skip to main content
US FlagAn official website of the United States government
dot gov icon
Official websites use .gov
A .gov website belongs to an official government organization in the United States.
https lock icon
Secure .gov websites use HTTPS
A lock ( lock ) or https:// means you've safely connected to the .gov website. Share sensitive information only on official, secure websites.


Title: CRUISE, a Tool for the Detection of Iterons in Circular Rep-Encoding Single-Stranded DNA Viruses
Iterons are short, repeated DNA sequences that are important for the replication of circular single-stranded DNA viruses. No tools that can reliably predict iterons are currently available. The CRUcivirus Iteron SEarch (CRUISE) tool is a computational tool that identifies iteron candidates near stem-loop structures in viral genomes.  more » « less
Award ID(s):
2025305
PAR ID:
10476554
Author(s) / Creator(s):
; ; ; ;
Editor(s):
Roux, Simon
Publisher / Repository:
ASM Press
Date Published:
Journal Name:
Microbiology Resource Announcements
Volume:
12
Issue:
1
ISSN:
2576-098X
Format(s):
Medium: X
Sponsoring Org:
National Science Foundation
More Like this
  1. Abstract DNA is not only a carrier of genetic information, but also a versatile structural tool for the engineering and self‐assembling of nanostructures. In this regard, the DNA template has dramatically enhanced the scalability, programmability, and functionality of the self‐assembled DNA nanostructures. These capabilities provide opportunities for a wide range of biomedical applications in biosensing, bioimaging, drug delivery, and disease therapy. In this review, the importance and advantages of DNA for programming and fabricating of DNA nanostructures are first highlighted. The recent progress in design and construction of DNA nanostructures are then summarized, including DNA conjugated nanoparticle systems, DNA‐based clusters and extended organizations, and DNA origami‐templated assemblies. An overview on biomedical applications of the self‐assembled DNA nanostructures is provided. Finally, the conclusion and perspectives on the self‐assembled DNA nanostructures are presented. 
    more » « less
  2. SUMMARY Genome editing technologies like CRISPR/Cas have greatly accelerated the pace of both fundamental research and translational applications in agriculture. However, many plant biologists are functionally limited to creating small, targeted DNA changes or large, random DNA insertions. The ability to efficiently generate large, yet precise, DNA changes will massively accelerate crop breeding cycles, enabling researchers to more efficiently engineer crops amidst a rapidly changing agricultural landscape. This review provides an overview of existing technologies that allow plant biologists to integrate large DNA sequences within a plant host and some associated technical bottlenecks. Additionally, this review explores a selection of emerging techniques in other host systems to inspire tool development in plants. 
    more » « less
  3. Abstract BackgroundTransgenic plants are essential for both basic and applied plant biology. Recently, fluorescent and colorimetric markers were developed to enable nondestructive identification of transformed seeds and accelerate the generation of transgenic plant lines. Yet, transformation often results in the integration of multiple copies of transgenes in the plant genome. Multiple transgene copies can lead to transgene silencing and complicate the analysis of transgenic plants by requiring researcher to track multiple T-DNA loci in future generations. Thus, to simplify analysis of transgenic lines, plant researchers typically screen transformed plants for lines where the T-DNA inserted in a single locus — an analysis that involves laborious manual counting of fluorescent and non-fluorescent seeds for screenable markers. ResultsTo expedite T-DNA segregation analysis, we developed SeedSeg, an image analysis tool that uses a segmentation algorithm to count the number of transformed and wild-type seeds in an image. SeedSeg runs a chi-squared test to determine the number of T-DNA loci. Parameters can be adjusted to optimize for different brightness intensities and seed sizes. ConclusionsBy automating the seed counting process, SeedSeg reduces the manual labor associated with identifying transgenic lines containing a single T-DNA locus. SeedSeg is adaptable to different seed sizes and visual transgene markers, making it a versatile tool for accelerating plant research. 
    more » « less
  4. Abstract Lipid‐coated microbubbles are an important class of gene delivery vehicles activated by ultrasound to locally deliver their DNA payloads to cells. Negatively charged DNA is electrostatically loaded onto the positively charged surface of microbubbles that contain a cationic lipid shell. Characterizing the zeta potential of individual cationic microbubbles to determine a population distribution and how this is affected by DNA complexation is critical to maximize DNA loading and circulation time. Traditional zeta potential analysis provides an ensemble charge measurement for a particle population but cannot measure individual particles to determine a distribution. Here, single‐particle tracking microelectrophoresis technology is applied to measure zeta potentials of individual microbubbles synthesized with different ratios of 1,2‐distearoyl‐3‐trimethylammonium‐propane (DSTAP) cationic lipid as well as loaded with increasing amounts of DNA. Results show that at 0 mol% DSTAP all microbubbles are negatively charged, and at 10 mol% half are positive. All particles are positive at 20 mol% DSTAP but the population shifts to negative values upon incubation with 0.01 pg DNA/microbubble. Analyzing zeta potential on the individual microbubble level is a powerful tool to understand DNA loading across a population of microbubbles and enables microbubble surface charge and nucleic acid loading optimization for delivery applications. 
    more » « less
  5. Abstract Tile‐based DNA self‐assembly is a powerful approach for nano‐constructions. In this approach, individual DNA single strands first assemble into well‐defined structural tiles, which, then, further associate with each other into final nanostructures. It is a general assumption that the lower‐level structures (tiles) determine the higher‐level, final structures. In this study, we present concrete experimental data to show that higher‐level structures could, at least in the current example, also impact on the formation of lower‐level structures. This study prompts questions such as: how general is this phenomenon in programmed DNA self‐assembly and can we turn it into a useful tool for fine tuning DNA self‐assembly? 
    more » « less