Monthly Archives: June 2017

During the past 20 years or so, DNA testing has become a household phrase. Television shows about tracing one's heritage and medical discoveries into the genetic links to illness have fed into this need to find one's origins or one's DNA pattern.

Now that is a possibility.

Sometimes people search their lineage out of curiosity. Family lore often carries untruths that people have believed for a few generations, and then they find out that the information was not accurate. Sometimes the curiosity stems from another desire.

"I have found that many people just want the information so that they can go on a trip and visit the geographic areas from which their ancestors came," said Marsha Peterson-Maass, a professional genealogist.

Whether it is an interest in ethnicity, lineage or medical predispositions, there is a commercial DNA test for finding out the answers.

"DNA testing technology is available for everyone, but first you need to figure out what test you want to take because there is usually a reason for why you are testing," said Peterson-Maass, during an "Understanding Commercial DNA Test Results" seminar at the Kankakee Public Library.

Peterson-Maass explained there are three different types of DNA, which include Autosomal DNA, mtDNA and Y-DNA. Each type tells something a little bit different about oneself and one's heritage.

1. Autosomal DNA offers the most extensive answers. It provides both kinship and medical results. It traces back six or possibly seven generations. Once tested, the testing company can identify other people already in its database, called cousins, who share long strings of matching DNA. (The matches are labeled cousins because somewhere back in the lineage, the two people came from a common couple pairing.)

In addition to lineage, this type of DNA also can identify physical traits and medical predispositions.

But, "I'd like to provide a word of caution here," Peterson-Maass said. "A predisposition does not mean that someone will definitely develop the condition, but if something in the report is scary, hiring a forensic genealogist through The Council for the Advancement of Forensic Genealogy to help understand the results can be a benefit."

2. mtDNA (mitochondrial DNA) offers deep ancestry information through the female line. Mitochondria are found in the cytoplasm of human cells, and while a mother passes it to every child, only daughters pass it on to the next generation. The mutation rate for mtDNA is only every 450 years or 22 generations, so having one person in a family tested is usually enough. Information found with a test for mtDNA would be able to tell a person what geographic area in which the matrilineal family line originated. It also is possible to find out what other family lines stemmed from the same origin and branched out elsewhere.

3. Y-DNA offers information passed only through males. It is the DNA on the Y-chromosome. Similar to mtDNA, Y-DNA also has a slow mutation rate. The mutation rate is about 150 to 200 years, so again, having one person tested in a family line is often enough to gather the results needed. Information about the origins of the patrilineal line can be found with a test for Y-DNA.

Commercial tests are available for each DNA type. At the moment, five companies offer commercial DNA testing: FamilyTreeDNA, DNA.Ancestry.com, 23andMe.com, Nat Geo and DNA Tribes.com. All of the companies offer some type of ethnicity report, but only 23andMe will give a chromosomal view, showing physical traits and medical predispositions.

Worried about a blood test? These testing companies use saliva samples swabbed at home and mailed in to the companies.

"It should be noted that DNA testing is not a magic solution and doesn't provide an instantaneous family tree," Peterson-Maass said. These tools work best in conjunction with traditional documentary research, she added.

It can get pricey. In general, costs for FamilyTreeDNA, DNA.Ancestry.com and 23andMe range from $59 to $99. FamilyTreeDNA offers mtDNA for $79 (for the full sequence, $199) and Y-DNA testing for $169 to $359. National Geographic offers mtDNA for $149. DNA Tribes testing starts at about $119.

And sometimes the results found can lead to further questions, as Al Mikel, a seminar attendee stated: "I just got my results from Ancestry.com, and they are something that I think I need to study."

More:
Thinking about testing your DNA? Here's what to know - Kankakee Daily Journal

June 19, 2017 by Stuart Mason Dambrot feature Fig. 1. Spontaneous formation of aligned DNA nanowires. (A) Schematic illustrations of the spontaneous formation of an array of DNA nanowires by the skin folding induced by water filaments containing DNA molecules. (B) Sequential optical microscope images of a droplet of DNA solution spreading over wrinkles (t = 5 min, 0.03); the wrinkle-to-fold transition occurs at the boundary and propagates with the edge of the droplet. (C) AFM image of an array of DNA nanowires extending from the boundary (t = 2 min, 0.02). The line profiles for each region are shown next to the image. (Scale bars: B, 50 m and C, 4 m.). Credit: Nagashimaa S, Haa HD, Kima DH, Komrljb A, Stone HA, Moon M-W (2017) Spontaneous formation of aligned DNA nanowires by capillarity-induced skin folding. Proc Natl Acad Sci USA 114:24 6233-6237.

(Phys.org)Nanowires fashioned from DNA (deoxyribonucleic acid)one of several type of molecular nanowires incorporating repeating molecular unitsare exactly that: Geometrically wire-like DNA-based nanostructures defined variously as having a 1~10 nm (109 m) diameter or a length-to-diameter ratio >1000. While nanowires can be made from several organic and inorganic materials, DNA nanowires have been shown to provide a range of valuable applications in programmed self-assembly1,2 of functional materialsincluding metallic and semiconductor nanowires for use in electronic devicesas well as biological, medical, and genetic analysis applications3,4,5. That being said, DNA nanowire adoption has been limited due to historical limitations in the ability to control their structural parametersspecifically, size, geometry and alignment. Recently, however, scientists at Korea Institute of Science and Technology and Princeton University leveraged the capillary forces of water containing DNA molecules to demonstrate size-controllable straight or undulated aligned DNA nanowires that were spontaneously formed by water entering wrinkled channels of a compressed thin skin on a soft substrate, which subsequently induced a wrinkle-to-fold transition.

Assistant Professor and lead author So Nagashima, Assistant Professor Andrej Komrlj, Donald R. Dixon '69 and Elizabeth W. Dixon Professor Howard A. Stone, and Principal Research Scientist Myoung-Woon Moon discussed the paper they and their co-authors published in Proceedings of the National Academy of Sciences. "I think that the most challenging aspect of devising our method for utilizing a thin skin template that responds to water by dynamically changing its surface morphology was finding the conditions where the wrinkle-to-fold transition occurs," Moon tells Phys.org. "The critical conditions as a function of the applied strain, initial wrinkle geometries, and thickness of the skin layer determined by oxygen plasma treatment duration were difficult to find." Moon adds that the observation technique for the dynamic transition was limited to only optical microscopes whose highest optical resolution falls between 100 to 1000 nm in the width of nanowires, this being due to the dynamic transition taking place at the submicron scale.

When inducing a template surface wrinkle-to-fold transition by exploiting the capillary forces of water containing DNA molecules, Stone points out, the observation that water changes the wrinkle-to-fold transition is new. "As far as we know, ours is the first study to show this effect, as is demonstrating one use of such folds for the alignment of DNA. Moreover, control of surface tension or resultant capillary forces and the area for fold formation is relatively hardand by adding DNA molecules to water, it appears that the surface tension is changed, so the fold transition length was shorter."

Template preparation used an oxygen plasma treatment of prestretched polydimethylsiloxane (or PDMS, a polymeric organosilicon compound) substrates for varying durations. "In fact," Moon explains, "the manipulation of PDMS with prestretching strain is a relatively well-developed method as is the oxygen plasma treatment: both have been discussed in the literature. We can make the samples with various sizes of a few millimeters to a few centimeters, which can be also made on much larger area." Moon notes that the researchers can also vary polydimethylsiloxane's mechanical propertiesto make it more stretchable, soft or flexibleby changing the ratio of elastomer and cross-linker for PDMS preparation.

A key aspect of the study was confirming that the new method reliably manipulates DNA nanowire size, geometry, and alignment. "By adjusting the conditions for stretching strain, plasma treatment duration, and post-compression of the stretched PDMS, DNA nanowires can be a half cylinder, a perfect cylinder, or undulated wire shape," Moon tells Phys.org. "By changing the wrinkle geometries such as the amplitudewhich is governed by the strainone can control the distance between wires in the fold channel." Wider distances between wires, he continues, can be accomplished by compressing the PDMS less, while compressing the substrate more yields smaller distances.

To address these challenges, the scientists discovered a transformation resulting from capillary forces that act at the edge of a water droplet that can, with only 1% compression, transform wrinkles into folds, which in the absence of a liquid drop form only at very high (~30%) compression. In addition, Moon adds, smaller substances such as biomolecules or nanoparticles can follow the water channel to form aligned 1-dimensional nanostructures. "Smaller is better. Less is more. We've found that the wrinkle-to-fold transition takes place more easily when the following factors become smaller: compression level, skin thickness, droplet volume, size of the sample surface, and static contact angles of droplets."

Based on their findings, the authors stated that their approach could lead to new ways of fabricating functional materials. "Our key finding is that one can change wrinkles into localized folds by simply exploiting the capillary forces of water on wrinkled surfaces under very small strain of about 1% in compression," Nagashima tells Phys.org. "Recent studies reported in the literature have demonstrated that such wrinkle-to-fold transitions can help develop systems that dynamically change their properties according to the surface morphology. However, inducing the transition in the absence of water is difficult to achieve in practice because, in general, large compression needs to be applied to the skin-substrate system, which hinders wider applications. Our study reveals that even 1% of compression, which is the critical level for creating wrinkles in our case, is large enough to trigger the transition to folds locally when water is present." Nagashima notes that while the compression level required to induce the transition might differ according to the skin-film system used, only a small compression level would be necessary in combination with water.

"This phenomenon can be considered a lithography-free method that allows for ready fabrication of arrays of nanomaterials, where their size, length, and periodicity could robustly be tuned," he continues. "Moreover, not only water but other liquids could be used to carry nanomaterials and to induce the wrinkle-to-fold transition."

Moon describes several examples of potential de novo fabrication and analysis techniques, including nanoscale lithography, nanoimprint, growth by chemical vapor deposition, and chemical reaction. "Our method can potentially be used for the fabrication of 1-dimensional nanowires or nanoarrays for application to DNA analysis with very dilute or small amounts of DNA; DNA templates as new metal or ceramic nanostructures; and DNA treatment devices for healing modified DNA. In addition, one can adopt this technique to handle protein, blood, or nanoparticles at nanoscale."

Komrlj and Stone tell Phys.org that one area of planned research is focused on nonlinear analysis and modeling for improved quantitative understanding of the capillarity-induced wrinkle-to-fold transition. "Since our system is composed of the mechanical behavior of the fold transition triggered by liquid surface tension, the wrinkle-to-fold transition that we've found is associated with large deformations where conventional linear elasticity theory does not apply. While the basic mechanisms can be explained within the linear theory, quantitative comparison with experiments can only be achieved by taking into account geometrical and material nonlinearities. We are therefore performing numerical simulations by coupling liquid surface tension and solid deformation, as well as performing analysis with perturbation series, where nonlinearities of elastic structures can be studied systematically."

"I also think that the challenges ahead are to find how to achieve larger areas for DNA pattern formation," Moon says. "In fact, our latest resultsobtained after this PNAS article was acceptedshows some impressive progress for the region with wrinkle-to-fold transition in larger areas, such as the entire area underneath a water droplet. Another area to be studied, Moon continues, concerns the fact that biological morphogenesis of skinsubstrate systems are ubiquitous in organisms where water is a major constituent. "We're trying to find situations where our findings are applicable. Active collaborations with experts in the field would be helpful."

The researchers might also investigate materials other than PDMS. "Yes. other polymers can work if they possess the basic factors to govern the fold transition, these being the thinness of the nano-skin and soft body materials, and surface hydrophilicity to ensure sufficient surface reaction with liquid," Moon notes.

Other possible future research interests and additional innovations mentioned by the authors include:

- theoretical analysis to elucidate the underlying physics related to the water-induced surface folding

- exploit the underlying physics to develop a robust and mass fabrication method for inducing the wrinkle-to-fold transition

- find and discuss morphological changes in nature where water is likely a key factor

- apply the current study's results to DNA analysis or DNA drug devices

- 2-D/3-D sensors, diagnostic tools, and drug-release systems

- templates for fabricating 1-dimensional nanomaterials

- methods for local patterning

"I believe that this work is beneficial to materials science for nanowire templates, mechanics for fluidic channels, and biology for quantitative analysis of DNA or other biomolecules," Moon concludes.

Explore further: Observation of the phase transition of liquid crystal defects for the first time

More information: Spontaneous formation of aligned DNA nanowires by capillarity-induced skin folding, PNAS (2017) 114:24 6233-6237, doi:10.1073/pnas.1700003114

Related:

1DNA nanowire fabrication, Nanotechnology (2006) 17:R14m https://core.ac.uk/download/pdf/1559975.pdf

2DNA-Templated Self-Assembly of Protein Arrays and Highly Conductive Nanowires, Science (2003) 301:5641 1882-1884, doi:10.1126/science.1089389

3Nanowire-Based Sensors for Biological and Medical Applications, IEEE Transactions on NanoBioscience (2016) 15:3 186-199, doi:10.1109/TNB.2016.2528258

4DNA-Based Applications in Nanobiotechnology, Journal of Biomedicine and Biotechnology (2010) Article ID 715295, doi:10.1155/2010/715295

5Nanowire nanosensors, Materials Today (2005) 8:5, doi:10.1016/S1369-7021(05)00791-1

2017 Phys.org

KAIST researchers observed the phase transition of topological defects formed by liquid crystal (LC) materials for the first time.

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Of wrinkles and wires: Capillarity-induced skin folding spontaneously forms aligned DNA nanowire - Phys.Org