115 posts · 70,059 views
Dispatches from the frontiers of systems biology.
Becky
115 posts
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- December 10, 2010
- 08:20 AM
- 292 views
Feces and phylogeny
by Becky in It Takes 30
A couple of weeks ago I wondered aloud about the question of whether diet-related changes in the nature of gut bacteria could have significant effects in evolution. The paper I was writing about at the time showed that flies fed different diets quickly began to prefer mates who had been fed the same diet, and [...]... Read more »
Ochman H, Worobey M, Kuo CH, Ndjango JB, Peeters M, Hahn BH, & Hugenholtz P. (2010) Evolutionary relationships of wild hominids recapitulated by gut microbial communities. PLoS biology, 8(11). PMID: 21103409
- December 7, 2010
- 05:30 AM
- 406 views
How long is a cell, and why?
by Becky in It Takes 30
A mammalian cell looks blobby and unstructured when you look at it in a tissue culture dish. The question of “why is it that shape?” tends not to leap to mind, in much the same way as it doesn’t when you look at a fried egg. And yet, there are real constraints on the shapes [...]... Read more »
Picone R, Ren X, Ivanovitch KD, Clarke JD, McKendry RA, & Baum B. (2010) A polarised population of dynamic microtubules mediates homeostatic length control in animal cells. PLoS biology, 8(11). PMID: 21103410
Takaku Y, Shimizu H, & Fujisawa T. (2010) Microtubules are involved in regulating body length in hydra. Developmental biology. PMID: 21047507
- December 3, 2010
- 08:54 AM
- 465 views
The astounding flexibility of life
by Becky in It Takes 30
This week’s big news is undoubtedly the discovery of a bacterium that can (if forced to) use arsenic in place of phosphorus. Though it’s being hyped as “completely different from any life on Earth”, it was in fact isolated from Mono Lake. The work was funded by NASA’s astrobiology division, who are interested in making [...]... Read more »
Wolfe-Simon, F, Blum, JS, Kulp, TR, Gordon, GW, Hoeft, SE, Pett-Ridge, J, Stolz,JF, Webb,SM, Weber, PK, Davies, PCW.... (2010) A bacterium that can grow by using arsenic instead of phosphorus. Science. info:/DOI: 10.1126/science.1197258
- December 3, 2010
- 05:30 AM
- 473 views
More microRNA mysteries
by Becky in It Takes 30
Since we only recently found out that microRNAs and small interfering RNAs (siRNAs) exist, and modulate gene expression, it’s perhaps not surprising that many aspects of their function are still puzzling. One mysterious feature is the fact that the efficacy of microRNAs and siRNAs in silencing mRNAs is rather unpredictable. For example, a single microRNA [...]... Read more »
Larsson E, Sander C, & Marks D. (2010) mRNA turnover rate limits siRNA and microRNA efficacy. Molecular systems biology, 433. PMID: 21081925
- November 30, 2010
- 05:30 AM
- 329 views
Is it me you like, or my bacteria?
by Becky in It Takes 30
When two populations of a species evolve in different directions — perhaps because they live on separate islands, with different food sources or different dangers — at some point individuals from the two populations become unwilling to mate with each other. This can increase the rate at which the two populations diverge, and thus the [...]... Read more »
Sharon G, Segal D, Ringo JM, Hefetz A, Zilber-Rosenberg I, & Rosenberg E. (2010) From the Cover: Commensal bacteria play a role in mating preference of Drosophila melanogaster. Proceedings of the National Academy of Sciences of the United States of America, 107(46), 20051-6. PMID: 21041648
- November 23, 2010
- 05:30 AM
- 412 views
Specifying sex in plants: the Q factor
by Becky in It Takes 30
Flowers and fruit are a great way for plants to take advantage of the mobility of insects and animals for their own purposes [and even to encourage moderately keen gardeners like me to spend significant amounts of money on propagating them]. It’s not quite clear when flowers first evolved, but in the mid-Cretaceous period (some [...]... Read more »
Airoldi CA, Bergonzi S, & Davies B. (2010) Single amino acid change alters the ability to specify male or female organ identity. Proceedings of the National Academy of Sciences of the United States of America, 107(44), 18898-902. PMID: 20956314
- November 19, 2010
- 10:52 AM
- 277 views
Reconciling robustness with evolvability
by Becky in It Takes 30
Marc Kirschner pointed me to this interesting recent paper about the evolvability of proteins (Philips et al. 2010. Robustness and evolvability in the functional anatomy of a PER-ARNT-SIM (PAS) domain, PNAS PMID: 20889915). What’s evolvability? It’s a term used to indicate the qualities of a molecule or organism that allow it to evolve effectively; the [...]... Read more »
Philip AF, Kumauchi M, & Hoff WD. (2010) Robustness and evolvability in the functional anatomy of a PER-ARNT-SIM (PAS) domain. Proceedings of the National Academy of Sciences of the United States of America, 107(42), 17986-91. PMID: 20889915
- November 16, 2010
- 06:59 AM
- 268 views
Redefining optimal
by Becky in It Takes 30
When you’re trying to use models to probe the behavior of a complex biological system, there usually comes a point where you have to “fit parameters”. This happens because the model is trying to build up a macroscopic picture from underlying features that may be impossible to measure. For example, in the case of tumor [...]... Read more »
Fernández Slezak D, Suárez C, Cecchi GA, Marshall G, & Stolovitzky G. (2010) When the optimal is not the best: parameter estimation in complex biological models. PloS one, 5(10). PMID: 21049094
- November 10, 2010
- 06:36 AM
- 340 views
The mysteries of blood
by Becky in It Takes 30
Be honest — would you have guessed that red blood cells are mysterious? No, I wouldn’t have either. They’re the simplest cells in our bodies, for goodness sake — they don’t even have DNA. All they do is carry hemoglobin around, picking up oxygen as they pass the lungs and gradually dumping it everywhere else. [...]... Read more »
Higgins, J., & Mahadevan, L. (2010) Physiological and pathological population dynamics of circulating human red blood cells. Proceedings of the National Academy of Sciences. DOI: 10.1073/pnas.1012747107
- November 9, 2010
- 05:30 AM
- 329 views
Surviving HIV
by Becky in It Takes 30
Untreated, HIV is normally a death sentence. But not quite always. A small number of people infected with HIV can survive for decades without symptoms. They’re called “elite controllers”, and — although the fact that they’re healthy makes them hard to identify with certainty — they’re thought to comprise less than 1% of the infected [...]... Read more »
The International HIV Controllers Study. (2010) The Major Genetic Determinants of HIV-1 Control Affect HLA Class I Peptide Presentation. Science. info:/10.1126/science.1195271
- November 2, 2010
- 07:11 AM
- 607 views
Bacterial electricity
by Becky in It Takes 30
What is electricity? It’s moving electrons. Every living thing moves electrons around, not just in nerves (for those of us that have them) but also in metabolism (oxidize one thing, reduce another). Is it possible to use this metabolic electricity to communicate with man-made devices? If you could, you might be able to make very [...]... Read more »
Jensen HM, Albers AE, Malley KR, Londer YY, Cohen BE, Helms BA, Weigele P, Groves JT, & Ajo-Franklin CM. (2010) Engineering of a synthetic electron conduit in living cells. Proceedings of the National Academy of Sciences of the United States of America. PMID: 20956333
- October 25, 2010
- 07:51 AM
- 461 views
Feed me, Seymour
by Becky in It Takes 30
The diversity of life is a puzzle for ecologists and evolutionary biologists. The principle of competitive exclusion suggests that if two species are competing for the same resource, one of them should eventually win and the other should become extinct. So if you have n different food sources, you should end up with (at most) [...]... Read more »
Jennings DE, Krupa JJ, Raffel TR, & Rohr JR. (2010) Evidence for competition between carnivorous plants and spiders. Proceedings. Biological sciences / The Royal Society, 277(1696), 3001-8. PMID: 20462904
- October 21, 2010
- 07:28 AM
- 523 views
To clot or not: the trigger for coagulation
by Becky in It Takes 30
Following up on the papers from the Alber lab I wrote about a few weeks ago, John Higgins pointed out this paper (Panteleev et al. 2010. Task-oriented modular decomposition of biological networks: trigger mechanism in blood coagulation. Biophys. J. 98 1751-1761), which also aims to use modeling to probe the mechanisms of clot formation. There’s [...]... Read more »
Panteleev MA, Balandina AN, Lipets EN, Ovanesov MV, & Ataullakhanov FI. (2010) Task-oriented modular decomposition of biological networks: trigger mechanism in blood coagulation. Biophysical journal, 98(9), 1751-61. PMID: 20441738
- October 14, 2010
- 08:15 AM
- 281 views
Repost: Controls are Cool
by Becky in It Takes 30
Many of you know that as a post-doc in Uri Alon’s lab, Galit Lahav caused a small revolution in our understanding of how the p53 network responds to DNA damage. By looking at single cells instead of populations, she showed that individual cells responding to the damage caused by gamma-irradiation show a series of stereotyped [...]... Read more »
Loewer A, Batchelor E, Gaglia G, & Lahav G. (2010) Basal dynamics of p53 reveal transcriptionally attenuated pulses in cycling cells. Cell, 142(1), 89-100. PMID: 20598361
- October 12, 2010
- 08:05 AM
- 601 views
Guest Post: The cellular postal system: more postmen don’t spoil the delivery
by Becky in It Takes 30
Bodo Stern writes: Remember the children’s game “Telephone” in which the first participant whispers a phrase to their neighbor who in turn whispers what they believe to have heard to the next player, and so on? The phrase announced by the final player often differs substantially and in hilarious ways from the original message. Luckily, [...]... Read more »
Wang F, Brown EC, Mak G, Zhuang J, & Denic V. (2010) A Chaperone Cascade Sorts Proteins for Posttranslational Membrane Insertion into the Endoplasmic Reticulum. Molecular cell. PMID: 20850366
- October 8, 2010
- 07:53 AM
- 413 views
Repost: The ancestor of the hairball
by Becky in It Takes 30
While we were playing “cite the oldest paper“, Pam Silver suggested this paper (Srb, AM and Horowitz, NH, 1944. The ornithine cycle in Neurospora and its genetic control. J. Biol. Chem 154 129-139), as a distant antecedent of the field we now call systems biology. Published only three years after Beadle and Tatum used Neurospora [...]... Read more »
Srb, AM, & Horowitz, NH. (1944) The ornithine cycle in Neurospora and its genetic control. J. Biol. Chem , 129-139. info:/
- October 5, 2010
- 06:43 AM
- 476 views
Do sea anenomes get jet lag?
by Becky in It Takes 30
A lot of effort has gone into understanding why we get jet lag, in other words understanding the molecular mechanism of the circadian clock. Circadian clocks are found in bacteria, fungi, plants and animals, and now a new paper from the Woods Hole Oceanographic Institution (Reitzel et al. 2010. Light entrained rhythmic gene expression in [...]... Read more »
Reitzel AM, Behrendt L, & Tarrant AM. (2010) Light Entrained Rhythmic Gene Expression in the Sea Anemone Nematostella vectensis: The Evolution of the Animal Circadian Clock. PloS one, 5(9). PMID: 20877728
- September 30, 2010
- 07:28 AM
- 723 views
Spider silk: the new Kevlar?
by Becky in It Takes 30
A recent article in PLoS One (Agnarsson et al. 2010. Bioprospecting finds the toughest biological material: extraordinary silk from a giant riverine orb spider. PLoS One 5 e11234 doi:10.1371/journal.pone.0011234) claims to have discovered the toughest known biomaterial: silk from “Darwin’s bark spider”, Caerostris darwini. The reason they looked at the properties of silk from this [...]... Read more »
Agnarsson I, Kuntner M, & Blackledge TA. (2010) Bioprospecting finds the toughest biological material: extraordinary silk from a giant riverine orb spider. PloS one, 5(9). PMID: 20856804
- September 29, 2010
- 07:18 AM
- 380 views
Paleopathology: do ancient cancers hold lessons for modern cancers?
by Becky in It Takes 30
Jagesh Shah sent me this intriguing recent review, which gives an overview of the results in a field I never knew existed: paleopathology. [I guess I kind of did know the field existed, from debates about whether Lincoln had Marfan syndrome and questions about whether "the royal disease" was hemophilia. Still, I didn't know how [...]... Read more »
David AR, Zimmerman MR. (2010) Cancer: an old disease, a new disease or something in between?. Nat Rev Cancer., 10(10), 728-733. info:/20814420
- September 27, 2010
- 07:11 AM
- 330 views
How do miRNAs affect protein production?
by Becky in It Takes 30
A recent paper from the Bartel and Weissman groups (Guo et al. Mammalian microRNAs predominantly act to decrease target mRNA levels, Nature 466 835-40, PMID: 20703300) provides an interesting snapshot of the journey of a field from consensus to controversy to (one day?) consensus again. At issue is the question of how microRNAs — small [...]... Read more »
Guo H, Ingolia NT, Weissman JS, & Bartel DP. (2010) Mammalian microRNAs predominantly act to decrease target mRNA levels. Nature, 466(7308), 835-40. PMID: 20703300
Hendrickson DG, Hogan DJ, McCullough HL, Myers JW, Herschlag D, Ferrell JE, & Brown PO. (2009) Concordant regulation of translation and mRNA abundance for hundreds of targets of a human microRNA. PLoS biology, 7(11). PMID: 19901979
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