Monday, May 31, 2010

Eat Local part II

The latest from the garden.

Spuds are one of those ineradicable plants, like horseradish or asparagus. Once you've planted them, you will have them forever. We last planted potatoes three or four years ago, but every year a couple of small plants come up. They're the nutritional and horticultural opposite of spinach: piles of starch and calories but not much else, and amazing yield. This is from two very sickly, spindly, single-stemmed plants that were buried in a patch of weeds and almost completely destroyed by slugs.

I'm sure that I left one pea-sized little spudling down there, and I'm sure I'll have the same thing next year.

Sunday, May 30, 2010

Eat Local

Here's about a third of our spinach crop.

This is from one eight-foot row from the garden in the far background. The other two thirds went into a fritatta that fed us for a couple of nights, and this is also about two meals worth. So, four meals. It is left as an exercise for the interested reader to figure out how many feet of spinach would need to be planted to end our household's dependence on imported spinach. (You can also figure in the chance of crop failure, as the row of lettuce right next to the spinach completely failed.) Chard's a much more productive crop in terms of meals per meter.

Saturday, May 29, 2010

Friday Fuligo, continued

The “dog barf” phase of Fuligo’s life is like the adult stage of a mayfly’s life. The mayfly larva lives for months as a predator in streams and lakes before spending a single day as a sexually reproducing result. The dog barf also lasts a single spectacular day devoted to reproduction, but it’s the last stage of a much longer predatory life.

Fuligo spends most of its life growing as a weird thing called a plasmodium. The plasmodium starts out as an ordinary eukaryotic cell, something like an amoeba. It’s mobile and predatory, and it engulfs any smaller cells it encounters as it creeps along its way. Unlike an amoeba, or any normal cell, it doesn’t divide as it grows. The cell just gets bigger, and BIGGER, and BIGGER. It copies its DNA, and its nucleus divides, so the result is a plasmodium: an enormous (well, a couple of centimeters) single cell membrane enclosing millions of nuclei. It has been reasonably compared to the title character in the B-movie classic “The Blob,” only instead of terrorizing Steve McQueen, it mows down bacteria and protozoa. If you’re lucky, you can sometimes see a plasmodium, a sort of film growing on moist humus.

When the time is right the Fuligo plasmodium gathers itself up and turns into the beautiful bumpy yellow blob we see. Its texture is like the fluffiest scrambled eggs, and I have read that it is cooked and eaten as such in Mexico—though I am not sufficiently adventurous to try it. If you see this in the morning, over the course of a single day it will turn tan and crusty, then brown and brittle. Break this, and you’ll get a cloud of black dust. The dust is spores, single cells that can spread on the wind and, in the right environment, repeat the cycle.

According to a recent hypothesis, the odd thing about Fuligo is that it not only eats protozoa as it oozes through the mulch, it actually incorporates some of their DNA into its own genome. This would be like me taking DNA from the asparagus that I ate last night and having the asparagus DNA woven into my own DNA—and that asparagus DNA would be found in the genomes of my descendants.

To briefly review, what makes Fuligo into Fuligo, and not asparagus or a human, is its genes. Fuligo DNA is transcribed to make RNA; that RNA either gets translated to make protein, or works as a catalytic RNA such as is found in the ribosomes. To a rough approximation, one gene encodes one protein or catalytic RNA. The sequence nucleotide bases in the DNA—A, T, G, and C—corresponds exactly to the sequence of nucleotide bases in the RNA transcript A, U (instead of T), G, and C. Likewise, the sequence of nucleotide bases in the RNA transcript corresponds in a precise way to the sequence of amino acids in the finished protein.

One hitch in this process is that the DNA often contains introns. Introns are sequences of DNA that occur in the middle of a gene, yet do not encode part of the finished catalytic RNA or protein. Eukaryotic organisms (like Fuligo, asparagus, and us) have lots of introns. As DNA is transcribed to make RNA, special enzymes snip the intron-encoded RNA out, and join together the remainder to make an RNA that can be much shorter than the DNA that it was transcribed from. The intron-encoded RNA is simply recycled.

Introns are a puzzle. They seem wasteful—the cell spends lots of energy replicating their DNA, making them into RNA, removing them from RNA transcripts, and recycling them. In fact, some people view them as “DNA parasites”: instead of an organism like a mosquito that reproduces at the expense of another organism, introns are DNA sequences that reproduce at the expense of another piece of DNA, the rest of the genome.

Most protozoa and a few fungi have particularly unusual introns. They are generally found in specific genes encoding the catalytic RNA of ribosomes. Class I introns are “self splicing”. They don’t need the help of any enzymes to do the cutting and pasting required to make a finished RNA. In fact, you can put RNA containing one of these introns by itself in a test-tube, and it will edit itself perfectly. The excised RNA will form itself into a stable little circle of RNA, and the rest of the RNA can go and do its job.

Different families of protozoa have different class I introns—the ones in different types of Tetrahymena look similar to each other, but different from the ones in different types of Acanthamoeba. Usually, the ribosomal RNA genes of these different protozoa contain one or two class I introns.

Fuligo is different. A group from Norway led by Steinar Johansen found that Fuligo’s ribosomal RNA genes have twelve class I introns. There’s a potentially easy explanation for this exuberance of introns. Duplication is a very common way for DNA sequences to evolve, so it’s possible that one class I intron could have been repeatedly duplicated. But the actual explanation is not so simple. Johansen found that most of the class I introns in Fuligo have no family resemblance to each other, so they’re not the result of duplications. In fact, one of the introns looks a lot like the ones from Tetrahymena. Another looks a lot like the ones from Naegleria. A third looks a lot like the ones from Acanthamoeba. These organisms, and a few others, are no more related to the Fuligo than you are—and yet, it looks like they contributed some DNA, specifically class I introns, to the dog-barf slime mold. A “family tree” of known class I introns shows this:

All the Fuligo introns are labeled Fse#### in bold; all the others are introns from other organisms. Generally, related organisms have related introns—for example, at the top of the figure, FseS1065 is a sibling of NmoL2563 and NmoL1949 and NaeL1926, which are all introns from related organisms in the genus Naegleria. Going down a little bit, you can see that the Fuligo introns FseS956, FseL1090, and FseL569 are closely related, and may have evolved by duplication from an ancestral intron. However, these are the only "sibling" introns in Fuligo.

Johansen proposes a wild hypothesis: The diverse protozoa eaten by the plasmodium stage of Fuligo have diverse class I introns. These are present (as the terrified protozoan is engulfed by the plasmodium) both in the protozoan genome, and as the little circles of RNA that are left over after the intron has been removed. It might be that the intron DNA gets mixed into the Fuligo DNA, or it might be that the intron RNA reverses its usual reaction—instead of snipping itself out, it pastes itself into a ribosomal RNA gene. Fuligo kills and eats the protozoan, but the protozoan reaches out of its grave and gives Fuligo a parting gift, a DNA parasite that it will never be rid of.

This is an unusual example of lateral gene transfer: the transfer of genetic material from one organism to another unrelated organism, uncoupled from reproduction. Typically, lateral gene transfer in Eukaryotes involves the transfer of a useful gene, one that enhances the fitness of the recipient, or something that is at least neutral. Here, we are shown the transfer not of a gene, but of a DNA parasite that may actually reduce the fitness of the recipient: a class I intron. Lateral gene transfer is rare in the Eukaryotic world (so I don’t worry about turning skinny and green when I eat asparagus), and this happened less than twelve times in the millions of years of Fuligo’s evolution. As Johansen says,

Perhaps the large number of introns accumulated in Fuligo [ribosomal RNA genes] reflects its natural behavior and promiscuous feeding habits and, thus, is a case in point of the phrase “you become what you eat.”

Eirik W. Lundblad, Christer Einvik, Sissel Rønning, Kari Haugli, and Steinar Johansen (2004). Twelve Group I Introns in the Same Pre-rRNA Transcript of the Myxomycete Fuligo septica: RNA Processing and Evolution. Molecular Biology and Evolution 21 (7), 1283-1293.

Friday, May 28, 2010

Friday not-Flora Fuligo

Fuligo septica, aka dog-vomit fungus, caca de luna, elf butter. About 8 cm.
It's not a fungus--it is no more closely related to fungi than it is to us. If you want to be precise, it is a Myxomycete, an "acellular slime mold." It turns out to have some real oddities in its genome, about which more later.

Thursday, May 27, 2010

Spring (continued)

Almost mowed this.

There's a reason it's called robin's-egg blue. It's hard to believe that the obese worm-suckers bouncing around our lawn came out of such tiny packages. This one appears to have been the victim of predation; there's a hole on the other side that looks a bit small for a chick to get out of.

Tuesday, May 25, 2010

Data, and my failure to provide it

I was the subject of a randomized telephone poll. There are a few things that I think are major impediments to the political life of this country. One is 24-hour news/opinion channels of any flavor, in which the constant barrage of data impedes any actual thinking. Another is the emphasis placed on polls, in which noise masquerades as data. Here was the first question in the telephone poll, asked by what sounded like a young woman who was dutifully, flatly, reading her script: Do you think the country is going in the right direction or the wrong direction?

Now, what does that mean? There’s plenty of stuff that is going to heck at high speed. But you know, compared with just ten years ago, we’ve elected a black man as a president, my gay friends are generally accepted in society, and I look at the students in my classes and I see many attitudes that represent a lot of progress from when I was a student. Am I supposed to take an arithmetic average of every factor? Or a median? I responded, unhelpfully, “I don’t know,” which was not part of the script. She checked with her supervisor, then soldiered on.

Most of the questions were about high school education. I was told I was supposed to answer them from the choices provided, but answering them honestly would have required me to know details about high school students and curricula that I simply don’t know. So I told them as much, and after a few minutes of questioning, the pollster gave up. I wasn’t trying to be difficult, just honest.

This made clear to me just how pernicious polling data is. It really is all about gut feelings—Stephen Colbert’s “truthiness”—and doesn’t have anything to do with a rational analysis of the situation. Then, the polls get reported and they feed forward onto themselves, because no one wants to be in the minority. And so decisions get made. All power to Luther H. Puttgrass!

Monday, May 24, 2010

Bracing for Fall and Beyond

I am assured that I’ll have a teaching spot for Introductory Microbiology at Davis in the Fall. I called the department secretary today and she told me that I have a contract to sign. I’m not sure if she means a “letter of intent” or a “contract”—as I’ve found out, Davis can easily just forget the former, while the latter has more binding power. So, it’s time to post this oldie but goodie (click to enlarge).

I’m still not sure about what is going on in the winter and spring. I’m told that it’s likely that I’ll split the microbial diversity class at Davis in the winter, which will be interesting. I’ve never team-taught, and I’ve never taught this class (though it is a favorite subject of mine).

I might be teaching at Sacramento State in the spring. I’ve sort of gotten used to the rhythm of uncertainty at Davis, which sometimes involves telling me that I’m going to be teaching a particular class for sure with 72 hours notice. I’m not used to the way it runs at Sac State, which has been like so:

Sacramento State (in March): We may possibly need instructors for these classes in the 2010-2011 year (shows two-page list of classes, including just about every class offered in the biology department.

Me (in March): Cool. I could easily do that one, that one, those, and that one in the fall semester, and that one, that one, these ones here, and that one in the spring. Here’s my application and relevant materials. When will you decide?

Sac State (in March): Oh, end of April, beginning of May.

Sac State (end of April, beginning of May):

Sac State (middle of May, via a letter addressed to “Alexis Appleman”): We were really impressed with the job you did teaching here last year. The students were very enthusiastic too.

Me (late May): Thanks. Um, have you guys decided anything yet?

Sac State: Er, no, not yet—but real soon, promise.

Me: Well, Davis just offered me something for Fall and I’m gonna take it.

Sac State: Shoot! You were at the top of a bunch of lists for Fall.

Me: Sorry, I guess. Bird in the hand, don’t you know. How about spring? Have you guys decided anything yet?

Sac State: Er, no, not yet—but real soon, promise.

We’ll see how this all plays out.

Bracing for summer

Spring is here, and I am busy trying to get myself ready for teaching introductory biology during the first summer session. This is a five week class, and it’s supposed to provide the students with a sound introduction to biology—the “origins and essence of life,” according to the title. The pedagogical feasibility of doing this is debatable. Right now I’m working on the syllabus, and the job is to try to eliminate everything that is not absolutely essential.

The task reminds me of the fable of the king who demanded from his sages a complete history of the world; they labored mightily and produced a brilliant 24 volume comprehensive chronicle, with analysis and explication. The king was a busy man, as kings are wont to be, and said he didn’t have time to read it. So, he demanded a shorter version, and the sages produced a single, condensed volume. This was still too much of a demand on the royal calendar, so he sent the sages away with the demand for an even more condensed and instructive account. The result was a single sentence: this, too, shall pass.

I don’t have to go quite that far in boiling things down, but I would say that I am leaving out a lot, and every slice of the editorial knife makes me wince. It comes down to a pretty similar conclusion: Given that life replicates itself in a universe where the second law of thermodynamics obtains, this, too, shall evolve.

There’s other headaches, and leading the pack is the new website that the university is insisting that I absolutely must use. I am not sure who designs these things. The previous website appears to have been designed by goatherds or HVAC technicians—but certainly not by anybody who ever had anything to do with college educaction. The new website manages to simultaneously be completely different, and yet exactly as user-hostile. Perhaps it was designed by a smithy.

Bonus academic link: Does teaching matter at (American) research universities? Given my personal experience, I would have to say that it is not the top of the list. There are many reasons to attend a big university, and good educations are possible at both, but if you want uniformly good teaching, go to a small liberal-arts college.

Monday Musical Offering

Miklós Rózsa: Six Bagatelles, Op. 12 Numbers 4, 5, and 6.

Friday, May 21, 2010

Friday Flora

Peas be with you. Few better things than going out in the yard and stuffing your face with sugar snap peas.

Thursday, May 20, 2010

Exciting Boring Big Small News

Headline writers are going to have a field day with this, and I am going to spend the next week wincing at the weird ways it will get portrayed in the news. Anyway, it’s finally happened: Craig Venter’s group has finally made an organism with a completely synthetic genome. Or, as the headlines will have it, “SCIENTISTS MAKE ARTIFICIAL LIFE!!1!” “OMG! FRANKENSTEIN!! RUN!!!”

Now, this is exciting, in that it represents an incredible technical tour de force. This is a project that Venter has been working on for several years now, and his group has overcome some formidable technical hurdles. He has taken raw, non-living ingredients, and made an entire genome out of them. This is easy to do for a single gene, or for a few thousand bases of DNA. Venter’s group has made DNA molecules of 1,077,947 bases, encoding about a thousand genes. His group has also figured out how to move this artificial genome into a cell, and have it displace the genome that was already there. To use Venter’s analogy, he has wiped the cell’s operating system and re-booted it with a new operating system.

However, this is also kind of boring. Venter’s group solved each of these technical problems, in isolation, over the last few years (see here for making a synthetic genome (which was not transplanted) and the reboot of a cell (with “natural,” not synthetic DNA)). Today’s news is simply that they have managed to do these things together. Most people who keep tabs on this kind of expected it to happen sooner, almost a year ago, and Venter himself has expressed some surprise that it’s taken so long.

This is big news, since it does open up a couple of cans of worms. There will be a bunch of hand-wringing, especially among those who have not been paying attention. (Half an hour after hearing the news, I heard the first wild conjectures about terrorists making killer superbugs. The commentator was apparently unaware of the tons—literally, thousands of kilograms—of genetically modified anthrax that the Soviet Union made, and thought that some schlub in a cave can do what Venter did.) Those who have been paying attention, including Venter, have been chewing on the ethical implications of this work for over a decade. The real big thing will be down the road. This is one step in the business plan of Venter’s company, Synthetic Genomics, which is to use purpose-built microorganisms to do all manner of useful things. They envision using these custom organisms to do everything from making hydrocarbons to, well, cleaning up oil spills.

And finally, it’s small news. This is a small step in Synthetic Genomics’ plan, and the organism that they’ve made is about as simple as possible. Its genes are the barest essentials. The cells are tiny, simple, and require a lot of help to grow. The only genetic material that these cells carry that is not about mere survival is a handful of genetic “watermarks,” regions of DNA that don’t encode anything, but have a distinctive sequence—a maker’s mark.

So, be excited, but try to be calmer than the headlines. More later.

Daniel G. Gibson, John I. Glass, Carole Lartigue, Vladimir N. Noskov, Ray-Yuan Chuang, Mikkel A. Algire, Gwynedd A. Benders, Michael G. Montague, Li Ma, Monzia M. Moodie, Chuck Merryman, Sanjay Vashee, Radha Krishnakumar, Nacyra Assad-Garcia, Cynthia Andrews-Pfannkoch, Evgeniya A. Denisova, Lei Young, Zhi-Qing Qi, Thomas H. Segall-Shapiro, Christopher H. Calvey, Prashanth P. Parmar, Clyde A. Hutchison, III, Hamilton O. Smith, J. Craig Venter (2010).
Creation of a Bacterial Cell Controlled by a Chemically Synthesized Genome. Science DOI: 10.1126

Wednesday, May 19, 2010

Screwy and Sociable

“Righty-tighty-lefty-loosey” is a handy mnemonic for pretty much every screw you’ll ever encounter. If you’ve ever met a backwards-threaded screw, it’s usually a signal that there’s something different that you need to pay attention to. The near-universality of a certain “handedness” also applies at the molecular level to all living things, and couple of recent discoveries show how a deviation from standard “handedness” functions as a signal that many Bacteria use to get each others’ attention.

A normal screw is the mirror image of a backwards-threaded screw, the same way your left hand is the mirror image of your right: they have identical composition but mirrored arrangement. Amino acids, the small building-blocks that make up every protein, can also be found in mirror-image forms. A molecule of right-handed alanine (or D-alanine, for Dextro alanine) is the mirror image of left-handed alanine (or L- alanine, for Laevo- alanine).

All the protein that you’re made of, and all the protein in every cell, is made of strings of L-amino acids. Very early in the history of life, L-amino acids became the standard for everything (the explanation for this is one of the nagging mysteries of the origin of life; there’s no reason why L-amino acids would work better than D-amino acids, and non-biological processes that produce amino acids produce a 50-50% mix of the two). One of the only places in the living world to find D-amino acids—the backwards-threaded screws of the living world—is in the cell walls of Bacteria.

The Bacterial cell wall is a meshwork of strings sugars woven together with chains of amino acids to make an astonishingly tough capsule (I think of the cell wearing a very snug sweater woven of Kevlar and wire). The amino acids found in the cell wall are all L-form, except D-alanine and D-glutamate.

The cell has dedicated enzymes to tweak the normal L-alanine and glutamate into their D- forms, and until recently this was what we knew about these odd amino acids.

A group led by Matthew Waldor found a previously unsuspected role for D-amino acids in the life of Bacteria. Their finding also undermines the common view that Bacteria are solitary organisms, but instead suggests that they have a social life that includes their siblings as well as bacteria of completely different species.

As is often the case in microbiology, the first clue came from an odd mutant bacterium. Normal cells are rod shaped, like a can of tennis balls, whether or not they are well fed or starving. The mutant was different: when it was well fed, it was rod shaped, but when they stopped growing because there was no more food, they swelled up into little spheres:

One odd thing about this phenomenon: if some of the “used” medium inhabited by spherical cells was added to well-fed mutant cells, they lost their rod shape and turned spherical within minutes. The mutants responded the same way to “used” medium from normal cells. This suggested that there was something produced by both normal and mutant cells as they ran out of food that acted as a signal; the mutant cells responded inappropriately, by turning into balls. It was fairly simple to purify the signal from the medium, and identify it as the D-form of four amino acids: Methionine, Leucine, Valine, and Isoleucine. So, as these bacteria begin to starve, they start pumping out lots of D-amino acids.

It takes a lot of energy for a cell to fill the growth medium with a high concentration of specially made D-amino acids, and energy is scarce as the cell is running out of food. However, it makes sense if the D-amino acids are a signal from one cell to its neighbors. Waldor’s group needed to find out the meaning of this signal, and the mutant cells provided a big hint. The mutant cells either can’t “hear” this signal or they misinterpret it, causing them to balloon out into spheres. Experience told the researchers that this was a sign that something was wrong with cell wall synthesis: changes in cell wall construction change the shape of the cell, and incidentally, some D-amino acids are found in the cell wall. The expectation was that going into starvation conditions would demand a thicker, tougher cell wall, and that the D-amino acids were a signal from one cell to another to strengthen the wall.

An analysis of the cell wall showed that this conjecture was only partly true. D-amino acids cause cells to significantly decrease cell wall synthesis; however, the composition of the cell wall changes, incorporating D-methionine as well as D-alanine and D-glutamate. The resulting cell wall, despite being thinner, is somewhat tougher than the cell wall of well-fed cells.

This result is cool, because the cells are acting in a seemingly altruistic manner: they are spending their own energy to “warn” other cells of impending hard times so they can change their cell walls. In studying animal behavior, such altruistic behavior is usually ascribed to “kin selection”—as long as an “altruistic” behavior benefits your relatives, the fitness of your genes will be improved. So, it makes a lot of sense to help your siblings, somewhat less sense to help your cousins, and no sense at all to help a total stranger. These bacteria, however, produce a signal that not only warns their own kind, but also just about every type of bacteria Waldor’s group checked.

Bacteria are usually grown in the laboratory, as in this study, as pure cultures suspended in liquid, but in the “real world”—for example, your bathtub, or on your teeth—they grow in diverse communities in a layer of slime called a biofilm. A biofilm is structured like raisin bread: individual bacterial cells of different types are arranged like raisins and nuts in a matrix of fibrous proteins and sugars. Biofilms are great for the Bacteria as long as there’s plenty of food. The cells get to stay in a good place, and are protected from threats in their environment (biofilms are notoriously resistant to antibiotics) and from drying out. However, if the food runs out, cells must escape the biofilm in order to survive.

The same D-amino acids that tell cells that hard times are coming also tell the cell that it’s time to leave the biofilm. Rich Losick and Roberto Kolter’s groups have extended Waldor’s discovery, and hinted at a way that this signal works. They exposed well-fed biofilms to “used” medium, and found that the biofilms rapidly dispersed. As with Waldor’s group, they found that only D-amino acids that were not part of the “well fed” cell wall had this effect, and that the unusual D-amino acids were being built into the cell wall as if the cells were being starved.

A key part of the biofilms that Losick and Kolter study is a long, stringy, sticky protein called Tas A. The Tas A protein can actually be seen using an electron microscope, and Losick and Kolter found that adding D-amino acids caused the cell to release the Tas A filaments.

Each Tas A protein filament is attached to the amino acids in the cell wall by a specific protein, YqxM. This protein is sensitive to D-amino acids—and once again, mutants help to show how. Losick and Kolter were able to find mutant cells that stayed in a biofilm even though D-amino acids were present. The only difference between these mutant cells and normal cells was one DNA base change in the gene that encodes YqxM.

The picture that emerges from these studies is that D-amino acids, the non-standard backwards screws of the biological world, are an important part of the life of Bacterial cells. Bacteria talk to each other in a language of D-amino acids. As starvation approaches, the cells in a biofilm release large amounts of D-amino acids; responding to this signal, the cells remodel and strengthen their cell walls and sever their ties to the biofilm. Losick and Kolter conclude by noting that this seems to be a general phenomenon in the bacterial world, and understanding the language of bacteria may allow us to tell problematic bacteria to go away. Infectious bacteria such as Staph aureus and Pseudomonas form medically troublesome biofilms that are quite resistant to antibiotics. However, they are sensitive to D-amino acids—and once expelled from a biofilm, these bacteria can be more easily killed.

Hubert Lam, Dong-Chan Oh, Felipe Cava, Constantin N. Takacs, Jon Clardy, Miguel A. de Pedro, Matthew K. Waldor (2009). D-Amino Acids Govern Stationary Phase Cell Wall Remodeling in Bacteria. Science 325: 1552-1555.

Ilana Kolodkin-Gal, Diego Romero, Shugeng Cao, Jon Clardy, Roberto Kolter, Richard Losick (2010). D-Amino Acids Trigger Biofilm Disassembly. Science 328: 627-629.

The Snail's Kiss

Found on a garbage can lid. The word of the day is "radula."

Tuesday, May 18, 2010

Microbiology + Legos = good

Amusing. Now I know how to pronounce "Beestjes," which is what Leeuwenhoek called 'em.


We just received our latest shipment of fly parasites in the mail.

If you've got yard chickens, you've got chicken poop. If you've got chicken poop, you get flies. In the past, we managed this problem with fly traps (which attract flies by smelling worse than chicken poop). Last year we started using biological control. There's a company that breeds parasitic wasps that lay their eggs in fly larvae. The eggs hatch in the fly pupa, and the wasps eat the developing fly from the inside. The fly dies, and wasps hatch out of the pupa.

So, what you get in the mail is an envelope of fly pupae that are just starting to produce zillions of teeny wasps (the guy in the photo is about 2mm; the big brown thing is a fly pupa). You dump these guys out where the chicken poop is, and they attack the flies. They work very well; we haven't had any fly problems at all.

As a microbiologist, I should write something about how the bacteria Wohlbachia manipulates the wasps' reproductive system. Instead, I'll quote Darwin:

I cannot persuade myself that a beneficent and omnipotent God would have designedly created parasitic wasps with the express intention of their feeding within the living bodies of Caterpillars.

And William Blake, who is a little too trippy for me:

Little Fly,
Thy summer's play
My thoughtless hand
Has brushed away.

Am not I
A fly like thee?
Or art not thou
A man like me?

For I dance
And drink, and sing,
Till some blind hand
Shall brush my wing.

If thought is life
And strength and breath
And the want
Of thought is death;

Then am I
A happy fly,
If I live,
Or if I die.

Monday, May 17, 2010

Monday Musical Offering

Miklós Rózsa: Six Bagatelles, Op. 12 Numbers 1, 2, and 3. Watch this space for numbers 4, 5, and 6.

Allez! Allez!

The Tour of California whizzed by our front door yesterday. Well, not quite our front door--if they did that, they would have had to go over speed bumps. But they were on Folsom Boulevard, half a block away.

This was the first stage, a mostly downhill run from Nevada City to the Capital. A perfect ride for a sprint finish, and the entire peleton was together, moving a lot faster than traffic on Folsom usually goes. Somewhere in there are such luminaries as Lance Armstrong, Tom Boonen, and Levi Leipheimer. Although some photons undoubtedly bounced off of them and into my eyeballs, I can't claim to have seen them here.

Sunday, May 16, 2010

Neadertals and Lateral Gene Transfer

The big buzz in the science news the last few days has been the finding that the genomes of modern European and Asian humans are actually between 1 and 4% Neandertal in origin. We share a common ancestor, but evolved separately. Most genes found in our last common ancestor evolved one way in us, but a different way in Neandertals. What really surprised the folks who did this study is that they found that while most humans have one version some genes (that evolved in the human lineage after humans and Neandertals diverged), the Eurasians have a different version—and that version is identical to the gene found in the Neandertal genome. This could have happened if these genes randomly changed in exactly the same way in both lineages, or if the genes evolved in Neandertals, then somehow moved into the human genome.

How did Neandertal genes get into the human genome? Humorists have jumped all over this with scenarios of beetle-browed Neandertals gettin’ it on with some modern types. But to a humorless biologist, this is an example of what is called “lateral gene transfer”, or the movement of genes between two distinct species. Lateral gene transfer doesn’t seem to have had that big an effect on human evolution—the Neandertal contribution to modern humanity is trivial—but lateral gene transfer can be of huge significance to Bacteria and Archaea. In some Bacteria, almost of a quarter of the genome got there by lateral gene transfer.

Lateral gene transfer changes prokaryotic evolution from a slow and linear process to a lightning fast and jumpy process. Prokaryotic genomes evolve slowly without lateral gene transfer. Evolving in isolation and relying on modification of existing genes, it is difficult to acquire radically new traits such as the ability to use light for energy. However, lateral gene transfer makes such changes possible and rapid. A small number of genes acquired by lateral gene transfer—a few thousand bases of DNA encoding a simple light-gathering machine—can change an organism into a phototroph. In the Bacteria and Archaea, lateral gene transfer seems almost free of constraints both in scale and effect. However, there are limits, and some of these were described in a clever study from Edward Rubin of the Joint Genome Institute.

I’ll preserve the modesty of the Bacteria involved, and refrain from discussing the mechanics of lateral gene transfer. Suffice it to say that it’s very easy to take a piece of DNA out of one bacterial cell and pop it into another cell—especially if the cell receiving the DNA is that workhorse of the lab, E. coli. In fact, because E. coli is so easy to transform with foreign DNA and grow, it has become the standard procedure to study genes from other organisms by moving them into E. coli. If you’re working on the genes of some eccentric bug that grows extremely slowly, and only in a growth medium of sheep’s guts, then you’ll want to move those genes into E. coli. In the last few years, entire genomes of other organisms have been put into E. coli. They’re not put in complete—there’s only room in the E. coli cell for a couple of dozen extra genes at a time—but one can make a “library” of E. coli cells carrying the entire genome of organism X. So, we laterally transfer genes one through 10 from organism X into this cell of E. coli; we laterally transfer genes five through 15 from organism X into that cell of E. coli; and so on until we have our library, each volume of which is an E. coli cell.

Nearly a hundred such “genomic libraries” have been made in E. coli, almost two million different individual volumes. This represents a lot of work by lots of different people over many years. The clever thing that Ed Rubin did was to analyze the results of all that work after other people did it.

Every so often, it’s impossible to make one of the volumes in a genomic library. Some genes simply can’t be transferred into E. coli. The DNA can be moved into the cell without difficulties, but the presence of that DNA in E. coli kills the cell. Rubin collected these failures in library-making help to establish the limits of lateral gene transfer.

How could a piece of DNA kill a cell? In some cases, the laterally-transferred DNA can encode a toxin; the “antitoxin” is on another piece of DNA that didn’t get transferred. Rubin’s group found very few examples of this. More often, the DNA that got transferred contained “safe” genes, but the expression of these genes was no longer controlled properly. So, the E. coli cell was essentially killed by too much of a good thing. The problem with these genes was not what they encoded, but how they were regulated. So, neither of these classes of genes is inherently untransferrable. The library-makers were simply unlucky.

The genes most difficult to transfer into E. coli were those encoding the basic machinery of the cell. In automotive terms, it was OK to transfer trim, paint, and upholstery. However, tinkering with the engine and the transmission was forbidden. So, there was no problem transferring genes for metabolizing different types of sugars—adding the ability to digest melibiose to E. coli is like adding a spoiler to your VW. However, transferring genes for ribosomes (the part of the cell that actually makes proteins) was difficult—a Lamborghini piston just won’t work in a VW.

Interestingly, successful lateral gene transfer was more difficult if the source of the DNA was closely related to E. coli. These genes could be similar enough to the E. coli genes that it will try to use their products, but different enough that the product doesn’t quite work. To return to our automotive analogy, if you’re building an engine and you need a 3/8 inch bolt, you’re likely to have a problem if the 3/8 bolt is mixed in with a bunch of 7/16 bolts. However, if the 3/8 inch bolt is mixed in with a bunch of wood screws, you won’t have any problems finding the right thing. Rubin’s group found that close relatives of E. coli typically had over a dozen genes that couldn’t be horizontally transferred into E. coli, while distant relatives often had no untransferrable genes. It’s as if Bacteria evolve by two different clocks. There is a slowly ticking clock for their “core” life functions, evolving by the stately march of mutation and selection and drift, and a rapidly buzzing timer for everything else, evolving by lateral gene transfer.

It’s interesting to compare lateral gene transfer in human evolution and microbial evolution. As we study more animal genomes, we’ll probably see a few more examples (Nancy Moran just reported that aphids have genes acquired from a fungus), but these will be oddities in the flow of animal evolution. On the other hand, in Bacteria, it’s news when we find that there are limits to what lateral gene transfer can do.

Rotem Sorek, Yiwen Zhu, Christopher J. Creevey, M. Pilar Francino, Peer Bork, Edward M. Rubin (2007). Genome-Wide Experimental Determination of Barriers to Horizontal Gene Transfer. Science 318, 1449-1452.

A. Martinez, A. S. Bradley, J. R. Waldbauer , R. E. Summons, E. F. DeLong (2007). Proteorhodopsin photosystem gene expression enables photophosphorylation in a heterologous host. Proceedings of the National Academy of Sciences (USA) 104(13):5590-5595

Flora of the week

Tillandsia, unknown species.
Click on photo to make it huge; actual size about 5 cm across. Stolen from my Mom's collection. They have been growing here in Sacramento under conditions which I would have expected to be lethal: excessively hot and dry in the summer, buried under dead leaves and dipping below freezing in winter. These conditions have proved fatal to a couple of species. However, this one seems to love it.

Wednesday, May 12, 2010

Not microbiology, but still cool

I go on about the cool things that modern imaging can see at the micro scale, but there's been plenty of advances in imaging at the macro scale that reveal stuff that's almost as amazing. Like this:
It's a landslide--on Mars. The blue arrow up at the top points to a probable meteorite that triggered it. For the full story, go here.

Tuesday, May 11, 2010

Insane in the (Outer) membrane

Okay, this is weird, even by Archaeal standards. That’s like saying that an outfit is eccentric, even by Lady Gaga standards. But this recent discovery about the structure of an unusual Archaeal cell is just a bit much: it takes one of the most basic features of cell structure and turns it inside out.

The Archaea are a group of organisms with small cells that are superficially similar to Bacteria. However, the genetic and biochemical differences between Bacteria and Archaea are as great as the differences between Bacteria and us, the Eukaryotes. Archaea have earned a reputation as oddballs. Many are “extremophiles,” living in environments with paint-peeling pH or scalding temperatures or pickling concentrations of brine. But in spite of all the differences between the Eukaryotes, Bacteria and Archaea, we are all descended from a common pool of ancestors, which accounts for our similarities: we all have inherited the same genetic coding and decoding system, and use similar mechanisms for getting energy.

This may look like a picture of Hoover Dam, but it’s actually a graphic explaining how almost every cell gets energy. There’s too much water upstream of the dam; there’s not enough water downstream of the dam. If you let water go through the dam, energy is released that you can use to do work—in this case, turn electrical generators. The system keeps recharging itself, as energy from the environment (the sun) does the work of lifting water back up into the atmosphere, eventually filling the river that feeds the dam.

This is how cells make energy. The cell’s membrane acts as a dam. Outside the cell, there are too many positive ions, while inside the cell there aren’t enough. If the cell lets positive ions in, energy is released that can do work. In this case, the energy drives a protein called ATPase that sits in the membrane. ATPase makes ATP, the chemical that powers just about everything in the cell. The cell keeps recharging itself by taking energy from the environment (sunlight or food) to push positive ions back out of the cell and “refilling” the reservoir (the outside of the cell).

The power from this “energized” membrane is used not only to make ATP, but also to move stuff into and out of the cell. There are a few cells that make ATP by a different mechanism, fermentation; but they still use much of their ATP to energize their membranes. An energized membrane is one of the hallmarks of any living cell, Bacterial, Eukaryotic, or Archaeal.
This universal mechanism for storing energy shows up in the architecture of every cell. In Bacteria, it’s like so:

The inner membrane is the energized membrane, where the ATPase is found. The ATP that is produced diffuses into the cell, where it is used to copy DNA and make proteins and power all the essential work of the cell. The space between the inner and outer membranes is small, less than 20% of the cell’s volume; it has a relatively high concentration of positive ions, and no ATP is found there.

Eukaryotes have mitochondria to make most of their ATP. The mitochondrion is actually evolved from bacteria that took up residence in the Eukaryotic cell, so we see basically the same arrangement of membranes and ATPase. The only difference is that special pores move ATP out of the mitochondrion and into the rest of the cell:

Archaeal cells are pretty much the same as Bacterial cells, except there’s no outer membrane. In every case, Bacterial, Eukaryotic, or Archaeal, the inner membrane is the energized membrane—the cell’s Hoover Dam.

Researchers led by Harald Huber of Regensberg, Germany, have been patiently studying the Archaean Ignicoccus hospitalis. This organism was found growing in near-boiling water at a geothermal vent in the Midatlantic Ridge, but it has been domesticated and grown in the laboratory in a mixture of hydrogen, elemental sulfur, and carbon dioxide at a temperature of 90 degrees Celsius. This passes for normal behavior in Archaea. The first surprise came in 2002 when Huber’s group used an electron microscope to examine these cells. What we’re looking at here is a very thin slice of a cell.

Now this is weird. There are clearly two membranes, and no cell wall. Bacteria generally have two membranes, but the Archea? No. And the space between the inner and outer membranes? HUGE! It’s 75% of the cell’s volume! In the Bacteria, that compartment is at most 20% of the cell’s volume. All the business of the cell—all the DNA, all the gene expression, all the synthesis of macromolecules and so on—goes on in the darker region, inside what we’ll call the inner membrane.

This bizarre structure raises questions. Since Ignicoccus’ structure resembles that of a Bacterium, Huber's group assumed it would be organized like a Bacterium, with an energized inner membrane. But why would so much of the cell—all that space between the membranes—not get any energy? So, they decided to look for ATPase. Since ATPase is too small to show up even in an electron microscope, they used a chemical trick to “tag” each molecule of ATPase with a little blob of gold. This shows up as a little black dot under an electron microscope. Here’s what they found; each black dot is a molecule of ATPase with a gold-tagged antibody stuck to it:

This picture makes as much sense to me as this:

I think that Huber’s group thought the same, so they checked and re-checked their result by a couple of completely different methods. The result was confirmed, and is baffling. The outer membrane is full of ATPase; the space between the membranes must get plenty of ATP. But all the DNA, all the gene expression, all the protein synthesis—all the stuff that consumes ATP—is going on inside the inner membrane. Nothing like a normal Archaeal cell, and nothing like a normal Bacterial cell.

The last page of the article describing this discovery is basically a long list of questions raised by this weird structure. Some of these questions are mechanical: if all the DNA and gene expression machinery is inside the inner membrane, how does ATP get through the inner membrane? What goes on in the space between membranes? Is the inner membrane energized? Even more puzzling are the evolutionary questions raised by Ignicoccus’ structure and the location of its ATPase. Ignicoccus is the only cell we know—perhaps in the entire world—with an energized outer membrane. Since all the other Archaea have just one membrane, it’s likely that Ignicoccus evolved from something with just one membrane. How did that happen? Is the outer membrane the recent addition—and if so, how did ATPase end up there? Is the inner membrane the recent addition—and if so, how did it evolve a mechanism to import ATP?

On the one hand, this discovery is not terribly significant; Ignicoccus is a niche player in a highly restricted environment, and it has no close relatives. On the other hand, it raises a lot of big questions about how such a freakish cell could evolve. These questions are relevant to us. A leading hypothesis for the origin of Eukaryotic cells posits that an Archaeal cell engulfed a bacterial cell; the Bacterium became the mitochondrion, while the Archaeal DNA was protected by an internal membrane. Huber notes that an Archaeal cell similar to Ignicoccus could be our great-great-to-the-gazillion-grandaddy.

Ulf Küpera, Carolin Meyerb, Volker Müllerc, Reinhard Rachelb, and Harald Hubera (2009). Energized outer membrane and spatial separation of metabolic processes in the hyperthermophilic Archaeon Ignicoccus hospitalis. PNAS 107:7, 3152-3156.

REINHARD RACHEL, IRITH WYSCHKONY, SABINE RIEHL and HARALD HUBER (2001). The ultrastructure of Ignicoccus: Evidence for a novel outer membrane and for intracellular vesicle budding in an archaeon. Archaea 1, 9-18.

Monday, May 10, 2010

Starting the top and back

The top of this violin is made from red pine—like the sides and back, recovered old-growth timber that has been soaking in the Great Lakes for a century. A single piece of wood is sawed in half in the most difficult direction, and the two halves are opened like opening a book. They will be joined to make a single, wide plank that is symmetrical about its center, or in wood jargon, bookended. The back is made from birch treated the same way.

The glue joint that holds together the bookended pieces must be absolutely precise. We tried using a friend's extremely fancy power joiner to do this. It was promised to deliver a perfect product in ten minutes, but it was about a tenth of a millimeter out of alignment, so we used hand tools--an extra-long joining plane, which makes extra-nice shavings.

Gluing together the two halves of the front and the back is very challenging. Professionals make it look easy; the glue tends to create a sort of suction between the two pieces of wood, so they simply drop them onto each other, rub them around for a few seconds, and then let them grab on to each other. I tried doing this, and it failed. I tried it again, and two more times, then went back to using clamps. The move of an amateur, but at least it worked.

Once the halves are together, one face must be planed absolutely flat.

Then, it's time to start removing all the wood that isn't part of the violin.

Saturday, May 8, 2010

Finishing the garland

The sides of the violin must be thin to save weight and make it sing nicely. However, it’s hard to glue the top and bottom to something that’s only a millimeter thick. So, linings are attached to the sides so that the top and bottom have about three millimeters to glue on to. I made the linings out of cedar, which is much easier to bend than birch. It is bent to fit the upper and lower bouts, and let into little channels in the corner blocks in the C-bouts.

Special high-tech clamps are used for gluing the linings. You can see that my violin looks exactly like the one in the how-to book.

Once the linings are in, the top surface of this frame must be made absolutely flat. A plane, followed by a piece of glass covered with sandpaper, do the trick.

Finally, the sides of the violin—the “garland”—is done. If you click on the picture, you can see the grain on the top block (over on the left) is going parallel to the sides. It should be perpendicular, like the bottom block. Learning!

On to the top and back!

A few bouts of learning

With the C-bouts in place, it's time to bend the upper and lower bouts and glue them on. First, the extra length of the C-bouts needs to be trimmed and the blocks need to be carved to make smoothly flowing corners. I've read that it is a common beginner mistake to make the corners too pointy, and I've certainly done this here. Another lesson learned! Yay!

Bending the wood for the upper bouts is difficult—instead of a “C”, the wood must make an “S”. I ended up cracking four strips of wood and burning one on the bending iron trying to make this curve. More learning! Yay!

After much colorful language, the bouts are bent. Time to glue them on.

Unfortunately, one of the upper bouts had a crack that didn’t show up until it was glued on--the stress of being held in place caused the wood to break. I had to break the piece off (hide glue allows you to do that), bend yet another piece of wood, and glue it on. Yet more learning! Yippee!

About this time, I found another mistake to learn from. The grain on the upper block is running the wrong way, so I’ll have to cut away most of the block and replace it. The learning never stops!

Finally, the upper and lower bouts are glued in place. The extra wood from the bouts is removed, and the corners are shaped using the plastic template as a guide. Almost done with the sides!