Tag Archives: research news

Standardized Notation for Biology, Finally

Molecular biologists are prodigious napkin users. We doodle. In the molecular biologist’s mind, enzymes and regulatory proteins look like roundish blobs, DNA and RNA are straight lines, and genes are boxes on top of the straight lines. Curved lines with arrows on their ends indicate relationships between these components: this protein stimulates that gene’s expression, the enzyme over here inhibits the one over there.

There are no standards for these symbols, so one biologist’s napkin doodle won’t be exactly the same as another biologist’s doodle of the same system. That wasn’t a big problem when researchers focused their entire careers on one or two genes, but with whole-genome sequencing now becoming routine, and gene regulation diagrams now incorporating hundreds or even thousands of components, it’s become almost impossible to understand the quirky “wiring diagrams” that now crowd the edges of every seminar speaker’s slides. We’ve outgrown the napkins.

Fortunately, someone is finally doing something about it. In the latest issue of Nature Biotechnology, a multi-institutional team of researchers presents a unified “systems biology graphical notation.” The standard isn’t perfect, or even complete, but it’s an excellent start. Now it’s up to the rest of the biology community to work on adopting it.

The journal is certainly doing its part. While most Nature content requires a subscription to view, the full text of the paper describing this standard is open-access. Click the wiring diagram to check it out.

Cell signaling diagram using new standardized notation.

Cell signaling diagram using new standardized notation.

Good News from Worm; Bad News for Worms

The latest issue of Science has some encouraging news about the state of global fisheries, which after decades of over-exploitation are, in a few cases, starting to recover. The researchers analyzed ten marine fisheries around the world, and found that half of them are showing signs of recovery after management programs got more stringent. Most of the fisheries they analyzed are well-regulated ones in developed countries’ territorial waters, so the results are slightly skewed, but it’s still an encouraging sign that world’s fish stocks aren’t a lost cause.

What initially caught my attention about this paper, though, was the first author’s name:

“Rebuilding Global Fisheries,” by B. Worm et al., Science, Vol. 325, 2009, p. 578-585.

You’d think he’d be against rebuilding fisheries, but maybe he just got hooked on the subject.

Bacteria Catch Some Air

A recent paper in PNAS highlights the lengths – and heights – bacteria go to in order to find suitable habitats. Actually, the bugs in this case are simply hitching a ride on dirt, their usual environment, as it gets picked up into the jet stream during African dust storms. That dirt, and its associated microbes, blows all the way across the Atlantic and lands as far away as the US mainland.

That’s all old news, but the new report shows that the biodiversity of that dirt is nearly as high after its transatlantic trip as it was at the beginning, with hundreds of species of bacteria in it. This imported jungle includes representatives from some nasty genera, too, like Francisella sp. and Bacillus anthracis. That could explain why some highly sensitive “biodefense” detector systems keep sounding false alarms – they could just be detecting the harmless bacteria-laden dust that’s been blowing through our skies for centuries.

Why would anthrax-containing dust from Africa be so harmless? For starters, the concentration of bacteria in the airborne particles is minuscule – the researchers in the new study had to concentrate air samples for several days in order to detect these organisms. Another issue is that the system the researchers used only detects snippets of microbial DNA, not actual live bacteria. That means it could be detecting organisms that actually died weeks earlier, and simply haven’t been fully broken down.

I asked Gary Andersen, the senior author on the paper, about that possibility, and here’s his reply:

Yes, our method picks up both live and dead. While it is true that dead bacteria transported in the air will be detected, bacterial and DNA degradation are fast processes. Therefore, we hypothesize that even the bacteria were alive at some point in their airborne transport. We amplified a 1500 bp gene and have found that sufficient amplification is only possible with high quality, non-degraded DNA.

He makes a good point about DNA degradation being quick, at least in most environments. However, it’s still possible that the organisms his team is detecting aren’t all capable of sprouting to life after their long journey.

This problem is becoming more important, as other groups are also using DNA-based assays to search for hard-to-culture organisms in the environment. For example, the recent report claiming to have found an extraordinarily small archaebacterium might actually be describing an obligate parasite. That would still be interesting, but somewhat less so than a free-living organism that tiny. Call me an old-fashioned microbiologist, but until I’ve seen a microbe actually cultured from a source, I’m not quite convinced it’s there.

Competition and Rotten Tricks

Microbes are consummate chemical warriors, producing numerous compounds that kill or repel their tiny competitors. The most successful antibiotics in medicine, for example, are almost all derived from naturally occurring chemicals that bacteria and fungi evolved to combat each other. But it seems this chemical warfare doesn’t stop at the microscopic scale, as Burkepile et al. show in the November issue of Ecology:

When we baited traps in a coastal marine ecosystem with fresh vs. microbe-laden fish carrion, fresh carrion attracted 2.6 times as many animals per trap as microbe-laden carrion. This resulted from fresh carrion being found more frequently and from attracting more animals when found. Microbe-laden carrion was four times more likely to be uncolonized by large consumers than was fresh carrion. In the lab, the most common animal found in our traps (the stone crab Menippe mercenaria) ate fresh carrion 2.4 times more frequently than microbe-laden carrion. Bacteria-removal experiments and feeding bioassays using organic extracts of microbe-laden carrion showed that bacteria produced noxious chemicals that deterred animal consumers.

In other words, when animals – including us – avoid a food because it smells rotten, we’re actually conceding our meal to the microbes, because of noxious compounds they probably evolved for precisely this purpose. Pretty clever for single-celled critters.

Deuterostomes Decoded – Stop the Presses!

Discover a new species of mammal, and your work will make front page news. Discover a whole new phylum of life – that’s the second-biggest categorization in biology – and hardly anyone will notice. At least, that seems to be the lesson from this report in last week’s issue of Nature. The researchers even put out a nice press release to put the work in context, but alas, Tom Brokaw doesn’t seem to be taking the bait.

Granted, the new phylum isn’t exactly photogenic. In fact, it’s nigh impossible to find a good image of its sole extant representative, the tiny, worm-like Xenoturbella that inhabits the depths of the Baltic Sea. But the new research, which used amino acid sequence comparisons to show that Xenoturbella is in fact in its own phylum, changes a lot of what we thought we knew about animals.

Sea star on aquarium.

The central issue is the classification of deuterostomes, one of the two superphyla in the animal kingdom and a major jumping-off point for discussions about evolutionary developmental biology. We’re deuterostomes. So are sea stars like the one pictured above. So is Xenoturbella, but nobody knew exactly where this weird Baltic worm fit into the lineage. In the new work, the researchers found that it is its own phylum.

Because Xenoturbella lacks a central nervous system, a digestive tract, and gonads (nobody’s figured out how it reproduces yet), putting this worm in its own phylum suggests that our common chordate ancestor also lacked those traits. In other words, brains and guts evolved multiple times in different animal lineages.

Think about that for a moment. The brain evolved multiple times, independently, not only in different deuterostome lineages but also in the other animal superphylum, protostomes. That suggests that a brain is so useful as to be nearly inevitable. Considering how far these independently-derived brains evolved in deuterostomes (Newton, Darwin, Einstein…) and protostomes (Frida), is it a stretch to say that given enough time, life naturally spawns abstract reasoning?

The Genes on the Chip Go Round and Round

For a story in the print edition of Bioscience Technology, I recently talked to several researchers working on microfluidic devices. These are silicon chips that move and mix tiny quantities of fluid, in order to carry out chemical reactions with minuscule amounts of material. Using small volumes also accelerates the reactions, so one can, for example, analyze the activities of dozens of enzymes in a few minutes.

The cutting edge of this technology is an approach called “digital microfluidics.” These nifty little devices use tiny electrically charged pads to move microscopic droplets at mind-bending speeds. Manipulating the current flowing to the pads makes the droplets scoot around, through the magical interaction of electricity and surface tension. Because there are no pipes, test tubes, or channels etched into the design, one can build generic chips with plain grids of pads on them, then use software to change the way the droplets move.

That has great potential in the lab, and it also makes good television. Check out this video from some researchers at Duke University, for example. That system is programmed to pull three droplets out of a larger sample, then send them spinning around a ring of electrodes, but it can just as easily be programmed to merge the droplets or do actual chemistry experiments.

The researchers’ home page explains the physics behind these eerie videos, and offers several other examples of this new genre.

Medical tests and pharmaceutical screening are the immediate big-money applications for microfluidics, but the technology has some interesting long-term potential as well. For example, Len Adleman built the first DNA computer more than a decade ago, and its actual processing speed exceeded even today’s supercomputers. However, it took Adleman a couple of weeks to do the pre- and post-processing on his DNA computer, making the system as a whole impractical.

Microfluidics could change that. Imagine a standard silicon computer that performs complex calculations by delegating them to an internal DNA processor. The DNA processor, a microfluidic device, could synthesize a set of PCR primers that encode all possible solutions, carry out an amplification reaction that selects the best of the billions of possible solutions it just synthesized, sequence this DNA “answer,” then transmit the sequence back to the silicon computer and clean itself up for the next question.

Does that sound like science fiction? Maybe you should watch the videos again and reconsider.

Speciation is Hard Work

How much energy does it take to produce a new species? The question had never occurred to me – or to most biologists, I suspect – but it’s the topic of a new mathematical modeling paper that just came out in the ”Proceedings of the National Academy of Sciences.” Normally, mathematical modeling results don’t catch my eye, but this one makes strong, testable predictions and explains some very old observations.

For example, we know that the tropics have greater biodiversity than the temperate zones. Even before Darwin, biologists were trying to explain why, but so far nobody’s really managed to figure it out. This new work offers a remarkably elegant solution. If the model is correct, then the evolution of a new species is just a very complex chemical reaction with a very high activation energy. Specifically, 10^23 Joules for certain species of oceanic plankton.

To arrive at that number, they created a set of equations that use well-characterized data like metabolic and reproductive rates as inputs, then predict the rate at which an organism will accumulate single-base mutations in its genome. Fast-reproducing plankton are ideal for this sort of analysis, because they have evolved many species and are well-represented in fossils. A 30-million-year scan of the fossil record provides a strong reality check for genetic comparisons of extant species.

The authors concede that other species will have different energy requirements for speciation, because the formula depends on the metabolic rate and reproductive time of the organism. Still, 10^23J is one heck of an expenditure. If you added up all of the fossil fuel energy consumed by all of the humans in the world for one year, it would be a bit less than the energy cost of producing one new species of plankton.