DNA Funtime: How to Stretch DNA and Put It Anywhere You Want (sort of)

journal.pone.0069058.g002_cropped

Ever since the days of Watson and Crick—and Franklin, but we won’t get into that right now—we’ve known that double-stranded DNA’s favorite shape is that of a helix. DNA also comes single-stranded and as a random coil, but regardless, as a type of strand, it stands to reason that if tension could somehow be applied to it, it could be elongated or “stretched.”

Why mess with the shape of DNA strands, single, double, random, or otherwise? Actually, when stretched out in all its glory, scientists hope that they may be able to do many things: map patterns in the DNA sequence, characterize chromosomal abnormalities, and possibly even directly read the genetic or epigenetic information right off its back…bone.

Stretching DNA is very tricky, as you might imagine, and requires fairly complicated (and slow) techniques that often create limitations. Particularly, once you’ve stretched the DNA, you’d like to set it down on a surface somewhere to have a look at it. To do this, scientists often need to use a liquid or solid “carrier,” like a pH-controlled solution, to get the DNA in contact with the depositing surface. However, problems can arise if the surface is fragile or otherwise incompatible with the carrier.

In an epic race to try to stretch DNA the fastest, cheapest, and best, scientists have been wracking their brains to come up with new ways in which this can be done. One of these is illustrated in a recently published PLOS ONE study, titled “Molecular Threading: Mechanical Extraction, Stretching and Placement of DNA Molecules from a Liquid-Air Interface,” where Harvard researchers developed a new method of stretching DNA that allows the strands to be deposited on many types of surfaces in a precise manner.

journal.pone.0069058.g001

The authors call this technique molecular threading, and the method is as follows: stick a special-coated glass microneedle into a DNA-containing droplet of solution, pull it out, and suspend the DNA segment in air until you are ready to put it down on the dry surface below (illustrated in the figure above and the video here).  This works because when you are pulling the DNA out of the droplet, there is an air-liquid interface between the droplet and the air that has the ever-so-convenient property known as surface tension. In a desperate fight to keep the droplet’s shape, the droplet molecules “hold on” to the pulled DNA molecule and create a restoring force that allows the molecule to be suspended in air. As the needle is lowered to the surface, the DNA molecule makes contact with it, and the substrate has enough weak forces to overcome the surface tension, so the DNA sticks to it. And, because threading stretches DNA in air rather than in liquid, the extended thread can be placed onto water-soluble, dry, or fragile surfaces. Voilà!

The researchers gadgeted out the apparatus so that they could monitor this high-throughput process in real-time, take pictures, introduce alternate positioning and angling, and make very precise needle movements. In addition, they made efforts to prevent droplet evaporation and make the straightest DNA strands that they could. The scientists took a look at their handiwork by introducing a fluorescent dye to the DNA and imaging the threads with both fluorescence and electron microscopy; the results of the fluorescence imaging can be seen as bright green lines (individual DNA strands!) in the image below.

journal.pone.0069058.g002

As with any technique, there are caveats and limitations, including the occasional multi-thread extraction and missing thread, but all in all, the authors believe that this technique produces cleaner, straighter, and more reproducible strands than other techniques, like molecular combing, and it also allows them to deposit more molecules closer together. Of course, more work is needed to improve the set up and understand exactly what is going on during stretching.

If you are interested in geeking out further on this topic, please check out the awesome instrument and method pics in the article here.

Citation: Payne AC, Andregg M, Kemmish K, Hamalainen M, Bowell C, et al. (2013) Molecular Threading: Mechanical Extraction, Stretching and Placement of DNA Molecules from a Liquid-Air Interface. PLoS ONE 8(7): e69058. doi:10.1371/journal.pone.0069058

Image and Video Credits: Figure 1, Figure 2, and Video S1 from the article

Wiley Launches New Journal – Regeneration

LSJ-13-57608-WOAI-VW-REG-Cover_180x240Wiley is thrilled to announce the launch of a new open access journal solely dedicated to regeneration and repair together with a team of high profile international editors – Regeneration. Regeneration  is a peer-reviewed, open access journal dedicated to the publication of papers covering regeneration and tissue repair in animals and plants.

Against the backdrop of basic research in developmental biology, and in conjunction with the ascendancy of stem cell biology, the time is ripe to explore the next frontier: natural and assisted healing and regeneration. The goal of the editors and publishers of Regeneration is to provide the first dedicated venue for research related to repair and regeneration in its many forms, and in all relevant species.

With an aging population in the Western world, a growing need for replacing organs is irrevocable, which has put emphasis on the need of increasing and enhancing research in regeneration and repair. Funding to the field has increased in recent years in most countries to further improve and grow the research and it is our hope that Regeneration will be instrumental in communicating these vital results to the community in the future.

The journal’s Editor-in-Chief is Susan V. Bryant, Research Professor and Associate Vice Chancellor for Research in the Department of Developmental and Cell Biology, University of California, Irvine.  Susan is supported by a diverse and internationally prominent Editorial Board of established scientists who have devoted their careers to regeneration and repair.

The journal will publish articles under the Creative Commons Attribution (CC BY) License, allowing authors to comply with Open Access Mandates. Authors are invited to submit articles via the journal’s online submission site, or ask the editorial office for more information about whether their article is suitable for this new journal.

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Read Ecology and Evolution Issue 3.10

ECE 3 10The latest issue of Ecology and Evolution is now live! Over 30 excellent articles free to read, download and share. ‘Interior Least Tern (Sternula antillarum) breeding distribution and ecology: implications for population-level studies and the evaluation of alternative management strategies on large, regulated rivers’ by Casey A. Lott et al. Below are some highlights from this issue:

purple_lock_open Dramatic response to climate change in the Southwest: Robert Whittaker’s 1963 Arizona Mountain plant transect revisited by Richard C. Brusca, et al.
Summary: Models analyzing how Southwestern plant communities will respond to climate change predict that increases in temperature will lead to upward elevational shifts of montane species. We tested this hypothesis by reexamining Robert Whittaker’s 1963 plant transect in the Santa Catalina Mountains of southern Arizona, finding that this process is already well underway. Our survey, five decades after Whittaker’s, reveals large changes in the elevational ranges of common montane plants, while mean annual rainfall has decreased over the past 20 years, and mean annual temperatures increased 0.25°C/decade from 1949 to 2011 in the Tucson Basin. Although elevational changes in species are individualistic, significant overall upward movement of the lower elevation boundaries, and elevational range contractions, have occurred. This is the first documentation of significant upward shifts of lower elevation range boundaries in Southwestern montane plant species over decadal time, confirming that previous hypotheses are correct in their prediction that mountain communities in the Southwest will be strongly impacted by warming, and that the Southwest is already experiencing a rapid vegetation change.

purple_lock_open Did the house mouse (Mus musculus L.) shape the evolutionary trajectory of wheat (Triticum aestivum L.)? by C. F. Morris, et al.
Summary: Wheat (Triticum aestivum L.) is one of the most successful domesticated plant species in the world. The majority of wheat carries mutations in the Puroindoline genes that result in a hard kernel phenotype. An evolutionary explanation, or selective advantage, for the spread and persistence of these hard kernel mutations has yet to be established. Here, we demonstrate that the house mouse (Mus musculus L.) exerts a pronounced feeding preference for soft over hard kernels. When allele frequencies ranged from 0.5 to 0.009, mouse predation increased the hard allele frequency as much as 10-fold. Studies involving a single hard kernel mixed with ~1000 soft kernels failed to recover the mutant kernel. Nevertheless, the study clearly demonstrates that the house mouse could have played a role in the evolution of wheat, and therefore the cultural trajectory of humankind.

purple_lock_open Quantitative genetic analysis of responses to larval food limitation in a polyphenic butterfly indicates environment- and trait-specific effects by Marjo Saastamoinen, et al.
Summary: Different components of heritability, including genetic variance (VG), are influenced by environmental conditions. Here, we assessed phenotypic responses of life-history traits to two different developmental conditions, temperature and food limitation. The former represents an environment that defines seasonal polyphenism in our study organism, the tropical butterfly Bicyclus anynana, whereas the latter represents a more unpredictable environment. We quantified heritabilities using restricted maximum likelihood (REML) procedures within an “Information Theoretical” framework in a full-sib design. Whereas development time, pupal mass, and resting metabolic rate showed no genotype-by-environment interaction for genetic variation, for thorax ratio and fat percentage the heritability increased under the cool temperature, dry season environment. Additionally, for fat percentage heritability estimates increased under food limitation. Hence, the traits most intimately related to polyphenism in B. anynana show the most environmental-specific heritabilities as well as some indication of cross-environmental genetic correlations. This may reflect a footprint of natural selection and our future research is aimed to uncover the genes and processes involved in this through studying season and condition-dependent gene expression.

Read other top articles in this issue >

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Brain and Behavior Issue 3.5 is Now Online

BRB 3 5The latest issue of Brain and Behavior looks at first language writing systems’ impact on second language word reading and examines the posterior insular cortex.  The cover features an image from, “Distinction between hand dominance and hand preference in primates: a behavioral investigation of manual dexterity in nonhuman primates (macaques) and human subjects” by Pauline Chatagny, Simon Badoud, Mélanie Kaeser, Anne-Dominique Gindrat, Julie Savidan, Michela Fregosi, Véronique Moret, Christine Roulin, Eric Schmidlin, and Eric M. Rouiller

Below is another article highlight, chosen by the editorial team. 

purple_lock_open The role of rs2237781 within GRM8 in eating behavior
By Marie-Therese Gast, Anke Tönjes, Maria Keller, Annette Horstmann, Nanette Steinle, Markus Scholz, Ines Müller, Arno Villringer, Michael Stumvoll, Peter Kovacs, and Yvonne Böttcher
Abstract: The glutamate receptor, metabotropic 8 gene (GRM8) encodes a G-protein-coupled glutamate receptor and has been associated with smoking behavior and liability to alcoholism implying a role in addiction vulnerability. Data from animal studies suggest that GRM8 may be involved in the regulation of the neuropeptide Y and melanocortin pathways and might influence food intake and metabolism. This study aimed to investigate the effects of the genetic variant rs2237781 within GRM8 on human eating behavior. 

Link to the full table on contents here.

Submit your research here.

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Pre-emptive cancellation costs far, far more than it saves


Bjorn Brembs: “What you’re saying here is that cancellations now are premature, because too few articles are actually available in green repositories? That libraries should hold off because otherwise we face access problems? If that is what you are saying here, then it may be worth spelling it out more clearly as for me that was not immediately obvious. Unintended consequences in publisher behavior (as you allude to above) aside, what is your opinion on using the funds of canceled subscriptions to improve repository functionality to improve green acess? This should only mean a brief interruption of service for much improved access shortly thereafter and a speeding up of the transition you envisage?”

1. Cancelling journals because their policies are Green — i.e., because they do not embargo Green OA self-archiving — is both absurd and destructive: It simply encourages journals to adopt embargoes.

2. Cancelling journals because (some of) their articles are Green is premature and self-defeating: Less than 20% of journal articles are unembargoed Green (i.e., immediate) OA today, and they are distributed randomly across all journals. Hence to cancel any particular journal because the proportion of its articles that is available Green today exceeds this global average is, again, just to penalize that journal, perversely (as well as jeopardizing the growth of Green OA itself, gratuitously).

The time to consider cancelling journals is once Green OA mandates and hence Green OA are at or near 100% globally, and hence the proportion of journal articles that are green OA is at or near 100%. At this point all journals will be at or near 100% and the global cancellation pressure will affect all of them, forcing them all to cut inessential costs, downsize, and convert to Fair Gold OA. (Then — and only then — is the time to redirect a fraction of each institution’s annual subscription cancellation windfall savings to pay the much-reduced Fair-Gold publication fees for the institution’s authors’ own annual article output, affordably and sustainably. Trying instead to start doing this now, pre-emptively — while percentage Green is still low, Green growth is still slow and unstable, subscriptions to core journals still have to be paid, and Fool’s Gold is still over-priced and double-paid (and double-dipped, if hybrid Fool’s-Gold) — would be a profound failure to think ahead.

In sum, to cancel journals now based on the percentage of their articles that are accessible as Green OA now would be as as short-sighted and futile as it would be counterproductive: Like the Finch Fiasco and , premature cancellation would only serve to delay the optimal and inevitable for yet another gratuitously lost decade.

(I begin to think that that might even serve as a fair punishment for all this seemingly endless readiness to run off in all directions but the right one, without troubling to think anything through even a few steps ahead!)

The Power of the Claw: Not Your Average “Soft” Material

Sep blog-tiger cropped

Earlier this month we gave you cuddling between affectionate lions. Lest we become overwhelmed by the desire to cuddle one of these (albeit adorable) feline predators ourselves, here is a look at exactly what one of their clawed paws could do to us, including to one of our toughest components: bone. In a PLOS ONE study published earlier this month, researchers tested the ability of claws to scratch the surface of bone. The effects of claw damage are often overlooked because claws are made of a material softer than bone. Contrary to expectations, however, these researchers found that claws produced recognizable bone damage.

The setup was simple: let a Kansas zoo tiger participating in their enrichment program spend an afternoon leisurely playing with carefully nested cow thigh bones, also called femora. To ensure that the cow femora were only accessible to tiger claws and not to tiger teeth, researchers bolted femora down into a log that was narrowly hollowed out—preventing the big cat from sticking his snout in.

Sep blog- cow femora

The result: impressively lacerated cow femora. Once tiger playtime was over, researchers removed the log, unbolted the femora, and microscopically examined the bone. Four scratches were clearly visible upon the bone’s surface. The scanning electron microscope (SEM) image below further highlights the depths of the tiger claw handiwork.

Sep blog-fomora scratches microscope

In this particular gouge, the main diagonal chasm in the image, the gulf made by the tiger’s claw penetrated the outer covering and subadjacent bone into the bony matrix. As we can see, tiger claws can do some damage.

Damage done to bone, however, is for the most part attributed to the effects of a predator’s teeth and not its claws, the reason being that measures of scratch resistance adhere to a so-called Mohs scale of mineral hardness. The Mohs scale is graded, with talc (1) as the softest material and diamond (10) as the hardest. On the scale, harder materials damage softer materials, but not vice versa. And in our case, bones are, in fact, harder than claws. Claws are made of the protein keratin—the same stuff is in hair, wool, nails, horns, and hooves—which scores a meager 2.5 on the Mohs scale. Bone, on the other hand, scores a much more formidable 5.0.

The current research, however, shows that we can expand our understanding of scratch resistance and mineral hardness to include the effects of softer materials striking harder materials, as long as we consider the kinetic energy involved, like the action of a tiger swatting or grabbing with its paw. In essence, more could be going on in the fossil record than previously thought.

Paleontologist and PLOS ONE Section Editor Andy Farke points out in the PLOS ONE blog The Integrative Paleontologist that fossils inevitably resurface as imperfect objects, which is, in part, what makes them so interesting: These fossils bear the visible marks in postpartum decay of a long and varied history. When studying bone narratives, paleontologists encounter everything from water damage to the bore marks of little critters. Including big-critter claw marks in the repertoire of possible bone modifications broadens this narrative and evidences, as the researchers themselves so aptly put it, the power of the claw.

For more information from the paleontologist perspective, check out blog posts on this article in The Integrative Paleontologist  by Dr. Farke and National Geographic.

Citation:

Rothschild BM, Bryant B, Hubbard C, Tuxhorn K, Kilgore GP, et al. (2013) The Power of the Claw. PLoS ONE 8(9): e73811. doi:10.1371/journal.pone.0073811

Image 1: Tiger by Dave Stokes

Image 2: doi:10.1371/journal.pone.0073811

Image 3: doi:10.1371/journal.pone.0073811

@Jay_Naidoo @Okcon “use the tool that you have to fight for justice and ethics”

Listening to @Jay_Naidoo’s plenary on Wednesday at #okcon I had a revelation.

What matters is Justice.

Jay’s twitter describes him as  Chairman of the Global Alliance for Improved Nutrition(GAIN), former Minister in Mandela Cabinet, founding GS of COSATU and political and social activist. Jay gave  us 30 minutes of breathtaking passion about what we must do for the world. I tweeted it and have recaptured my tweets (below).  Jay urged us to action – at the end Andrew Stott (chair) asked

“what is most import thing for us to do in the next week?”

Jay:   “use the tool that YOU have to bring justice and ethics”

That has changed the rest of my life. The key word is JUSTICE. That’s what the OKF is about. That’s what my software is about. That’s what this blog is about. And it was the theme running through the whole of #okcon. We develop tools (blogs, protocols, Python, Java, CKAN, Open Spending, Panton Principles, etc.) to make the world a just society.

Jay articulated Nelson Mandela’s passion on stage – it was as if it was Mandela speaking. If you were not at the session is is the must-watch 30 minutes of #okcon – and watch it all.

Here are my tweets from Jay – the order doesn’t matter. Read them and then go out and fight for justice.

when you are poor the only food is junk food.

“one person one vote” => “one person one gigabyte” (of information)

we can now hold leaders to account. Citizenry must be informed and make power accountable

“we have liberated ourselves from the chains of secrecy”. Where is the money for the library and toilets?

when people know the truth and their rights they become unstoppable. Everyone of us is a journalist and whistleblower

give us (digital) tools for accountability.

SA has second most transparent budget in world. We have to make it understandable. Create a revolution

can we translate understanding of budget into local funding to deliver schools, etc.

SA delivered a political miracle .

old generation cannot tell young what they should do but must support them.

Andrew Stott asks  how do we make this happen.  we must give young people a voice . innovation to deliver a better society

Have to defeat language of denialism . We must be advocates of building society where we care about what happens to planet

money that belongs to our people (in S A) is stolen. Governance should be brought to ordinary people through Open Data

We must bring back ethics and accountability

How do we make our democracy work. How create livelihoods. S Africa now lags behind Kenya.

[telcoms in Africa]. Must design this (from bankrupt beginnings) to provide justice

technology has led to death of geography but not death of injustice

Live a life of truth. Undiluted truth. Then you will challenge injustice wherever it stands

how to we bring compassion into the cold steel of technology. Our technology is built from blood spilt in the Congo

[recalls Mandela] – “fighting poverty is not an act of charity, it is an act of justice”.

stand up and do something

Build a tsunami of hope and accountability – your job is to be accountable and serve society

“Overflowing of positive energy that makes us want to be better people”

tackle global malnutrition. Billion people will go to bed today without food

we have brought the world to its knees. What could we have done with the wasted financial millions. The problem remains

You must be brave like Steve Biko. Nothing to lose but your chains.

 

 

#okcon (first) thoughts (blog, hack)+ in Geneva Public Library

My blogging comes in fits and start. I sometimes used to feel upset if I didn’t blog each day. But now I two major imperatives – to blog and to hack Liberation Software. And for the last few weeks the software has been on top.

Also I have had technical problems. I have been using Word to author blogs since (a) I didn’t like WordPress interface (b) I can only use it online (unless you tell me different) and (c) I spent some time experimenting with Word’s voice recognition software (d) it was more convenient to use Word to create compound documents with included images. (c) no longer holds. (d) started to fail badly and doesn’t seem to have a cure. Word/Wordpress gave useless error messages, failed to upload, created multiple posts with same title, etc.

So I am coming back to using WordPress. I think it’s clunky but I have no alternative. It means I can only blog at certain times of the day and have to spend extra time uploading the images. But I have to do it.

Wow! I can copy. Maybe it’s not so bad. (BTW this is Chuff, the OKF okapi).  Animals are not allowed in libraries so he/she/it is sleeping in the hotel. I love public libraries – they have a sense of calm, quiet but also centuries of history of the struggle for freedom. See http://switzerland-geneva.com/attractions/library.html . They have free wifi. And there’s a student cafe in the next building.

My mind has been blown at #okcon. I need to blog on at least the following:

  • Mat Todd’s fantastic, world changing, session yesterday on Open Source Drug Discovery. The world has a crisis in dscovering new pharmaceuticals and, IMO, Open Knowledge and collaboration is a critical part. Without it we shall not defeat Neglected Tropical Diseases (NTD) or antibiotic resistance. We have to change the way we work.
  • Jay Naidoo’s completely inspirational talk yesterday. He is a colleagues of Mandela and brought the same massive message. (“South Africa was the political/democratic miracle of the twentieth century”). Jay brought me one word – JUSTICE – which is transforming the way I now see Open Knowledge. That is what we are about.
  • OKF itself. We are now a major resource for bettering the world. Some years ago I started telling people “Wikipedia is the digital triumph of the 2000′s. OKFN will be the triumph of the 2010s.” (I don’t think I ever wrote this). I now believe it.
  • Chuff. Down! Your time will come. In Berlin 2014. (This shows I can do strikethroughs).

But I also need to hack. Content-mining will be massive and I am making a contribution through PDF-hacking (#ami2). I’m now very close to nearly faultless conversion of BioMedCentral PDFs to semantic XML. Ross Mounce, Matt Wills and I will be starting on this in earnest next month for phylogenetic trees. It’s been desperately hard work and it’s really only because I don’t have a day-job I can give it the obsessiveness it needs. But #ami2 can do simple tables (nobody can do complex tables because there are no semantics describing them). #ami2 can do diagrams if the EPS strokes and characters are still there. I’ve done a complex phylo tree and am pleased with progress. (I’ll blog all this later).

So I’m going into blog-hack-blog-hack mode… (blog, hack)+ in regex-speak. The hacking takes precedence.

So maybe WordPress is now easier to use than it used to be – we’ll see. I might even try SVG later.

 

Latest Article Alert from Respiratory Research

The following new articles have just been published in Respiratory Research

For articles using Author Version-first publication you will see a provisional PDF corresponding to the accepted manuscript. In these instances, the fully formatted Final Version PDF and full text (HTML) versions will follow in due course.

Research
A randomized, controlled trial to evaluate the effect of an