scholarly journals Seeds for effective oligonucleotide design

2021 ◽  
Author(s):  
Lucian Ilie ◽  
Silvana Ilie ◽  
Shima Khoshraftar ◽  
Anahita Mansouri Bigvand
Keyword(s):  
Dna Oligonucleotides ◽  
Spaced Seeds

Background DNA oligonucleotides are a very useful tool in biology. The best algorithms for designing good DNA oligonucleotides are filtering out unsuitable regions using a seeding approach. Determining the quality of the seeds is crucial for the performance of these algorithms. Results We present a sound framework for evaluating the quality of seeds for oligonucleotide design. The F - score is used to measure the accuracy of each seed. A number of natural candidates are tested: contiguous (BLAST-like), spaced, transitions-constrained, and multiple spaced seeds. Multiple spaced seeds are the best, with more seeds providing better accuracy. Single spaced and transition seeds are very close whereas, as expected, contiguous seeds come last. Increased accuracy comes at the price of reduced efficiency. An exception is that single spaced and transitions-constrained seeds are both more accurate and more efficient than contiguous ones. Conclusions Our work confirms another application where multiple spaced seeds perform the best. It will be useful in improving the algorithms for oligonucleotide design.

scholarly journals Seeds for effective oligonucleotide design

2021 ◽  
Author(s):  
Lucian Ilie ◽  
Silvana Ilie ◽  
Shima Khoshraftar ◽  
Anahita Mansouri Bigvand
Keyword(s):  
Dna Oligonucleotides ◽  
Spaced Seeds

Background DNA oligonucleotides are a very useful tool in biology. The best algorithms for designing good DNA oligonucleotides are filtering out unsuitable regions using a seeding approach. Determining the quality of the seeds is crucial for the performance of these algorithms. Results We present a sound framework for evaluating the quality of seeds for oligonucleotide design. The F - score is used to measure the accuracy of each seed. A number of natural candidates are tested: contiguous (BLAST-like), spaced, transitions-constrained, and multiple spaced seeds. Multiple spaced seeds are the best, with more seeds providing better accuracy. Single spaced and transition seeds are very close whereas, as expected, contiguous seeds come last. Increased accuracy comes at the price of reduced efficiency. An exception is that single spaced and transitions-constrained seeds are both more accurate and more efficient than contiguous ones. Conclusions Our work confirms another application where multiple spaced seeds perform the best. It will be useful in improving the algorithms for oligonucleotide design.

scholarly journals Optical Monitoring of the Production Quality of Si-Nanoribbon Chips Intended for the Detection of ASD-Associated Oligonucleotides

Micromachines ◽  
2021 ◽  
Vol 12 (2) ◽  
pp. 147
Author(s):  
Kristina A. Malsagova ◽  
Tatyana O. Pleshakova ◽  
Vladimir P. Popov ◽  
Igor N. Kupriyanov ◽  
Rafael A. Galiullin ◽  
...  
Keyword(s):  
Production Quality ◽  
Autism Spectrum ◽  
Covalent Immobilization ◽  
Biological Macromolecules ◽  
Label Free ◽  
Raman Scattering Spectroscopy ◽  
Dna Oligonucleotides ◽  
Highly Sensitive ◽  
Highly Sensitive Detection

Gas-phase etching and optical lithography were employed for the fabrication of a silicon nanoribbon chip (Si-NR chip). The quality of the so-fabricated silicon nanoribbons (Si-NRs) was monitored by optical Raman scattering spectroscopy. It was demonstrated that the structures of the Si-NRs were virtually defect-free, meaning they could be used for highly sensitive detection of biological macromolecules. The Si-NR chips were then used for the highly sensitive nanoelectronics detection of DNA oligonucleotides (oDNAs), which represent synthetic analogs of 106a-5p microRNA (miR-106a-5p), associated with the development of autism spectrum disorders in children. The specificity of the analysis was attained by the sensitization of the Si-NR chip sur-face by covalent immobilization of oDNA probes, whose nucleotide sequence was complementary to the known sequence of miR-106a-5p. The use of the Si-NR chip was demonstrated to al-low for the rapid label-free real-time detection of oDNA at ultra-low (~10−17 M) concentrations.

scholarly journals DNA-Templated Fluorescent Silver Nanoclusters Inhibit Bacterial Growth While Being Non-Toxic to Mammalian Cells

Molecules ◽  
2021 ◽  
Vol 26 (13) ◽  
pp. 4045
Author(s):  
Lewis Rolband ◽  
Liam Yourston ◽  
Morgan Chandler ◽  
Damian Beasock ◽  
Leyla Danai ◽  
...  
Keyword(s):  
Mammalian Cells ◽  
Antibacterial Properties ◽  
Silver Nanoclusters ◽  
Metal Nanoclusters ◽  
Fluorescent Properties ◽  
Dna Oligonucleotides ◽  
Mammalian Cell Lines ◽  
History Of ◽  
The Stability

Silver has a long history of antibacterial effectiveness. The combination of atomically precise metal nanoclusters with the field of nucleic acid nanotechnology has given rise to DNA-templated silver nanoclusters (DNA-AgNCs) which can be engineered with reproducible and unique fluorescent properties and antibacterial activity. Furthermore, cytosine-rich single-stranded DNA oligonucleotides designed to fold into hairpin structures improve the stability of AgNCs and additionally modulate their antibacterial properties and the quality of observed fluorescent signals. In this work, we characterize the sequence-specific fluorescence and composition of four representative DNA-AgNCs, compare their corresponding antibacterial effectiveness at different pH, and assess cytotoxicity to several mammalian cell lines.

scholarly journals Fast and accurate correction of optical mapping data via spaced seeds

2019 ◽  
Vol 36 (3) ◽  
pp. 682-689
Author(s):  
Leena Salmela ◽  
Kingshuk Mukherjee ◽  
Simon J Puglisi ◽  
Martin D Muggli ◽  
Christina Boucher
Keyword(s):  
Error Correction ◽  
Optical Mapping ◽  
Correction Method ◽  
Supplementary Information ◽  
The Novel ◽  
Mapping Data ◽  
Error Correction Method ◽  
Spaced Seeds ◽  
Many Core

Abstract Motivation Optical mapping data is used in many core genomics applications, including structural variation detection, scaffolding assembled contigs and mis-assembly detection. However, the pervasiveness of spurious and deleted cut sites in the raw data, which are called Rmaps, make assembly and alignment of them challenging. Although there exists another method to error correct Rmap data, named cOMet, it is unable to scale to even moderately large sized genomes. The challenge faced in error correction is in determining pairs of Rmaps that originate from the same region of the same genome. Results We create an efficient method for determining pairs of Rmaps that contain significant overlaps between them. Our method relies on the novel and nontrivial adaption and application of spaced seeds in the context of optical mapping, which allows for spurious and deleted cut sites to be accounted for. We apply our method to detecting and correcting these errors. The resulting error correction method, referred to as Elmeri, improves upon the results of state-of-the-art correction methods but in a fraction of the time. More specifically, cOMet required 9.9 CPU days to error correct Rmap data generated from the human genome, whereas Elmeri required less than 15 CPU hours and improved the quality of the Rmaps by more than four times compared to cOMet. Availability and implementation Elmeri is publicly available under GNU Affero General Public License at https://github.com/LeenaSalmela/Elmeri. Supplementary information Supplementary data are available at Bioinformatics online.

Immunoferritin localization of intracellular antigens in positively stained frozen sections

1978 ◽  
Vol 36 (2) ◽  
pp. 168-169
Author(s):  
K. T. Tokuyasu
Keyword(s):  
Surface Tension ◽  
Water Surface ◽  
Thin Layers ◽  
The Other ◽  
Positive Staining ◽  
Frozen Sections ◽  
The Past ◽  
Ultrathin Frozen Sections ◽  
Definition Of

During the past investigations of immunoferritin localization of intracellular antigens in ultrathin frozen sections, we found that the degree of negative staining required to delineate u1trastructural details was often too dense for the recognition of ferritin particles. The quality of positive staining of ultrathin frozen sections, on the other hand, has generally been far inferior to that attainable in conventional plastic embedded sections, particularly in the definition of membranes. As we discussed before, a main cause of this difficulty seemed to be the vulnerability of frozen sections to the damaging effects of air-water surface tension at the time of drying of the sections.Indeed, we found that the quality of positive staining is greatly improved when positively stained frozen sections are protected against the effects of surface tension by embedding them in thin layers of mechanically stable materials at the time of drying (unpublished).

Lithography below 100 nm

1983 ◽  
Vol 41 ◽  
pp. 96-99
Author(s):  
L. D. Jackel
Keyword(s):  
Spatial Distribution ◽  
Electron Beam ◽  
Electron Scattering ◽  
Electron Beam Lithography ◽  
Substrate Material ◽  
Local Electron ◽  
Electron Dose ◽  
Positive Resist ◽  
Exposure Process

Most production electron beam lithography systems can pattern minimum features a few tenths of a micron across. Linewidth in these systems is usually limited by the quality of the exposing beam and by electron scattering in the resist and substrate. By using a smaller spot along with exposure techniques that minimize scattering and its effects, laboratory e-beam lithography systems can now make features hundredths of a micron wide on standard substrate material. This talk will outline sane of these high- resolution e-beam lithography techniques.We first consider parameters of the exposure process that limit resolution in organic resists. For concreteness suppose that we have a “positive” resist in which exposing electrons break bonds in the resist molecules thus increasing the exposed resist's solubility in a developer. Ihe attainable resolution is obviously limited by the overall width of the exposing beam, but the spatial distribution of the beam intensity, the beam “profile” , also contributes to the resolution. Depending on the local electron dose, more or less resist bonds are broken resulting in slower or faster dissolution in the developer.

Convergent Beam Electron Diffraction

1978 ◽  
Vol 36 (3) ◽  
pp. 304-315
Author(s):  
G. Lehmpfuhl
Keyword(s):  
Electron Diffraction ◽  
Diffraction Pattern ◽  
Crystal Surface ◽  
Diffraction Spot ◽  
Crystal Thickness ◽  
Large Area ◽  
Electron Microscopic ◽  
Additional Information ◽  
Microscopic Investigations

Introduction In electron microscopic investigations of crystalline specimens the direct observation of the electron diffraction pattern gives additional information about the specimen. The quality of this information depends on the quality of the crystals or the crystal area contributing to the diffraction pattern. By selected area diffraction in a conventional electron microscope, specimen areas as small as 1 µ in diameter can be investigated. It is well known that crystal areas of that size which must be thin enough (in the order of 1000 Å) for electron microscopic investigations are normally somewhat distorted by bending, or they are not homogeneous. Furthermore, the crystal surface is not well defined over such a large area. These are facts which cause reduction of information in the diffraction pattern. The intensity of a diffraction spot, for example, depends on the crystal thickness. If the thickness is not uniform over the investigated area, one observes an averaged intensity, so that the intensity distribution in the diffraction pattern cannot be used for an analysis unless additional information is available.

Observability of Very Thick Specimen by Using Transmission Scanning Electron Microscope

1971 ◽  
Vol 29 ◽  
pp. 26-27
Author(s):  
K. Shibatomi ◽  
T. Yamanoto ◽  
H. Koike
Keyword(s):  
Electron Microscope ◽  
Image Quality ◽  
Scanning Electron Microscope ◽  
Chromatic Aberration ◽  
Image Contrast ◽  
Objective Lens ◽  
Thick Specimen ◽  
Transmission Electron ◽  
Scanning Electron

In the observation of a thick specimen by means of a transmission electron microscope, the intensity of electrons passing through the objective lens aperture is greatly reduced. So that the image is almost invisible. In addition to this fact, it have been reported that a chromatic aberration causes the deterioration of the image contrast rather than that of the resolution. The scanning electron microscope is, however, capable of electrically amplifying the signal of the decreasing intensity, and also free from a chromatic aberration so that the deterioration of the image contrast due to the aberration can be prevented. The electrical improvement of the image quality can be carried out by using the fascionating features of the SEM, that is, the amplification of a weak in-put signal forming the image and the descriminating action of the heigh level signal of the background. This paper reports some of the experimental results about the thickness dependence of the observability and quality of the image in the case of the transmission SEM.

The Current Situation in Chemical Stabilization of Biological Materials

1972 ◽  
Vol 30 ◽  
pp. 132-133
Author(s):  
John H. Luft
Keyword(s):  
Electron Microscopy ◽  
Electron Microscope ◽  
Osmium Tetroxide ◽  
Molecular Level ◽  
Cross Linking ◽  
Chemical Stabilization ◽  
Specimen Preparation ◽  
Sufficient Condition ◽  
Radio Telescopes

With information processing devices such as radio telescopes, microscopes or hi-fi systems, the quality of the output often is limited by distortion or noise introduced at the input stage of the device. This analogy can be extended usefully to specimen preparation for the electron microscope; fixation, which initiates the processing sequence, is the single most important step and, unfortunately, is the least well understood. Although there is an abundance of fixation mixtures recommended in the light microscopy literature, osmium tetroxide and glutaraldehyde are favored for electron microscopy. These fixatives react vigorously with proteins at the molecular level. There is clear evidence for the cross-linking of proteins both by osmium tetroxide and glutaraldehyde and cross-linking may be a necessary if not sufficient condition to define fixatives as a class.

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