Pure Biology
apalazzo | August 28, 2006(This is an intro to a n upcoming entry.)
When I was an undergrad, working in a lab at McGill, my then boss Morag Park would joke that Phosphoinositides were at the center of the universe.
What did she mean by that? Well inositol metabolism seemed to be involved in everything, including oncogenesis and cell migration the only two important cellular activities.
So what the hell is inositol, phosphoinositides and all those inositol metabolites? I'll make this simple and then overload your neocortex. Inositol is a sugar polyalcoholcyclohexane molecule. It's hydroxyl groups can be phosphorylated…
apalazzo | August 27, 2006This is the newest from the Blobel lab.
Note to all "they've discovered everything" types: this finding shows how much we know about how cells operate.
Background: As I've described before the nucleus and the cytoplasm are two cellular compartments that are kept apart by the Nuclear Pore Complex (NPC). This mega-assembly of proteins is the gate (or the bouncer) of the nucleus - pass it and you can gain access to the nucleus from the cytoplasm (or vice versa). NPCs sit in the nuclear envelope, an extension of the ER that covers the chromosomes.
Nuclear proteins are synthesized in the…
apalazzo | August 24, 2006OK this post was a warm up for today.
Microtubules are long hollow polymers. They are also polar. Their minus ends are inert and are found towards the cell center while their plus ends grow and shrink and are found towards the cell periphery.
Question: Why are microtubules hollow?
Well you might think that a tube provides more strength and is less flexible. Now that might be true for a cluster of microtubules bunched up together, but beyond a couple of micrometers, single microtubules are as limp as a wet noodle.
Could there be another role?
Others have claimed that various micro "cargo"…
apalazzo | August 22, 2006The Cytoskeleton. Now that's what you call a misnomer. It is one of the most fascinating, yet misunderstood, macromolecular assemblies of the cell. Yes, the cytoskeleton can act as a scafold onto which the rest of the cell is drapped (so to speak), but in reality the cytoskeleton is a dynamic responsive network that can mold the cell and organize the cell's contents to maximize inner-cell differentiation. Perhaps a bettler title is the psychoskeleton, as one noted researcher once called it.
Take the microtubule cytoskeleton. This is a highly dynamic structure that grows and shrinks constantly…
apalazzo | August 19, 2006Not so long ago I wrote about piRNA. After reading a bit more, there are some points I'd like to make:
- It would seem that piRNA (read this for background) are required for proper spermiogenesis.
- The argonaute family members associated with piRNA (Piwi, Miwi, Mili, Riwi ...) are only expressed in testes.
- The piRNA transcripts all come from specific loci in the genome.
It would seem like the piRNA may be processed fragments of a few transcripts that are transcribed from certain promoters within the genome. These piRNA don't seem to recognize retrotransposons or other "selfish genes" so…
apalazzo | August 17, 2006Wow, centrosomes attract a strange crowd.
Strange theories about centrosomes are plentiful. Some quacks have claimed that they are , "the eyes of the cell", some sort of quantum pulse generator that secretes consciousness and now a turbine.
Ian Musgrave at Panda's thumb posted a summary of how ID proponents ... really don't have a clue about centrosome research.
(Also FrinkTank proposes its own centrosome theory - sorry Dan, I guess two central spots is a lot sexier than theories on cancer/dedifferentiation.)
apalazzo | August 16, 2006(in the best possible way)
I'm scanning through Science when BAM:
He's imaging RNA polymerase as it transcribes DNA .... nucleotide by freakin' nucleotide ... it's sequencing at the individual molecule level.
(To all those thinking about the future of biology and day dreaming of "big biology", this is where it's at ... single molecule enzymology.)
Ref:
William J. Greenleaf and Steven M. Block
Single-Molecule, Motion-Based DNA Sequencing Using RNA Polymerase
Science (2006) 313:801
apalazzo | August 16, 2006Yes I wrote about centrosome kissing and then ... another paper appears in Nature Cell Biology.
But this time it's not in mammalian cells but in yeast. Remember what I once said:
prokaryotic (bacterial) strategy: out-multiply your neighbors
eukaryotic strategy: out-sophisticate your neighbors
yeast strategy: shed many of your eukaryotic tools and go back to out-multiplying your neighbors
Durring cell division in eukaryotes, microtubules that eminate from two centrosomes form a spindle. The spindle microtubules act to yank the duplicated chromosomes to each daugther cell. But microtubules are…
apalazzo | August 12, 2006A new paper provides evidence that certain RNAs associate with centrosomes and may represent a centrosomal RNA genome. Furthermore this potential genome includes an enzyme that could copy the centrosomal associated RNA. But first some background.
For many years, there have been scientists interested in the mysterious entity called the centrosome. Often refered to as the black hole of the eukaryotic cell, these intracellular structures (see red dots) are often located next to the nucleus (blue), where the microtubule cytoskeleton (green) converges (called the microtubule organizing center).…
apalazzo | August 8, 2006There is a paper in last week's Science that describes a proofreading mechanism in prokaryotic (i.e. bacterial) RNA Polymerase, the enzyme responsible for transcribing DNA into RNA. When RNA Pol incorporates the wrong base into a growing RNA, the enzyme moves two steps back and cleaves the dinucleotide fragment (the mismatched DNA-RNA base pair plus the preceding pair DNA-RNA pair).
So far that's OK. RNA Pol can correct mistakes and thus can transcribe with increased fidelity etc. But the cool part is that the data from this paper supports a model where the mismatched nucleotide participates…
apalazzo | August 8, 2006A paper from a week or so, describes a method for detecting regions in the genome where DNA wrapping takes place. So what (you may asked) is DNA wrapped around?
Nucleosomes!
Each nucleosome (red balls in the cartoon) contains 8 histone proteins (two each of Histone 2A, 2B, 3 and 4). In addition, histone 1 (yellow in the diagram) hangs out at the periphery and is involved in linking neighboring nucleosomes together (we think). Histones are not only the most conserved eukaryotic proteins but also the most abundant. In fact, if you were to run a protein gel and stain for total proteins (by…
apalazzo | August 5, 2006You can find almost anything on Youtube.
Here is a video from Nikon (maker of great microscopes) of mouse fibroblasts (connective tissue cells) dividing and migrating around a coverslip.
Ah, this is why I became a cell biologist. Look at those guys go! (And to think that some would call them bags of molecules -which they are ... but they are pure beauty) Also notice that the cells must contract and round up just before they divide.
While you're at it visit Nikon U. a web resource for microscopy.
apalazzo | August 5, 2006Well two weeks ago in Science, two reports came out about yet another species of small RNA ... rasiRNA ... uhm ... piRNA (OK they haven't harmonized their nomenclature yet).
So here is a brief review of the types of RNA:
- mRNA (messenger RNA). These are the RNAs that encode polypeptide chains.
- rRNA (ribosomal RNA). These form the core structure of the ribosome. The ribosome is the enzyme that translates the tri-nucleotides, to amino acids. In this way it synthesizes (or "translates") proteins from mRNAs.
- tRNAs (transfer RNA). These are used by the ribosome to translate the tri-nucleotie…
apalazzo | August 2, 2006Heatwave = sitting inside a dark room and doing some work. It's funny I'm laptopless, and my life still revolves around computers (this one is attached to my microscope). Since I haven't been keeping up with the latest, all I have to show you are some nice pics of Endoplasmic Reticulum (ER). Enjoy:
Here's a closer shot (different cell):
Here is just a picture of fluorescent protein in a hepathocyte (kidney cell). Note the negative stain (absence of fluorescence) labels some organelles and some filaments:
And last, here is a cell expressing a fluorescent ER marker, but the poor cell just…
apalazzo | July 28, 2006Yes this is the surprising result interpretation of Jonathan Weissman's paper in Science. For non cell biologists, click here first, to get some background on the unfolded protein response (UPR) and ER associated degradation (ERAD). And to learn about some recent developments on ERAD, click here.
OK on to the HARDCORE cell biology ...
Remember under UPR conditions cells want to stop translating ER targeted proteins and instead synthesize chaperones and ERAD components. UPR inhibits translation through PERK (see the post on UPR) but what happens to the mRNA that encodes ER targeted proteins?…
apalazzo | July 27, 2006Well I was going to write about J. Weissman's new paper, but Pedro (from our lab) published his work TODAY (I knew it was coming out soon ...)
His paper and YET ANOTHER paper from the Weissman group made the cover of the latest issue of Cell:
They deal with the nitty-gritty of ERAD (to learn more on ERAD see this morning's post).
I won't go through the Weissman paper (the one in Cell that is), as I've yet to read it, but I can give you the summary of Pedro's work.
He discovered that ERAD works through three different complexes. Each complex is responsible for pulling a different class of…
apalazzo | July 27, 2006Need to analyze your DNA, protein or Gene (or do a one of a gadzillion other bioinformatic operations?) Well fortunately you live in the internet age.
But where to start?
From the Nucleic Acids Research Journal: A compilation of molecular biology web servers: 2006 update on the Bioinformatics Links Directory.
And the main database: http://bioinformatics.ubc.ca/resources/links_directory/narweb2006/ (If I were you I would bookmark this excellent site, it lists almost every web based application out there ...)
apalazzo | July 27, 2006OK today I'll talk about yet another paper from Jonathan Weissman's group at UCSF ... but I'll write it up in two parts. This post will be generally background about the ER and its ability to degrade proteins.
When many scientists think about "cellular functions", diagrams of the central dogma of biology (DNA=>RNA=>protein) pop into their head. But sorting out the good stuff (properly processed mRNA, well folded proteins) from the bad stuff (misprocessed mRNA, misfolded protein) is equally important.
Proteins can be divided into two classes, those that have to cross a membrane (membrane…
apalazzo | July 26, 2006In my last post, I forgot to link to these great movies of migrating fibroblasts (available as online supplements to the arginylation paper), that illustrate how beta-actin arginylation can alter cellular behavior.
So the assay is simple, grow fibroblasts until they fill up the coverslip as a single layer of cells (or monolayer). At this stage the cells will stop dividing (by a process known as "contact inhibition of cell growth"). Then the researcher can scratch the monolayer thus removing a strip of cells. The surviving cells present at the wound edge will at once migrate into the wound.…
apalazzo | July 26, 2006In cells, actin polymers dictate cell morphology.
Actin filaments can adopt several conformations, they can be bundled into large microfilaments (often called stress fibers; here "mf" - electron micrograph taken from the Borisy lab webpage) or arranged in a meshwork (as seen in the second electron micrograph). One actin isomer (gamma-actin) predominates in the stress fibers that are concentrated in the cell body, while another (beta-actin) predominates in the actin meshwork found in the leading edge of migrating cells. In fact, the generation of this meshwork right at the tip of the cell (…