Complete Genomic Sequence of an Australian Sindbis Virus Isolated 44 Years Ago Reveals Unique Indels in the E2 and nsP3 Proteins.
Ontology highlight
ABSTRACT:
SUBMITTER: Pickering P
PROVIDER: S-EPMC6522784 | biostudies-literature | 2019 May
REPOSITORIES: biostudies-literature
Publications
Complete Genomic Sequence of an Australian Sindbis Virus Isolated 44 Years Ago Reveals Unique Indels in the E2 and nsP3 Proteins.
Pickering Paul P Aaskov John G JG Liu Wenjun W
Microbiology resource announcements 20190516 20
The complete genome sequence of a Sindbis virus (SINV) strain (SINV_AUS_1975_18953) isolated in Australia in 1975 from <i>Culex annulirostris</i> mosquitoes revealed unique deletions in amino acid positions 182 to 184 and 201 to 228 of the E2 envelope protein and multiple indels in the nonstructural protein 3 (nsP3). ...[more]
Similar Datasets
Project description:There is little evidence for the role of plant foods in the dispersal of early modern humans into new habitats globally. Researchers have hypothesised that early movements of human populations through Island Southeast Asia and into Sahul were driven by the lure of high-calorie, low-handling-cost foods, and that the use of plant foods requiring processing was not common in Sahul until the Holocene. Here we present the analysis of charred plant food remains from Madjedbebe rockshelter in northern Australia, dated to between 65 kya and 53 kya. We demonstrate that Australia's earliest known human population exploited a range of plant foods, including those requiring processing. Our finds predate existing evidence for such subsistence practices in Sahul by at least 23ky. These results suggest that dietary breadth underpinned the success of early modern human populations in this region, with the expenditure of labour on the processing of plants guaranteeing reliable access to nutrients in new environments.
| S-EPMC7026095 | biostudies-literature
Project description:The family Birnaviridae are a group of non-enveloped double-stranded RNA viruses which infect poultry, aquatic animals and insects. This family includes agriculturally important pathogens of poultry and fish. Recently, next-generation sequencing technologies have identified closely related birnaviruses in Culex, Aedes and Anopheles mosquitoes. Using a broad-spectrum system based on detection of long double-stranded RNA, we have discovered and isolated a birnavirus from Aedes notoscriptus mosquitoes collected in northern New South Wales, Australia. Phylogenetic analysis of Aedes birnavirus (ABV) showed that it is related to Rotifer birnavirus, a pathogen of microscopic aquatic animals. In vitro cell infection assays revealed that while ABV can replicate in Aedes-derived cell lines, the virus does not replicate in vertebrate cells and displays only limited replication in Culex- and Anopheles-derived cells. A combination of SDS-PAGE and mass spectrometry analysis suggested that the ABV capsid precursor protein (pVP2) is larger than that of other birnaviruses and is partially resistant to trypsin digestion. Reactivity patterns of ABV-specific polyclonal and monoclonal antibodies indicate that the neutralizing epitopes of ABV are SDS sensitive. Our characterization shows that ABV displays a number of properties making it a unique member of the Birnaviridae and represents the first birnavirus to be isolated from Australian mosquitoes.
| S-EPMC7552023 | biostudies-literature
Project description:We describe a near-complete, three-dimensionally preserved skeleton of a metatherian (relative of modern marsupials) from the middle Eocene (Lutetian: 44-43 million years ago) Lülük member of the Uzunçarşıdere Formation, central Turkey. With an estimated body mass of 3-4 kg, about the size of a domestic cat (Felis catus) or spotted quoll (Dasyurus maculatus), it is an order of magnitude larger than the largest fossil metatherians previously known from the Cenozoic of the northern hemisphere. This new taxon is characterised by large, broad third premolars that probably represent adaptations for hard object feeding (durophagy), and its craniodental morphology suggests the capacity to generate high bite forces. Qualitative and quantitative functional analyses of its postcranial skeleton indicate that it was probably scansorial and relatively agile, perhaps broadly similar in locomotor mode to the spotted quoll, but with a greater capacity for climbing and grasping. Bayesian phylogenetic analysis of a total evidence dataset comprising 259 morphological characters and 9kb of DNA sequence data from five nuclear protein-coding genes, using both undated and "tip-and-node dating" approaches, place the new taxon outside the marsupial crown-clade, but within the clade Marsupialiformes. It demonstrates that at least one metatherian lineage evolved to occupy the small-medium, meso- or hypo-carnivore niche in the northern hemisphere during the early Cenozoic, at a time when there were numerous eutherians (placentals and their fossil relatives) filling similar niches. However, the known mammal fauna from Uzunçarşıdere Formation appears highly endemic, and geological evidence suggests that this region of Turkey was an island for at least part of the early Cenozoic, and so the new taxon may have evolved in isolation from potential eutherian competitors. Nevertheless, the new taxon reveals previously unsuspected ecomorphological disparity among northern hemisphere metatherians during the first half of the Cenozoic.
| S-EPMC5559079 | biostudies-literature
Project description:Full genome sequencing of two bovine rotavirus A (RVA) strains isolated in Japan in 2019 revealed two genotype constellations; one had a constellation of G8-P[1]-I2-R2-C2-M2-A3-N2-T9-E2-H3. Thereupon, genotype T9 carried by RVA/Bovine-tc/JPN/AH1041/2022/G8P[1], constitutes a rare NSP3 genotype, and only two unusual Japanese bovine RVA strains have thus far been reported to carry this genotype. The other RVA/Bovine-tc/JPN/AH1207/2022/G6P[5] strain possessed a constellation of G6-P[5]-I2-R2-C2-M2-A3-N2-T6-E2-H3. Phylogenetic analyses indicate that the majority of gene segments were most closely related to Japanese bovine RVAs, suggesting that both strains might have derived through multiple reassortment events from RVA strains circulating within Japanese cattle. The emergence of RVA strains in Japan and their reassortment with locally circulating atypical RVAs could have implications for current vaccination strategies.
| S-EPMC10539819 | biostudies-literature
Project description:Sindbis virus (SINV), the prototype alphavirus, contains a macro domain in the highly conserved N-terminal region of nonstructural protein 3 (nsP3). However, the biological role of the macro domain is unclear. Mutations of amino acids 10 and 24 from asparagine to alanine in the ADP-ribose binding region of the macro domain impaired SINV replication and viral RNA synthesis particularly in neurons, but did not alter binding of poly(ADP-ribose). Mutation at position 10 had the greatest effect and caused nsP3 instability in neurons, decreased SINV-induced death of mature, but not immature neurons, and attenuated virulence in 2 week-old, but not 5 day-old mice. A compensatory mutation at amino acid 31 in the macro domain of nsP3, as well as reversion of mutated amino acid 10, occurred during replication of double mutant SINV in vitro and in vivo. The nsP3 macro domain is important for SINV replication and age-dependent susceptibility to encephalomyelitis.
| S-EPMC2683903 | biostudies-literature
Project description:Four heteropod lizard trackways discovered in the Hasandong Formation (Aptian-early Albian), South Korea assigned to Sauripes hadongensis, n. ichnogen., n. ichnosp., which represents the oldest lizard tracks in the world. Most tracks are pes tracks (N?=?25) that are very small, average 22.29?mm long and 12.46?mm wide. The pes tracks show "typical" lizard morphology as having curved digit imprints that progressively increase in length from digits I to IV, a smaller digit V that is separated from the other digits by a large interdigital angle. The manus track is 19.18?mm long and 19.23?mm wide, and shows a different morphology from the pes. The predominant pes tracks, the long stride length of pes, narrow trackway width, digitigrade manus and pes prints, and anteriorly oriented long axis of the fourth pedal digit indicate that these trackways were made by lizards running bipedally, suggesting that bipedality was possible early in lizard evolution.
| S-EPMC5814403 | biostudies-literature
Project description:A three-dimensional reconstruction of Sindbis virus at 7.0 Å resolution presented here provides a detailed view of the virion structure and includes structural evidence for key interactions that occur between the capsid protein (CP) and transmembrane (TM) glycoproteins E1 and E2. Based on crystal structures of component proteins and homology modeling, we constructed a nearly complete, pseudo-atomic model of the virus. Notably, this includes identification of the 33-residue cytoplasmic domain of E2 (cdE2), which follows a path from the E2 TM helix to the CP where it enters and exits the CP hydrophobic pocket and then folds back to contact the viral membrane. Modeling analysis identified three major contact regions between cdE2 and CP, and the roles of specific residues were probed by molecular genetics. This identified R393 and E395 of cdE2 and Y162 and K252 of CP as critical for virus assembly. The N-termini of the CPs form a contiguous network that interconnects 12 pentameric and 30 hexameric CP capsomers. A single glycoprotein spike cross-links three neighboring CP capsomers as might occur during initiation of virus budding.
| S-EPMC3407685 | biostudies-literature
Project description:Understanding the timing and character of the expansion of Homo sapiens out of Africa is critical for inferring the colonization and admixture processes that underpin global population history. It has been argued that dispersal out of Africa had an early phase, particularly ~130-90 thousand years ago (ka), that reached only the East Mediterranean Levant, and a later phase, ~60-50?ka, that extended across the diverse environments of Eurasia to Sahul. However, recent findings from East Asia and Sahul challenge this model. Here we show that H. sapiens was in the Arabian Peninsula before 85?ka. We describe the Al Wusta-1 (AW-1) intermediate phalanx from the site of Al Wusta in the Nefud desert, Saudi Arabia. AW-1 is the oldest directly dated fossil of our species outside Africa and the Levant. The palaeoenvironmental context of Al Wusta demonstrates that H. sapiens using Middle Palaeolithic stone tools dispersed into Arabia during a phase of increased precipitation driven by orbital forcing, in association with a primarily African fauna. A Bayesian model incorporating independent chronometric age estimates indicates a chronology for Al Wusta of ~95-86?ka, which we correlate with a humid episode in the later part of Marine Isotope Stage 5 known from various regional records. Al Wusta shows that early dispersals were more spatially and temporally extensive than previously thought. Early H. sapiens dispersals out of Africa were not limited to winter rainfall-fed Levantine Mediterranean woodlands immediately adjacent to Africa, but extended deep into the semi-arid grasslands of Arabia, facilitated by periods of enhanced monsoonal rainfall.
| S-EPMC5935238 | biostudies-literature
Project description:Here we present one of the world's oldest examples of large-scale and formalized water management, in the case of the Liangzhu culture of the Yangtze Delta, dated at 5,300-4,300 years cal B.P. The Liangzhu culture represented a peak of early cultural and social development predating the historically recorded Chinese dynasties; hence, this study reveals more about the ancient origins of hydraulic engineering as a core element of social, political, and economic developments. Archaeological surveys and excavations can now portray the impressive extent and structure of dams, levees, ditches, and other landscape-transforming features, supporting the ancient city of Liangzhu, with an estimated size of about 300 ha. The results indicate an enormous collective undertaking, with unprecedented evidence for understanding how the city, economy, and society of Liangzhu functioned and developed at such a large scale. Concurrent with the evidence of technological achievements and economic success, a unique relationship between ritual order and social power is seen in the renowned jade objects in Liangzhu elite burials, thus expanding our view beyond the practicalities of water management and rice farming.
| S-EPMC5748178 | biostudies-literature
Project description:Fluctuating climate is a hallmark of Earth. As one transcends deep into Earth time, however, both the evidence for and the causes of climate change become difficult to establish. We report geochemical and sedimentological evidence for repeated, short-term climate fluctuations from the exceptionally well-preserved ?1.4-billion-year-old Xiamaling Formation of the North China Craton. We observe two patterns of climate fluctuations: On long time scales, over what amounts to tens of millions of years, sediments of the Xiamaling Formation record changes in geochemistry consistent with long-term changes in the location of the Xiamaling relative to the position of the Intertropical Convergence Zone. On shorter time scales, and within a precisely calibrated stratigraphic framework, cyclicity in sediment geochemical dynamics is consistent with orbital control. In particular, sediment geochemical fluctuations reflect what appear to be orbitally forced changes in wind patterns and ocean circulation as they influenced rates of organic carbon flux, trace metal accumulation, and the source of detrital particles to the sediment.
| S-EPMC4378410 | biostudies-literature