33 research outputs found
Application of mismatch detection methods in DNA computing
In many implementations of DNA computing, reliable detection of hybridization is of prime importance. We have applied several well-established DNA mutation scanning methods to this problem. Since they have been developed for speed and accuracy, these technologies are very promising for DNA computing. We have benchmarked a heteroduplex migration assay and enzymatic detection of mismatches on a 4 variable instance of 3SAT, using a previously described blocking algorithm. The first method is promising, but yielded ambiguous results. On the other hand, we were able to distinguish all perfect from imperfect duplexes by means of a CEL I mismatch endonuclease assay.Animal science
Enhancement of Arabidopsis growth characteristics using genome interrogation with artificial transcription factors
Plant science
DNA computing of solutions to knapsack problems
Algorithms and the Foundations of Software technologyMicrobial Biotechnolog
Parallel deep transcriptome and proteome analysis of zebrafish larvae
BackgroundSensitivity and throughput of transcriptomic and proteomic technologies have advanced tremendously in recent years. With the use of deep sequencing of RNA samples (RNA-seq) and mass spectrometry technology for protein identification and quantitation, it is now feasible to compare gene and protein expression on a massive scale and for any organism for which genomic data is available. Although these technologies are currently applied to many research questions in various model systems ranging from cell cultures to the entire organism level, there are few comparative studies of these technologies in the same system, let alone on the same samples. Here we present a comparison between gene and protein expression in embryos of zebrafish, which is an upcoming model in disease studies.ResultsWe compared Agilent custom made expression microarrays with Illumina deep sequencing for RNA analysis, showing as expected a high degree of correlation of expression of a common set of 18,230 genes. Gene expression was also found to correlate with the abundance of 963 distinct proteins, with several categories of genes as exceptions. These exceptions include ribosomal proteins, histones and vitellogenins, for which biological and technical explanations are discussed.ConclusionsBy comparing state of the art transcriptomic and proteomic technologies on samples derived from the same group of organisms we have for the first time benchmarked the differences in these technologies with regard to sensitivity and bias towards detection of particular gene categories in zebrafish. Our datasets submitted to public repositories are a good starting point for researchers interested in disease progression in zebrafish at a stage of development highly suited for high throughput screening technologies.Animal science
Identification of common carp innate immune genes with whole-genome sequencing and RNA-seq data
169Computer Systems, Imagery and MediaAnimal science
Fabrication of Atomically Precise Nanopores in Hexagonal Boron Nitride
We demonstrate the fabrication of individual nanopores in hexagonal boron
nitride (hBN) with atomically precise control of the pore size. Previous
methods of pore production in other 2D materials create pores of irregular
geometry with imprecise diameters. By taking advantage of the preferential
growth of boron vacancies in hBN under electron beam irradiation, we are able
to observe the pore growth via transmission electron microscopy, and terminate
the process when the pore has reached its desired size. Careful control of beam
conditions allows us to nucleate and grow individual triangular and hexagonal
pores with diameters ranging from subnanometer to 6nm over a large area of
suspended hBN using a conventional TEM. These nanopores could find application
in molecular sensing, DNA sequencing, water desalination, and molecular
separation. Furthermore, the chemical edge-groups along the hBN pores can be
made entirely nitrogen terminated or faceted with boron-terminated edges,
opening avenues for tailored functionalization and extending the applications
of these hBN nanopores.Comment: 5 pages, 6 figure