Genetics & Politics

By way of smithsonianlibraries:

One of ten drawings illustrating Louis Agassiz’s lectures on comparative embryology, delivered before the Lowell Institute in Boston, 1848-49. Want to see them all?

Why yes, I would love to see them all. And now a little tidbit from the 9th Edition of Developmental Biology by Scott Gilbert,

The first known study of comparative developmental anatomy was undertaken by Aristotle in the fourth century BCE.

He continues,

There was remarkable little progress in embryology for the two thousand years following Aristotle

In other words, there’s still a lot to explore.

(via scientificillustration)

By way of wetwareontologies:

Folding@home aims to understand protein misfolding and accelerate drug design for disease research. It uses Markov state models, in diagram, to model the possible shapes and folding pathways a protein can take as it condenses from its initial randomly-coiled state (left) into its native 3D structure (right).

My favorite models.

Figure 7. Example of BioCompiler motif declarations.

1. (a) Logical not operator,
2. (b) Green fluorescence actuator,
3. (c) IPTG sensor
4. (d) A non-branching logical and operator. Terminators are not shown in the gene network diagrams for simplicity.

From the abstract: To address the gap between DNA synthesis and circuit design capabilities, we present a platform that enables synthetic biologists to express desired behavior using a convenient high-level biologically-oriented programming, Proto. The high level specification is compiled, using a regulatory motif based mechanism, to a gene network, optimized, and then converted to a computational simulation for numerical verification.

Source: Automatic Compilation from High-Level Biologically-Oriented Programming Language to Genetic Regulatory Networks [PLoS One]

Image Caption: The sea slug Chromodoris reticulata sheds and regrows its penis between matings. MATTHEW OLDFIELD/SCIENCE PHOTO LIBRARY

Just in time for Valentine’s Day [Nature], some sea slug action for all of you sea slug fans,

In total, the team observed 108 pairings, and noticed that individuals that had recently donated sperm seemed to be incapable of doing so again for at least 24 hours. When the researchers looked into this more closely, they noticed that the animals unplugged their penises from their partners and crawled away with their penises dragging along beside them: about 20 minutes later, the slugs discarded their penises. The authors realized that the nudibranchs were not donating sperm again within the 24-hour period because they did not have the necessary anatomy with which to do so.

I have nothing to add here.

By way of Aqua Velvet, Health and Disease © 1965 Time Inc.

This drawing on the back cover indicates the influence of external forces on the body’s interior condition.

This relationship has been reinvigorated recently on the covers of popular magazines by what is known as epigenetics. What is known about epigenetics and the environment [Nature Reviews] is limited (in comparison to similar areas of study) but there’s a growing [Heredity] body of work and thus plenty more that needs to be said at the molecular level.

By way of berksbiology,

Unless the CS students finish the robot revolution before you finish the cephalopod one.

Hilarious. With that said, while reading for a protein informatics course  I came across a passage that is relevant to the comic,

Consider, for instance, the rise of molecular biology as a discipline. We think of Watson and Crick as molecular biologists, not as an ornithologist and a physicist. The first molecular biologists were a motley crew of misfits and revolutionaries with no particularly relevant training, many of them ex-physicists. These physicists didn’t waste much time identifying themselves as physicists any more. They viewed themselves as a new kind of biologist. They burned their bridges. Max Delbrück dropped physics and started studying phage replication because it seemed like the fastest, best way to crack the molecular basis of heredity. It’s hard to imagine molecular biology making such dramatic progress if it had involved forming interdisciplinary teams of physicists and biologists. The molecular biologists were viewed as naive infidels. Biochemist Erwin Chargaff sniffed that ‘‘molecular biology is the practice of biochemistry without a license’’.

Molecular biologists even worried about what to call themselves, like we argue over whether we’re computational biologists or bioinformaticians. Any revolution needs to find the right slogan to unify under. Francis Crick explained, ‘‘I myself was forced to call myself a molecular biologist because when inquiring clergymen asked me what I did, I got tired of explaining that I was a mixture of crystallographer, biophysicist, biochemist, and geneticist, an explanation which in any case they found too hard to grasp’’.

To encourage the rise of new disciplines as successful as molecular biology, we need to encourage individuals to leave old disciplines behind and forge new fields.

Antedisciplinary science, Sean Eddy, PLoS Comput Biol. 2005 June; 1(1): e6. [PLoS link so you can read it for free! YAY!]

Stem Cells/Immunology from bmscartoons (follow them)

Presentation: “Serendipity 3: The Role of TLR3 in Nuclear Reprogramming”
Presenter: Avantika Chitre  (2^nd year BMS student)
Paper: Lee J, et al. Activation of innate immunity is required for efficient nuclear reprogramming. Cell. 2012 Oct 26;151(3):547-58.

In a nutshell:

Arguably one of the most remarkable feats of modern medicine is organ transplantation.   Who could have imagined centuries ago that we would someday be able to remove a patient’s damaged kidney or liver and replace it with that of another human being?  This process, however, carries significant risks, including limited availability of donor organs and possible rejection of the foreign tissue.  What if we could bypass all of that by growing and using the patient’s own healthy tissue? 

What if we could grow a new liver for a patient using his or her skin cells?  What if we could regrow neurons in patients with degenerative diseases such as Alzheimer’s? This is the hope of regenerative medicine—developing the ability to replace damaged tissue or stimulate its healing. 

Groundbreaking progress in the field was made in the lab of UCSF’s own Nobel-prize-winning Shinya Yamanaka.  It was found that four proteins (the transcription factors Oct4, Sox2, Klf4, and c-Myc) could be used to reprogram mature cells into induced pluripotent stem cells, or iPS cells.  Not only does this discovery allow researchers to bypass the ethical concerns of experimentation with embryonic stem cells, but it also introduces the possibility of taking mature cells in the body and reprogramming them into another cell type for regenerative purposes.

Something that works well in the lab, however, does not always translate to success in the clinic.  One of the reprogramming methods is introducing these proteins, now dubbed the Yamanaka factors, into cells using a virus.  This poses the risk of turning on cancer-causing genes—is it worth it to get a new kidney only to develop cancer shortly afterwards?  Another technique is the use of purified proteins, but this has proven to be significantly less effective than use of viruses.

The authors of this paper set out to determine the reason for this decreases in reprogramming efficiency.  They found that using any virus, not just one that introduces (one of) the Yamanaka factors, improved efficiency, and hypothesized that this might be due to activation of the immune system by the virus.  Indeed, they uncovered a possible role for the immune component TLR3.  Stimulating the TLR3 pathway allowed for more efficient reprogramming.  In support of the role of the immune system was the observation that the TLR3 pathway induced epigenetic changes, which are necessary for cellular reprogramming.  Perhaps by stimulating the immune system, then, we can reprogram cells into iPS cells more safely and efficiently and come one step closer to the goals of regenerative medicine.  

The Yamanaka factors as super heroes but in a story written by Alan Moore.