The Molbio Carnival: second edition

Welcome everybody! I’m glad you found us here at the second stop of the traveling MolBio carnival. If you’ve got an eye for the small and tiny you have arrived at the right address, as our rides and bazaars are specialized in molecular and cellular biology! I’ll be happy guide you along the carnival grounds and show you all the great contributors.

Getting there
No point in organizing a carnival without means of getting there! These contributions are about cellular spaces and molecular localization and trafficking within the cell.

Lab Rat discusses the problems of getting proteins to the outer membrane of bacteria and folding them properly among the way. To cross all the obstacles the proteins encounter along the way, they are guided by the BAM chaperone protein. Interestingly, BAM itself is chaperoned by Skp! This Skp can be turned on and off, giving bacteria the power to decide when and where proteins are shuttled to the outer membrane.

An anonymous contributor on the ‘You’d Prefer an Argonaute’ blog discusses a paper on microRNAs. The main question addressed in this paper is whether these miRNAs can be delivered to other cells in small vesicles. While the researchers indeed find miRNAs in these vesicles, the author of the blogposts suggest other experiments and controls that should reveal the truth about this new mechanism.

Grant Jacobs from Code for life has submitted a great primer on the coiling of bacterial DNA. Being small, bacteria have to be smart about their space. DNA is not excluded from this principle, since unstretched the entire thread of DNA would be orders of magnitude larger than the bacteria itself! Bacteria use special proteins to compact the DNA and recent research has uncovered how these proteins form a continuous scaffold to which the DNA can associate.

In for the thrill
In this section of the carnival grounds, you’ll find thrill rides that are not for the faint of heart. in here you’ll find posts on extreme colds, the highest altitudes and zombie enzymes to statisfy your need for adrenaline and thrills.

In a guest post on MolBio Research Highlights, Cristopher Dieni blogs about what keeps the wood frog warm during the freezing winter nights. It turns out that the humble glucose molecule plays a central role in the cryoprotection of these amphibians. Since the blogpost is written by a scientist on his own work, it contains nice peeks behind the curtains of the research process. If you want to know some of the considerations and afterthoughts and work go into, go check it out!

Michael Clarkson brings in a sinister chill over the carnival grounds by discussing zombie enzymes on his blog. Mutations that were thought to ‘kill’ certain HIV enzymes, only impair the enzyme’s activity! If you only check if the enzymes bind their substrate they could appear dead, while they still have catalyzing activity. Michael contributed to the research himself and rightly warns that our understanding of protein mutations is based on a few examples from fewer species, so the right assays are required to see if the enzyme is truly dead.

Torah Kachur contributes a post from far-away Tibet! Unlike the Tibetans, Torah was struggling with the low oxygen in the mountainous country. Tibetan people have some adaptations that allow them to live at high altitudes. Read the blogpost if you want to know more about one of the genes that allows Tibetans to cope with one of the harshest environments on this planet!

Carnival hubbub
The noisy bazaars on the carnival grounds fill the air with chatter and shouting. These posts are all about the noise and chaos that is intrinsic to life, and the ways life has found to reduce some of that noise.

On the It Takes Thirty blog, Becky Ward blogs about two different signalling circuits that have something in common: they weren’t doing what scientists expected them to do. Instead of a linear relationship between the input and ouput, the circuits responded to fold changes. Signalling by fold change guarantees the reliability and consistency of the developmental pathways by making the whole system is more robust to noise. For the whole story, check out the entire blogpost!

Iddo Friedberg from Byte Size Biology pumps up the volume with the finding that bacteria are incredibly noisy! While they don’t actually make much sound, they’re incredibly noisy in terms of protein production and gene expression. Additionally, they discovered that mRNA and protein expression levels don’t correlate at all. But somehow, atop of all that noise, ordered systems arise, suggesting that there are other noise reducing or amplifying mechanisms that still need to be discovered.

The second blogpost contributed by Becky Ward has everything to do with signalling pathways and noise reduction. The subject of this post is the Notch pathway, which plays a major role in determining the destiny of cells during embryonal development (“You’ll be a nerve cell. And you there hiding in that corner, you’re a endothelial cell from now on!”). The ligand of Notch, Delta, can behave in two very different ways to Notch signalling. This makes the whole system a kind of phenotypic switch!

The hawkers and peddlers try to attract your attention with varying visual and auditory signals. These blogposts are about the signals within our cells and on top of their genes that make us into who whe are.

Sally Church discusses the darker side of Notch signalling by highlighting the role it could play in proliferating cancers. Notch might be partly responsible for angiogenesis, or the growth of new blood vessels in a malignant tumour. The good news is that in mouse models, a combination treatment of standard drugs and drugs that reduce Notch activity were more effective than either drug treatment would have been alone. Read all about it here!

A blogpost on epigenetic inheritance appeared on Phased, by Michael Scott Long. Epigenetics is an exciting field of science that studies the modifications of DNA that come and go (‘on top’ of the normal genome, hence ‘epi’-genetics), and which are sometimes inherited. Long discusses a new piece of software to analyze these epigenetic modifications, to hopefully shed some light on the role of epigenetics in health and disease.

That’s it for this month’s edition of The MolBio Carnival. You can check future hosts and past editions on the Carnival’s home page. Be sure to subscribe to the RSS feed to receive notifications and summaries when new editions of the Carnival are posted. Also, you are welcomed to submit your best molbio blog articles to the next edition of The MolBio Carnival which will be hosted by Alexander Knoll over at Alles was lebt. More info here!

In the meantime, enjoy the carnival and beware of zombie enzymes!

Arold ST, Leonard PG, Parkinson GN, & Ladbury JE (2010). H-NS forms a superhelical protein scaffold for DNA condensation. Proceedings of the National Academy of Sciences of the United States of America PMID: 20798056

Bosco DA, Eisenmesser EZ, Clarkson MW, Wolf-Watz M, Labeikovsky W, Millet O, & Kern D (2010). Dissecting the Microscopic Steps of the Cyclophilin A Enzymatic Cycle on the Biological Substrate HIV Capsid by NMR. Journal of molecular biology PMID: 20708627

Goentoro L, & Kirschner MW (2009). Evidence that fold-change, and not absolute level, of beta-catenin dictates Wnt signaling. Molecular cell, 36 (5), 872-84 PMID: 20005849

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