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Life, Volume 10, Issue 3 (March 2020) – 12 articles

Cover Story (view full-size image): The Platanistoidea clade, as here redefined, is a toothed whale group that appeared in the late Oligocene and, nowadays, represented only by the Asian river dolphin Platanista gangetica. Here, we present new significant platanistoid material from the Chilcatay Formation (19–18 Ma, Peru). Two new genera and species, the hyper-longirostrine Ensidelphis riveroi and the squalodelphinid Furcacetus flexirostrum, are described together with new specimens of the squalodelphinid Notocetus vanbenedeni and fragmentary platanistid remains of aff. Araeodelphis . The fossils examined here further confirm the high diversity and disparity of platanistoids during the early Miocene. Morphofunctional considerations of the entire platanistoid assemblage of the Chilcatay Formation suggest high trophic partitioning of this peculiar cetacean paleocommunity. View this paper
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12 pages, 958 KiB  
Article
Low Long Terminal Repeat (LTR)-Retrotransposon Expression in Leaves of the Marine Phanerogam Posidonia Oceanica L.
by Alberto Vangelisti, Flavia Mascagni, Gabriele Usai, Lucia Natali, Tommaso Giordani and Andrea Cavallini
Life 2020, 10(3), 30; https://doi.org/10.3390/life10030030 - 24 Mar 2020
Cited by 4 | Viewed by 2324
Abstract
Seagrasses as Posidonia oceanica reproduce mostly by vegetative propagation, which can reduce genetic variability within populations. Since, in clonally propagated species, insurgence of genetic variability can be determined by the activity of transposable elements, we have estimated the activity of such repeat elements [...] Read more.
Seagrasses as Posidonia oceanica reproduce mostly by vegetative propagation, which can reduce genetic variability within populations. Since, in clonally propagated species, insurgence of genetic variability can be determined by the activity of transposable elements, we have estimated the activity of such repeat elements by measuring their expression level in the leaves of plants from a Mediterranean site, for which Illumina complementary DNA (cDNA) sequence reads (produced from RNAs isolated by leaves of plants from deep and shallow meadows) were publicly available. Firstly, we produced a collection of retrotransposon-related sequences and then mapped Illumina cDNA reads onto these sequences. With this approach, it was evident that Posidonia retrotransposons are, in general, barely expressed; only nine elements resulted transcribed at levels comparable with those of reference genes encoding tubulins and actins. Differences in transcript abundance were observed according to the superfamily and the lineage to which the retrotransposons belonged. Only small differences were observed between retrotransposon expression levels in leaves of shallow and deep Posidonia meadow stands, whereas one TAR/Tork element resulted differentially expressed in deep plants exposed to heat. It can be concluded that, in P. oceanica, the contribution of retrotransposon activity to genetic variability is reduced, although the nine specific active elements could actually produce new structural variations. Full article
(This article belongs to the Section Plant Science)
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14 pages, 1326 KiB  
Article
Diatom-Derived Polyunsaturated Aldehydes Are Unlikely to Influence the Microbiota Composition of Laboratory-Cultured Diatoms
by Chloe L. Eastabrook, Paul Whitworth, Georgina Robinson and Gary S. Caldwell
Life 2020, 10(3), 29; https://doi.org/10.3390/life10030029 - 24 Mar 2020
Cited by 3 | Viewed by 3649
Abstract
Diatom-derived oxylipins, including polyunsaturated aldehydes (PUA), are considered to have infochemical, allelochemical and bacteriostatic properties, with plausible roles as grazing deterrents and regulators of inter- and intraspecific competition. However, the extent and mechanisms of how PUA influence diatom–bacteria interactions remain unresolved. In this [...] Read more.
Diatom-derived oxylipins, including polyunsaturated aldehydes (PUA), are considered to have infochemical, allelochemical and bacteriostatic properties, with plausible roles as grazing deterrents and regulators of inter- and intraspecific competition. However, the extent and mechanisms of how PUA influence diatom–bacteria interactions remain unresolved. In this study, impacts on the diversity of the associated bacterial communities (microbiota) of two contrasting Skeletonema marinoi strains (a PUA and a non-PUA producer) were investigated under three nitrate conditions in batch culture. Further, the response of the culture microbiota was studied when spiked with PUA at ecologically relevant concentrations (86nM octadienal and 290nM heptadienal). Of the 741 identified OTUs, Proteobacteria was the most abundant phylum (62.10%), followed by Bacteroidetes (12.33%) and Firmicutes (6.11%). Escherichia/Shigella were the most abundant genera for all treatments. Similar communities were present in both spiked and non-spiked cultures suggesting they can tolerate PUA exposure at realistic concentrations. This study suggests that PUA are not major drivers of diatom–bacteria interactions in laboratory cultures. Full article
(This article belongs to the Section Microbiology)
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15 pages, 1111 KiB  
Review
Biogenic Metal Nanoparticles: A New Approach to Detect Life on Mars?
by Marta Filipa Simões, Cristiane Angélica Ottoni and André Antunes
Life 2020, 10(3), 28; https://doi.org/10.3390/life10030028 - 20 Mar 2020
Cited by 15 | Viewed by 4420
Abstract
Metal nanoparticles (MNPs) have been extensively studied. They can be produced via different methods (physical, chemical, or biogenic), but biogenic synthesis has become more relevant, mainly for being referred by many as eco-friendly and more advantageous than others. Biogenic MNPs have been largely [...] Read more.
Metal nanoparticles (MNPs) have been extensively studied. They can be produced via different methods (physical, chemical, or biogenic), but biogenic synthesis has become more relevant, mainly for being referred by many as eco-friendly and more advantageous than others. Biogenic MNPs have been largely used in a wide variety of applications, from industry, to agriculture, to health sectors, among others. Even though they are increasingly researched and used, there is still space for exploring further applications and increasing their functionality and our understanding of their synthesis process. Here, we provide an overview of MNPs and biogenic MNPs, and we analyze the potential application of their formation process to astrobiology and the detection of life on Mars and other worlds. According to current knowledge, we suggest that they can be used as potential biosignatures in extra-terrestrial samples. We present the advantages and disadvantages of this approach, suggest further research, and propose its potential use for the search for life in future space exploration. Full article
(This article belongs to the Special Issue Life on Mars)
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62 pages, 12508 KiB  
Article
Extensive Diversity and Disparity of the Early Miocene Platanistoids (Cetacea, Odontoceti) in the Southeastern Pacific (Chilcatay Formation, Peru)
by Giovanni Bianucci, Christian de Muizon, Mario Urbina and Olivier Lambert
Life 2020, 10(3), 27; https://doi.org/10.3390/life10030027 - 18 Mar 2020
Cited by 23 | Viewed by 8281
Abstract
Several aspects of the fascinating evolutionary history of toothed and baleen whales (Cetacea) are still to be clarified due to the fragmentation and discontinuity (in space and time) of the fossil record. Here we open a window on the past, describing a part [...] Read more.
Several aspects of the fascinating evolutionary history of toothed and baleen whales (Cetacea) are still to be clarified due to the fragmentation and discontinuity (in space and time) of the fossil record. Here we open a window on the past, describing a part of the extraordinary cetacean fossil assemblage deposited in a restricted interval of time (19–18 Ma) in the Chilcatay Formation (Peru). All the fossils here examined belong to the Platanistoidea clade as here redefined, a toothed whale group nowadays represented only by the Asian river dolphin Platanista gangetica. Two new genera and species, the hyper-longirostrine Ensidelphis riveroi and the squalodelphinid Furcacetus flexirostrum, are described together with new material referred to the squalodelphinid Notocetus vanbenedeni and fragmentary remains showing affinities with the platanistid Araeodelphis. Our cladistic analysis defines the new clade Platanidelphidi, sister-group to Allodelphinidae and including E. riveroi and the clade Squalodelphinidae + Platanistidae. The fossils here examined further confirm the high diversity and disparity of platanistoids during the early Miocene. Finally, morphofunctional considerations on the entire platanistoid assemblage of the Chilcatay Formation suggest a high trophic partitioning of this peculiar cetacean paleocommunity. Full article
(This article belongs to the Section Paleontology)
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14 pages, 3167 KiB  
Article
Circumnutation and Growth of Inflorescence Stems of Arabidopsis thaliana in Response to Microgravity under Different Photoperiod Conditions
by Yuanyuan Wu, Junyan Xie, Lihua Wang and Huiqiong Zheng
Life 2020, 10(3), 26; https://doi.org/10.3390/life10030026 - 18 Mar 2020
Cited by 7 | Viewed by 3826
Abstract
Circumnutation is a periodic growth movement, which is an important physiological mechanism of plants to adapt to their growth environments. Gravity and photoperiod are two key environmental factors in regulating the circumnutation of plants, but the coordination mechanism between them is still unknown. [...] Read more.
Circumnutation is a periodic growth movement, which is an important physiological mechanism of plants to adapt to their growth environments. Gravity and photoperiod are two key environmental factors in regulating the circumnutation of plants, but the coordination mechanism between them is still unknown. In this study, the circumnutation of Arabidopsis thaliana inflorescence stems was investigated on board the Chinese recoverable satellite SJ-10 and the Chinese spacelab TG-2. Plants were cultivated in a special plant culture chamber under two photoperiod conditions [a long-day (LD) light: dark cycle of 16:8 h, and a short-day (SD) light: dark cycle of 8:16 h]. The plant growth and movements were followed by two charge-coupled device (CCD) cameras. The parameter revealed a daily (24 h) modulation on both TG-2 and SJ-10, under both the LD and the SD conditions. The inhibition of circumnutation was more apparent by microgravity under the SD in comparison with that under the LD condition, suggesting the synergistic effects of the combined microgravity and photoperiod on the circumnutation in space. In addition, an infradian rhythm (ca. 21 days long) on the TG-2 was also observed. Full article
(This article belongs to the Special Issue Space Experiments for Astrobiology)
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18 pages, 1015 KiB  
Review
Spectrum of Light as a Determinant of Plant Functioning: A Historical Perspective
by Oxana S. Ptushenko, Vasily V. Ptushenko and Alexei E. Solovchenko
Life 2020, 10(3), 25; https://doi.org/10.3390/life10030025 - 17 Mar 2020
Cited by 15 | Viewed by 5047
Abstract
The significance of the spectral composition of light for growth and other physiological functions of plants moved to the focus of “plant science” soon after the discovery of photosynthesis, if not earlier. The research in this field recently intensified due to the explosive [...] Read more.
The significance of the spectral composition of light for growth and other physiological functions of plants moved to the focus of “plant science” soon after the discovery of photosynthesis, if not earlier. The research in this field recently intensified due to the explosive development of computer-controlled systems for artificial illumination and documenting photosynthetic activity. The progress is also substantiated by recent insights into the molecular mechanisms of photo-regulation of assorted physiological functions in plants mediated by photoreceptors and other pigment systems. The spectral balance of solar radiation can vary significantly, affecting the functioning and development of plants. Its effects are evident on the macroscale (e.g., in individual plants growing under the forest canopy) as well as on the meso- or microscale (e.g., mutual shading of leaf cell layers and chloroplasts). The diversity of the observable effects of light spectrum variation arises through (i) the triggering of different photoreceptors, (ii) the non-uniform efficiency of spectral components in driving photosynthesis, and (iii) a variable depth of penetration of spectral components into the leaf. We depict the effects of these factors using the spectral dependence of chloroplast photorelocation movements interlinked with the changes in light penetration into (light capture by) the leaf and the photosynthetic capacity. In this review, we unfold the history of the research on the photocontrol effects and put it in the broader context of photosynthesis efficiency and photoprotection under stress caused by a high intensity of light. Full article
(This article belongs to the Section Plant Science)
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18 pages, 1150 KiB  
Review
Is the Application of Plant Probiotic Bacterial Consortia Always Beneficial for Plants? Exploring Synergies between Rhizobial and Non-Rhizobial Bacteria and Their Effects on Agro-Economically Valuable Crops
by Esther Menéndez and Ana Paço
Life 2020, 10(3), 24; https://doi.org/10.3390/life10030024 - 12 Mar 2020
Cited by 30 | Viewed by 6518
Abstract
The overgrowth of human population and the demand for high-quality foods necessitate the search for sustainable alternatives to increase crop production. The use of biofertilizers, mostly based on plant probiotic bacteria (PPB), represents a reliable and eco-friendly solution. This heterogeneous group of bacteria [...] Read more.
The overgrowth of human population and the demand for high-quality foods necessitate the search for sustainable alternatives to increase crop production. The use of biofertilizers, mostly based on plant probiotic bacteria (PPB), represents a reliable and eco-friendly solution. This heterogeneous group of bacteria possesses many features with positive effects on plants; however, how these bacteria with each other and with the environment when released into a field has still barely been studied. In this review, we focused on the diversity of root endophytic rhizobial and non-rhizobial bacteria existing within plant root tissues, and also on their potential applications as consortia exerting benefits for plants and the environment. We demonstrated the benefits of using bacterial inoculant consortia instead of single-strain inoculants. We then critically discussed several considerations that farmers, companies, governments, and the scientific community should take into account when a biofertilizer based on those PPBs is proposed, including (i) a proper taxonomic identification, (ii) the characterization of the beneficial features of PPB strains, and (iii) the ecological impacts on plants, environment, and plant/soil microbiomes. Overall, the success of a PPB consortium depends on many factors that must be considered and analyzed before its application as a biofertilizer in an agricultural system. Full article
(This article belongs to the Section Microbiology)
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13 pages, 1479 KiB  
Article
The Effects of Salts and Osmoprotectants on Enzyme Activities of Fructose-1,6-biphosphate Aldolases in a Halotolerant Cyanobacterium, Halothece sp. PCC 7418
by Siripat Ngoennet, Masaki Honda, Tanutcha Patipong, Takashi Hibino, Rungaroon Waditee-Sirisattha and Hakuto Kageyama
Life 2020, 10(3), 23; https://doi.org/10.3390/life10030023 - 09 Mar 2020
Cited by 5 | Viewed by 2813
Abstract
The halotolerant cyanobacterium, Halothece sp. PCC 7418, possesses two classes of fructose-1,6-bisphosphate aldolase (FBA): H2846 and H2847. Though class I (CI)-FBA H2846 is thought to be associated with salt tolerance, the regulatory mechanisms, molecular characteristics, and expression profiles between H2846 and class II [...] Read more.
The halotolerant cyanobacterium, Halothece sp. PCC 7418, possesses two classes of fructose-1,6-bisphosphate aldolase (FBA): H2846 and H2847. Though class I (CI)-FBA H2846 is thought to be associated with salt tolerance, the regulatory mechanisms, molecular characteristics, and expression profiles between H2846 and class II (CII)-FBA H2847 have scarcely been investigated. Here, we show that the accumulation of the H2846 protein is highly responsive to both up- and down-shock with NaCl, whereas H2847 is constitutively expressed. The activity of CI- and CII-FBA in cyanobacterial extracts is correlated with the accumulation patterns of H2846 and H2847, respectively. In addition, it was found that these activities were inhibited by NaCl and KCl, with CII-FBA activity strikingly inhibited. It was also found that the CI-FBA activity of recombinant H2846 was hindered by salts and that this hindrance could be moderated by the addition of glycine betaine (GB), whereas no moderation occurred with other potential osmoprotectant molecules (proline, sucrose, and glycerol). In addition, a phylogenetic analysis showed that CI-FBAs with higher similarities to H2846 tended to be distributed among potential GB-synthesizing cyanobacteria. Taken together, our results provide insights into the independent evolution of the CI- and CII-FBA gene families, which show distinct expression profiles and functions following salt stress. Full article
(This article belongs to the Section Microbiology)
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20 pages, 2595 KiB  
Article
Evolving Always-Critical Networks
by Marco Villani, Salvatore Magrì, Andrea Roli and Roberto Serra
Life 2020, 10(3), 22; https://doi.org/10.3390/life10030022 - 04 Mar 2020
Cited by 2 | Viewed by 2957
Abstract
Living beings share several common features at the molecular level, but there are very few large-scale “operating principles” which hold for all (or almost all) organisms. However, biology is subject to a deluge of data, and as such, general concepts such as this [...] Read more.
Living beings share several common features at the molecular level, but there are very few large-scale “operating principles” which hold for all (or almost all) organisms. However, biology is subject to a deluge of data, and as such, general concepts such as this would be extremely valuable. One interesting candidate is the “criticality” principle, which claims that biological evolution favors those dynamical regimes that are intermediaries between ordered and disordered states (i.e., “at the edge of chaos”). The reasons why this should be the case and experimental evidence are briefly discussed, observing that gene regulatory networks are indeed often found on, or close to, the critical boundaries. Therefore, assuming that criticality provides an edge, it is important to ascertain whether systems that are critical can further evolve while remaining critical. In order to explore the possibility of achieving such “always-critical” evolution, we resort to simulated evolution, by suitably modifying a genetic algorithm in such a way that the newly-generated individuals are constrained to be critical. It is then shown that these modified genetic algorithms can actually develop critical gene regulatory networks with two interesting (and quite different) features of biological significance, involving, in one case, the average gene activation values and, in the other case, the response to perturbations. These two cases suggest that it is often possible to evolve networks with interesting properties without losing the advantages of criticality. The evolved networks also show some interesting features which are discussed. Full article
(This article belongs to the Section Synthetic Biology and Systems Biology)
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22 pages, 2915 KiB  
Review
Evolution of Life on Earth: tRNA, Aminoacyl-tRNA Synthetases and the Genetic Code
by Lei Lei and Zachary F Burton
Life 2020, 10(3), 21; https://doi.org/10.3390/life10030021 - 02 Mar 2020
Cited by 25 | Viewed by 9093
Abstract
Life on Earth and the genetic code evolved around tRNA and the tRNA anticodon. We posit that the genetic code initially evolved to synthesize polyglycine as a cross-linking agent to stabilize protocells. We posit that the initial amino acids to enter the code [...] Read more.
Life on Earth and the genetic code evolved around tRNA and the tRNA anticodon. We posit that the genetic code initially evolved to synthesize polyglycine as a cross-linking agent to stabilize protocells. We posit that the initial amino acids to enter the code occupied larger sectors of the code that were then invaded by incoming amino acids. Displacements of amino acids follow selection rules. The code sectored from a glycine code to a four amino acid code to an eight amino acid code to an ~16 amino acid code to the standard 20 amino acid code with stops. The proposed patterns of code sectoring are now most apparent from patterns of aminoacyl-tRNA synthetase evolution. The Elongation Factor-Tu GTPase anticodon-codon latch that checks the accuracy of translation appears to have evolved at about the eight amino acid to ~16 amino acid stage. Before evolution of the EF-Tu latch, we posit that both the 1st and 3rd anticodon positions were wobble positions. The genetic code evolved via tRNA charging errors and via enzymatic modifications of amino acids joined to tRNAs, followed by tRNA and aminoacyl-tRNA synthetase differentiation. Fidelity mechanisms froze the code by inhibiting further innovation. Full article
(This article belongs to the Section Origin of Life)
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23 pages, 1795 KiB  
Perspective
The Future of Origin of Life Research: Bridging Decades-Old Divisions
by Martina Preiner, Silke Asche, Sidney Becker, Holly C. Betts, Adrien Boniface, Eloi Camprubi, Kuhan Chandru, Valentina Erastova, Sriram G. Garg, Nozair Khawaja, Gladys Kostyrka, Rainer Machné, Giacomo Moggioli, Kamila B. Muchowska, Sinje Neukirchen, Benedikt Peter, Edith Pichlhöfer, Ádám Radványi, Daniele Rossetto, Annalena Salditt, Nicolas M. Schmelling, Filipa L. Sousa, Fernando D. K. Tria, Dániel Vörös and Joana C. Xavieradd Show full author list remove Hide full author list
Life 2020, 10(3), 20; https://doi.org/10.3390/life10030020 - 26 Feb 2020
Cited by 54 | Viewed by 22612
Abstract
Research on the origin of life is highly heterogeneous. After a peculiar historical development, it still includes strongly opposed views which potentially hinder progress. In the 1st Interdisciplinary Origin of Life Meeting, early-career researchers gathered to explore the commonalities between theories and approaches, [...] Read more.
Research on the origin of life is highly heterogeneous. After a peculiar historical development, it still includes strongly opposed views which potentially hinder progress. In the 1st Interdisciplinary Origin of Life Meeting, early-career researchers gathered to explore the commonalities between theories and approaches, critical divergence points, and expectations for the future. We find that even though classical approaches and theories—e.g., bottom-up and top-down, RNA world vs. metabolism-first—have been prevalent in origin of life research, they are ceasing to be mutually exclusive and they can and should feed integrating approaches. Here we focus on pressing questions and recent developments that bridge the classical disciplines and approaches, and highlight expectations for future endeavours in origin of life research. Full article
(This article belongs to the Section Origin of Life)
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23 pages, 1116 KiB  
Review
A Comprehensive Review of the Nutraceutical and Therapeutic Applications of Red Seaweeds (Rhodophyta)
by João Cotas, Adriana Leandro, Diana Pacheco, Ana M. M. Gonçalves and Leonel Pereira
Life 2020, 10(3), 19; https://doi.org/10.3390/life10030019 - 26 Feb 2020
Cited by 114 | Viewed by 11065
Abstract
The red seaweed group (Rhodophyta) is one of the phyla of macroalgae, among the groups Phaeophyceae and Chlorophyta, brown and green seaweeds, respectively. Nowadays, all groups of macroalgae are getting the attention of the scientific community due to the bioactive substances they produce. [...] Read more.
The red seaweed group (Rhodophyta) is one of the phyla of macroalgae, among the groups Phaeophyceae and Chlorophyta, brown and green seaweeds, respectively. Nowadays, all groups of macroalgae are getting the attention of the scientific community due to the bioactive substances they produce. Several macroalgae products have exceptional properties with nutraceutical, pharmacological, and biomedical interest. The main compounds studied are the fatty acids, pigments, phenols, and polysaccharides. Polysaccharides are the most exploited molecules, which are already widely used in various industries and are, presently, entering into more advanced applications from the therapeutic point of view. The focuses of this review are the red seaweeds’ compounds, its proprieties, and its uses. Moreover, this work discusses new possible applications of the compounds of the red seaweeds. Full article
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