of Bergen, Bergen 5007, Norway
| | - Min Shi
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan 430074, China
| | - Huan Liu
- Tianjin Institute of Geology and Mineral Resources, China Geological Survey, Tianjin 300170, China
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Tomescu AMF, Klymiuk AA, Matsunaga KKS, Bippus AC, Shelton GWK. Microbes and the Fossil Record: Selected Topics in Paleomicrobiology. THEIR WORLD: A DIVERSITY OF MICROBIAL ENVIRONMENTS 2016. [DOI: 10.1007/978-3-319-28071-4_3] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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Herkovits J, Castañaga LA, D'Eramo JL, Jourani VP. Living organisms influence on environmental conditions: pH modulation by amphibian embryos versus aluminum toxicity. CHEMOSPHERE 2015; 139:210-215. [PMID: 26126231 DOI: 10.1016/j.chemosphere.2015.05.025] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/26/2014] [Revised: 05/02/2015] [Accepted: 05/06/2015] [Indexed: 06/04/2023]
Abstract
The LC10, 50 and 90/24h of aluminum for Rhinella arenarum embryos at complete operculum stage were 0.55, 0.75 and 1mgAl(3+)/L respectively. Those values did not change significantly by expanding the exposure period till 168h. The aluminum toxicity was evaluated in different pH conditions by means of a citrate buffer resulting for instance, 1mgAl(3+)/L at pH 4, 4.1, 5 and 6 in 100%, 70%, 35% and 0% of lethality respectively. As an outstanding feature, the embryos changed the pH of the maintaining media both in the case of Al(3+) or citrate buffer treatments toward neutral. 10 embryos in 40mL of AMPHITOX solution were able to increase the pH from 4.2 to 7.05, a fact related with a metabolic shift resulting in an increase in nitrogen loss as ammonia. Our study point out the natural selection of the most resistant amphibian embryos both for pH or aluminum as well as the capacity of living organisms (as a population) to alter their chemical environment toward optimal conditions for their survival. As these facts occur at early life stages, it expand the concept that living organisms at ontogenic stages are biomarker of environmental signatures of the evolutionary process (Herkovits, 2006) to a global Onto-Evo concept which imply also the feedback mechanisms from living organisms to shape environmental conditions in a way that benefits them.
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Affiliation(s)
- Jorge Herkovits
- Instituto de Ciencias Ambientales y Salud, Fundacion PROSAMA, Paysandú 752, 1405 Buenos Aires, Argentina.
| | - Luis Alberto Castañaga
- Instituto de Ciencias Ambientales y Salud, Fundacion PROSAMA, Paysandú 752, 1405 Buenos Aires, Argentina
| | - José Luis D'Eramo
- Instituto de Ciencias Ambientales y Salud, Fundacion PROSAMA, Paysandú 752, 1405 Buenos Aires, Argentina
| | - Victoria Platonova Jourani
- Instituto de Ciencias Ambientales y Salud, Fundacion PROSAMA, Paysandú 752, 1405 Buenos Aires, Argentina
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Abergel C, Legendre M, Claverie JM. The rapidly expanding universe of giant viruses: Mimivirus, Pandoravirus, Pithovirus and Mollivirus. FEMS Microbiol Rev 2015; 39:779-96. [PMID: 26391910 DOI: 10.1093/femsre/fuv037] [Citation(s) in RCA: 158] [Impact Index Per Article: 17.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/15/2015] [Indexed: 12/31/2022] Open
Abstract
More than a century ago, the term 'virus' was introduced to describe infectious agents that are invisible by light microscopy and capable of passing through sterilizing filters. In addition to their extremely small size, most viruses have minimal genomes and gene contents, and rely almost entirely on host cell-encoded functions to multiply. Unexpectedly, four different families of eukaryotic 'giant viruses' have been discovered over the past 10 years with genome sizes, gene contents and particle dimensions overlapping with that of cellular microbes. Their ongoing analyses are challenging accepted ideas about the diversity, evolution and origin of DNA viruses.
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Affiliation(s)
- Chantal Abergel
- Structural and Genomic Information Laboratory, UMR 7256 (IMM FR 3479) Centre National de la Recherche Scientifique & Aix-Marseille University, 13288 Marseille, France
| | - Matthieu Legendre
- Structural and Genomic Information Laboratory, UMR 7256 (IMM FR 3479) Centre National de la Recherche Scientifique & Aix-Marseille University, 13288 Marseille, France
| | - Jean-Michel Claverie
- Structural and Genomic Information Laboratory, UMR 7256 (IMM FR 3479) Centre National de la Recherche Scientifique & Aix-Marseille University, 13288 Marseille, France Assistance Publique des Hôpitaux de Marseille, La Timone, 13005 Marseille, France
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Abstract
Biologists used to draw schematic “universal” trees of life as metaphors illustrating the history of life. It is indeed a priori possible to construct an organismal tree connecting the three major domains of ribosome encoding organisms: Archaea, Bacteria and Eukarya, since they originated by cell division from LUCA. Several universal trees based on ribosomal RNA sequence comparisons proposed at the end of the last century are still widely used, although some of their main features have been challenged by subsequent analyses. Several authors have proposed to replace the traditional universal tree with a ring of life, whereas others have proposed more recently to include viruses as new domains. These proposals are misleading, suggesting that endosymbiosis can modify the shape of a tree or that viruses originated from the last universal common ancestor (LUCA). I propose here an updated version of Woese’s universal tree that includes several rootings for each domain and internal branching within domains that are supported by recent phylogenomic analyses of domain specific proteins. The tree is rooted between Bacteria and Arkarya, a new name proposed for the clade grouping Archaea and Eukarya. A consensus version, in which each of the three domains is unrooted, and a version in which eukaryotes emerged within archaea are also presented. This last scenario assumes the transformation of a modern domain into another, a controversial evolutionary pathway. Viruses are not indicated in these trees but are intrinsically present because they infect the tree from its roots to its leaves. Finally, I present a detailed tree of the domain Archaea, proposing the sub-phylum neo-Euryarchaeota for the monophyletic group of euryarchaeota containing DNA gyrase. These trees, that will be easily updated as new data become available, could be useful to discuss controversial scenarios regarding early life evolution.
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Affiliation(s)
- Patrick Forterre
- Unité de Biologie Moléculaire du Gène chez les Extrêmophiles, Département de Microbiologie, Institut Pasteur , Paris, France ; Institut de Biologie Intégrative de la cellule, Université Paris-Saclay , Paris, France
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Abstract
Animals evolved in seas teeming with bacteria, yet the influences of bacteria on animal origins are poorly understood. Comparisons among modern animals and their closest living relatives, the choanoflagellates, suggest that the first animals used flagellated collar cells to capture bacterial prey. The cell biology of prey capture, such as cell adhesion between predator and prey, involves mechanisms that may have been co-opted to mediate intercellular interactions during the evolution of animal multicellularity. Moreover, a history of bacterivory may have influenced the evolution of animal genomes by driving the evolution of genetic pathways for immunity and facilitating lateral gene transfer. Understanding the interactions between bacteria and the progenitors of animals may help to explain the myriad ways in which bacteria shape the biology of modern animals, including ourselves.
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Affiliation(s)
- Rosanna A Alegado
- Department of Oceanography, Center for Microbial Oceanography: Research and Education, Sea Grant College, University of Hawai'i Mānoa, Honolulu, Hawaii 96822
| | - Nicole King
- Howard Hughes Medical Institute and the Department of Molecular and Cell Biology, University of California, Berkeley, California 94720
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The 2.1 Ga old Francevillian biota: biogenicity, taphonomy and biodiversity. PLoS One 2014; 9:e99438. [PMID: 24963687 PMCID: PMC4070892 DOI: 10.1371/journal.pone.0099438] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2014] [Accepted: 05/14/2014] [Indexed: 11/20/2022] Open
Abstract
The Paleoproterozoic Era witnessed crucial steps in the evolution of Earth's surface environments following the first appreciable rise of free atmospheric oxygen concentrations ∼2.3 to 2.1 Ga ago, and concomitant shallow ocean oxygenation. While most sedimentary successions deposited during this time interval have experienced thermal overprinting from burial diagenesis and metamorphism, the ca. 2.1 Ga black shales of the Francevillian B Formation (FB2) cropping out in southeastern Gabon have not. The Francevillian Formation contains centimeter-sized structures interpreted as organized and spatially discrete populations of colonial organisms living in an oxygenated marine ecosystem. Here, new material from the FB2 black shales is presented and analyzed to further explore its biogenicity and taphonomy. Our extended record comprises variably sized, shaped, and structured pyritized macrofossils of lobate, elongated, and rod-shaped morphologies as well as abundant non-pyritized disk-shaped macrofossils and organic-walled acritarchs. Combined microtomography, geochemistry, and sedimentary analysis suggest a biota fossilized during early diagenesis. The emergence of this biota follows a rise in atmospheric oxygen, which is consistent with the idea that surface oxygenation allowed the evolution and ecological expansion of complex megascopic life.
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Antcliffe JB, Callow RHT, Brasier MD. Giving the early fossil record of sponges a squeeze. Biol Rev Camb Philos Soc 2014; 89:972-1004. [DOI: 10.1111/brv.12090] [Citation(s) in RCA: 126] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2012] [Revised: 01/16/2014] [Accepted: 01/30/2014] [Indexed: 11/27/2022]
Affiliation(s)
- Jonathan B. Antcliffe
- Department of Zoology; University of Oxford; South Parks Road Oxford OX1 3PS U.K
- Department of Earth Sciences; University of Bristol; Wills Memorial Building, Queen's Road Bristol BS81RJ U.K
| | - Richard H. T. Callow
- Department of Geology and Petroleum Geology; School of Geosciences, University of Aberdeen; Meston Building Aberdeen AB24 3UE U.K
| | - Martin D. Brasier
- Department of Earth Sciences; Oxford University; Parks Road Oxford OX13PR U.K
- Department of Earth Sciences; Memorial University of Newfoundland; 300 Prince Philip Drive St John's A1B 3X5 Canada
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Kempes CP, Okegbe C, Mears-Clarke Z, Follows MJ, Dietrich LEP. Morphological optimization for access to dual oxidants in biofilms. Proc Natl Acad Sci U S A 2014; 111:208-13. [PMID: 24335705 PMCID: PMC3890773 DOI: 10.1073/pnas.1315521110] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
A major theme driving research in biology is the relationship between form and function. In particular, a longstanding goal has been to understand how the evolution of multicellularity conferred fitness advantages. Here we show that biofilms of the bacterium Pseudomonas aeruginosa produce structures that maximize cellular reproduction. Specifically, we develop a mathematical model of resource availability and metabolic response within colony features. This analysis accurately predicts the measured distribution of two types of electron acceptors: oxygen, which is available from the atmosphere, and phenazines, redox-active antibiotics produced by the bacterium. Using this model, we demonstrate that the geometry of colony structures is optimal with respect to growth efficiency. Because our model is based on resource dynamics, we also can anticipate shifts in feature geometry based on changes to the availability of electron acceptors, including variations in the external availability of oxygen and genetic manipulation that renders the cells incapable of phenazine production.
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Affiliation(s)
- Christopher P. Kempes
- Exobiology Branch, National Aeronautics and Space Administration Ames Research Center, Moffett Field, CA 94035
- Control and Dynamical Systems, California Institute of Technology, Pasadena, CA 91125
- SETI Institute, Mountain View, CA 94034
- Department of Earth, Atmospheric and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, MA 02139; and
| | - Chinweike Okegbe
- Department of Biological Sciences, Columbia University, New York, NY 10027
| | | | - Michael J. Follows
- Department of Earth, Atmospheric and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, MA 02139; and
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Oxygen dynamics in the aftermath of the Great Oxidation of Earth's atmosphere. Proc Natl Acad Sci U S A 2013; 110:16736-41. [PMID: 24082125 DOI: 10.1073/pnas.1315570110] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The oxygen content of Earth's atmosphere has varied greatly through time, progressing from exceptionally low levels before about 2.3 billion years ago, to much higher levels afterward. In the absence of better information, we usually view the progress in Earth's oxygenation as a series of steps followed by periods of relative stasis. In contrast to this view, and as reported here, a dynamic evolution of Earth's oxygenation is recorded in ancient sediments from the Republic of Gabon from between about 2,150 and 2,080 million years ago. The oldest sediments in this sequence were deposited in well-oxygenated deep waters whereas the youngest were deposited in euxinic waters, which were globally extensive. These fluctuations in oxygenation were likely driven by the comings and goings of the Lomagundi carbon isotope excursion, the longest-lived positive δ(13)C excursion in Earth history, generating a huge oxygen source to the atmosphere. As the Lomagundi event waned, the oxygen source became a net oxygen sink as Lomagundi organic matter became oxidized, driving oxygen to low levels; this state may have persisted for 200 million years.
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Koschwanez JH, Foster KR, Murray AW. Improved use of a public good selects for the evolution of undifferentiated multicellularity. eLife 2013; 2:e00367. [PMID: 23577233 PMCID: PMC3614033 DOI: 10.7554/elife.00367] [Citation(s) in RCA: 87] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2012] [Accepted: 02/14/2013] [Indexed: 01/05/2023] Open
Abstract
We do not know how or why multicellularity evolved. We used the budding yeast, Saccharomyces cerevisiae, to ask whether nutrients that must be digested extracellularly select for the evolution of undifferentiated multicellularity. Because yeast use invertase to hydrolyze sucrose extracellularly and import the resulting monosaccharides, single cells cannot grow at low cell and sucrose concentrations. Three engineered strategies overcame this problem: forming multicellular clumps, importing sucrose before hydrolysis, and increasing invertase expression. We evolved populations in low sucrose to ask which strategy they would adopt. Of 12 successful clones, 11 formed multicellular clumps through incomplete cell separation, 10 increased invertase expression, none imported sucrose, and 11 increased hexose transporter expression, a strategy we had not engineered. Identifying causal mutations revealed genes and pathways, which frequently contributed to the evolved phenotype. Our study shows that combining rational design with experimental evolution can help evaluate hypotheses about evolutionary strategies. DOI:http://dx.doi.org/10.7554/eLife.00367.001 Life first appeared on Earth more than 3 billion years ago in the form of single-celled microorganisms. The diverse array of complex life forms that we see today evolved from these humble beginnings, but it is not clear what triggered the evolution of multicellular organisms from single cells. One of the simplest multicellular eukaryotes is the yeast, Saccharomyces cerevisiae—a fungus that has been used for centuries in baking and brewing and, more recently, as a model organism in molecular biology. Yeast cells feed on sugar (sucrose), but are unable to absorb it directly from their surroundings. Instead they secrete an enzyme called invertase, which breaks down the sucrose into simpler components that cells can take up with the help of sugar transporters. However, single yeast cells living in a low-sucrose environment face a problem: most of the simple sugars that they produce diffuse out of reach. To overcome this difficulty, the cells could form multicellular clumps, which would enable each cell to consume the sugars that drift away from its neighbours. Alternatively, the cells could increase their production of invertase, or they could begin to take up sucrose directly. Using genetic engineering, Koschwanez et al. produced three strains of yeast, each with one of these traits, and confirmed that all three strategies do indeed help fungi to grow in low sucrose. But could any of these traits evolve spontaneously? To test this possibility, Koschwanez et al. introduced wild-type yeast cells into a low-sucrose environment and studied any populations of cells that managed to survive. Of 12 that did, 11 had acquired the ability to form multicellular clumps, while 10 had increased their expression of invertase. Surprisingly, none had evolved the ability to import sucrose. However, 11 of the populations that survived also displayed an adaptation that the researchers had not predicted beforehand: they all expressed higher levels of the sugar transporters that take up sucrose breakdown products. The work of Koschwanez et al. suggests that the benefits of being able to share invertase and, therefore, simple sugars, may have driven the evolution of multicellularity in ancient organisms. Moreover, their use of rational design (engineered mutations) combined with experimental evolution (allowing colonies to grow under selection pressure and studying the strategies that they adopt) offers a new approach to studying evolution in the lab. DOI:http://dx.doi.org/10.7554/eLife.00367.002
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Affiliation(s)
- John H Koschwanez
- FAS Center for Systems Biology and Department of Molecular and Cellular Biology , Harvard University , Cambridge , United States
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Lepland A, Melezhik VA, Papineau D, Romashkin AE, Joosu L. 7.7 The Earliest Phosphorites: Radical Change in the Phosphorus Cycle During the Palaeoproterozoic. READING THE ARCHIVE OF EARTH’S OXYGENATION 2013. [DOI: 10.1007/978-3-642-29670-3_7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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Oviparity or viviparity? That is the question…. Reprod Biol 2012; 12:259-64. [PMID: 23153695 DOI: 10.1016/j.repbio.2012.09.001] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2011] [Accepted: 04/05/2012] [Indexed: 11/24/2022]
Abstract
The modes of reproduction undoubtedly represent one of the most critical life-history traits because they profoundly affect fitness and survival. The parent-offspring conflict over the degree of parental investment may be the main selective factor in the evolution of reproduction. Although the modes of sexual reproduction are remarkably diversified in animals, the traditional typology spanning three classes does not seem to be adequate to clarify the level of parental investment. Thus, lecithotrophy does not provide any information on the retention of the zygotes inside the parent's body and matrotrophy only indicates that nutrients are provided by mother but does not make any distinction between various types of maternal care. I here present a scientific typology of the reproductive modes comprising five classes: ovuliparity, oviparity, ovo-viviparity, histotrophic viviparity and hemotrophic viviparity. Based on the development stage of the zygote and on its interrelation with the parent, my classification details the degree of contrivances by which animals provide alternative parental investment in their offspring. Hence, this typology possesses a great heuristic value, both in reproduction and evolutionary biology. These different modes of reproduction do represent a sequence, with ovuliparity being the most primitive and hemotrophic viviparity the most advanced mode. Lastly, the comparative analysis of different reproductive modes in vertebrates suggests that climatic conditions (cold) could be one of the strongest selection pressures for extending egg retention and the establishment of viviparity.
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