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1.
Nature ; 574(7779): 527-531, 2019 10.
Artigo em Inglês | MEDLINE | ID: mdl-31645719

RESUMO

The known diversity of tetrapods of the Devonian period has increased markedly in recent decades, but their fossil record consists mostly of tantalizing fragments1-15. The framework for interpreting the morphology and palaeobiology of Devonian tetrapods is dominated by the near complete fossils of Ichthyostega and Acanthostega; the less complete, but partly reconstructable, Ventastega and Tulerpeton have supporting roles2,4,16-34. All four of these genera date to the late Famennian age (about 365-359 million years ago)-they are 10 million years younger than the earliest known tetrapod fragments5,10, and nearly 30 million years younger than the oldest known tetrapod footprints35. Here we describe Parmastega aelidae gen. et sp. nov., a tetrapod from Russia dated to the earliest Famennian age (about 372 million years ago), represented by three-dimensional material that enables the reconstruction of the skull and shoulder girdle. The raised orbits, lateral line canals and weakly ossified postcranial skeleton of P. aelidae suggest a largely aquatic, surface-cruising animal. In Bayesian and parsimony-based phylogenetic analyses, the majority of trees place Parmastega as a sister group to all other tetrapods.


Assuntos
Fósseis , Filogenia , Vertebrados/anatomia & histologia , Animais , Teorema de Bayes , Palato/anatomia & histologia , Federação Russa , Crânio/anatomia & histologia , Vertebrados/classificação
2.
Rinsho Ketsueki ; 60(9): 1063-1069, 2019.
Artigo em Japonês | MEDLINE | ID: mdl-31597828

RESUMO

In modern hematology, research on hematopoiesis and blood cells in vertebrates, such as birds, reptiles, amphibians, and fish, is lagging. This is because there are many experimental constraints when selecting subjects other than humans and mice as research subjects. Currently, the availability of flow cytometry to count classified nucleated blood cells and utilization of whole genome information have led to novel findings. For example, in case of amphibian hematopoiesis studies, megakaryocytes have been found to be present in African clawed frogs (Xenopus laevis), which do not have platelets but have circulating nucleated thrombocytes. Moreover, we shed light on several mysteries, such as the C-terminal region in human TPO molecules not being found in birds, amphibians, and fish TPO molecules and the functional universalities of mutant CALR-MPL binding and EPO-EphB4 binding, in conjunction with comparative hematology.


Assuntos
Hematologia , Megacariócitos/citologia , Trombopoese , Vertebrados , Animais , Plaquetas , Genoma , Histologia Comparada , Humanos , Camundongos
3.
Nat Ecol Evol ; 3(8): 1233-1240, 2019 08.
Artigo em Inglês | MEDLINE | ID: mdl-31263232

RESUMO

The evolution of vertebrates from an ancestral chordate was accompanied by the acquisition of a predatory lifestyle closely associated to the origin of a novel anterior structure, the highly specialized head. While the vertebrate head mesoderm is unsegmented, the paraxial mesoderm of the earliest divergent chordate clade, the cephalochordates (amphioxus), is fully segmented in somites. We have previously shown that fibroblast growth factor signalling controls the formation of the most anterior somites in amphioxus; therefore, unravelling the fibroblast growth factor signalling downstream effectors is of crucial importance to shed light on the evolutionary origin of vertebrate head muscles. By using a comparative RNA sequencing approach and genetic functional analyses, we show that several transcription factors, such as Six1/2, Pax3/7 and Zic, act in combination to ensure the formation of three different somite populations. Interestingly, these proteins are orthologous to key regulators of trunk, and not head, muscle formation in vertebrates. Contrary to prevailing thinking, our results suggest that the vertebrate head mesoderm is of visceral and not paraxial origin and support a multistep evolutionary scenario for the appearance of the unsegmented mesoderm of the vertebrates new 'head'.


Assuntos
Anfioxos , Animais , Regulação da Expressão Gênica no Desenvolvimento , Mesoderma , Somitos , Vertebrados
5.
Nature ; 571(7765): 333-334, 2019 07.
Artigo em Inglês | MEDLINE | ID: mdl-31308528
6.
BMC Evol Biol ; 19(1): 143, 2019 07 12.
Artigo em Inglês | MEDLINE | ID: mdl-31299890

RESUMO

BACKGROUND: Our laboratory identified ADGRL4/ELTD1, an orphan GPCR belonging to the adhesion GPCR (aGPCR) family, as a novel regulator of angiogenesis and a potential anti-cancer therapeutic target. Little is known about how ADGRL4/ELTD1 (and aGPCRs in general) function, a problem compounded by a lack of known ligands or means of activation. With this in mind, we turned to computational evolutionary biology with the aim of better understanding ADGRL4/ELTD1. RESULTS: We identified ADGRL4/ELTD1 as a highly conserved early angiogenic gene which emerged in the first true vertebrates (bony fish) approximately 435 million years ago (mya), evolving alongside key angiogenic genes VEGFR2 and DLL4. We identified 3 evolutionary ADGRL4/ELTD1 variants based on EGF domain deletions with variant 2 first emerging 101 mya (95% CI 96-105) in Afrotheria and 82 mya (95% CI 76-89) in Primates. Additionally, conservation mapping across all orthologues reveals highest level conservation in EGF Ca binding domain 1, suggesting that this motif plays an essential role, as well as specific regions of the GAIN domain, GPS motif and 7TM domain, suggesting possible activation mechanisms and ligand binding positions. Additionally, we found that ADGRL4/ELTD1 (a member aGPCR family 1) is possibly ancestral to members of aGPCR family 2. CONCLUSION: This work establishes ADGRL4/ELTD1's evolution, sheds light on its possible activation and ligand binding zones, and establishes the first temporal references for the emergence of ADGRL4/ELTD1 variants during vertebrate evolution. Our approach is applicable to the greater aGPCR family and opens up new avenues for future experimental work.


Assuntos
Sequência Conservada , Evolução Molecular , Neovascularização Fisiológica , Receptores Acoplados a Proteínas-G/genética , Vertebrados/genética , Animais , Adesão Celular , Sistemas de Liberação de Medicamentos , Peixes/genética , Humanos , Neovascularização Fisiológica/genética , Filogenia , Domínios Proteicos , Receptores Acoplados a Proteínas-G/química , Deleção de Sequência , Fatores de Tempo
7.
BMC Evol Biol ; 19(1): 144, 2019 07 16.
Artigo em Inglês | MEDLINE | ID: mdl-31311498

RESUMO

BACKGROUND: Rapid accumulation of vertebrate genome sequences render comparative genomics a powerful approach to study macro-evolutionary events. The assessment of phylogenic relationships between species routinely depends on the analysis of sequence homology at the nucleotide or protein level. RESULTS: We analyzed mRNA GC content, codon usage and divergence of orthologous proteins in 55 vertebrate genomes. Data were visualized in genome-wide landscapes using a sliding window approach. Landscapes of GC content reveal both evolutionary conservation of clustered genes, and lineage-specific changes, so that it was possible to construct a phylogenetic tree that closely matched the classic "tree of life". Landscapes of GC content also strongly correlated to landscapes of amino acid usage: positive correlation with glycine, alanine, arginine and proline and negative correlation with phenylalanine, tyrosine, methionine, isoleucine, asparagine and lysine. Peaks of GC content correlated strongly with increased protein divergence. CONCLUSIONS: Landscapes of base- and amino acid composition of the coding genome opens a new approach in comparative genomics, allowing identification of discrete regions in which protein evolution accelerated over deep evolutionary time. Insight in the evolution of genome structure may spur novel studies assessing the evolutionary benefit of genes in particular genomic regions.


Assuntos
Composição de Bases/genética , Evolução Molecular , Exoma/genética , Proteínas/genética , Vertebrados/genética , Animais , Códon/genética , Genoma , Humanos , Mamíferos/genética , Filogenia , RNA Mensageiro/genética , RNA Mensageiro/metabolismo , Répteis/genética
8.
Zebrafish ; 16(5): 469-476, 2019 10.
Artigo em Inglês | MEDLINE | ID: mdl-31295059

RESUMO

To adequately connect zebrafish medical models to human biology, it is essential that gene nomenclature reflects gene orthology. Analysis of gene phylogenies and conserved syntenies shows that the zebrafish gene currently called wnt11 (ENSDARG00000004256, ZFIN ID: ZDB-GENE-990603-12) is not the ortholog of the human gene called WNT11 (ENSG00000085741); instead, the gene currently called wnt11r (ENSDARG00000014796, ZFIN ID: ZDB-GENE-980526-249) is the zebrafish ortholog of human WNT11. Genomic analysis of Wnt11-family genes suggests a model for the birth of Wnt11-family gene ohnologs in genome duplication events, provides a mechanism for the death of a Wnt11-family ohnolog in mammals after they diverged from birds, and suggests revised nomenclature to better connect teleost disease models to human biology.


Assuntos
Evolução Biológica , Vertebrados/metabolismo , Proteínas Wnt/metabolismo , Animais , Genoma , Humanos , Família Multigênica/genética , Sintenia , Terminologia como Assunto , Vertebrados/genética , Proteínas Wnt/classificação , Proteínas Wnt/genética
9.
BMC Evol Biol ; 19(1): 117, 2019 06 10.
Artigo em Inglês | MEDLINE | ID: mdl-31182024

RESUMO

BACKGROUND: The branchiostegal series consists of an alignment of bony elements in the posterior portion of the skull of osteichthyan vertebrates. We trace the evolution of the number of elements in a comprehensive survey that includes 440 extant and 66 extinct species. Using a newly updated actinopterygian tree in combination with phylogenetic comparative analyses, we test whether osteichthyan branchiostegals follow an evolutionary trend under 'Williston's law', which postulates that osteichthyan lineages experienced a reduction of bony elements over time. RESULTS: We detected no overall macroevolutionary trend in branchiostegal numbers, providing no support for 'Williston's law'. This result is robust to the subsampling of palaeontological data, but the estimation of the model parameters is much more ambiguous. CONCLUSIONS: We find substantial evidence for a macroevolutionary dynamic favouring an 'early burst' of trait evolution over alternative models. Our study highlights the challenges of accurately reconstructing macroevolutionary dynamics even with large amounts of data about extant and extinct taxa.


Assuntos
Evolução Biológica , Extinção Biológica , Fósseis , Vertebrados/anatomia & histologia , Animais , Biodiversidade , Modelos Teóricos , Filogenia , Tamanho da Amostra , Crânio/anatomia & histologia , Fatores de Tempo
10.
Malar J ; 18(1): 187, 2019 May 30.
Artigo em Inglês | MEDLINE | ID: mdl-31146762

RESUMO

BACKGROUND: The propensity of different Anopheles mosquitoes to bite humans instead of other vertebrates influences their capacity to transmit pathogens to humans. Unfortunately, determining proportions of mosquitoes that have fed on humans, i.e. Human Blood Index (HBI), currently requires expensive and time-consuming laboratory procedures involving enzyme-linked immunosorbent assays (ELISA) or polymerase chain reactions (PCR). Here, mid-infrared (MIR) spectroscopy and supervised machine learning are used to accurately distinguish between vertebrate blood meals in guts of malaria mosquitoes, without any molecular techniques. METHODS: Laboratory-reared Anopheles arabiensis females were fed on humans, chickens, goats or bovines, then held for 6 to 8 h, after which they were killed and preserved in silica. The sample size was 2000 mosquitoes (500 per host species). Five individuals of each host species were enrolled to ensure genotype variability, and 100 mosquitoes fed on each. Dried mosquito abdomens were individually scanned using attenuated total reflection-Fourier transform infrared (ATR-FTIR) spectrometer to obtain high-resolution MIR spectra (4000 cm-1 to 400 cm-1). The spectral data were cleaned to compensate atmospheric water and CO2 interference bands using Bruker-OPUS software, then transferred to Python™ for supervised machine-learning to predict host species. Seven classification algorithms were trained using 90% of the spectra through several combinations of 75-25% data splits. The best performing model was used to predict identities of the remaining 10% validation spectra, which had not been used for model training or testing. RESULTS: The logistic regression (LR) model achieved the highest accuracy, correctly predicting true vertebrate blood meal sources with overall accuracy of 98.4%. The model correctly identified 96% goat blood meals, 97% of bovine blood meals, 100% of chicken blood meals and 100% of human blood meals. Three percent of bovine blood meals were misclassified as goat, and 2% of goat blood meals misclassified as human. CONCLUSION: Mid-infrared spectroscopy coupled with supervised machine learning can accurately identify multiple vertebrate blood meals in malaria vectors, thus potentially enabling rapid assessment of mosquito blood-feeding histories and vectorial capacities. The technique is cost-effective, fast, simple, and requires no reagents other than desiccants. However, scaling it up will require field validation of the findings and boosting relevant technical capacity in affected countries.


Assuntos
Anopheles/fisiologia , Mosquitos Vetores/fisiologia , Espectrofotometria Infravermelho , Aprendizado de Máquina Supervisionado , Vertebrados/sangue , Animais , Sangue , Galinhas/sangue , Comportamento Alimentar , Feminino , Cabras/sangue , Especificidade de Hospedeiro , Humanos , Modelos Logísticos , Malária/sangue
11.
Parasit Vectors ; 12(1): 328, 2019 Jun 28.
Artigo em Inglês | MEDLINE | ID: mdl-31253201

RESUMO

BACKGROUND: Anaplasma phagocytophilum is currently regarded as a single species. However, molecular studies indicate that it can be subdivided into ecotypes, each with distinct but overlapping transmission cycle. Here, we evaluate the interactions between and within clusters of haplotypes of the bacterium isolated from vertebrates and ticks, using phylogenetic and network-based methods. METHODS: The presence of A. phagocytophilum DNA was determined in ticks and vertebrate tissue samples. A fragment of the groEl gene was amplified and sequenced from qPCR-positive lysates. Additional groEl sequences from ticks and vertebrate reservoirs were obtained from GenBank and through literature searches, resulting in a dataset consisting of 1623 A. phagocytophilum field isolates. Phylogenetic analyses were used to infer clusters of haplotypes and to assess phylogenetic clustering of A. phagocytophilum in vertebrates or ticks. Network-based methods were used to resolve host-vector interactions and their relative importance in the segregating communities of haplotypes. RESULTS: Phylogenetic analyses resulted in 199 haplotypes within eight network-derived clusters, which were allocated to four ecotypes. The interactions of haplotypes between ticks, vertebrates and geographical origin, were visualized and quantified from networks. A high number of haplotypes were recorded in the tick Ixodes ricinus. Communities of A. phagocytophilum recorded from Korea, Japan, Far Eastern Russia, as well as those associated with rodents had no links with the larger set of isolates associated with I. ricinus, suggesting different evolutionary pressures. Rodents appeared to have a range of haplotypes associated with either Ixodes trianguliceps or Ixodes persulcatus and Ixodes pavlovskyi. Haplotypes found in rodents in Russia had low similarities with those recorded in rodents in other regions and shaped separate communities. CONCLUSIONS: The groEl gene fragment of A. phagocytophilum provides information about spatial segregation and associations of haplotypes to particular vector-host interactions. Further research is needed to understand the circulation of this bacterium in the gap between Europe and Asia before the overview of the speciation features of this bacterium is complete. Environmental traits may also play a role in the evolution of A. phagocytophilum in ecotypes through yet unknown relationships.


Assuntos
Anaplasma phagocytophilum/genética , Biota , Evolução Molecular , Filogenia , Anaplasma phagocytophilum/isolamento & purificação , Animais , Ásia , Chaperonina 60/genética , Ecótipo , Europa (Continente) , Geografia , Haplótipos , Ixodes/microbiologia , Vertebrados/microbiologia
12.
BMC Evol Biol ; 19(1): 126, 2019 06 18.
Artigo em Inglês | MEDLINE | ID: mdl-31215418

RESUMO

BACKGROUND: L-ascorbate (Vitamin C) is an important antioxidant and co-factor in eukaryotic cells, and in mammals it is indispensable for brain development and cognitive function. Vertebrates usually become L-ascorbate auxothrophs when the last enzyme of the synthetic pathway, an L-gulonolactone oxidase (GULO), is lost. Since Protostomes were until recently thought not to have a GULO gene, they were considered to be auxothrophs for Vitamin C. RESULTS: By performing phylogenetic analyses with tens of non-Bilateria and Protostomian genomes, it is shown, that a GULO gene is present in the non-Bilateria Placozoa, Myxozoa (here reported for the first time) and Anthozoa groups, and in Protostomians, in the Araneae family, the Gastropoda class, the Acari subclass (here reported for the first time), and the Priapulida, Annelida (here reported for the first time) and Brachiopoda phyla lineages. GULO is an old gene that predates the separation of Animals and Fungi, although it could be much older. We also show that within Protostomes, GULO has been lost multiple times in large taxonomic groups, namely the Pancrustacea, Nematoda, Platyhelminthes and Bivalvia groups, a pattern similar to that reported for Vertebrate species. Nevertheless, we show that Drosophila melanogaster seems to be capable of synthesizing L-ascorbate, likely through an alternative pathway, as recently reported for Caenorhabditis elegans. CONCLUSIONS: Non-Bilaterian and Protostomians seem to be able to synthesize Vitamin C either through the conventional animal pathway or an alternative pathway, but in this animal group, not being able to synthesize L-ascorbate seems to be the exception rather than the rule.


Assuntos
Ácido Ascórbico/metabolismo , Eucariotos/enzimologia , Eucariotos/genética , Evolução Molecular , L-Gulonolactona Oxidase/genética , Animais , Drosophila melanogaster/genética , Eucariotos/classificação , Eucariotos/metabolismo , Genoma , L-Gulonolactona Oxidase/química , L-Gulonolactona Oxidase/metabolismo , Modelos Moleculares , Filogenia , Vertebrados/classificação , Vertebrados/genética
13.
BMC Evol Biol ; 19(1): 128, 2019 06 20.
Artigo em Inglês | MEDLINE | ID: mdl-31221090

RESUMO

BACKGROUND: The hypothesis that vertebrates have experienced two ancient, whole genome duplications (WGDs) is of central interest to evolutionary biology and has been implicated in evolution of developmental complexity. Three-way and Four-way paralogy regions in human and other vertebrate genomes are considered as vital evidence to support this hypothesis. Alternatively, it has been proposed that such paralogy regions are created by small-scale duplications that occurred at different intervals over the evolution of life. RESULTS: To address this debate, the present study investigates the evolutionary history of multigene families with at least three-fold representation on human chromosomes 1, 2, 8 and 20. Phylogenetic analysis and the tree topology comparisons classified the members of 36 multigene families into four distinct co-duplicated groups. Gene families falling within the same co-duplicated group might have duplicated together, whereas genes belong to different co-duplicated groups might have distinct evolutionary origins. CONCLUSION: Taken together with previous investigations, the current study yielded no proof in favor of WGDs hypothesis. Rather, it appears that the vertebrate genome evolved as a result of small-scale duplication events, that cover the entire span of the animals' history.


Assuntos
Evolução Molecular , Duplicação Gênica , Família Multigênica , Vertebrados/genética , Animais , Cromossomos Humanos , Genoma Humano , Humanos , Invertebrados/classificação , Invertebrados/genética , Filogenia , Vertebrados/classificação
14.
J Environ Radioact ; 207: 7-14, 2019 Oct.
Artigo em Inglês | MEDLINE | ID: mdl-31151051

RESUMO

Preliminary values of whole organism concentration ratio (CRwo-soil) were derived for terrestrial vertebrates of an Australian tropical savanna environment. Wildlife groups included bird, bat, ground-dwelling mammal and reptile. Sample data for some of the wildlife groups (bird and bat in particular) were limited. The bird and bat CRwo-soil values were generally lower than the ground-dwelling mammal and reptile CRwo-soil values based on the available data. Arithmetic mean CRwo-soil values for two species of native marsupial and two species of non-native placental were not significantly different (p < 0.05) when tested using a one-way analysis of variance. The results hinted at possible sampling efficiencies for terrestrial vertebrates. However, verification with additional data was recommended. Used cautiously, the CRwo-soil values may assist in environmental assessments of Australian uranium mining sites. They also enhance the available data on radionuclide transfer to wildlife for use internationally.


Assuntos
Monitoramento Ambiental , Poluentes Ambientais/metabolismo , Metais/metabolismo , Radioisótopos/metabolismo , Vertebrados/metabolismo , Animais , Austrália , Pradaria
15.
Dokl Biol Sci ; 485(1): 40-43, 2019 Mar.
Artigo em Inglês | MEDLINE | ID: mdl-31197592

RESUMO

We describe a vertebrate assemblage from the Pleistocene deposits of the Taurida karst cave discovered in 2018 in central Crimea (Zuya village, Belogorsk raion). The assemblage is correlated with Late Villafranchian faunas of the Eastern Mediterranean and has an approximate age of 1.8-1.5 Ma.


Assuntos
Biodiversidade , Cavernas , Fósseis/anatomia & histologia , Vertebrados/classificação , Animais , Dente/anatomia & histologia , Vertebrados/anatomia & histologia
16.
Nucleic Acids Res ; 47(14): 7306-7320, 2019 08 22.
Artigo em Inglês | MEDLINE | ID: mdl-31165881

RESUMO

Double-stranded DNAs are usually present in the form of linear B-form double-helix with the base pairs of adenine (A) and thymine (T) or cytosine (C) and guanine (G), but G-rich DNA can form four-stranded G-quadruplex (G4) structures, which plays important roles in transcription, replication, translation and protection of telomeres. In this study, a RNA recognition motif (RRM)-containing protein, BmLARK, was identified and demonstrated to bind G4 structures in the promoters of a transcription factor BmPOUM2 and other three unidentified genes of Bombyx mori, as well as three well-defined G4 structures in the human genes. Homologous LARKs from Bombyx mori, Drosophila melanogaster, Mus musculus and Homo sapiens bound G4 structures in BmPOUM2 and other genes in B. mori and H. sapiens. Upon binding, LARK facilitated the formation and stability of the G4 structure, enhancing the transcription of target genes. The G4 structure was visualized in vivo in cells and testis from invertebrate B. mori and vertebrate Chinese hamster ovary (CHO) cells. The results of this study strongly suggest that LARK is a novel and conserved G4-binding protein and that the G4 structure may have developed into an elaborate epigenetic mechanism of gene transcription regulation during evolution.


Assuntos
Proteínas de Transporte/metabolismo , DNA/metabolismo , Proteínas de Drosophila/metabolismo , Quadruplex G , Proteínas de Insetos/metabolismo , Proteínas de Ligação a RNA/metabolismo , Animais , Bombyx/citologia , Bombyx/genética , Bombyx/metabolismo , Células CHO , Proteínas de Transporte/genética , Linhagem Celular , Cricetinae , Cricetulus , DNA/genética , Proteínas de Drosophila/genética , Drosophila melanogaster/genética , Drosophila melanogaster/metabolismo , Evolução Molecular , Regulação da Expressão Gênica , Humanos , Proteínas de Insetos/genética , Invertebrados/genética , Invertebrados/metabolismo , Camundongos , Proteínas de Ligação a RNA/genética , Vertebrados/genética , Vertebrados/metabolismo
17.
Nat Commun ; 10(1): 2200, 2019 05 16.
Artigo em Inglês | MEDLINE | ID: mdl-31097702

RESUMO

Multiple factors modulate microbial community assembly in the vertebrate gut, though studies disagree as to their relative contribution. One cause may be a reliance on captive animals, which can have very different gut microbiomes compared to their wild counterparts. To resolve this disagreement, we analyze a new, large, and highly diverse animal distal gut 16 S rRNA microbiome dataset, which comprises 80% wild animals and includes members of Mammalia, Aves, Reptilia, Amphibia, and Actinopterygii. We decouple the effects of host evolutionary history and diet on gut microbiome diversity and show that each factor modulates different aspects of diversity. Moreover, we resolve particular microbial taxa associated with host phylogeny or diet and show that Mammalia have a stronger signal of cophylogeny. Finally, we find that environmental filtering and microbe-microbe interactions differ among host clades. These findings provide a robust assessment of the processes driving microbial community assembly in the vertebrate intestine.


Assuntos
Biodiversidade , Evolução Biológica , Comportamento Alimentar/fisiologia , Microbioma Gastrointestinal/genética , Vertebrados/microbiologia , Animais , Conjuntos de Dados como Assunto , Interações entre Hospedeiro e Microrganismos/fisiologia , Filogenia , RNA Ribossômico 16S/genética , RNA Ribossômico 16S/isolamento & purificação , Vertebrados/fisiologia
18.
Arch Virol ; 164(8): 2147-2151, 2019 Aug.
Artigo em Inglês | MEDLINE | ID: mdl-31111261

RESUMO

Posaviruses and posa-like viruses are unclassified viruses with sequence similarity to viruses of the order Picornavirales. They have been reported in various vertebrates and invertebrates. We identified 11 posavirus-like sequences in porcine feces and performed phylogenic analysis. Previously reported Japanese posaviruses and those identified in this study clustered with posavirus 1, 4, and 7 and husavirus 1, while five viruses branched into three independent lineages, tentatively named posavirus 10, 11, and 12. Interestingly, posaviruses, except for posavirus 8 and 9, husaviruses, and rasaviruses, formed a cluster consisting of viruses only from pigs, humans, and rats, while posavirus 8 and 9, fisavirus, and basaviruses clustered with posa-like viruses from invertebrates.


Assuntos
Fezes/virologia , Invertebrados/virologia , Vertebrados/virologia , Vírus/classificação , Vírus/genética , Animais , Análise por Conglomerados , Genoma Viral/genética , Humanos , Japão , Metagenômica/métodos , Filogenia , Vírus de RNA/genética , Ratos , Análise de Sequência de DNA/métodos , Suínos
19.
BMC Bioinformatics ; 20(Suppl 7): 192, 2019 May 01.
Artigo em Inglês | MEDLINE | ID: mdl-31074372

RESUMO

BACKGROUND: The Iridoviridae family is categorized into five genera and clustered into two subfamilies: Alphairidovirinae includes Lymphocystivirus, Ranavirus (GIV), and Megalocystivirus (TGIV), which infect vertebrate hosts and Betairidovirinae includes Iridovirus and Chloriridovirus, which infect invertebrate hosts. Clustered Iridoviridae subfamilies possess host-specific characteristics, which can be considered as exclusive features for in-silico prediction of effective epitopes for vaccine development. A voting mechanism-based linear epitope (LE) prediction system was applied to identify and endorse LE candidates with a minimum length requirement for each clustered subfamily RESULTS: The experimental results showed that four conserved epitopes among the Iridovirideae family, one exclusive epitope for invertebrate subfamily and two exclusive epitopes for vertebrate family were predicted. These predicted LE candidates were further validated by ELISA assays for evaluating the strength of antigenicity and cross antigenicity. The conserved LEs for Iridoviridae family reflected high antigenicity responses for the two subfamilies, while exclusive LEs reflected high antigenicity responses only for the host-specific subfamily CONCLUSIONS: Host-specific characteristics are important features and constraints for effective epitope prediction. Our proposed voting mechanism based system provides a novel approach for in silico LE prediction prior to vaccine development, and it is especially powerful for analyzing antigen sequences with exclusive features between two clustered groups.


Assuntos
Infecções por Vírus de DNA/imunologia , Epitopos/imunologia , Interações Hospedeiro-Patógeno/imunologia , Invertebrados/imunologia , Iridoviridae/imunologia , Vertebrados/imunologia , Proteínas Virais/imunologia , Animais , Infecções por Vírus de DNA/virologia , Invertebrados/virologia , Iridoviridae/classificação , Iridoviridae/genética , Vertebrados/virologia
20.
Nat Ecol Evol ; 3(6): 919-927, 2019 06.
Artigo em Inglês | MEDLINE | ID: mdl-31110252

RESUMO

Predator-prey interactions in natural ecosystems generate complex food webs that have a simple universal body-size architecture where predators are systematically larger than their prey. Food-web theory shows that the highest predator-prey body-mass ratios found in natural food webs may be especially important because they create weak interactions with slow dynamics that stabilize communities against perturbations and maintain ecosystem functioning. Identifying these vital interactions in real communities typically requires arduous identification of interactions in complex food webs. Here, we overcome this obstacle by developing predator-trait models to predict average body-mass ratios based on a database comprising 290 food webs from freshwater, marine and terrestrial ecosystems across all continents. We analysed how species traits constrain body-size architecture by changing the slope of the predator-prey body-mass scaling. Across ecosystems, we found high body-mass ratios for predator groups with specific trait combinations including (1) small vertebrates and (2) large swimming or flying predators. Including the metabolic and movement types of predators increased the accuracy of predicting which species are engaged in high body-mass ratio interactions. We demonstrate that species traits explain striking patterns in the body-size architecture of natural food webs that underpin the stability and functioning of ecosystems, paving the way for community-level management of the most complex natural ecosystems.


Assuntos
Ecossistema , Cadeia Alimentar , Animais , Tamanho Corporal , Comportamento Predatório , Vertebrados
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