Ontology highlight
ABSTRACT:
PROVIDER: PRJNA449946 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Zika virus (ZIKV) is a mosquito-transmitted positive-sense RNA virus in the family Flaviviridae. ZIKV infections are associated with neurodevelopmental deficiencies termed Congenital Zika Syndrome. ZIKV strains are grouped into three phylogenetic lineages: East African, West African, and Asian, which contains the American lineage. RNA virus genomes exist as genetically-related sequences. The heterogeneity of these viral populations is implicated in viral fitness, and genome diversity is correlated to virulence. This study examines genetic diversity of representative ZIKV strains from all lineages utilizing next generation sequencing (NGS). Inter-lineage diversity results indicate that ZIKV lineages differ broadly from each other; however, intra-lineage comparisons of American ZIKV strains isolated from human serum or placenta show differences in diversity when compared to ZIKVs from Asia and West Africa. This study describes the first comprehensive NGS analysis of all ZIKV lineages and posits that sub-consensus-level diversity may provide a framework for understanding ZIKV fitness during infection.
2018-12-31 | E-MTAB-5945 | biostudies-arrayexpress
Project description:Infectious pancreatic necrosis virus (IPNV) is an aquatic virus that causes acute infection in freshwater and marine fish. The stage-specific expression of TNFα regulates Bad/Bid-mediated apoptosis and RIP1/ROS-mediated secondary necrosis in IPNV-infected fish cells. Using microRNA microarray and real-time quantitative PCR assays, the expression patterns of microRNA were characterized in different replication stages of IPNV or stimulation of LPS.
2011-12-31 | GSE30262 | GEO
Project description:Cassava mosaic disease (CMD) suppresses cassava yields across the tropics. It has been reported that landraces lose CMD resistance after regeneration through de novo morphogenesis. We sequenced WGBS data of 14 samples.
2022-05-27 | GSE192748 | GEO
Project description:With the advent of advanced sequencing technology, studies of RNA viruses have shown that genetic diversity contribute to both attenuation and virulence. The differences in genetic diversity of wild-type Asibi virus and 17D-204 vaccine provides an unique opportunity to investigate RNA population theory in the context of a well described live attenuated vaccine. Utilizing infectious clone-derived viruses containing some of the amino acid substitutions that differentiate yellow fever wild-type Asibi strain from 17D vaccine and recovered in a controlled experiment, establishes that the genetic diversity differences that exist between wild-type Asibi and 17D-204 vaccine viruses are not influenced by either different passage history or source of samples, but rather resulted from the attenuation of wild-type Asibi virus to yield the 17D vaccine sub-strains.
2018-10-16 | E-MTAB-6614 | biostudies-arrayexpress
Project description:Picocyanobacteria from the genus Synechococcus are ubiquitous in ocean waters. Their phylogenetic and genomic diversity suggests ecological niche differentiation, but the selective forces influencing this are not well defined. Marine picocyanobacteria are sensitive to Cu toxicity, so adaptations to this stress could represent a selective force within, and between, “species” also known as clades. We compared Cu stress responses in cultures and natural populations of marine Synechococcus from two co-occurring major mesotrophic clades (I and IV). Using custom microarrays and proteomics to characterize expression responses to Cu in the lab and field, we found evidence for a general stress regulon in marine Synechococcus. However, the two clades also exhibited distinct responses to copper. The Clade I representative induced expression of genomic island genes in cultures and Southern California Bight populations, while the Clade IV representative downregulated Fe-limitation proteins. Copper incubation experiments suggest that Clade IV populations may harbor stress-tolerant subgroups, and thus fitness tradeoffs may govern Cu-tolerant strain distributions. This work demonstrates that Synechococcus has distinct adaptive strategies to deal with Cu toxicity at both the clade and subclade level, implying that metal toxicity and stress response adaptations represent an important selective force for influencing diversity within marine Synechococcus populations.
2016-10-28 | GSE89262 | GEO
Project description:ZIKV strains belong to three phylogenetic lineages: East African, West African, and Asian/American. RNA virus genomes exist as populations of genetically-related sequences whose heterogeneity may impact viral fitness, evolution, and virulence. The genetic diversity of representative ZIKVs (N=7) from each lineage was examined using next generation sequencing (NGS) paired with downstream Shannon entropy calculation and single nucleotide variant (SNV) analysis. This comprehensive analysis of ZIKV genetic diversity provides insight into the genetic diversity of ZKIV and repository of SNV positions across lineages.
2019-07-30 | E-MTAB-7771 | biostudies-arrayexpress
Project description:Proteomics data used in the evaluation of Micromonas pusilla as part of a larger comparison associated with marine diversity and ancestral characteristics of land plants
2016-01-26 | MSV000079483 | MassIVE