115 posts · 70,296 views
For decades now, the biological community has been focused on the question of how cells transmit information from place to place. It’s a central problem if you want to understand pretty much anything about cell behavior. A signal to grow, for example, might start when a growth factor arrives on the outside of a cell, [...]... Read more »
There was a time when we viewed bacterial cells as mere bags of randomly mixed molecules. Lacking the obvious compartmentalization of eukaryotic cells, bacteria were viewed as being completely unstructured. But increasing numbers of studies seem to show clearly defined localization patterns for proteins in bacteria. One example is that the main proteases responsible for [...]... Read more »
There was a time when we viewed bacterial cells as mere bags of randomly mixed molecules. Lacking the obvious compartmentalization of eukaryotic cells, bacteria were viewed as being completely unstructured. But increasing numbers of studies seem to show clearly defined localization patterns for proteins in bacteria. One example is that the main proteases responsible for regulated proteolysis in bacteria — the Clp proteases (pronounced “clip”) — have been observed in se........ Read more »
Perhaps not quite as exciting as revivified dinosaurs, but still amazing: plants from the late Paleolithic era are claimed to have been regenerated from fossil material (Yashina et al. 2012. Regeneration of whole fertile plants from 30,000-y-old fruit tissue buried in Siberian permafrost. PNAS doi:10.10.73/pnas.1118386109). This has very little to do with systems biology, but I was interested and thought you would be too. Perhaps I could trace some kind of connection (did you know that our Ar........ Read more »
Yashina, S., Gubin, S., Maksimovich, S., Yashina, A., Gakhova, E., & Gilichinsky, D. (2012) Regeneration of whole fertile plants from 30,000-y-old fruit tissue buried in Siberian permafrost. Proceedings of the National Academy of Sciences. DOI: 10.1073/pnas.1118386109
Jeremy Gunawardena recently wrote a very nice minireview about the lessons of the Michaelis-Menten equation for model-building (also available here). Michaelis-Menten is an equation with many lessons for modern systems biologists (as I’ve discussed before) and is so deeply ingrained in biochemistry that I am sure that most people who learn about it regard it as simply a fact of life; but instead, it is a simplified way of expressing certain facts about life, i.e. a model. ... Read more »
Gunawardena J. (2012) Some lessons about models from Michaelis and Menten. Molecular biology of the cell, 23(4), 517-9. PMID: 22337858
Viruses are the ultimate hackers of biological systems. Synthetic biologists might begin to catch up in a billion years or so, depending, of course, on how strong the evolutionary pressures on them are. But for now, for frighteningly elegant and complex interventions in cellular behavior, viruses are hard to beat. And that means that when you find a virus messing with your system, you can learn a lot from how it achieves its effects.
A recent paper (Maynard et al. 2012. Competing pathways ........ Read more »
Maynard ND, Macklin DN, Kirkegaard K, & Covert MW. (2012) Competing pathways control host resistance to virus via tRNA modification and programmed ribosomal frameshifting. Molecular systems biology, 567. PMID: 22294093
The protein folding problem, as it’s called, has been confounding biologists for decades. Unlike a strand of RNA or DNA, which can be relied upon to follow a few rather simple rules dominated by base pairing, a string of amino acids seems to have so many possible ways to interact with itself as to defy [...]... Read more »
Marks, D., Colwell, L., Sheridan, R., Hopf, T., Pagnani, A., Zecchina, R., & Sander, C. (2011) Protein 3D Structure Computed from Evolutionary Sequence Variation. PLoS ONE, 6(12). DOI: 10.1371/journal.pone.0028766
I like bees, and for a brief and mostly happy period was the host of the Stern/Rudner Swarm — a pair of hives maintained by Bodo Stern and David Rudner that resided in my garden. My job was to grow the flowers and take a share of the resulting honey. Sadly they failed to make it through last winter. I suspect that the problem for these particular hives was the lack of a convenient water source rather than one of the many diseases that seem to be decimating bees worldwide, but it’........ Read more »
Koch H, & Schmid-Hempel P. (2011) Socially transmitted gut microbiota protect bumble bees against an intestinal parasite. Proceedings of the National Academy of Sciences of the United States of America. PMID: 22084077
I recently gave a short talk to a group of post-docs who had organized their own mini-symposium and workshop as a way of bringing the Harvard post-doc community in systems biology together. Those of you who haven't worked in the Boston area may be surprised that we need special events to bring together a community that is separated by only ~4 miles, but in fact the trip from Harvard's main campus in Cambridge to Harvard Medical School in Boston is a frustrating and lengthy one. Much........ Read more »
Klein AM, & Lande-Diner L. (2011) The critical discussion group: fostering personal and scientific growth. Molecular cell, 44(2), 167-9. PMID: 22017864
One of the things we wonder about a lot in biology is what is going on inside a cell. We have many ways to get at partial answers — Western blots, GFP fusions, transcriptional profiling, various proteomic techniques — and the number and power of these approaches is increasing. Here’s a new window on the internal state of a cell that makes use of a fundamental process of biology: the presentation of peptides by the class I MHC complex (Caron et al. 2011. The MHC I immunopeptid........ Read more »
Caron E, Vincent K, Fortier MH, Laverdure JP, Bramoullé A, Hardy MP, Voisin G, Roux PP, Lemieux S, Thibault P.... (2011) The MHC I immunopeptidome conveys to the cell surface an integrative view of cellular regulation. Molecular systems biology, 533. PMID: 21952136
Boy, it’s hard to get back into the rhythm of blogging once you stop. It’s been a busy few weeks — if you read the Initiative in Systems Pharmacology post you know a little bit about why, but also there have been a number of grant and fellowship deadlines, and on top of that we’re recruiting this year. In short, the day job has been taking up (even) more of the evening than it usually does. I like to be busy, but there is such a thing as going too far. However, somewha........ Read more »
I’ve been thinking recently about this year’s iGEM Jamboree, which is coming up soon. For those of you who don’t know, iGEM, the international Genetically Engineered Machines competition, challenges undergraduate students and high school students to make useful machines out of biological parts and implement them in living cells. The ideas are always interesting — usually somewhere between creative and wild, actually — and the Jamboree is where the different teams (165 of them this year........ Read more »
Ramsay, J., Williamson, N., Spring, D., & Salmond, G. (2011) A quorum-sensing molecule acts as a morphogen controlling gas vesicle organelle biogenesis and adaptive flotation in an enterobacterium. Proceedings of the National Academy of Sciences. DOI: 10.1073/pnas.1109169108
When I pouted last week about the fact that other writers had beaten me to the punch in discussing an interesting recent paper on the fitness benefits of clumping in yeast, I had somehow failed to notice that another, similarly fascinating, paper on a related topic had just come out from the Bassler lab (Nadell and Bassler 2011. A fitness trade-off between local competition and dispersal in Vibrio cholerae biofilms. PNAS doi:10.1073/pnas.1111147108). This paper is looking at the formation of b........ Read more »
Nadell CD, & Bassler BL. (2011) A fitness trade-off between local competition and dispersal in Vibrio cholerae biofilms. Proceedings of the National Academy of Sciences of the United States of America. PMID: 21825170
Our immune system has quite a problem on its hands: it needs to notice and fight off invaders of all kinds, including bacteria and viruses that evolve extremely rapidly relative to us. There are two obvious strategies for dealing with such attackers: the first is to look for a hard-to-change tag that the attacker usually carries, rather as one army recognizes and attacks the uniform of another. This is the strategy a neutrophil uses in recognizing the formylated peptides produced by bacteria. T........ Read more »
Arnaout, R., Lee, W., Cahill, P., Honan, T., Sparrow, T., Weiand, M., Nusbaum, C., Rajewsky, K., & Koralov, S. (2011) High-Resolution Description of Antibody Heavy-Chain Repertoires in Humans. PLoS ONE, 6(8). DOI: 10.1371/journal.pone.0022365
Lots has been written about the scientific method (and even I have written about it in a minor way in the past). The cycle of “make hypothesis, make predictions, test predictions, revise hypothesis, repeat” is the main thing people focus on when talking about how scientific progress happens. What’s less talked about is where the hypothesis comes from in the first place, which starts with someone (maybe you, dear reader) noticing something that needs to be explained. This is ........ Read more »
Kondrashov N, Pusic A, Stumpf CR, Shimizu K, Hsieh AC, Xue S, Ishijima J, Shiroishi T, & Barna M. (2011) Ribosome-mediated specificity in Hox mRNA translation and vertebrate tissue patterning. Cell, 145(3), 383-97. PMID: 21529712
When you’re sick — whether you just have a mild headache or you’re at risk of a heart attack — it’s likely that the drug that will be used to treat you is either a natural product or a human-made copy of a molecule originally found in nature. About half of the drugs on the market today were discovered by screening collections of small molecules made by bacteria, fungi, snails, leeches and other such creatures. Though the pharmaceutical industry has made serious ef........ Read more »
Zhu F, Qin C, Tao L, Liu X, Shi Z, Ma X, Jia J, Tan Y, Cui C, Lin J.... (2011) Clustered patterns of species origins of nature-derived drugs and clues for future bioprospecting. Proceedings of the National Academy of Sciences of the United States of America. PMID: 21768386
Ah, courtship. That crazy time when you'll do almost anything to show off for your potential mate: drink too much, fight with rivals, play chicken with cars, and generally behave in ways that make you shudder in later life. The courtship rituals of suburbia are complex enough, but they pale in comparison to the behaviors some animals show. Why do these rituals evolve? Darwin hypothesized that both sex-specific ornamentation, such as the tail of the peacock (bling, if you will), and elaborate ........ Read more »
I talk a lot about drug-resistant bacteria and why we should worry about their inexorable rise — the most recent example of which is chronicled here. Now I want to offer you another thing to worry about: drug-resistant fungi. It’s the same general problem — when you use a drug that inhibits the growth of [...]... Read more »
Spitzer M, Griffiths E, Blakely KM, Wildenhain J, Ejim L, Rossi L, De Pascale G, Curak J, Brown E, Tyers M.... (2011) Cross-species discovery of syncretic drug combinations that potentiate the antifungal fluconazole. Molecular systems biology, 499. PMID: 21694716
We often talk, often rather vaguely, about instincts and how they shape our behavior (my instinctive reaction was…, etc.). Predator-prey interactions are one place where instincts are real, and really matter. A cat that doesn’t realize that a little scuttling squeaky thing is also a good meal probably won’t be welcome in the barn of [...]... Read more »
Ferrero DM, Lemon JK, Fluegge D, Pashkovski SL, Korzan WJ, Datta SR, Spehr M, Fendt M, & Liberles SD. (2011) Detection and avoidance of a carnivore odor by prey. Proceedings of the National Academy of Sciences of the United States of America. PMID: 21690383
Once again, an interesting Theory Lunch talk has inspired me to write a blog post. Last Friday’s talk was from Mike White, who described (among other things) his lab’s efforts to understand the transcriptional behavior of the prolactin gene. This gene is primarily expressed in the pituitary, and controls the production of milk in breastfeeding [...]... Read more »
Harper CV, Finkenstädt B, Woodcock DJ, Friedrichsen S, Semprini S, Ashall L, Spiller DG, Mullins JJ, Rand DA, Davis JR.... (2011) Dynamic analysis of stochastic transcription cycles. PLoS biology, 9(4). PMID: 21532732
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