Today, I learned that much of the success of polio eradication in the Western hemisphere could be attributed to a vaccine delivery strategy employed throughout Central and South America. Between the 1960's-80's, a number of countries throughout the region started campaigns to immunize every child. Brazil specifically held a series of national immunization days, a strategy later adopted by other countries in the region. I'm not sure how many countries still actively maintain national immunization days or how effective they've been for diseases besides poliomyelitis. It's a bit disheartening to imagine the opposition such an approach would receive here in the US.

Today I learned about Merisopedia, a genus of cyanobacteria. Species in this genus grow in rectangular grids. They look like this:

Well-regimented. From Photomicrographs of the freshwater algae Vol. 2 by Yamagishi and Akiyama, 1984.

Merisopedia species can be found all over the planet, including the Amazon, China, and Nigeria.

Who nose why skin's the way it is

Today I read about an interaction between two occupants of the human microbiome. The authors really do their findings a disservice by repeatedly referring to them in the context of the "nostril microbiome". What they really discuss is Staphylococcus aureus and various species of Propionibacterium. Both can be found in a variety of skin locations and especially on the face. Propionibacterium - and especially P. acne - is famous for causing the inflammation associated with all manner of nasty skin conditions. S. aureus is famous for causing many similar but often more medically worrisome infections. This paper shows how they might work together.*

Long story short: it's coproporphyrin III. Propionibacterium produces it and S. aureus uses it as a sign to start making biofilms.  A biofilm phenotype can improve survival in the face of the immune system, antibiotics, or even just physical stress.

Citation:
Wollenberg, M. S., Claesen, J., Escapa, I. F., Aldridge, K. L., Fischbach, M. A., and Lemon, K. P. (2014). Propionibacterium-Produced Coproporphyrin III Induces Staphylococcus aureus Aggregation and Biofilm Formation. mBio 5, e01286-14-.

*Anthropomorphism is to be avoided when discussing microbes. The English language, unfortunately, offers many opportunities for anthropomorphism-based rhetoric. In this case, "work together" is a bit misleading as this may not be a coordinated biological phenomenon. It may simply result from one species releasing a molecule and another species noticing it.

I just found out about the BioFabric project today. It claims to offer a networking visualization method superior to traditional node and edge graphs. Nearly anything is preferable to a hairball network so I'm fairly intrigued, plus their quick demonstration looks neat. I'm starting to work with some very large networks (approaching 50,000 edges, at least) so it's nice to have visualization options.

A post I came across on the StackExchange English Language and Usage forum today asked the following question:

Is there a word or phrase that means to plant my idea in someone else’s mind so they think it is their own idea?

This is immediately followed by a mention of Inception, of course. I'm wondering if the verb incept couldn't be used for such a task. Transitively, it's an occasional synonym for ingest, though I haven't heard it used that way in recent memory.

Others on the forum suggested insinuate, brainwash, inculate, and suggest. Most of these don't seem quite right as they only include one half of the exchange of ideas; I might suggest or insinuate something without successfully landing the idea in your mind. Inculate is a historical euphemism in English and a current one in Italian, so that one's not ideal either.

The limiting factor is, as usual, mutual intelligibility.

Today, I learned that ImageMagick will do about 90% of routine image editing tasks in 10% of the time they usually take.

Here's the music for today. Yes, all seven hours of it. (No, don't listen to seven hours of this unless you're planning to sleep like a highly relaxed log.)

Here's a neat little thing, and an example of Twitter being used well for once: @congressedits. It sends out a tweet every time an anonymous English Wikipedia editor with an IP corresponding to any Congress office makes any edits. Thus far, it mostly just shows that some Congress staffers likely have obscenely dull jobs.

The code behind it, a script called anon, is here. It's in CoffeeScript, with which I'm not terribly familiar, potentially due to my general suspicion of Javascript. It may be worth exploring further for small coding tasks in the future.

Confusingly-named and located universities include:

• Miami University of Oxford, OH
• Indiana University of Pennsylvania
• American World University - OK, it's just an online-only unaccredited school

I'm sure there are additional examples.

Update: Cal U.

This is today's music. This entire album sounds like it should be the soundtrack to an alternative version of the Cosmos TV series completely lacking Sagan, Neil Degrasse Tyson, or any other human at all.

Today, I learned that the anaerobic gut microbiome occupant Bifidobacterium longum has been explored as a potential vector for treating cancer with gene therapy. B. longum is generally considered non-pathogenic and beneficial: it helps to balance pH in the gut, in part through production of lactic acid. A gut with the wrong pH can become susceptible to infection by bacterial pathogens. B. longum is added to some foods and supplements as a probiotic for this reason.

So what's going on with that gene therapy? A paper in 2000 by Yazawa et al. used a mouse model for an initial feasibility study. Though it doesn't appear that they actually used the method for tumor reduction, they did show that B. longum into mice with lung tumors could only be found in tumor tissue after 168 hours. That's presumably because the bacteria require an anaerobic (or, at least a hypoxic) environment to survice. Ideally, this means that B. longum bearing some kind of anti-tumor factor could be injected into or near a tumor with no pathogenic effect on any other tissues. B. longum can be killed off using common antibiotics; Yazawa et al. used ampicillin, though they only tried it in vitro. I'd be worried about long-term use with immunocompromised patients, though the exact anti-tumor material in play may be another critical factor.

The same research group was apparently still working on the idea as of 2010, when they published this review. A 2013 study by a different group looks like it had some success in using Bifidobacterium longum subsp. infantis as part of a method for treating bladder cancer in a mouse model.* This 2014 study just coated their Bifidobacterium in selenium, an elemental micronutrient which may have anti-tumor properties.


*I don't have access to the article so I'm not sure how well the method worked. The authors claim their treatment "exhibited the highest level of apoptosis" compared to controls so that could just mean they had a statistically-significant but limited effect on tumors. Cancer therapy isn't really my field so I'll give them the benefit of the doubt.

Sea stars. (Or, picoplankton from the Pacific.) Photo from Daniel Vaulot on Wikimedia Commons.

The oceans of our planet are so immense that it's often difficult to accurately determine what their occupants are up to. A recent paper in Science focuses on picoplankton, the tiniest ocean occupants but also the most widespread. It's a segment of life driven by photosynthesis (in the photo above, all the small orange dots are photosynthetic cyanobacteria). The new study found that the day-light cycle has an effect on more than just the dominant photosynthetic species, however. Non-photosynthetic, heterotrophic microbes also appeared to exhibit differences as a result of available sunlight.

This summary offers a more detailed breakdown.

I read a review article about phage therapy today (citation below*) with the following opening sentence:

The human gut contains approximately 10¹⁵ bacteriophages (the ‘phageome’), probably the richest concentration of biological entities on earth.

Is that claim actually true? They cite this Lepage et al. Gut paper; those folks estimate that 10¹⁴ microorganisms (that is, distinct cells) live in any single human gut. We usually guess that an environment contains at least 10 times as many individual bacteriophage as potential host cells, so 10¹⁵ bacteriophages doesn't seem like a bad estimate. That being said, could there be a more densely-populated reservoir out there? I've seen population counts for chickens as high as 19 billion but I wasn't able to find any estimates of their gut microbiome diversity. We know they're a potential reservoir of pathogens and their population exceeds that of humanity.

Update: I've been thinking about this and realized that the phrase "richest concentration of biological entities" likely refers to a single human gut rather than the sum of all human gut microbiomes and viriomes. I like to think about ecological niches on a grand scale; the total number of different variations in phage genomes is higher when we include every similar environment in the total rather than the contents of just one human gut. My qualms about the superlative remain. I'd suspect that some sewer systems may contain richer, more diverse arrays of phages, and that's without employing much creativity. Could other species on this planet maintain more diverse microbiomes and/or viriomes?



*Dalmasso M, Hill C, Ross RP (2014) Exploiting gut bacteriophages for human health. Trends in microbiology 22: 399–405.

This is the kind of music I listen to while in the lab:

When I'm feeling rushed, I listen to the same thing, just faster. 
(Yes, I made that. My inspiration was several hours of staring at protein interaction networks.)

Power couples

I read about mutualism today. There has been - and continues to be - a long-running debate regarding the evolution of mutualism. The problem has often come down to a lack of evidence: we can be fairly confident that symbiotic mutualism is a real phenomenon but it's not always easy to demonstrate. We also know that many of the best examples of mutualism, such as chloroplasts, are the result of extensive evolution. Can mutualism emerge mutation, given the right circumstances for symbiotic partnerships to emerge?

A recent paper by Horn and Murray and accompanying summary article in Science show how it can happen. It's a neat, simple demonstration which would make a great elementary science class project.

Citation:
Horn EFY, Murray AW (2014) Niche engineering demonstrates a latent capacity for fungal-algal mutualism. Science 345: 94–98.

Gotta keep it clean.

This is what my desktop looked like on December 8, 2003. Yes, I used Kazaa, the Uber of the early 00's (see previous blog entry). Other items of note:

• Matching GUI and Winamp skin. Looks like I was listening to Hybrid - If I Survive. It was probably this remix, actually.
• Fruity Loops Studio 4, the perfect software package for the young, enterprising electronic musician on a severely limited budget.
• A Temporary Desktop Folder. Nothing temporary about it. That's where every document goes.
• Both AIM and Trillian. This version of Trillian crashed every 10 minutes or so.
• I was not as cyberpunk in real life as this desktop may imply.

Remember Napster? How about Kazaa? Do you remember how popular they were and how blatantly illegal they were? The illegality was blatant but revolutionary. It was emblematic of a myopic but resolute spirit still actively pervasive among new companies, especially those providing new mechanisms for old grey markets.

The ongoing fracas about Uber and Lyft always brings that spirit to mind. Some folks in my city are excited about its possibilities. I'm conflicted about it, honestly. Just as Napster, Kazaa, and all the other early file-sharing methods rendered music sharing painless, these new companies are simplifying ride sharing. People could and did share music before the internet made it easy and they certainly still do so. They also continue to share cars, even on an unofficial paid basis.

Here's why I'm conflicted, though:

1. Taxis are terrible but I'm glad they're regulated. I'm generally in favor of regulating services: there's always some liability issue should something go wrong during a business transaction. Uber and Lyft really need some very specific safety regulations before I'm convinced they should supplant the existing taxi system.
2. I'm increasingly worried about the distancing effect of turning human interactions into apps. Is that old-fashioned?*
3. Uber and Lyft frame their business concepts as creative destruction. I don't see anything terribly creative about it. They're organizing existing systems in a patently illegal way and discarding every logical reason why the laws exist. If that's the only way this system can be improved, then I suppose I'll get used to it. In the meantime, I'll continue to be suspicious. 

*I do really like knowing how much a taxi ride will cost up-front, though. That's a clear advantage of these new services and it's obscene that the old taxi companies couldn't provide it.