1. Directed evolution and selection of biostable l-DNA aptamers with a mirror-image DNA polymerase | Nature Biotechnology
- Author: www.nature.com
- Date Submitted: 07/10/2021 02:30 AM
- Average star voting: (4.97/5 stars and 95369 reviews)
- Summary: Mirror-image aptamers made from chirally inverted nucleic acids are nuclease-resistant and exceptionally biostable, opening up opportunities for unique applications. However, the directed evolution and selection of mirror-image aptamers directly from large randomized l-DNA libraries has, to our knowledge, not been demonstrated previously. Here, we developed a ‘mirror-image selection’ scheme for the directed evolution and selection of biostable l-DNA aptamers with a mirror-image DNA polymerase. We performed iterative rounds of enrichment and mirror-image polymerase chain reaction (PCR) amplification of l-DNA sequences that bind native human thrombin, in conjunction with denaturing gradient gel electrophoresis (DGGE) to isolate individual aptamers and l-DNA sequencing-by-synthesis to determine their sequences. Based on the selected l-DNA aptamers, we designed biostable thrombin sensors and inhibitors, which remained functional in physiologically relevant nuclease-rich environments, even in the presence of human serum that rapidly degraded d-DNA aptamers. Mirror-image selection of biostable l-DNA aptamers directly from large randomized l-DNA libraries greatly expands the range of biomolecules that can be targeted, broadening their applications as biostable sensors, therapeutics and basic research tools. Mirror-image PCR and l-DNA sequencing-by-synthesis enable the directed evolution and selection of functional l-DNA aptamers.
- Match with the search results: Jun 6, 2022 … Mirror-image aptamers made from chirally inverted nucleic acids are nuclease-resistant and exceptionally biostable, opening up opportunities …
2. Highest-Resolution Images of DNA Reveal It’s Surprisingly Jiggly
- Author: gizmodo.com
- Date Submitted: 04/04/2019 08:49 AM
- Average star voting: (3.9/5 stars and 43830 reviews)
- Summary: Scientists have captured the highest-resolution images ever taken of DNA, revealing previously unseen twisting and squirming behaviors.
- Match with the search results: Feb 16, 2021 … Scientists have captured the highest-resolution images ever taken of DNA, revealing previously unseen twisting and squirming behaviors.
3. IMAGE: high-powered detection of genetic effects on DNA methylation using integrated methylation QTL mapping and allele-specific analysis – Genome Biology
- Author: genomebiology.biomedcentral.com
- Date Submitted: 03/18/2020 10:50 AM
- Average star voting: (3.89/5 stars and 19832 reviews)
- Summary: Identifying genetic variants that are associated with methylation variation—an analysis commonly referred to as methylation quantitative trait locus (mQTL) mapping—is important for understanding the epigenetic mechanisms underlying genotype-trait associations. Here, we develop a statistical method, IMAGE, for mQTL mapping in sequencing-based methylation studies. IMAGE properly accounts for the count nature of bisulfite sequencing data and incorporates allele-specific methylation patterns from heterozygous individuals to enable more powerful mQTL discovery. We compare IMAGE with existing approaches through extensive simulation. We also apply IMAGE to analyze two bisulfite sequencing studies, in which IMAGE identifies more mQTL than existing approaches.
- Match with the search results: Oct 24, 2019 … IMAGE: high-powered detection of genetic effects on DNA methylation using integrated methylation QTL mapping and allele-specific analysis.
4. Cisco DNA Center User Guide, Release 2.1.2 – Manage Software Images [Cisco DNA Center]
- Author: www.cisco.com
- Date Submitted: 07/09/2019 11:36 PM
- Average star voting: (3.75/5 stars and 93466 reviews)
- Summary: Manage Software Images
- Match with the search results: Aug 2, 2022 … Image Repository: Cisco DNA Center stores all the unique software images according to image type and version. You can view, import, and delete …
5. Image Encryption Algorithm Based on DNA Encoding and Chaotic Maps
- Author: www.hindawi.com
- Date Submitted: 07/12/2021 10:23 AM
- Average star voting: (3.78/5 stars and 45036 reviews)
- Summary: We propose a new image encryption algorithm based on DNA sequences combined with chaotic maps. This algorithm has two innovations: (1) it diffuses the pixels by transforming the nucleotides into corresponding base pairs a random number of times and (2) it confuses the pixels by a chaotic index based on a chaotic map. For any size of the original grayscale image, the rows and columns are fist exchanged by the arrays generated by a logistic chaotic map. Secondly, each pixel that has been confused is encoded into four nucleotides according to the DNA coding. Thirdly, each nucleotide is transformed into the corresponding base pair a random number of time(s) by a series of iterative computations based on Chebyshev’s chaotic map. Experimental results indicate that the key account of this algorithm is 1.536 × 10127, the correlation coefficient of a 256 × 256 Lena image between, before, and after the encryption processes was 0.0028, and the information entropy of the encrypted image was 7.9854. These simulation results and security analysis show that the proposed algorithm not only has good encryption effect, but also has the ability to repel exhaustive, statistical, differential, and noise attacks.
- Match with the search results: However, using only DNA encoding to encrypt images is not secure. Therefore, we combine chaos encryption technology and image encryption based on DNA computing …
6. Automatic DNA Diagnosis for 1D Gel Electrophoresis Images using Bio-image Processing Technique – BMC Genomics
- Author: bmcgenomics.biomedcentral.com
- Date Submitted: 07/27/2021 07:05 PM
- Average star voting: (3.66/5 stars and 58903 reviews)
- Summary: DNA gel electrophoresis is a molecular biology technique for separating different sizes of DNA fragments. Applications of DNA gel electrophoresis include DNA fingerprinting (genetic diagnosis), size estimation of DNA, and DNA separation for Southern blotting. Accurate interpretation of DNA banding patterns from electrophoretic images can be laborious and error prone when a large number of bands are interrogated manually. Although many bio-imaging techniques have been proposed, none of them can fully automate the typing of DNA owing to the complexities of migration patterns typically obtained. We developed an image-processing tool that automatically calls genotypes from DNA gel electrophoresis images. The image processing workflow comprises three main steps: 1) lane segmentation, 2) extraction of DNA bands and 3) band genotyping classification. The tool was originally intended to facilitate large-scale genotyping analysis of sugarcane cultivars. We tested the proposed tool on 10 gel images (433 cultivars) obtained from polyacrylamide gel electrophoresis (PAGE) of PCR amplicons for detecting intron length polymorphisms (ILP) on one locus of the sugarcanes. These gel images demonstrated many challenges in automated lane/band segmentation in image processing including lane distortion, band deformity, high degree of noise in the background, and bands that are very close together (doublets). Using the proposed bio-imaging workflow, lanes and DNA bands contained within are properly segmented, even for adjacent bands with aberrant migration that cannot be separated by conventional techniques. The software, called GELect, automatically performs genotype calling on each lane by comparing with an all-banding reference, which was created by clustering the existing bands into the non-redundant set of reference bands. The automated genotype calling results were verified by independent manual typing by molecular biologists. This work presents an automated genotyping tool from DNA gel electrophoresis images, called GELect, which was written in Java and made available through the imageJ framework. With a novel automated image processing workflow, the tool can accurately segment lanes from a gel matrix, intelligently extract distorted and even doublet bands that are difficult to identify by existing image processing tools. Consequently, genotyping from DNA gel electrophoresis can be performed automatically allowing users to efficiently conduct large scale DNA fingerprinting via DNA gel electrophoresis. The software is freely available from http://www.biotec.or.th/gi/tools/gelect .
- Match with the search results: Dec 9, 2015 … The image processing workflow comprises three main steps: 1) lane segmentation, 2) extraction of DNA bands and 3) band genotyping classification …