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We stress test this new codec in silico and found it to be robust up to petabyte-scale designs: only 10 imperfectly synthesized strands, each missing up to 30% are needed for sequence reconstruction. This will be a valuable exploit until we reach single DNA template storage...pic.twitter.com/B16OfHIBen
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We tested out this new codec by synthesizing "Eureka!" and show that data can be retrieved from as little as 10 imperfectly synthesized strands, each missing up to 30%! To make sure we retrieve the data, we do have to sequence more strands.pic.twitter.com/x0r92wHutR
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Recovering erasures even with multiple strands representing a single sequence can be tough, but never fear! We added "synchronization" nucleotides to our sequence design to improve sequence reconstruction.pic.twitter.com/oJEqbLAVqf
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We synthesize "hello world!" and sequence *all* produced strands. Data can be retrieved from strands matching sequence design (i.e., # of bases per sequence). Analyses show 1. extension length varies (TdT has sequence bias) 2. deletions predominate (TdT is distributive).pic.twitter.com/El2FXaiqR7
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Our approach requires balancing the kinetic activity of two enzymes that compete for free nucleoside triphosphates (TdT adds as apyrase depletes) to yield net synthesis of short homopolymers. We then encode data as transitions between non-identical nucleotides.pic.twitter.com/Z4vmAdUeXK
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Pleased to share our work for storing digital data in DNA: https://rdcu.be/bFu9b ! We describe de novo DNA synthesis with enzymes (no terminators!) and devise a highly tolerant error-correction codec for perfect data retrieval. Here are some highlights:pic.twitter.com/2VQx6HtEIK
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587 core genes are required to maintain wildtype growth rate. 278 (~47%) are homologous to essentials found in E. coli and V. cholerae. Remaining 309 genes are enriched for respiration. Majority of core genes are located on chr1. So it seems that chr2 is mostly dispensable...pic.twitter.com/N8PRP3c7JX
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Every gene can be scored for fitness by using only a couple of flasks, thanks to pooling. We profile genes under different growth media and found a number of nonfunctional duplications. (Beware! We were burned in another study when using the 'wrong' duplicate...)pic.twitter.com/hWi8zwFEym
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After failing for years to make a saturating transposon library, we devised a pooled CRISPRi system for gene knockdown. gRNA counts (
@illumina) over time is a proxy for gene fitness. We synthesized a 13,567 CRISPRi library (@Agilent) which targets 99.7% of predicted ORFs (4,565).pic.twitter.com/p9LLaqGmSg
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We produced the ~5.2MB closed genome (
@PacBio) which is 1.5MB bigger than E. coli but split into two chromosomes. Mapped (@nanopore) replication origins and termini for each chromosome. Genes and pathways annotated with RAST. Total time for these parts of the study ~6 months.pic.twitter.com/11lMUKnlK2
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LB3 (LB with 3% final NaCl w/v) is a robust growth medium easily accessible to most labs. The brilliant
@brandogw and@MoKhalilLab designed microchemostats to visualize V.nat's (left) incredible growth rate, which is 2x faster than E. coli (right) at 37C.pic.twitter.com/jX0qcrdYtCPrikaži ovu nit -
Sun doesn't set on the British SynBio empire
#SB7conf @DrTomEllis@glen_gowerspic.twitter.com/D9PYvQMMYW
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