Pure Biology
apalazzo | November 6, 2006I heard about this paper (Deng and Hochstrasser. Nature (06) 443:827-831) and took a look at it over the weekend. Wow! There are lots of goodies in there. And it showcases how manipulable yeast are. (As you can tell I am really jealous of researchers who use yeast as a model system.)
The premise of the paper is not bad either.
There had been some rumours that proteins could get degraded within the nucleus through the ubiquitin/proteosome pathway. Now to some this idea was heretical but this new paper gives some mechanistic info into how this process occurs.
Doa10p is an E3 ligase, that is…
apalazzo | October 31, 2006OK sorry for the lack of updates. I've been rereading lots of mlp literature. Mlp = myosin like proteins. These are found on nucleoplasmic face of the nuclear pore complex (NPC) and seem to filter what goes out of the nucleus, specifically unspliced mRNA precursors. It's old data so I won't go over it here. I recently bumped into the latest instalment of the dynamin in the mitochondria saga.
Jodi Nunnari's group has a paper in Cell about how Mgm1, a dynamin like protein found in the inner mitochondrial matrix, is required for inner-membrane fusion in mitos.
I just don't get the whole thing,…
apalazzo | October 26, 2006At that same meeting over the past weekend, I heard Tim Mitchison give an interesting talk about mitosis and pharmacogenetics. For any of you who don't know, Tim's lab has been at the fore front of analyzing how the mitotic spindle operates. Tim was the first to visualize microtubules, the major constituents of the spindle, in a live cell. In his seminar, he led us on a tour of 20 years of thought about mitosis. In the past 5 years Tim had been involved in developing drugs that would inhibit mitosis and thus be used as a treatment against cancer. He was responsible for setting up the ICCB,…
apalazzo | October 25, 2006Does this type of expression profile look familiar?
From my limited experience from these types of pan-tissue blots, it would seem like every damn protein is expressed in testes.
Why?
All they do is make sperm (i.e. swimming machines). I mean sure these little guys are complicated, but compared to the liver which plays the role of the body's pharmacist, or the brain with it's supposed unquantifiable complexity, you'd expect that testes should be relatively simple. And as for "making a new human", sperm provide DNA and little else. Most of the important stuff is found in the oocyte. Face it…
apalazzo | October 23, 2006Again some interesting thoughts about problem solving in biological systems ... ripped off of a seminar intro from this weekend's retreat. Here goes ...
Scientists are tinkerers. We need tools to get inside a system and manipulated it to understand what is going on and to ultimately test our theories. So what are our tools? And what are the major parameters that we must consider when using our tools.
This weekend I heard a great talk by Kevan Shokat of UCSF. In his intro Dr Shokat made a great point in detailing the two most important features in manipulating biological systems: specificity…
apalazzo | October 13, 2006One of the problems in modern day biomedical research is turning on/off protein expression.
In order to control in vivo protein levels, many researchers have reverted to genetically tractable organisms such as yeast and worms. In the September issue of Cell, there's a cool paper by Banaszynski et al., who developed reagents so that you can pharmacological manipulate the expression of any protein in the cell.
They take advantage of the FKBP-rapamycin-FRB system, where the addition of a drug (rapamycin) promotes the association of two proteins (FKBP and FRB). Using Yellow fluorescent protein-…
apalazzo | October 10, 2006Just came back from Montreal. We attended a wedding, a thanksgiving feast, and countless outings. Basically lots of eating and drinking. I just read at ScienceSampler that interfering with actin polymerization enhances ethanol tolerance. If only I knew. The only question left is that will it cure your hangover?
(Actually it shouldn't as hangovers are produced mainly from sulfide consumption + dehydration.)
Ref:
Increased Ethanol Resistance and Consumption in Eps8 Knockout Mice Correlates with Altered Actin Dynamics
Nina Offenhäuser, Daniela Castelletti, Lisa Mapelli, Blanche Ekalle Soppo,…
apalazzo | October 2, 2006OK a breif history of RNA interference.
1990 Rich Jorgensen at the University of Arizona wanted to make petunias a deeper purple. His group tried expressing extra copies of the same gene and ... he got white flowers. The very gene he wanted to overexpress got turned off. This effect was named "cosuppression".
Cossupression was then seen in other plants and fungi. Plant virologists also found that plants expressing viral genes, or simply small bits of viral RNA that did not encode for any protein, developed resistance to the virus from which the genes originally came from.
1993 Victor Ambrose'…
apalazzo | October 2, 2006About a month ago I wrote an entry on centrosomal RNA. Turns out that the work was not "out of Bob Palazzo's lab" as I asserted but from Mark Alliegro's Lab.
His lab has been working on this project for quite a while and he tells me that more's on the way. (In fact from the little note he sent me the new data sounds VERY cool, but I'll wait till the next paper(s) comes out to tell you more).
apalazzo | October 2, 2006We all thought that it was a bit early, but VERY deserved. Also can I add this:
The Daily Transcript 1: Thomson Scientific 0.
For anyone not in the basic biomedical sciences, the two biggest revolutions in the past 10 years have been RNA interference (RNAi) and fluorescent protein technology. The two techniques allowed us to perform genetics in higher eukaryotes and to visualize proteins over time. When both came on the scene it was truly amazing. People first gossiped about both technologies and the buzz spread fast. Within months everyone was using the technique to probe their field of…
apalazzo | September 28, 2006Here is an illustration from a recent PLoS Biology paper:
Two complexes:
1- miRNA. Imperfect base pairing between the small RNA and the target. This complex sorts the RNA to p-bodies (processing bodies) where other proteins join in. The mRNA is either destroyed or stored.
2- siRNA. Perfect base pairing. The mRNA is destroyed and that's it.
A picture is worth a thousand words.
Ref:
Chu Cy, Rana TM
Translation Repression in Human Cells by MicroRNA-Induced Gene Silencing Requires RCK/p54.
PLoS Biol (2006) 4(7): e210
apalazzo | September 27, 2006Newest from PLoS Biology:
Raj A, Peskin CS, Tranchina D, Vargas DY, Tyagi S
Stochastic mRNA Synthesis in Mammalian Cells.
PLoS Biol (2006) 4(10): e309
The authors genomically incorporated a gene with
32 tandem copies of a 43-base-pair probe-binding sequence at the 3â² end of a coding sequence for a fluorescent protein
into CHO (chinese hamster overy) cells and probed fixed cells with fluorescent oligos (in other words they used FISH). The high signal (32 oligos/transcript) allowed the group to see individual mRNAs. The incorporated gene was under an inducible promoter.
What did they find?…
apalazzo | September 20, 2006There is a nice post by Coffee Mug at Gene Expression on non-coding RNAs (ncRNAs). This post was provoked by a paper in Annual Review of Neuroscience. In light of my post on the recent Eric Lander and David Spector's talks, here's a snippet:
There are more ncRNAs than you thought:
- Half of the "full-length long Japan" library of human cDNA clones appear to be non-coding. Anti-jargon: cDNA (complementary DNA) is sequence read off of RNA backwards. This group tried to take a very large scale unbiased picture of the RNAs floating around in human cells and did bioinformatics to guess whether…
apalazzo | September 19, 2006Biology is filled with feedback loops and other natural buffers to promote homeostasis. In the latest Nature, there is a ... cute ... paper about how the RNA export factor Tap (aka NXF1) mediates the nuclear export of an alternatively spliced form of it's own mRNA transcript. (For more background on the mechanism of nuclear export of mRNA, click here).
Viruses like the Mason-Pfizer monkey virus can exploit our mRNA export pathway by having their transcripts bind directly to export factors such as Tap. The RNA elements that bind Tap are called constitutive export elements (CTEs). In a hunt for…
apalazzo | September 15, 2006Looks like this season's lecture series has started.
Yesterday evening I saw a talk by Eric Lander, head of the Broad Institute. Now normally I do not blog about my results and I do not blog about what I hear at seminars. It just doesn't feel right. Scientists work very hard at obtaining results and I don't want to start telling the world about their preliminary data. But I can give you some "factoids" from the talk ... very interesting stuff. (In addition, it would be very hard to scoop anything done at the Broad.)
He started off his talk with the neatest analysis of the 20th century. Gregor…
apalazzo | September 13, 2006I gave lab meeting yesterday and I'm exhausted. Here something I presented.
(First the images then the explanation)
Image 1:
Image 2:
Signal sequences are short stretches of protein that are recognized by the signal recognition particle and direct the protein to be inserted into the endoplsmic reticulum (ER). Similarly there are protein stretches that target newly synthesized proteins to mitochondria. Signal sequences are hydrophobic, while mitochondrial targeting sequences are amphipathic helices.
What is an amphipathic helix? Poly-peptide chains tend to either line up next to each other…
apalazzo | September 5, 2006I discovered this wonderful website: Peoples Archives. In it you'll find interviews with some of the greatest thinkers of the 20th century. I just finished listening to Sydney Brenner and Francis Crick and am now listening to Renato Dulbecco.
Dulbecco, a protege of Giuseppe Levi, moved to Salvador Luria's Lab at the University of Indiana in 1947. Like many of the founders of Molecular Biology, Dulbecco started off by studying phage. Phages are to bacteria what viruses are to our cells. Back then the greatest mystery of all was the nature of the unit of inheritance (i.e. genes). Phages were…
apalazzo | September 2, 2006Just a quick lab advertisement, my bay mate Yoko and my boss Tom have a review article in Cell about how morphological differences between various regions of the endoplasmic reticulum (ER) are representative of functional differences.
You can divide the ER into 3 morphological parts.
- The Nuclear Envelope (which can be further divided into an outer nuclear membrane and inner nuclear membrane)
- Peripheral ER sheets
- Peripheral ER tubes
As I've mentioned before, a main focus of our lab (the Rapoport lab) concerns the mechanism of how newly synthesized protein is translocated into the ER.…
apalazzo | September 1, 2006See this entry for background on inositols. Inositol-6-phosphate (aka Inositol hexaphosphate, phytic acid, phytate) is a strange compound.
Apparently plants make loads of it, and it is thought that they use this molecule to store phosphate. Also it would seem that lots of cancer researchers have been throwing this compound onto oncogenic cell lines. Apparently IP6 works to inhibit cell growth ... but as to it's effectiveness in vivo, I don't know. Phytate is also sold as a dietary supplement. But lets talk about its known cellular functions. Now it turns out that IP6 is a co-factor required…
apalazzo | August 29, 2006Well I was reading BK's excellent blog Life of a Lab Rat (an opinion piece from the Guardian "Only biology is safe and, as everybody knows, biology is science for girls." WTF?)
When I came upon a link to this great entry on x-ray crystallography (here is some background on what the hell x-ray crystallography is). My current lab is a remarkable mix of various disciplines in the life sciences ... we have biochemists, cell biologists and x-ray crystallographers. We non-crystallographers have had many discussions about that last group. They are a curious breed of biologists ... well really…