A related note about corpses.

Today I learned about the story of Elmer McCurdy:

In December 1976, during filming at Queens Park (A.K.A. The Pike), of the television show The Six Million Dollar Man episode "Carnival of Spies" (#4.17) (1977), a crew member was moving what was thought to be a wax mannequin that was hanging from a gallows. When the mannequin's arm (some accounts say finger) broke off, it was discovered that it was in fact embalmed and mummified human remains. Later, when medical examiner Thomas Noguchi opened the mummy's mouth for other clues, he was surprised to find a 1924 penny and a ticket from Sonney Amusement's Museum of Crime in Los Angeles.

Long story short: the guy got shot in 1911, got mummified, got turned into a sideshow attraction, and somehow became a prop on a California boardwalk.

"the corpse progresses through several forensically recognized stages of decomposition, including Fresh (before decomposition begins), Active Decay, which includes Bloating and Rupture, and Advanced Decay"

Creepy-spooky microbiology fact: Grave soil differs in biochemical composition from other soils. It's probably due to the action of microbial communities. Along the same rapidly-decomposing lines, forensic investigators may be able to use microbes to estimate a corpse's time of death in much the same way they may use insects.

Salt of the earth

The word of the day is 'saltern'. That's a place where salt is made. We've been doing that (making salt, that is) since prehistoric times, but what's even more interesting about salterns is how rich they are in salt-loving microorganisms. One such group is the Ectothiorhodospiraceae, or purple sulfur bacteria. They just love salt. That, and sulfur. 

There's no conclusion here. I just really enjoy microorganisms with exotic lifestyles.

Check it off

As part of my quest to find ever duller subjects to blog about, I will now briefly discuss web-based task managers. These are bits of software (let's avoid that badly-abused term 'app', shall we?) designed to replace all the usefulness of a pen and pad of paper, at least when they're used for keeping track of lists. Electronic solutions offer benefits like sorting, accessibility, and categorization, all of which can be performed on paper with the right combination of tabs and color-coding. Even so, no notebook matches the Internet's ability to make the same bits of information available everywhere, all the time. The end goal is to decrease the amount of friction between conceptualizing a task and actually completing it.

So here's a bit of pro and con:

• Pen and paper. It's easy, requires no power or data connection and looks great in a Lisa Frank Trapper Keeper.* It also cannot exist in more than one place at once. That may be a feature rather than a bug if security is a concern.
• A text file. The digital equivalent of pen n' paper, this option is cheap and flexible. It does require access to wherever the file happens to be, though placing it in a Dropbox solves that issue handily. Even so, mobile devices find editing text files challenging. I'm not sure why. Text editors also aren't ideal environments for sorting tasks though they are great for searching, especially when regular expressions are involved.
• Remember The Milk.  I used this for a while last year after migrating from the maddeningly minimal Google Tasks. It's free-ish, plays well with Google Apps of various sorts, and parses natural language very smoothly (i.e., you can enter a task as "eat ham on Wednesday" and it will understand when the task should happen). The -ish is an issue as the web interface is free but the mobile version won't sync tasks more than once a day without a $25/year pro account. The interface used to be genuinely ugly on all platforms but appears to have improved recently. It has plenty of features and active support. That added cost is really the only downside but it's a notable one.
• Astrid. This isn't even a real option any longer as the Astrid team got bought out (read: consumed and digested) by Yahoo** a few months back. It's sad. Astrid ran smoothly on all kinds of platforms, looked great, and allowed for shared lists. Now it's all gone.
• Wunderlist. This option may, in fact, be on its second iteration (Wunderlist2) and is primarily a mobile application. At least, I had daily problems with its interface: tasks would disapper, buttons would become invisible, and most recently I couldn't even log in to my account. The entire project has a Web 2.5 sheen which is attractive until the point at which it works slowly. Even worse, there is no option to export tasks to anything other than a bloated, difficult-to-import-with-other-software JSON file. I used Wunderlist for about six months and just couldn't tolerate all the bugs.
• Toodledo. Just started using this one. It's rich in features but I'll have to use it a while to see if they're useful. The desktop web interface has some really basic usability issues, but hey, it's all free.

Next week, I plan to discuss the care and handling of airborne sawdust. Stay tuned, kids!

*I was blissfully immune from the Trapper Keeper trend when it was endemic. Have students ever been so excited about personal organization since that time?

**Or, more officially, YAHOO!

Yes, that is correct, more dumb Excel tricks

For personal future reference and otherwise: how to hide text in Excel but retain the formatting. Just change the Format to ;;;. That's all it takes.

See also: this blog post.

Learning to love mothballs

Today, I learned about the existence of a bacterial species named Polaromonas naphthalenivorans. This lil' guy* fits into the mysterious, often baffling category of extremophile bacteria - that is, species capable of living in environments we normally wouldn't consider habitable. Originally isolated from a coal-tar-contaminated aquifer somewhere in the northeastern US,** P. naphthalenivorans can grow using naphthalene as its only carbon source. It's not terribly surprising, as naphthalene is a major component of coal tar (and was originally isolated from coal tar, in fact), so this species is just working with what it has. It's still rather odd as naphthalene is toxic and a suspected carcinogen. Those kind of rules don't always apply to bacteria.

Dividing P. naphthalenivorans cells. Micrograph is from the Joint Genome Institute (JGI). See this page for more details.

Most people are familiar with naphthalene as a component of mothballs. This paper suggests that a whole metabolic community could subsist on naphthalene, or at least could adapt to its presence. Evolution is great that way!

*Literary anthropomorphism is a constant danger when discussing animals and especially when discussing microbes since it's difficult to understand why they do what they do. I will rarely, however, avoid an opportunity to make bacteria seem cute. They're already tiny, and tiny things are cute, right?

**A paper describing the aquifer describes it using little more detail than "A single truckload of coal tar was buried in a forested area in the northeastern United States." This MicrobeWiki page says it's in South Glens Falls, New York. There's a lab at Cornell that likes to work there. As far as they know, the local drinking water isn't contaminated with coal tar or anything like that.

Goofy Excel tricks episode #1048577

Just a quick trick I learned today about how to make Excel search a series of values and return one or more corresponding adjacent values for each. I'd normally use VLOOKUP for such a thing but the function only returns the first match it finds. How about situations when I have more than one match, like this one:
A   elephant
B   truck
C   large rock
D   pudding
B   gopher

in which I want to know which values are adjacent to value 'B'?

Googling a bit provided this convenient and non-obvious answer. The general function is:
=INDEX([the values you want to return], SMALL(INDEX(([the search value]=[the values being searched])*(MATCH(ROW([the values being searched]), ROW([the values being searched])))+([the search value]<>[the values being searched])*1048577, 0, 0), COLUMN(A1)))


The function will return one matched value at a time, so to get the other matched values to appear in the same row just copy it over to the adjacent cells in the row. It will return #REF! if the search value isn't found.


Don't forget to make references static as needed, i.e. $A$4:$A$979. The 1048577 is to convert the function from an array function into a normal one, I think. Not really sure what that COLUMN(A1) part is doing. Maybe it's just to establish where the upper-leftmost cell is.


This post is mostly for my own edification but I hope it was helpful. To me. Most people don't use Excel arrays for things that are better suited to a bit of SQL, right?

For future reference: to remove bromophenol blue stains from clothing, soak with ethanol, dry with paper towel, then spray with Windex or something similar and dry again. It's not just the isopropanol in the Windex - I think the surfactants help, too.

For future reference: the Excel escape character is not a slash. It is a tilde, i.e. searching for ? performs a wildcard search but ~? will return question marks.

No big deal. Just some big viruses.

Searching PubMed for the keyword "giant virus" always provides some fun results. That's not what I did today - though I do recommend trying it sometime - as the recent reports about oversized viruses have been spreading like some kind of very small causative agent of infectious disease.

Here's the first one: the isolation of a Mimivirus from a patient with pneumonia. The particular viral isolate is more than 550 nanometers wide and has a 1.23 megabase genome. For reference, that's huge. For a better reference, that's about the width of an average E. coli cell and a genome in the same size range as many of the more genetically streamlined bacteria (it's more than twice as large as the tiny Mycoplasma genitalium genome, though that's about as minimal as known bacterial genomes get). Most viruses we know of aren't quite this massive, though Mimiviruses and other record-holders for viral size share the characteristic of infecting Acanthamoeba polyphaga amoebae. So if this new mimivirus infects amoebae, is it pathogenic to humans as well? The authors of this paper seem to think so. As always, further viral isolates will be necessary. (The actual paper is right on the other side of this concrete paywall.) 

If you thought that mimivirus was big and/or had a silly name, check out the Pandoraviruses. These viral isolates average more than 700 nanometers in diameter and bear genomes of, in at least one case, more than 2 megabases. They were found in sediments and mud where amoebae are plentiful. There are some hyperbolic news reports out there about these new viruses already so I'll just pick some interesting bits out of the paper itself:

Unlike eukaryotic DNA viruses and phages, which first synthesize and then fill their capsids, the tegument and internal compartment of the Pandoravirus particles are synthesized simultaneously, in a manner suggestive of knitting, until the particles are fully formed and closed.

Knitting viruses. Don't tell Pinterest. Not yet.

The high percentage (93%) of CDSs without recognizable homolog (ORFans), the alien morphological features displayed by P. salinus, and its atypical replication process raised the concern that the translation of its genes into proteins might not obey the standard genetic code, hence obscuring potential sequence similarities.

The authors are trying to say that these viruses are almost suspiciously strange. It's not uncommon to see large chunks of viral genome sequences that don't look like any known sequence, but when you're talking about genomes larger than many bacterial ones then this becomes a sizable reservoir of new, uncharacterized genes and proteins. They may be more familiar than we can initially tell.

...their DNA polymerase does cluster with those of other giant DNA viruses, suggesting the controversial existence of a fourth domain of life ... The absence of Pandoravirus-like sequences from the rapidly growing environmental metagenomic databases suggests either that they are rare or that their ecological niche has never been prospected. However, the screening of the literature on Acanthamoeba parasites does reveal that Pandoravirus-like particles had been observed 13 years ago ... although not interpreted as viruses. 

So these viruses aren't totally alien. They've been around for at least 13 years! Probably even longer,* though exactly how much longer may determine how controversial that claim about the "fourth domain of life" becomes.

Citations follow.

Saadi, H., Pagnier, I., Colson, P., Cherif, J. K., Beji, M., Boughalmi, M., … Raoult, D. (2013). First Isolation of Mimivirus in a Patient With Pneumonia. Clinical infectious diseases: an official publication of the Infectious Diseases Society of America. doi:10.1093/cid/cit354.

Philippe, N., Legendre, M., Doutre, G., Coute, Y., Poirot, O., Lescot, M., … Abergel, C. (2013). Pandoraviruses: Amoeba Viruses with Genomes Up to 2.5 Mb Reaching That of Parasitic Eukaryotes. Science, 341(6143), 281–286. doi:10.1126/science.1239181.

* Some varieties of amoebae may have been around as long ago as the Neoproterozoic Era, or between 1,000 and 541 million years ago. If there were amoebae then viruses with amoebic hosts may have also been present.

New job, same as the old job

I'm finding this report on the growth of temporary work in the US quite interesting. It's at least partially because I've worked temp jobs before, even immediately after finishing the undergraduate stages of my ongoing academic career. The unnerving thing about each job wasn't the uncertainty, the mediocre pay or the lack of decent benefits. Rather, it was the sense that you could serve as a critical element of a larger whole yet retain absolutely no role in your long-term fate with the company. Anyway, here are some bits from the report I found especially damning:

Every year, a tenth of all U.S. workers finds a job at a staffing agency.

That's both temporary and contract workers. The American Staffing Association states that staffing agencies employ more than 2.9 million people in the US every day. That time factor is the critical element here -- these may not be the same 2.9 million employees from one day to the next.

“We’re seeing just more and more industries using business models that attempt to change the employment relationship or obscure the employment relationship,” said Mary Beth Maxwell, a top official in the Labor Department’s Wage and Hour Division. 

Obscuring the employment relationship doesn't initially seem like an ideal goal but it certainly looks like an effective way to turn formerly long-term employment into a more commitment-free model.

“I think our industry has been good for North America, as far as keeping people working,” said Randall Hatcher, president of MAU Workforce Solutions, which supplies temps to BMW. “I get laid off by Employer A and go over here to Employer B, and maybe they have a job for me. People get a lot of different experiences. An employee can work at four to five different companies and then maybe decide this is what I want to do.”

This kind of attitude reminds me of the whole "self-deportation" idea. Nothing with that much uncertainty can be a solid long-term solution. There will always be enough work for everyone but not at the same time. Traditionally, this problem was alleviated by unions, though clearly they come with their own issues. Aren't they worth a try for temp workers?

A 2004 order by the National Labor Relations Board barred temp workers from joining with permanent workers for collective bargaining unless both the temp agency and the host company agree to the arrangement.

Oops, maybe not.

Only 8 percent get health insurance from their employers, compared with 56 percent of permanent workers. What employers don’t provide, workers get from the social safety net, i.e., taxpayers.

And don’t look for Obamacare to fix it. Under the law, employers must provide health coverage only to employees who average 30 hours a week or more. After pressure from the temp industry and others, the IRS ruled that companies have up to a year to determine if workers qualify. 

Health care, or the lack thereof, may be the most worrisome element of the growth of temp work. If most of the temp job growth is in industrial jobs, more people will continue to be at risk of experiencing injuries they will never be able to afford. Many of them may not even work for a single employer more than a year, or when they do, they still won't be able to afford the plans the employers offer (in my experience, the plan wasn't exactly cost-competitive).

This whole problem is genuinely worrisome from numerous perspectives. It's yet another economic maelstrom waiting to happen, with the added stench of Industrial Age exploitation swirling throughout.

Time to BRCA the habit

The US Supreme Court has ruled that human genes cannot be patented. That's great news until we stop to consider what a human gene includes. The ruling bars patents on original human DNA, presumably in any variation of its sequence. That is, I couldn't file a patent for the sequence of my favorite human gene or of any of its alleles. The ruling does specifically permit any implementation or subsequent product made using that sequence, up to and including synthesis of cDNA. By means of awkward simile, that's like prohibiting patents on maple trees (or, at least, the concept and structure of a maple tree) but permitting patents on maples grown in a tree farm. There's still plenty of room for perfectly legitimate patents to be granted and for new products to be protected. I'm just concerned that this ruling stops well short of actually resolving the issue of what kinds of biological material can or can't be patented.

We've reached the point at which the whole "natural" vs. "artificial" dichotomy just doesn't pass muster anymore. Advancements in synthetic biology promise to blur a line that wasn't especially crisp to begin with, especially when discussing raw DNA sequences. The SCOTUS ruling states "cDNA does not present the same obstacles to patentability as naturally occurring, isolated DNA segments...creation of a cDNA sequence from mRNA results in an exons-only molecule that is not naturally occurring." The issue here really shouldn't be whether cDNA of a patented sequence could be found in a human (that is, without influence by outside factors like viruses), but rather that the cDNA still bears exactly the same protein-coding message as the RNA transcript does, just in an edited format.

We can, of course, get more philosophical about the issue and debate what constitutes a "human" gene. At least eight percent of the sequenced human genome is made up of retroviral sequences. Some of them even code for things in active use. There have also been suspected instances of bacterial sequences jumping into the genome of their human host. I suppose each of these issues will create their own legal issues when the time comes, i.e. the next time a biomedical company gets overzealous about their intellectual property. In the meantime, this new ruling will have to suffice.

Update: I like the 2010 district court ruling. It went farther than today's SCOTUS ruling.

"We shot lightning"

Hello! Here is a neat timelapse of a particularly large and impressive storm. Not anywhere near me, and not my video, but quite striking nonetheless. That's it for now!

Golden eggs

I just got back from visiting my lovely lady counterpart in Germany. In lieu of describing the whole trip, here is a photo of a gold-plated silver chicken.

Click here and see if you can find this guy. Hint: he's smaller than the average rooster.

Many, many more photos, presented with no context at all, are present here.  Nope, that link is no longer operational. Photos available upon request.

Do you have a second?

Every 15 minutes, someone averages a sum of events over an arbitrary period of time. No, I don't have a citation for that. It's standard practice to assume that frequencies are infrequently constant yet are much easier to understand if we can apply some kind of linear assumptions to them. That's perfectly fine, especially when we don't really know when the event in question is more or less likely to happen. This approach is used in science and medical journalism with the intent of breaking down impossibly huge numbers (i.e., 50 thousand deaths due to Ocelot Fever) into something more human-readable.

The problem arises when the level of granularity imposed by averaging over time obfuscates the reasons why the events happen at all. If MADD tells us that "In 2011, 9,878 people died in drunk driving crashes - one every 53 minutes", what do we really learn? That single number, (9,878 deaths / 53 minutes) is so specific that it disregards critical time-related factors like the weekend.*

I was planning to do an XKCD-inspired bit of Googling** and search for results of a few arbitrary frequencies to find out what happens at those times, every time. The results are too ghastly to share as most of the assumed events involve death, dismemberment, or assault. So, for the sake of diversity, I'll pull a few numbers from everysecond.info instead:

• Every second, Johnny Depp makes $2.92. The guy makes $92 million a year. Economists do use hourly pay or yearly salary to estimate how much an individual's time is worth, such that any period of time is "worth" however much they would have earned had they spent it working for pay. This can lead to some rather ludicrous estimates when inappropriately applied. We know Johnny Depp isn't actually working continuously despite his numerous sources of income. Even so, a number like $2.92/sec doesn't really provide us with any context to Mr. Depp's economic situation.
• Every second, 194 videos are watched on Myspace. What a perfect example! The statistic is from 2009. Some big changes have happened since then. Even so, it's fun to imagine Myspace users draining what's left of their attenuated attention spans on single-second videos. Hundreds of them every second!
• Every second, cows emit 250 kgs of methane in the United States. It's already difficult to imagine what a single kilogram of methane looks like,*** much less how what happens to it when the next second's round of methane arrives. Even so, cows don't continuously emit methane and they may emit more or less of it depending on what they're eating. Those factors can't even be considered when we break things down into seconds or even hours. If I observe a cow swish its tail three hundred times in an hour, perhaps I can safely claim 5 tail swishes per minute. Expanding the observation to a thousand cows over the course of months or years would render per-minute or per-second estimates useless without a greater knowledge of the relationship between cow tails and time.

All I'm saying is that averaging massive numbers over time is misleading at best and dangerously myopic at worst. These are situations best handled by probabilities, not solid quantities and linear relationships. Averaging such an immense quantity over such a small period of time distorts our understanding of both quantities.


*This paper's thesis in brief: young people like to drink for fun on the weekends. To be fair, the study subjects were Swiss rather than the usual Americans. I'll refrain from griping about social science research for now.

**I have this nagging suspicion that this actually was an XKCD piece at some point. If so, go read that again too. It was probably pretty entertaining.

***250 kg of methane is 375 thousand liters, if that helps.

Get well soon

Here is a use for one of the strange but inevitable results of modern society: singing greeting cards. The materials in one of those cards, plus a cheap resistor and capacitor, are enough to assemble a perfectly usable pulse sensor. The original paper suggests that this off-the-shelf solution could be used in an educational setting. 

A little Googling shows that a number of pulse sensors are available or can be made for all kinds of platforms.

• This one is intended for use with Arduino. Total cost is ~$25, not counting whatever it's attached to.
• For comparison, this one is a more clinical model. I can only imagine how much it costs.
• This setup uses an optical approach instead of a piezoelectric one. It seems like overkill, possibly because the signal requires a lot of amplification.

I'm imagining an art project in which a viewer's heart rate changes the intensity of lights in a room or turns certain appliances (i.e., a fan or a radio) on or off at certain rate thresholds. Even something like a cheap knock-off of this bike helmet seems entirely feasible. 

More like "Nope! Share, Fool!"

It's worrisome to see politics bleed into science. It's even more alarming to see sources of scientific funding dry up because they don't fit a specific agenda. The National Science Foundation, under directive from Congress, recently cut off funding for political science research except for that "promoting national security or the economic interests of the United States." It's a rather general guideline for a specific field. It also reveals how legislators feel about the role of any science and when it deserves to be funded: we want results, we want them now, and we want we certainly don't need any context.


The NSF spent more than $7 billion last year. It's where 20 percent of the money for federally-funded research in the US comes from. That total goes a long way and contributes to numerous fields, from engineering to education. It's only a matter of time before some Congressman decides an entire field of research doesn't need federal funding at all.

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.

I suppose the most important thing is just to know where to look.

The refrigerator room down the hall from my lab looks like it finally got fixed; it's constantly running at around 4 degrees C. Here's hoping it stays that way as it will make an ideal home for all our media.

I wonder how those rooms get installed in buildings.

The paper for today is:

Parks, J.M. et al. (2013). The Genetic Basis for Bacterial Mercury Methylation. Science, 339(6125), pp. 1332-1335. doi:10.1126/science.1230667.

(There is a tiny dog in this room and its constant yelpings and mewlings are making it quite hard to absorb this material.)

This is a quick little report about the genes used by mercury-methylating microbes to do their mercury-methylating work. The authors already knew about the corrinoid iron-sulfur protein (CFeSP) used to methylate metallic clusters on acetyl-CoA synthases, so they began to look for something similar in the genomes of mercury-methylating bacteria. They did find one within a Desulfovibrio desulfuricans genome along with a gene for a putatively associated ferredoxin. It's not just D. desulfuricans, either: the same pair of genes appears to be present in 51 other genome sequences, at least a few of which are known to be mercury-methylators. Beyond the bioinformatics, D. desulfuricans deletion mutants without these two genes appeared to grow normally yet had almost none of their usual Hg-methylating ability.

It is entirely possible that the two target genes in this study - referred to the authors as hgcA and hgcB - have some other functions. The genomes of some distantly related species do appear to contain hgcAB orthologs, including a set in the recently isolated Methanomassiliicoccus luminyensis, a commensal human gut-dwelling archaeon. It isn't clear why many of these species code for these enzymes or need anything like them at all. Studies of microbial metal metabolism look like another job for the "sequence everything that moves" approach.

Another Cytoscape quirk - when importing data, redundant pairs of interactions are usually - but not always - ignored. This is a problem when I actually want to see how many different sets of data produced the same interactions, so doing such a comparison may be a better job for Excel.

Cytoscape also has trouble importing VizMapper settings almost all the time. Sometimes importing the settings then saving and reloading the network irons out any bugs.

Edit: I figured out the problem with failure to recognize redundancy. Cytoscape ignores redundant entries if the interacting nodes are presented in the same order, so Node1 (pp) Node2 only gets added to the network once even if the data set includes it twice with different attributes, i.e. if Node1 (pp) Node2 from Data Set 1 and Node1 (pp) Node2 from Data Set 2 are both in the input file. If Node1 (pp) Node2 and Node2 (pp) Node1 are both in the input file, though, both interactions are retained despite just being the inverse of each other. A solution: import the attribute as an interaction type.

Argh, why is Google discontinuing Reader? Do people not use RSS feeds anymore? I know that the Big G really just wants to roll everything up into Google Plus Sign but they're hardly transparent about why they discontinue services like that. It's poor service (though not customer service, as evidenced by that internet adage along the lines of "if you're not paying anything, you're not the customer, you're the product).

An interesting note from a 2010 review of pathogenic E. coli by Croxen and Finlay in Nature Reviews Micro:

Intriguingly, EHEC can sense the hormones adrenaline and noradrenaline from host cells, as well as the quorum-sensing molecule auto-inducer 3 (AI-3) from gastrointestinal cells, to regulate motility and T3SS expression... Sensing of these molecules is required for virulence of EHEC in animal models and presents a new interaction that should be taken into account when considering pathogen–host interactions.

Some kind of a localization factor, perhaps, as adrenaline receptors are indeed present in the gastrointestinal tract.

It would be nice to actually accomplish something new in lab today but I'm spending an awful lot of time on small jobs like sending plasmid samples to labs in Austria and cleaning off plastic dishes so they can be sterilized (that job wouldn't even be necessary if said dishes didn't cost nearly $200 for a case of 60, but I guess lab materials are just obscenely expensive). There's also a bacterial pathogenesis exam tomorrow morning to study for. That material is generally fun to read, at least.

One hand washes the other.

I posted this generative text project on Facebook but it's something I'll want to come back to again. These kinds of project are just so neat in every sense of the word. I know they aren't that complex in their implementation but it's all a matter of presentation and how context deeply influences our understanding of even perfectly uninspiring text. The source is all here on Github. A selection (anything this project generates is a selection, anyway, as with the Twitter implementation it's nearly infinite, though the possible maximum number of tweets comes to mind):

...I saw stretched upon his back, and gazing up straight at the terrible sun, the man I was seeking. I saw about Miss Vivian's death to-day, and I was afraid Hal would be all alone fretting. I saw that William Oke, in his heart, thoroughly looked down upon all his neighbours. I saw only a snapshot of her, which showed her to be beautiful. I saw smoke in the chimney this evening. I saw a man talking with a woman there, at your door. I saw some beauties there a while ago. I saw tears in their eyes, tears of joy for the honors paid me; and especially, said they, for the manner in which I had received them. I saw her in the prisoners' dock, the Katusha betrayed by me, in a prisoner's cloak, condemned to penal servitude through a strange mistake, and my own fault. I saw them! The damage amounted to seventeen rupees, eight annas. I saw my Indian fall to the ground. I saw it in his desperate face. I saw my daughter at the theatre in London. I saw her only to love her; nor was it a common passion she inspired in me. I saw absolutely nothing else on the floor...

And so on. The Twitter version obviously doesn't benefit from being studded with excess punctuation but it does feel more like an authentic stream of consciousness, or maybe a stream of collective unconsciousness.

I went over to the MCV hospital cafeteria for lunch today. Lunch is quite inexpensive there due to the VCU discount, though the minor health risks of eating in a hospital are sometimes worrisome. Hospitals are just chock full of pathogens.

I saw Kristin and Joana from the Christie lab briefly while waiting in line at the cafeteria. Kristin said she referred someone to my lab who was looking for places for new microbiology graduate students to do rotations. It would be helpful to have some more help in the lab to handle small projects or even just to provide some fresh ideas. Hopefully any new students won't have to undergo extensive lab-skills training, especially if they're not going to stay around longer than the terms of a single rotation period.

At least I'm not the only victim of contamination right now:

Sergei Bulat,  a researcher at the Laboratory of Eukaryote Genetics at the St. Petersburg Nuclear Physics Institute, originally told RIA that they that "call it unidentified and 'unclassified' life."they found new signs of life after examining water samples from the subglacial Lake Vostok.

However, on Saturday the Eukaryote Genetics Laboratory head Vladimir Korolyov, spoke to Interfax News Agency, and said that they actually did not find any new signs of life. He said they just found contaminants.

Ugh, I got into lab today and discovered the following:

1. My yeast transformations performed last Wednesday appear to have yielded no transformant colonies at all.
2. The majority of the transformants for our last set of transformations may in fact be contaminants. 
3. My lab PI may not be in the office this week.

I'm becoming quite irritated with the research I'm trying to accomplish in this lab. These should be incredibly basic protocols but we're having little to no success at all with them. I'm almost completely out of variables to test and few of the options I've tested before have expanded our understanding of what is preventing our yest from transforming. All I know is that some of the plasmid stocks we already have are, in fact, incorrectly labeled. All this together is just impeding any process I could be making on an actual project.

Danielle and I were up in Delaware and PA this past weekend setting up wedding things. We got a site scheduled and a photographer booked, plus Danielle got measured for her dress. We also got to sit down and have brunch with the bulk of the Wedding Party Participants and sort out the basic details, i.e. when the event is and what they should (or shouldn't, mostly) be wearing at the time. We also went to see a movie with Danielle's mother and sister, which was watchable, mostly. Entertaining, perhaps.

(The movie was Oz: The Great and Powerful, which I will review parenthetically as follows: bright and colorful but predictable in Titanic proportions.)

This lab at UCLA is doing some pretty neat stuff with very small microscopes. I read about them in the Feb 2013 National Geographic but the article was very vague on details. They're working on developing mobile devices that can diagnose diseases like malaria using microscopy. Very useful.

I'm in Delaware for the day and I am currently petting a cat with one eye.

Today's paper is: 

Cissé, O. H., Pagni, M., & Hauser, P. M. (2012). De novo assembly of the Pneumocystis jirovecii genome from a single bronchoalveolar lavage fluid specimen from a patient. mBio, 4(1), e00428-12. American Society for Microbiology. doi:10.1128/mBio.00428-12.

Pneumocystis jirovecii is a fungus that isn't usually pathogenic but is deadly to immunocompromised patients, most prominently those with AIDS.  As with many other parasitic microbes colonizing human tissues, P. jirovecii can't be cultured in the lab. This disadvantage makes working with P. jirovecii nearly impossible if researchers seek to use genetic or molecular techniques. This looks like a case for sequencing! Wait, no, hold on. Researchers generally need to culture microbes to get enough genomic DNA for sequencing. The authors of this paper bypass that issue by collecting the fungus direct from the lungs of infected patients (they also used immunoprecipitation and random amplification, so this by no means an instance of single-cell sequencing).

Collecting samples of bronchoalveolar lavage fluid (or, if you prefer, the ridiculous-sounding acronym BALFs) provides plenty of fungus to work with. The samples are also rich in other genetic material from human cells, bacteria, viruses, and on occasion other species of Pneumocystis. The authors had to extract the P. jirovecii genome from the mess -- luckily, the genome of related species and rat pathogen P. carinii has already been sequenced and partially assembled. Process of elimination allowed for removal of the non-Pneumocystis sequences, then genome comparison and RNAseq helped finish and annotate the rest. More than just a de novo genome assembly using a messy metagenomic data source, this work is an example of how availability of massive quantities of genomic data make some projects entirely feasible.

It's a snowy, slushy mess out there! It's certainly been more wintry in Richmond before but rarely the kind of weather in which trees actively pelt me with slushballs on the walk to campus. It's still snowing, too. Danielle and I were planning on driving to Delaware this evening or tomorrow morning so I hope most of it gets cleaned up by then.

Today's paper is: Rao and Black - Structure and assembly of bacteriophage T4 head (2010) Virology Journal.

The T4 head structure. Looks kinda like a pineapple.

This is a review of the essential observations of the phage T4 head structure. Next to the famous lambda phage, T4 and its fellow T-even phages may be some of the most closely-studied viruses. T4 has that classic phage structure: an icosohedral head, a contractile tail, and a baseplate at the end of the tail, plus six spindly fibers on the baseplate. Cryo-EM has helped to define the structures of the primary T4 head proteins (gp23 and gp24) down to about 0.3 nm or 3 angstrom, which is a resolution that's hard to improve on. The gp23 protein demonstrates the classical HK97 fold and relies upon the E. coli chaperone GroEL and a phage-encoded cochaperone gp31 to reach its final form.

The paper digresses a bit to discuss phage display. I wasn't aware of how this technique was being used in recent years, but antigens fused to T4 capsids have been shown to be effective vaccines against foot and mouth disease virus, anthrax toxin and potentially even tumor metastasis. The authors aren't clear about how phage help with vaccine delivery. I suspect that they may have improved long-term storage capabilities when compared to antigen alone but the overall number of fusion proteins is limited by copy number per phage capsid; it can't really exceed the 870 copies of Soc already bound to the capsid and may also be limited by steric hindrance. Displaying antigens on phage rather than on their own may increase the immune response but I'm curious if it makes sense to use phage instead of a chemical adjuvant. The folks who did the anti-tumor study cite some references claiming as much and also claim that phage have the benefit of causing few side effects. I'd still call potential disruption of enteric bacteria a notable side effect.

Other interesting notes about the T4 capsid:

• The T4 packaging motor packages DNA at about 2 kb/s. It's an ATP-dependent process - no silly physics tricks here, though it's incredibly efficient (the authors state that this motor is "...approximately twice as powerful as a typical automobile engine", whatever they mean by 'typical'). The T4 genome is 171 kb so the motor gets the whole thing and then some packaged in less than 5 minutes. The authors must have summarized some numbers as a constant rate of 2000 kb/s should get it all packaged in less than 2 minutes, so the rest of the time may proceed more slowly or may be subject to something like strand slippage.
• The structure of the T4 portal complex is conserved across many phages and in HSV, which is really just an overgrown phage anyway. Studies really don't agree about how it works and I'm not inclined to bet on any one model at the moment.

A few departmental mailing lists just sent out a message about the Life Sciences building losing power due to a generator test between 1 and 3 PM. I really wish we were given more advance notice about these kinds of things.

Ugh, I'm fighting off a cold today. It's nothing serious, though sometimes I would rather have a decent excuse to stay home and avoid spreading disease, as I would with a slightly more virulent infection. It doesn't really help that I've been feeling directionless in the lab lately. I think one of the plasmid stocks is mislabeled and I can't seem to get our yeast strains to mate with any decent efficiency.

Today I discovered that a plasmid I thought was one thing was, in fact, another. I suspect it was mislabeled. I also suspect that I will take the blame for not verifying its identity sooner. At least we know now.

Danielle and I visited a couple yard sales and an estate sale this morning in search of a nice desk to replace the rather unstable Ikea one she is currently using. No luck, though it was interesting to see how many strange statuettes a person can accumulate in a lifetime.

In Cytoscape, you can select a subset of nodes including all edge types between those nodes by doing the following: use a filter to select nodes by edge type, then select all nodes connected by selected edges (or Ctrl+7). Follow by selecting adjacent edges (Alt+E). This will select a subnetwork determined by the filtered edge type but including the other edges (i.e. if you'd like to determine which nodes are connected by more than one edge of differing types). Don't forget to actually create the new subnetwork using the button on the toolbar.

Today I learned that Astrid doesn't handle shared tasks very well, despite this feature being central to its marketing. As with all free web services I can't complain too much. The problems aren't as apparent when using the iOS app and may in fact be solved by accessing the account through the app. It's hard to tell.

Hey blog. How are you doin'?

Today I was glad to hear that A Bit of Fry and Laurie was back on Netflix.