There aren't as many videos about yawning out there as you might think.

This Slate article about a supposed phenomenon known as ASMR is a few months old but it's still an interesting subject*. ASMR, or the Autonomous Sensory Meridian Response** is a rather general term for a collection of subtle but pleasurable psychological and physical reactions to what appears to be gentle or indirect stimuli. It can reportedly be triggered by gentle whispering, light touching, or even just the implication of receiving care from another person. Crinkling food wrappers, sorting silverware, or examining groceries also seem to produce ASMR for some individuals.

I don't experience this phenomenon. I generally remain skeptical about unexplained phenomena, too, especially when they're endemic to the Internet. Despite my skepticism I can't help but wonder if ASMR is really just a way to collectively codify a set of real psychological phenomena previously considered too minor to observe or too difficult to quantify. Everyday life is rich in dull but enjoyable moments. Perhaps mass communication just offers them in a more concentrated format, much like it does with news. Information overload is a real issue, too, if not a psychological one. It's the result of an inability to distinguish signal from noise; perhaps ASMR is pleasurable because it requires observation of a small signal (like Bob Ross' whispered instructions, for instance) in a low-noise background. It's relaxing because there isn't a lot of stimulus competing for the recipient's attention but it's stimulating because it's direct.

What's considered ASMR may truly be a collection of phenomena all related to the same set of primarily audiovisual stimuli. I think it's safe to suggest that the limbic system is involved and that much of the reaction is subconscious. It's reported to be not quite but almost orgasmic, much like yawning or sneezing are sometimes described. The Slate article above also suggests some potentially Freudian parent-child reaction but I think that may just be confirmation bias; Youtube participation may skew toward female users.

It would be interesting to see what range of stimuli repeatedly produce ASMRs in those who feel them. Do gently-worded threats do it? What about calming medical interviews in foreign languages?


*This sentence originally ended "...but it's been making the rounds again." That's how the last entry begins and it's kind of an embarrassing phrase to use anyway. Calling attention to it kinda defeats the purpose of editing but now it's not redundant, at least.

**It's really kind of a curious name for the phenomena. I'd generally expect unexplained psychological responses to acquire more pseudo-scholastic and less clinical names, i.e. Morgellons. Perhaps that's one distinction between a pleasurable unexplained phenomenon and a collective delusion.

Hunka burnin' love

There's a web game called No One Has To Die that's been making the gaming-blog rounds. I don't intend this to be a gaming blog per se but this particular game is really quite good. Without giving too much away, it an excellent example of how even the smallest dose of interactivity can turn a fairly average story into a multifaceted one by virtue of player choice. The venerable Choose Your Own Adventure books did that too, of course, but aren't those really games, too? Either way, No One Has To Die isn't even that much more fun than flipping around a paperback to avoid the "bad" endings, but in this case it's clearly intentional. Perhaps most games can be reduced to repeating different permutations of the same actions until the desired result is reached.

As cheap as free?

It now costs about $3000 to $5000 to sequence a human genome. That cost is 10,000x less than the same effort had required just 10 years ago. Obviously we can't get the technology to be much cheaper, right? The sequencing machinery itself is growing cheaper: as of last year, a decent next-generation sequencer could be purchased for $80,000 to $120,000 or so, down from half-million dollar models from just a few years ago. The limiting factor here may be how the machines are intended for research purposes. A well-funded lab can certainly afford to spend hundreds of thousands of dollars on a single machine, to say nothing of the reagents required to actually get data out of it.

Ubiquitous DNA sequencing has the potential to upend nearly everything we know about personalized medicine, but only if it's not cost-prohibitive. Basic molecular biological techniques certainly have applications in clinical or diagnostic environments. Sequencing could really go beyond that and become relevant to everyday folks. It could just be a matter of having a streamlined, automated system, with samples sent elsewhere. A recent start-up called uBiome offers to characterize the microbiome of just about anything you'd like for less than $100. They aren't specific about how they got their costs so low, but I'm assuming they're just doing the usual 16S rRNA amplification and some quick next-gen sequencing. That's one way to create demand for incredibly cheap sequencing technologies.

Let's wax futurist about the potential of super-cheap, publicly-available nucleotide sequencing:

• Breakfast cereal manufacturers can offer free microbiome sequencing in every box of Cap'n Bran Flakes to show how their product might contribute to a healthy gut.
• Vending machines can offer genome screening on demand to screen for potential genetic maladies (but do people ever use those drugstore blood pressure screening machines? Are they secretly some kind of Scientologist apparatus?)
• Speaking of drugstores, pharmacies could do quick screens for genetic predisposition to adverse drug reactions before they actually dispense said drugs.
• Labs could spend money on more practical things, like this electronic ice bucket. Oh yeah. 

Virulence Factors is the punk band that never was*

It seems like every time I hit up Google for a quick answer to a science question I find a new database. In this case, the question was "does the Vibrio pathogenicity island produce an infective phage particle on its own?" It's really just a question best answered by a review article rather than a database, but I found a nice map of the pathogenicity island in question. Very helpful, plus this VFDB site may be helpful in the future despite, sadly, appearing inactive since 2008.**

*Virulence Factor is apparently a band from Chicago. They're kind of Evanescence-metal. Unlike the above database, Virulence Factor remains active.

**Oh, wait, no! There's a new version of VFDB.

A membrane protein specific to Staph?

So I was poking around in some gene orthology databases and found a family of uncharacterized proteins conserved in Staphylococcus. It's at least in S. aureus COL. Though the protein family is largely undescribed, some annotations seem to suggest it's a M50B family metalloendopeptidase.

Pretty pictures

No radiation, but it is diatomic

This is a scanning electron micrograph of a diatom, a single-celled organism and a type of phyoplankton. Diatoms are known for the varied appearance, specifically that of their silica-based outer walls, also known as frustules. This diatom isn't naturally red - that's just the false color - but it does naturally have that radiation-warning pattern.
The image is from Anne Weston of the  London Research Institute of Cancer Research UK and is a 2012 Wellcome Image Award winner.

Babies on strike

Found while looking for tuberculosis-related public health posters:

Infants Local 23

This is a poster from the Library of Congress archives. Perhaps babies just aren't well-organized.

Here's a pretty neat example of technological time travel: media preservation folks at Indiana University found gramophone records printed into books from the late 19th century. The records aren't solid media. They're just ink-based reproductions of the grooves found on records. From these grooves we can produce waveform images and from the images we can produce audio. The original authors of these reproduced records explicitly intended their work to be accessible in the future, though they clearly didn't foresee technology like scanners or audio editing software.

There are other, earlier examples of hand-engraved waveforms. Here's one from 1806, mentioned in the link above but looped by me just for fun:

I listened to this TED talk by Allan Savory today. TED talks are usually rich in big ideas and poor in specifics. This one is certainly no exception. Even so, it illustrates one potential example of an established phenomenon proving to be somewhat less than the absolute truth.

Savory explains how global climate change isn't just due to an overabundance of burning carbon sources. It's also due to rampant desertification. Many former grasslands have, over the course of the last century or so, lost most of their natural plant life and groundcover, exposing the soil to the elements and increasing water loss by evaporation. The area no longer serves as carbon storage. Savory proposes that the only solution (and here's where I start to get skeptical, at least due to his claims of the "only solution") is to mimic the effects of natural animal movement patterns with livestock. Large herds of cattle usually don't stay in one place for long: they graze for a while and move on to the proverbial greener pastures. Some success has been had in planning the grazing patterns of domestic livestock such that they keep moving through arid areas and stimulate plant growth rather than just consuming it all. The improved plant growth should prevent or even reverse large swaths of desert and allow for enough carbon storage to reduce atmospheric carbon to pre-industrial levels.

It would be nice to think that reversing carbon-based climate change is as easy as shuffling around livestock. I worry about how well the theory scales up; what assumptions are being made about how much desert land can really be reverted to grassland? Do these plans require more livestock than we currently have? What's the potential impact on methane levels? Allan Savory has been talking about holistic resource management for decades, but some actual models of its potential impact on climate change would be nice to see. I presume they exist somewhere. (There's plenty of climate-bloggery about Savory's hypotheses out there but much of it looks less than open-minded.)

It's a lovely shade of orange.

I found this in a lab cleanout today: SDS Tris-Glycine Butter. Not the best thing to put on a baked potato, even if it wasn't more than a decade old.

Guess who's BCKDK (this is BCKDK, or at least its structure). Image by Wikipedia user Emw.

Speaking of awkward acronyms: BCKDK.
It's branched-chain alpha-ketoacid dehydrogenase kinase, an enzyme critical to amino acid metabolism in humans. Defects in BCKDK are linked with some forms of autism.

A single residue change appears to confer the disease phenotype.

Creating new methods is great for three reasons:

1. It allows old phenomena to be explored in new ways.
2. It provides other researchers with more options.
3. It permits creation of ludicrous acronyms.

A recent paper by Moreno et al. in Molecular Systems Biology is an example of cases 1 and 3. Perhaps it will someday be useful to researchers studying protein-protein interactions, but for now, SPLIFF looks like a good way to visualize interactions found by other assays (i.e., yeast two-hybrid).

But I'm getting ahead of myself. This is a method called SPLIFF. It's about lighting up cells. Somebody got a little carried away with that acronym.

SPLIFF is a Split-Ubiquitin method and indicates protein-protein interactions within cells though the ratio fluorescence produced by two auto-fluorescent reporter proteins. Assays for protein-protein interactions usually use a growth phenotype or a colorimetric reporter to indicate interactions, so SPLIFF may offer more clearly quantifiable, temporally-sensitive results. The authors also show how SPLIFF, like other fluorescence-based methods, can localize interactions within cells. The protein interactions are reportedly detected instantaneously.  Hopefully this method can weed out some of the false-positives in two-hybrid interaction screens.

Citation:
Moreno, D., Neller, J., Kestler, H., Kraus, J., Dünkler, A., & Johnsson, N. (2013). A fluorescent reporter for mapping cellular protein-protein interactions in time and space Molecular Systems Biology, 9 DOI: 10.1038/msb.2013.3

Here's an interesting example of emergent properties.

In short, it's essentially a topology-based approach to solving a classical optimization problem. Quite novel, really, though it's not clear if the solution offers a whole lot of benefit over brute force calculation in terms of saved computation time. The paper is here.

What struck me as particularly interesting was the authors' proposal to physically implement their "blob" model:

...it would be satisfying if this virtual material could be implemented and embodied in a real physical substrate with the desired physical (for example visco-elastic, free energy minimisation) properties.

What would this accomplish? I'm not saying that it wouldn't be a neat, cheap engineering project to build an elastic blob capable of solving traveling salesman problems, it just doesn't seem like any kind of a job for real-world models.

Jeff Jones, & Andrew Adamatzky (2013). Computation of the Travelling Salesman Problem by a Shrinking Blob arXiv arXiv: 1303.4969v2

Here's a paper dealing with a frequently worrisome issue:

Shrestha, P. M., Nevin, K. P., Shrestha, M., & Lovley, D. R. (2013). When Is a Microbial Culture “Pure”? Persistent Cryptic Contaminant Escapes Detection Even with Deep Genome Sequencing. mBio, 4(2). doi:10.1128/mBio.00591-12
Microbiologists, like most biologists, like to have neatly organized categories and taxonomies available at all times. We work with individual species, specific strains of those species, and often mutants of those strains. If we grow our chosen organisms and they don't behave as expected, we generally assume that contamination occurred somewhere along the line or that a new mutation transpired. The usual preventative measure is simply to ensure that cultures start from single cells of the desired strain.

Shrestha et al. seem to have had some issues with culture contamination. This group works with Geobacter sulfurreducens strain DL1 in studies of microbial fuel cells. As they were attempting to isolate G. sulfurreducens strains with mutations enabling them to be more electrically conductive, they managed to isolate a strain later named KN400. This strain was great at conducting current but clearly wasn't just a mutant of DL1: sequencing showed that the new strain likely differed by more than 27,000 SNP's, or far more mutations than any lab-based methods of selection were likely to create.

The authors sought to clarify the origins of G. sulfurreducens strain KN400. Next-gen sequencing showed that a sequence specific to KN400 could be found in the original DL1 cultures, though out of more than 10⁷ sequence copies, fewer than 300 were the KN400 sequence. The new strain wasn't a new mutant at all. Subsequent growth studies found that even repeated rounds of restreaking cells on solid medium still yielded colonies with minute but detectable levels of the cryptic KN400 strain. Shrestha et al. suggest that their intense electrical conductivity-based selective pressures may have been the only reason they were able to isolate KN400 at all.

It's still not clear how G. sulfurreducens KN400 lives alongside the DL1 strain so well. My guess is that KN400 is actually an instance of a separate but phylogenetically related chromosome copy acting as a mobile genetic element. Cultures of the DL1 strain consistently maintain KN400 cells at low levels, so some variety of fitness benefit must be conferred to the entire culture or we'd expect the minority cells to just get selected against. There's clearly something strange going on with this bacterial species but it may be an ongoing process.

It was my birthday this past weekend! Danielle made a lovely cake:

You got your chocolate in my peanut butter, intentionally.

and a lovely phage:

Not pictured: crocheted phage in lysogenic state.

It also seemed like an appropriate time for this:

A birthday cake is no place for a cow.

Gatsogiannis, C., Lang, A. E., Meusch, D., Pfaumann, V., Hofnagel, O., Benz, R., Aktories, K., et al. (2013). A syringe-like injection mechanism in Photorhabdus luminescens toxins. Nature, advance on. Nature Publishing Group, a division of Macmillan Publishers Limited. All Rights Reserved. doi:10.1038/nature11987

Didn't read this one yet, but the abstract contains the phrase "vuvuzela-shaped channel" so it should be interesting.

Glud, R. N., Wenzhöfer, F., Middelboe, M., Oguri, K., Turnewitsch, R., Canfield, D. E., & Kitazato, H. (2013). High rates of microbial carbon turnover in sediments in the deepest oceanic trench on Earth. Nature Geoscience, advance on. Nature Publishing Group. doi:10.1038/ngeo1773.

This is a small letter about Challenger Deep, the deepest point in Earth's oceans. Located within the southern extent of the Mariana Trench, this spot is nearly 11,000 meters deep. It's pretty chilly down there - about 2.5 degrees C - but more importantly it's under extremely high pressure. Wikipedia tells me it's more than 16,000 psi or about 1,099 times surface pressure. This doesn't stop bacterial growth: Glud et al. found that two sediment samples from this deep spot contained, on average, nearly 10⁷ prokaryotic cells per cubic centimeter. Shallower sites nearby were also dense with microbial life but not nearly as rich as the Challenger Deep samples. 

Glud et al. suggest that deep-sea trenches like the Mariana may serve to naturally funnel fresh sediment downward, providing essential nutrients for microbial growth at extreme depths. Further analysis of these deep-sea microbes could show how they've adapted to such specialized metabolic demands. 

I went to a lecture today by Tim Read from Emory University. He discussed comparative genomics, specifically of Bacillus and Chlamydiaceae species and strains. The history of the latter is rather interesting: researchers thought these bacteria were actually viruses until the 1960s (due to the advent of electron microscopy, of course) as they couldn't culture them on artificial media. It's a group full of pathogens with wide host ranges but small, highly conserved genomes so it would be useful to know more about.

This review served as a basis for some new additions to the Chlamydophila psittaci Wikipedia page.

I've been thinking lately about that internet-adage, "if you're not paying anything, you're not the customer, you're the product." It comes up whenever someone, frequently the user of some free or freemium service, complains about sudden changes in terms of use or status of their service. The Instagram fracas last year and the Google Reader shutdown this year serve as good examples. Being a customer or a product of either of the two service may be possible but I'm not convinced that the above adage accurately describes any one individual's relationship with a company.

Every consumer is a customer and a product. We all do the whole exchanging-money-for-goods-and-services thing regularly. We all serve as marketing for these products and services as well. It might be the obvious tag on a pair of jeans or it may be more like membership in a club of fellow consumers (i.e.,  diehard Apple fans or anyone eating at Chik-fil-A after its recent PR issues). This marketing is provided free of charge. So are word-of-mouth recommendations, Facebook likes, discarded packaging, stock purchases, and any other interaction with a corporate entity, public or private. Even if all publicity isn't really good publicity, any continually increasing level of interaction with a company builds identity. That's almost priceless.

It's all just bacterial media. Photo from Flickr user Jepster.

Here is a paper:


Levkovich, T., Poutahidis, T., Smillie, C., Varian, B. J., Ibrahim, Y. M., Lakritz, J. R., Alm, E. J., et al. (2013). Probiotic bacteria induce a “glow of health”. (G. P. Kobinger, Ed.)PloS one, 8(1), e53867. Public Library of Science. doi:10.1371/journal.pone.0053867

This one looked like it was going to be silly. Most papers with quotations in the title tend to have that sense of "summarizing an idea with an adage" or just "excessive use of punctuation." Describing any observable phenomenon a "glow" rather than a glow really ought to give readers pause. We do live in an age when experimental animals can be engineered to literally glow. Is it a stretch to assume that the authors of this paper are trying out some new GFP-fusions with proteins indicative of healthy animal phenotypes?

Yes. This assumption would be wrong. This paper is about yogurt.

The authors claim that eating probiotic yogurt is associated with what they repeatedly describe as a 'glow of health,' sometimes with quotes and at least once without. I'll give them the benefit of the doubt as far as describing observable phenomena goes: the authors are all affiliated with MIT rather than Yoplait and they primarily discuss mice. For mice, the 'glow of health' includes thick, shiny hair and lustrous skin. These experimental animals were fed Lactobacillus reuteri within yogurt and on its own. As compared with control mice, the bacteria-eating mice were indeed significantly shinier and had thicker skin. All of these effects may be related to levels of the anti-inflammatory cytokine IL-10, as those 'glow'-ing traits weren't seen in mice without IL-10.


Some select quotes:

Taken together with our earlier data, this led us to postulate that probiotic bacteria induce host physiological changes including a more acidic pH resulting in radiant skin and shiny hair signaling peak health and fertility and thus a good reproductive investment.

(A good reproductive investment for the bacteria or the host?)

Extrapolation from data of mice to humans suggests that excessive inflammation in the form of uncontrolled IL-17A subverts scalp hair growth, and this may be remedied by eating probiotic bacteria such as L. reuteri, but interpretation is complicated by disparities in hair on scalp versus other body sites of these species [37]. Nonetheless, aged male mice eating probiotics displayed Il-10-dependent dense fur together with elevated testosterone and increased virility (data not shown) when compared with mice eating control diet alone. It is unknown whether eating of probiotic yogurt may forestall or reverse follicular activities of hormones in human subjects.  

This study leaves me with a bad taste in my mouth. The authors fail to address the actual differences between a probiotic-yogurt-based diet and the control diet; bacteria may just be more nutritive than the usual rat food. The sample size also doesn't appear to be larger than 20 animals in any one group. Last year's GM corn study had some similar issues. Even so, it's always interesting to see product claims (or even conventional wisdom, though I suspect it's still mostly marketing) put to the test.