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"It is not currently possible to compute an organism from its genome, performing the transformation so efficiently executed by embryos, but two articles in this issue, by Gerstein et al. on page 1775 (1) and the modENCODE Consortium on page 1787 (2), bring this goal closer." (see full article, subscription not required FTW!)
One person's junk DNA is another persons treasure.
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"Mashing up a multitude of cells in order to study them obliterates key differences between cells, researchers have come to realize. That's why more and more scientists are opting to take the measure of individual cells." (subscription required)
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""For the first time, we have a complete archaeological picture of wine production dating back 6,100 years," said Gregory Areshian, co-director of the excavation and assistant director of UCLA's Cotsen Institute of Archaeology."
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Cool. Codon usage modulates trasncription speed and subsequent post-translational modification. The paper.
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Cool. Codon usage modulates trasncription speed and subsequent post-translational modification.
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A simply amazing look back at ads from the earliest days of selling personal computers. [via @russb]
The subtlety of life – clever codon usage
Here’s a paper from September I haven’t had a chance to comment on.
Zhang et al reported in Science (review, paper – subscription required) how two almost identical protein sequences can have different translational modifications. In this case, β-actin and γ-actin are 98% identical, the differences are marginal and don’t explain why one protein is modified with arginine and the other is not.
The difference is actually quite subtle – there is one amino acid in the protein sequence that is lysine in both proteins, but the codons in the RNA are different. That difference is enough to change the relative translation speed of β-actin so that it rapidly folds and gets arginylated but not degraded as happens in the slower translation of γ-actin. In the end, this affects the relative lifetime of each protein in the cell, leading to differential functions.
That’s so cool.
It seems like every so often, things we view as well understood turn out to have another layer of subtlety built in. For example, differential codon usage is usually considered a synonymous change, nothing momentous. Sure, there’s been studies of codon usage relative to the abundance of corresponding tRNAs and how that might be used to modulate abundance of a protein (a quick Google search revealed some interesting codon-usage papers). But I think this case is novel, differential codon usage actually affecting the post-translational modification of a protein simply by tweaking the speed of translation.
How might we create a codon usage table that takes into account tRNA abundance, contribution to translational speed of different codons, and speed of post-translational processes to be able to model and predict things like the differences between the functions of β-actin and γ-actin.
Also, how prevalent is this subtle effect on post-translational modification and how susceptible is it to breaking and causing trouble in a cell?
image from Science review (found via Google images, mind you)
Co-operative evolution of the immune system in humans?
Lee and Mazmanian, from Caltech, published this great review in Science on microbes in the gut and how different bacteria might have been involved in the evolution of the human immune system.
Link (subscription required): Has the Microbiota Played a Critical Role in the Evolution of the Adaptive Immune System? by Yun Kyung Lee and Sarkis K. Mazmanian
They discuss research that shows different bacteria modulating the maturation and function of different types of T-cells. And this modulation not only affects what happens immunologically in the gut, but also the rest of the body.
The thought is that this modulation not only keeps the body from rejecting the bacteria outright, but also might provide a protective environment favoring that bacteria, including keeping out other competing bacteria. They also suggest some potential connection with auto-immunity as well.
How cool is that?
Of course, all this requires a proper balance of bacterial populations and T-cell modulation – any imbalance can lead to disease. Indeed, they use the term “pathobionts” for bacteria that normally colonize the gut without adverse affects, but still remain pathogenic under certain circumstances.
There has been lots of research in understanding the molecular mechanisms that underly our relationship as host to a whole ecosystem of bacteria in and on our body. This review provides a great overview of what’s known about the potential modulation of the evolution of our immunity. It’s worth a read if you can get the paper.
Image from striatic
links for 2011-01-13
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Analyst says, "“If someone is taking pictures at a party, those are almost immediately posted to Facebook, and kids expect to find them there,’’ he said. “Those kids may already be lost to printing pictures out, Polaroid-style.’’"
Yeah, but there are 25-55 y.o. moms who would be printing out oodles of pics. Yeah, folks post to FB, but the real pics are printed out on Shutterfly and the like and sent to family and friends. I say printing pics still has legs.
More on bacteria and asthma
There’s a theory going around to explain the rise in asthma: we’re too clean. Research in the past 5 years has slowly been teasing out how this might be.
Link (subscription required): Bacteria and Asthma: Untangling the Links by Jennifer Couzin-Frankel, Science
Scientists have been studying the difference in the incidence of asthma in babies born by cesarian and babies born through vaginal birth, where they are exposed to birth canal bacteria and fungi; or the incidence in children who receive lots of antibiotics or not. Children who are born by C-section or receive lots of antibiotics have a higher incidence of asthma.
Another study is comparing the bacterial flora of children from farms and from non-farm rural settings – farm kids seem to get less asthma.
So far, the link between bacterial diversity and asthma has been an association not proof that bacteria are causing or inhibiting the development of asthma. Yet, it does point to a future where we are less aseptic, less clean in the post-Pasteurian sort of way.
What do you think?
Image from net_efekt
links for 2011-01-12
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"I think we’re in the awkward, adolescent stage of Mass Media adoption of social media. Eventually more sane minds will prevail and attention and praise will flow towards more nuanced design. Less is more my friends, really."
Indeed.
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[via @harvestpower]
links for 2011-01-11
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"Fear the Asian carp. The fish jump several feet into the air. And they are big–up to 80 pounds. They'll slap a fisherman in the face with their tails, and leave him with a black eye…if he's lucky. They've been known to break jaws."
I trust in humanity's ability to strip a resource – we need to make these fish palatable, then overfishing will take care of the rest. [Disclaimer: I like carp!]
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"His real dream came true, he said, when he began selling his fresh mushrooms at a few farmers markets, including the Saturday market in Chico. "It kind of makes me feel complete," he said. "Otherwise, I'd feel like the preacher that preaches but never goes to church."
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"The human body teems with microbes. In this, the first of two features, Asher Mullard looks at the global efforts to catalogue this vast 'microbiome'. In the second, Apoorva Mandavilli meets the surgeons who have a rare opportunity to watch an ecosystem being established as they transplant guts from one person to another."
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"What can microbiologists who study human bowels learn from those who study the bowels of Earth?"
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I really like the "fitness landscapes" in this review.
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"Scientists are struggling to make sense of the expanding scientific literature. Corie Lok asks whether computational tools can do the hard work for them."
Yeah. Info-swim.
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(subscription required, FAIL)
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(subscription required, FAIL)
The new germ theory
Lizzie Buchen from Nature (link below) wrote a great article on some cool work folks are doing to change the way we view bacteria.
For example, one group (like a joke, it’s a microbiologist of extremophiles, a neonatologist, and a human microbial geneticist) is studying the effect of bacteria on a devastating intestinal disease in premature babies. They want to know if there’s a role or not for bacteria in this disease.
What’s interesting is that up to now, most understanding of bacteria in humans has been stuff that is pathogenic and can be cultured easily. Bringing in someone who is skilled at finding and characterizing microbes from extremely inhospitable places might help discover new things about our own microbiota.
I don’t know if it’s because I’m all interested now in human microbial ecology or if indeed there has been a resurgence in the study of human microbiology, all I know is that not a week goes by without a new paper or review in this area.
Quite exciting, isn’t it?
Here’s the article: Microbiology: The new germ theory in Nature (no subscription required FTW!).
links for 2011-01-10
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"Oonincx says that based on these results, insects do seem to put more of their food into growing plump and less into polluting the atmosphere than do traditional livestock. "The species I've looked at so far suggest that insects could be a more environmentally friendly alternative," he says."
But what about bacteria and yeast?
links for 2011-01-09
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"After months of speculation about what will happen to the Gulf oil spill, it turns out Mother Nature has rolled up her sleeves and dispatched with a lot of the gas released along with it—in just four months."
Useful bugs!
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from the @onetruecathal