4 research outputs found
Hidden Addressing Encoding for DNA Storage
DNA is a natural storage medium with the advantages of high storage density and long service life compared with traditional media. DNA storage can meet the current storage requirements for massive data. Owing to the limitations of the DNA storage technology, the data need to be converted into short DNA sequences for storage. However, in the process, a large amount of physical redundancy will be generated to index short DNA sequences. To reduce redundancy, this study proposes a DNA storage encoding scheme with hidden addressing. Using the improved fountain encoding scheme, the index replaces part of the data to realize hidden addresses, and then, a 10.1Â MB file is encoded with the hidden addressing. First, the Dottup dot plot generator and the Jaccard similarity coefficient analyze the overall self-similarity of the encoding sequence index, and then the sequence fragments of GC content are used to verify the performance of this scheme. The final results show that the encoding scheme indexes with overall lower self-similarity, and the local thermodynamic properties of the sequence are better. The hidden addressing encoding scheme proposed can not only improve the utilization of bases but also ensure the correct rate of DNA storage during the sequencing and decoding processes
Proteomic Basis of Stress Responses in the Gills of the Pacific Oyster <i>Crassostrea gigas</i>
The
Pacific oyster <i>Crassostrea gigas</i> is one of
the dominant sessile inhabitants of the estuarine intertidal zone,
which is a physically harsh environment due to the presence of a number
of stressors. Oysters have adapted to highly dynamic and stressful
environments, but the molecular mechanisms underlying such stress
adaptation are largely unknown. In the present study, we examined
the proteomic responses in the gills of <i>C. gigas</i> exposed
to three stressors (high temperature, low salinity, and aerial exposure)
they often encounter in the field. We quantitatively compared the
gill proteome profiles using iTRAQ-coupled 2-D LC–MS/MS. There
were 3165 identified proteins among which 2379 proteins could be quantified.
Heat shock, hyposalinity, and aerial exposure resulted in 50, 15,
and 33 differentially expressed gill proteins, respectively. Venn
diagram analysis revealed substantial different responses to the three
stressors. Only xanthine dehydrogenase/oxidase showed a similar expression
pattern across the three stress treatments, suggesting that reduction
of ROS accumulation may be a conserved response to these stressors.
Heat shock caused significant overexpression of molecular chaperones
and production of <i>S</i>-adenosyl-l-methionine,
indicating their crucial protective roles against protein denature.
In addition, heat shock also activated immune responses, Ca<sup>2+</sup> binding protein expression. By contrast, hyposalinity and aerial
exposure resulted in the up-regulation of 3-demethylubiquinone-9 3-methyltransferase,
indicating that increase in ubiquinone synthesis may contribute to
withstanding both the osmotic and desiccation stress. Strikingly,
the majority of desiccation-responsive proteins, including those involved
in metabolism, ion transportation, immune responses, DNA duplication,
and protein synthesis, were down-regulated, indicating conservation
of energy as an important strategy to cope with desiccation stress.
There was a high consistency between the expression levels determined
by iTRAQ and Western blotting, highlighting the high reproducibility
of our proteomic approach and its great value in revealing molecular
mechanisms of stress responses
Proteomic Basis of Stress Responses in the Gills of the Pacific Oyster <i>Crassostrea gigas</i>
The
Pacific oyster <i>Crassostrea gigas</i> is one of
the dominant sessile inhabitants of the estuarine intertidal zone,
which is a physically harsh environment due to the presence of a number
of stressors. Oysters have adapted to highly dynamic and stressful
environments, but the molecular mechanisms underlying such stress
adaptation are largely unknown. In the present study, we examined
the proteomic responses in the gills of <i>C. gigas</i> exposed
to three stressors (high temperature, low salinity, and aerial exposure)
they often encounter in the field. We quantitatively compared the
gill proteome profiles using iTRAQ-coupled 2-D LC–MS/MS. There
were 3165 identified proteins among which 2379 proteins could be quantified.
Heat shock, hyposalinity, and aerial exposure resulted in 50, 15,
and 33 differentially expressed gill proteins, respectively. Venn
diagram analysis revealed substantial different responses to the three
stressors. Only xanthine dehydrogenase/oxidase showed a similar expression
pattern across the three stress treatments, suggesting that reduction
of ROS accumulation may be a conserved response to these stressors.
Heat shock caused significant overexpression of molecular chaperones
and production of <i>S</i>-adenosyl-l-methionine,
indicating their crucial protective roles against protein denature.
In addition, heat shock also activated immune responses, Ca<sup>2+</sup> binding protein expression. By contrast, hyposalinity and aerial
exposure resulted in the up-regulation of 3-demethylubiquinone-9 3-methyltransferase,
indicating that increase in ubiquinone synthesis may contribute to
withstanding both the osmotic and desiccation stress. Strikingly,
the majority of desiccation-responsive proteins, including those involved
in metabolism, ion transportation, immune responses, DNA duplication,
and protein synthesis, were down-regulated, indicating conservation
of energy as an important strategy to cope with desiccation stress.
There was a high consistency between the expression levels determined
by iTRAQ and Western blotting, highlighting the high reproducibility
of our proteomic approach and its great value in revealing molecular
mechanisms of stress responses
Comparative Genomics Reveals Evolutionary Drivers of Sessile Life and Left-right Shell Asymmetry in Bivalves
Bivalves are species-rich mollusks with prominent protective roles in coastal ecosystems. Across these ancient lineages, colony-founding larvae anchor themselves either by byssus production or by cemented attachment. The latter mode of sessile life is strongly molded by left-right shell asymmetry during larval development of Ostreoida oysters such as Crassostrea hongkongensis. Here, we sequenced the genome of C. hongkongensis in high resolution and compared it to reference bivalve genomes to unveil genomic determinants driving cemented attachment and shell asymmetry. Importantly, loss of the homeobox gene Antennapedia (Antp) and broad expansion of lineage-specific extracellular gene families are implicated in a shift from byssal to cemented attachment in bivalves. Comparative transcriptomic analysis shows a conspicuous divergence between left-right asymmetrical C. hongkongensis and symmetrical Pinctada fucata in their expression profiles. Especially, a couple of orthologous transcription factor genes and lineage-specific shell-related gene families including that encoding tyrosinases are elevated, and may cooperatively govern asymmetrical shell formation in Ostreoida oysters