Bats, Primates, and the Evolutionary Origins and Diversification of Mammalian Gammaherpesviruses

ABSTRACTGammaherpesviruses (γHVs) are generally considered host specific and to have codiverged with their hosts over millions of years. This tenet is challenged here by broad-scale phylogenetic analysis of two viral genes using the largest sample of mammalian γHVs to date, integrating for the first time bat γHV sequences available from public repositories and newly generated viral sequences from two vampire bat species (Desmodus rotundusandDiphylla ecaudata). Bat and primate viruses frequently represented deep branches within the supported phylogenies and clustered among viruses from distantly related mammalian taxa. Following evolutionary scenario testing, we determined the number of host-switching and cospeciation events. Cross-species transmissions have occurred much more frequently than previously estimated, and most of the transmissions were attributable to bats and primates. We conclude that the evolution of theGammaherpesvirinaesubfamily has been driven by both cross-species transmissions and subsequent cospeciation within specific viral lineages and that the bat and primate orders may have potentially acted as superspreaders to other mammalian taxa throughout evolutionary history.IMPORTANCEIt has long been believed that herpesviruses have coevolved with their hosts and are species specific. Nevertheless, a global evolutionary analysis of bat viruses in the context of other mammalian viruses, which could put this widely accepted view to the test, had not been undertaken until now. We present two main findings that may challenge the current view of γHV evolution: multiple host-switching events were observed at a higher rate than previously appreciated, and bats and primates harbor a large diversity of γHVs which may have led to increased cross-species transmissions from these taxa to other mammals.

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Evolution and Potential Function in Molluscs of Neuropeptide and Receptor Homologues of the Insect Allatostatins

Frontiers in Endocrinology ◽

10.3389/fendo.2021.725022 ◽

2021 ◽

Vol 12 ◽

Author(s):

Zhi Li ◽

João C. R. Cardoso ◽

Maoxiao Peng ◽

João P. S. Inácio ◽

Deborah M. Power

Keyword(s):

Immune Response ◽

Meta Analysis ◽

Evolutionary Analysis ◽

Expression Of Genes ◽

Peptide Precursors ◽

Peptide Precursor ◽

Mollusc Species ◽

Species Specific ◽

First Time ◽

G Protein Coupled

The allatostatins (ASTs), AST-A, AST-B and AST-C, have mainly been investigated in insects. They are a large group of small pleotropic alloregulatory neuropeptides that are unrelated in sequence and activate receptors of the rhodopsin G-protein coupled receptor family (GPCRs). The characteristics and functions of the homologue systems in the molluscs (Buccalin, MIP and AST-C-like), the second most diverse group of protostomes after the arthropods, and of high interest for evolutionary studies due to their less rearranged genomes remains to be explored. In the present study their evolution is deciphered in molluscs and putative functions assigned in bivalves through meta-analysis of transcriptomes and experiments. Homologues of the three arthropod AST-type peptide precursors were identified in molluscs and produce a larger number of mature peptides than in insects. The number of putative receptors were also distinct across mollusc species due to lineage and species-specific duplications. Our evolutionary analysis of the receptors identified for the first time in a mollusc, the cephalopod, GALR-like genes, which challenges the accepted paradigm that AST-AR/buccalin-Rs are the orthologues of vertebrate GALRs in protostomes. Tissue transcriptomes revealed the peptides, and their putative receptors have a widespread distribution in bivalves and in the bivalve Mytilus galloprovincialis, elements of the three peptide-receptor systems are highly abundant in the mantle an innate immune barrier tissue. Exposure of M. galloprovincialis to lipopolysaccharide or a marine pathogenic bacterium, Vibrio harveyi, provoked significant modifications in the expression of genes of the peptide precursor and receptors of the AST-C-like system in the mantle suggesting involvement in the immune response. Overall, our study reveals that homologues of the arthropod AST-systems in molluscs are potentially more complex due to the greater number of putative mature peptides and receptor genes. In bivalves they have a broad and varying tissue distribution and abundance, and the elements of the AST-C-like family may have a putative function in the immune response.

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Bark traits, decomposition and flammability of Australian forest trees

Australian Journal of Botany ◽

10.1071/bt16258 ◽

2017 ◽

Vol 65 (4) ◽

pp. 327 ◽

Cited By ~ 4

Author(s):

Saskia Grootemaat ◽

Ian J. Wright ◽

Peter M. van Bodegom ◽

Johannes H. C. Cornelissen ◽

Veronica Shaw

Keyword(s):

Forest Tree ◽

Remarkable Feature ◽

Interspecific Differences ◽

Eucalypt Plantations ◽

Physical Traits ◽

Key Driver ◽

Multiple Species ◽

Species Specific ◽

First Time ◽

Different Tissues

Bark shedding is a remarkable feature of Australian trees, yet relatively little is known about interspecific differences in bark decomposability and flammability, or what chemical or physical traits drive variation in these properties. We measured the decomposition rate and flammability (ignitibility, sustainability and combustibility) of bark from 10 common forest tree species, and quantified correlations with potentially important traits. We compared our findings to those for leaf litter, asking whether the same traits drive flammability and decomposition in different tissues, and whether process rates are correlated across tissue types. Considerable variation in bark decomposability and flammability was found both within and across species. Bark decomposed more slowly than leaves, but in both tissues lignin concentration was a key driver. Bark took longer to ignite than leaves, and had longer mass-specific flame durations. Variation in flammability parameters was driven by different traits in the different tissues. Decomposability and flammability were each unrelated, when comparing between the different tissue types. For example, species with fast-decomposing leaves did not necessarily have fast-decomposing bark. For the first time, we show how patterns of variation in decomposability and flammability of bark diverge across multiple species. By taking species-specific bark traits into consideration there is potential to make better estimates of wildfire risks and carbon loss dynamics. This can lead to better informed management decisions for Australian forests, and eucalypt plantations, worldwide.

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The Morphological and Anatomical Traits of the Leaf in Representative Vinca Species Observed on Indoor- and Outdoor-Grown Plants

Plants ◽

10.3390/plants10040622 ◽

2021 ◽

Vol 10 (4) ◽

pp. 622

Author(s):

Alexandra Ciorîță ◽

Septimiu Cassian Tripon ◽

Ioan Gabriel Mircea ◽

Dorina Podar ◽

Lucian Barbu-Tudoran ◽

...

Keyword(s):

Spongy Parenchyma ◽

Palisade And Spongy Parenchyma ◽

Chemical Composition Of Plants ◽

Ultrastructural Characteristics ◽

Species Specific ◽

Microscopy Techniques ◽

First Time ◽

Thick Layers ◽

Space Ratio ◽

Indoor And Outdoor

Morphological and anatomical traits of the Vinca leaf were examined using microscopy techniques. Outdoor Vinca minor and V. herbacea plants and greenhouse cultivated V. major and V. major var. variegata plants had interspecific variations. All Vinca species leaves are hypostomatic. However, except for V. minor leaf, few stomata were also present on the upper epidermis. V. minor leaf had the highest stomatal index and V. major had the lowest, while the distribution of trichomes on the upper epidermis was species-specific. Differentiated palisade and spongy parenchyma tissues were present in all Vinca species’ leaves. However, V. minor and V. herbacea leaves had a more organized anatomical aspect, compared to V. major and V. major var. variegata leaves. Additionally, as a novelty, the cellular to intercellular space ratio of the Vinca leaf’s mesophyll was revealed herein with the help of computational analysis. Lipid droplets of different sizes and aspects were localized in the spongy parenchyma cells. Ultrastructural characteristics of the cuticle and its epicuticular waxes were described for the first time. Moreover, thick layers of cutin seemed to be characteristic of the outdoor plants only. This could be an adaptation to the unpredictable environmental conditions, but nevertheless, it might influence the chemical composition of plants.

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AlphaFold at CASP13

Bioinformatics ◽

10.1093/bioinformatics/btz422 ◽

2019 ◽

Vol 35 (22) ◽

pp. 4862-4865 ◽

Cited By ~ 48

Author(s):

Mohammed AlQuraishi

Keyword(s):

Protein Structure ◽

Protein Sequence ◽

Structure Prediction ◽

Computational Prediction ◽

Data Bank ◽

Academic Community ◽

Physical Contact ◽

Evolutionary Analysis ◽

History Of ◽

First Time

Abstract Summary: Computational prediction of protein structure from sequence is broadly viewed as a foundational problem of biochemistry and one of the most difficult challenges in bioinformatics. Once every two years the Critical Assessment of protein Structure Prediction (CASP) experiments are held to assess the state of the art in the field in a blind fashion, by presenting predictor groups with protein sequences whose structures have been solved but have not yet been made publicly available. The first CASP was organized in 1994, and the latest, CASP13, took place last December, when for the first time the industrial laboratory DeepMind entered the competition. DeepMind's entry, AlphaFold, placed first in the Free Modeling (FM) category, which assesses methods on their ability to predict novel protein folds (the Zhang group placed first in the Template-Based Modeling (TBM) category, which assess methods on predicting proteins whose folds are related to ones already in the Protein Data Bank.) DeepMind's success generated significant public interest. Their approach builds on two ideas developed in the academic community during the preceding decade: (i) the use of co-evolutionary analysis to map residue co-variation in protein sequence to physical contact in protein structure, and (ii) the application of deep neural networks to robustly identify patterns in protein sequence and co-evolutionary couplings and convert them into contact maps. In this Letter, we contextualize the significance of DeepMind's entry within the broader history of CASP, relate AlphaFold's methodological advances to prior work, and speculate on the future of this important problem.

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Ribosome profiling in Streptococcus pneumoniae reveals the role of methylation of 23S rRNA nucleotide G748 on ribosome stalling

10.1101/2020.12.21.423859 ◽

2020 ◽

Author(s):

Tatsuma Shoji ◽

Akiko Takaya ◽

Yoko Kusuya ◽

Hiroki Takahashi ◽

Hiroto Kawashima

Keyword(s):

Streptococcus Pneumoniae ◽

Ribosome Profiling ◽

23S Rrna ◽

Ribosome Stalling ◽

70S Ribosome ◽

Exit Tunnel ◽

Species Specific ◽

Peptidyltransferase Center ◽

First Time

2.Abstract(1) BackgroundMany nucleotides in 23S rRNA are methylated post-transcriptionally by methyltransferases and cluster around the peptidyltransferase center (PTC) and the nascent peptidyl exit tunnel (NPET) located in 50S subunit of 70S ribosome. Biochemical interactions between a nascent peptide and the tunnel may stall ribosome movement and affect expression levels of the protein. However, no studies have shown a role for NPET on ribosome stalling using an NPET mutant.(2) ResultsA ribosome profiling assay in Streptococcus pneumoniae demonstrates for the first time that an NPET mutant exhibits completely different ribosome occupancy compared to wild-type. We demonstrate, using RNA footprinting, that changes in ribosome occupancy correlate with changes in ribosome stalling. Further, statistical analysis shows that short peptide sequences that cause ribosome stalling are species-specific and evolutionarily selected. NPET structure is required to realize these specie-specific ribosome stalling.(3) ConclusionsResults support the role of NPET on ribosome stalling. NPET structure is required to realize the species-specific and evolutionary conserved ribosome stalling. These findings clarify the role of NPET structure on the translation process.

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Sperm chemotaxis is driven by the slope of the chemoattractant concentration field

eLife ◽

10.7554/elife.50532 ◽

2020 ◽

Vol 9 ◽

Cited By ~ 1

Author(s):

Héctor Vicente Ramírez-Gómez ◽

Vilma Jimenez Sabinina ◽

Martín Velázquez Pérez ◽

Carmen Beltran ◽

Jorge Carneiro ◽

...

Keyword(s):

Marine Invertebrates ◽

Strongylocentrotus Purpuratus ◽

Concentration Field ◽

Stimulus Function ◽

Frequency Entrainment ◽

Sperm Chemotaxis ◽

Coupling Force ◽

Species Specific ◽

First Time ◽

Fundamental Requirement

Spermatozoa of marine invertebrates are attracted to their conspecific female gamete by diffusive molecules, called chemoattractants, released from the egg investments in a process known as chemotaxis. The information from the egg chemoattractant concentration field is decoded into intracellular Ca2+ concentration ([Ca2+]i) changes that regulate the internal motors that shape the flagellum as it beats. By studying sea urchin species-specific differences in sperm chemoattractant-receptor characteristics we show that receptor density constrains the steepness of the chemoattractant concentration gradient detectable by spermatozoa. Through analyzing different chemoattractant gradient forms, we demonstrate for the first time that Strongylocentrotus purpuratus sperm are chemotactic and this response is consistent with frequency entrainment of two coupled physiological oscillators: i) the stimulus function and ii) the [Ca2+]i changes. We demonstrate that the slope of the chemoattractant gradients provides the coupling force between both oscillators, arising as a fundamental requirement for sperm chemotaxis.

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A Three-Pool Model Dissecting Readily Releasable Pool Replenishment at the Calyx of Held

Scientific Reports ◽

10.1038/srep09517 ◽

2015 ◽

Vol 5 (1) ◽

Cited By ~ 8

Author(s):

Jun Guo ◽

Jian-long Ge ◽

Mei Hao ◽

Zhi-cheng Sun ◽

Xin-sheng Wu ◽

...

Keyword(s):

Time Course ◽

Current View ◽

Vesicle Recycling ◽

Releasable Pool ◽

Readily Releasable Pool ◽

Central Synapse ◽

Pool Model ◽

Underlying Mechanisms ◽

First Time ◽

Intense Stimulation

Abstract Although vesicle replenishment is critical in maintaining exo-endocytosis recycling, the underlying mechanisms are not well understood. Previous studies have shown that both rapid and slow endocytosis recycle into a very large recycling pool instead of within the readily releasable pool (RRP) and the time course of RRP replenishment is slowed down by more intense stimulation. This finding contradicts the calcium/calmodulin-dependence of RRP replenishment. Here we address this issue and report a three-pool model for RRP replenishment at a central synapse. Both rapid and slow endocytosis provide vesicles to a large reserve pool (RP) ~42.3 times the RRP size. When moving from the RP to the RRP, vesicles entered an intermediate pool (IP) ~2.7 times the RRP size with slow RP-IP kinetics and fast IP-RRP kinetics, which was responsible for the well-established slow and rapid components of RRP replenishment. Depletion of the IP caused the slower RRP replenishment observed after intense stimulation. These results establish, for the first time, a realistic cycling model with all parameters measured, revealing the contribution of each cycling step in synaptic transmission. The results call for modification of the current view of the vesicle recycling steps and their roles.

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The “good, the bad and the double-sword” effects of exposure to MPs and their organic additives on N2-fixing bacteria

10.1101/2020.07.21.210740 ◽

2020 ◽

Author(s):

Víctor Fernández-Juárez ◽

Xabier López-Alforja ◽

Aida Frank-Comas ◽

Pedro Echeveste ◽

Antoni Bennasar-Figueras ◽

...

Keyword(s):

Posidonia Oceanica ◽

Dioctyl Phthalate ◽

Benthic Organisms ◽

Protein Overexpression ◽

Organic Additives ◽

Physical Interactions ◽

High Concentrations ◽

Species Specific ◽

Micro Organisms ◽

First Time

AbstractThe accumulation of microplastics (MPs) pollution at depths suggests the susceptibility of benthic organisms (e.g. seagrasses and their associated macro- and micro-organisms) to the effects of these pollutants. Little is known about the direct effects of MPs and their organic additives on marine bacteria, e.g. in one of the most ecologically significant groups, the diazotrophs or N2-fixing bacteria. To fill this gap of knowledge, we exposed marine diazotrophs found in association with the endemic Mediterranean seagrass Posidonia oceanica to pure MPs which differ in physical properties (e.g. density, hydrophobicity and/or size), namely, polyethylene (PE), polypropylene (PP), polyvinyl chloride (PVC) and polystyrene (PS) and to their most abundant associated organic additives (e.g. fluoranthene, 1,2,5,6,9,10-hexabromocyclododecane [HBCD] and dioctyl-phthalate [DEHP]). Growth, protein overexpression, direct physical interactions between MPs and bacteria, phosphorus (P) acquisition mechanisms and N2-fixation rates were evaluated. Our results show species-specific responses of the autotrophic and heterotrophic N2-fixing bacteria tested and the responses were dependent on the type and concentration of MPs and additives. N2-fixing cyanobacteria were positively affected by environmental and high concentrations of MPs (e.g. PVC), as opposed to heterotrophic strains, that were only positively affected with high concentrations of ∼120 µm-size MPs (detecting the overexpression of proteins related to plastic degradation and C-transport), and negatively affected by 1 µm-size PS beads. Generally, the organic additives (e.g. fluoranthene) had a deleterious effect in both autotrophic and heterotrophic N2-fixing bacteria and the magnitude of the effect is suggested to be dependent on bacterial size. We did not find evidences that specific N2-fixation rates were significantly affected by exposure to MPs, albeit changes in bacterial abundance can affect the bulk N2-fixation rates. In summary, we reported for the first time, the beneficial (the “good”), deleterious (the “bad”) and/or both (the “double-sword”) effects of exposure to MPs and their organic additives on diazotrophs found in association with seagrasses.

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Species-specific patterns of the use of burrows of Upogebia Leach, 1814 (Decapoda: Gebiidea: Upogebiidae) by the symbiotic alpheid shrimps Stenalpheops anacanthus Miya, 1997 and Athanas japonicus Kubo, 1936 (Decapoda: Caridea: Alpheidae) as revealed by laboratory quantification

Journal of Crustacean Biology ◽

10.1093/jcbiol/ruaa095 ◽

2020 ◽

Author(s):

Yumi Henmi ◽

Gyo Itani

Keyword(s):

Evolutionary Biology ◽

Evolutionary History ◽

The Body ◽

Symbiotic Relationship ◽

Use Patterns ◽

Species Specific ◽

Burrow Use ◽

First Time ◽

The Relationship ◽

Observation Period

Abstract Many alpheid shrimps live symbiotically on the body surface or inside the bodies of other invertebrates, while others use burrows made by other animals. The burrow symbiosis of alpheid shrimps is poorly studied in the context of ecology, probably because the cryptic infaunal nature of the relationship is hard to observe. The limited knowledge of the pattern of burrow use by alpheid shrimps leaves a gap in our understanding of their evolutionary history. We described and compared the behavior of Stenalpheops anacanthus Miya, 1997 and Athanas japonicus Kubo, 1936, two alpheid species living symbiotically in the burrows of the same host, Upogebia yokoyai Makarov, 1938. We found that both alpheid species used U. yokoyai burrows in aquaria, but their burrow use patterns were quite different. The average time taken for S. anacanthus to enter the burrow for the first time was much shorter (1 min) than that of A. japonicus (13 min). Subsequently, S. anacanthus made longer use of the burrow (80% of the observation period) than A. japonicus (49%). The tail-first exit frequency, which may indicate a sudden expulsion from the burrow by the host, was more frequent in A. japonicus (25%) than in S. anacanthus (7%). Such differences could be attributed to the nature of the symbiotic relationship, obligate in S. anacanthus but facultative in A. japonicus. Because of the diversity of symbiotic lifestyles, there is considerable potential to study the ecology and evolutionary biology of burrow-symbiotic alpheids further.

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Genetic characterization of a novel picornavirus in Algerian bats: co-evolution analysis of bat-related picornaviruses

Scientific Reports ◽

10.1038/s41598-019-52209-2 ◽

2019 ◽

Vol 9 (1) ◽

Cited By ~ 1

Author(s):

Safia Zeghbib ◽

Róbert Herczeg ◽

Gábor Kemenesi ◽

Brigitta Zana ◽

Kornélia Kurucz ◽

...

Keyword(s):

Geographical Location ◽

Data Sets ◽

Evolutionary Analysis ◽

Evolutionary Patterns ◽

Host Genus ◽

Evolution Analysis ◽

Zoonotic Viruses ◽

History Of ◽

First Time

Abstract Bats are reservoirs of numerous zoonotic viruses. The Picornaviridae family comprises important pathogens which may infect both humans and animals. In this study, a bat-related picornavirus was detected from Algerian Minioptreus schreibersii bats for the first time in the country. Molecular analyses revealed the new virus originates to the Mischivirus genus. In the operational use of the acquired sequence and all available data regarding bat picornaviruses, we performed a co-evolutionary analysis of mischiviruses and their hosts, to authentically reveal evolutionary patterns within this genus. Based on this analysis, we enlarged the dataset, and examined the co-evolutionary history of all bat-related picornaviruses including their hosts, to effectively compile all possible species jumping events during their evolution. Furthermore, we explored the phylogeny association with geographical location, host-genus and host-species in both data sets.

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