chronobiology
clock | July 13, 2007A short post from April 17, 2005 that is a good starting reference for more detailed posts covering recent research in clock genetics (click on spider-clock icon to see the original).
As I have mentioned before, there was quite an angst in the field of chronobiology around 1960s about the lack of undestanding of circadian and other rhythms at cellular and subcellular levels. Experiment involved manipulation of the environment (e.g,. light cycles) and observing outputs (e.g., wheel-running rhythms), while treating the clock, even if its anatomical location was known, as a "black box".…
clock | July 12, 2007A new paper just came out today on PLoS-Biology: Glucocorticoids Play a Key Role in Circadian Cell Cycle Rhythms. The paper is long and complicated, with many control experiments, etc, so I will just give you a very brief summary of the main finding.
One of the three major hypotheses for the origin of circadian clocks is the need to shield sensitive cellular processes - including cell division - from the effects of UV radiation by the sun, thus relegating it to night-time only:
The cyclic nature of energetic availability and cycles of potentially degrading effects of the sun's ultraviolet…
clock | July 11, 2007
Chad wrote a neat history of (or should we say 'evolution of') clocks, as in "timekeeping instruments". He points out the biological clocks are "...sort of messy application, from the standpoint of physics..." and he is right - for us biologists, messier the better. We wallow in mess, cherish ambiguity and relish in complexity. Anyway, he is talking about real clocks - things made by people to keep time. And he starts with a simple definition of what a clock is:
In order to really discuss the physics of timekeeping, you need to strip the idea of a clock down to the absolute bare…
clock | June 19, 2007"Is sunshine good for you?" is the latest Ask a ScienceBlogger question and Nick Anthis did a great job answering it - focusing on the circadian aspects of the need for sunlight - in his response here. Excellent and quite correct, if I may say so, (and I had trouble commenting on his blog, so I'll put it here) except perhaps the details of the Viagra paper.
clock | June 15, 2007
Microarrays have been used in the study of circadian expression of mammalian genes since 2002 and the consensus was built from those studies that approximately 15% of all the genes expressed in a cell are expressed in a circadian manner. I always felt it was more, much more.
I am no molecular biologist, but I have run a few gels in my life. The biggest problem was to find a control gene - one that does not cycle - to make the comparisons to. Actin, which is often used in such studies as control, cycled in our samples. In the end, we settled on one of the subunits of the ribosome as we…
clock | May 26, 2007Back in the late 1990s, when people first started using various differential screens, etc. looking for elusive "genes for sleep", I wrote in my written prelims (and reprinted it on my blog several years later):
Now the sleep researchers are jumping on the bandwagon of molecular techniques. They are screening for differences in gene expression between sleeping and awake humans (or rats or mice), searching quite openly for the "genes for sleep". Every time they "fish out" a gene, it turns out to be Protein kinase A, a dopamine receptor, or something similar with a general function in the brain…
clock | May 23, 2007When it's someone's birthday it is nice to give presents, or a flower. Perhaps a whole boquet of roses. But if the birthday is a really big round number, like 300, and the birthday boy is the one who actually gave names to many of those flowers, it gets a little tougher. Perhaps you may try to do something really difficult and build, actually plant, a Flower Clock. After all, it was Carl von Linne, aka Carolus Linnaeus, today's birthday celebrator, who invented the flower clock. He drew it like this, but he never actully built one:
The first one to make (and write down) an observation…
clock | May 22, 2007
If this gets more widely known (and, with this post, I am trying to help it become so), you can just imagine the jokes about the new challenges to the aviation industry and the renewed popularity of the Mile High Club, or the cartoons utilizing the phallic shape of airplanes!
Hamsters on Viagra Have Less Jet Lag, Research Shows (also Viagra helps jet-lagged hamsters, maybe humans, too: study and Viagra 'improves jet lag'):
Hamsters given Pfizer Inc.'s Viagra adapted more quickly to changes in their internal clocks, scientists said.
Hamsters given sildenafil, the chemical name of the drug…
clock | May 21, 2007Far too gene-centered for my taste, but an excellent chronobiology primer (pdf) nonetheless.
clock | May 18, 2007
As we mentioned just the other day, studying animal behavior is tough as "animals do whatever they darned please". Thus, making sure that everything is controlled for in an experimental setup is of paramount importance. Furthermore, for the studies to be replicable in other labs, it is always a good idea for experimental setups to be standardized. Even that is often not enough. I do not have access to Science but you may all recall a paper from several years ago in which two labs tried to simultaneously perform exactly the same experiment in mice, using all the standard equipment,…
clock | May 6, 2007
This is going to be a challenging post to write for several reasons. How do I explain that a paper that does not show too much new stuff is actually a seminal paper? How do I condense a 12-page Cell paper describing a gazillion experiments without spending too much time on details of each experiment (as much as I'd love to do exactly that)? How do I review it calmly and critically without gushing all over it and waxing poetically about its authors? How do I put it in proper theoretical and historical perspective without unnecessarily insulting someone? I'll give it a try and we'll see…
clock | May 1, 2007One chronobiological pioneer is leaving and another one is coming in. Gene Block is going to UCLA and Joe Takahashi is leaving Northwestern (What are Fred Turek and others going to do there without him? What happens to the Howard Hughes institute?) and coming in to head the new Center for Circadian and Systems Biology. A very interesting game of musical chairs. Stay tuned.
clock | April 26, 2007Thus reports The Scientist:
Researchers from three different labs have identified a new circadian gene in the mouse, according to two papers in Science and one paper in Cell published online this week. Mutagenesis screens revealed that mutations in a protein called FBXL3 lengthen the mouse circadian period by several hours, and biochemical analyses showed that FBXL3 is necessary for degradation of key circadian clock proteins.
I'll probably have something more to say once I get hold of the actual papers.
In a perfect world, the three groups would have done Open Notebook science, found each…
clock | April 25, 2007Cold Spring Harbor 72nd Symposium: Clocks & Rhythms, May 30 - June 4, 2007. Abstract deadline is way past due, but just to go and be there (and blog from there) would be super-awesome.
clock | April 22, 2007This is the first study I know that directly tested this - the effects of rotating shifts on longevity - in humans, though some studies of night-shift nurses have shown large increases in breast cancers, stomach ulcers and heart diseases, and similar studies have been done in various rodents and fruitflies:
Working in shifts shortens life span: Study:
A study of 3,912-day workers and 4,623 shift workers of the Southeastern Central Railway in Nagpur showed the former lived 3.94 years longer than their counterparts on shift duties, said the study by Atanu Kumar Pati of The School of Life…
clock | April 20, 2007Yup, that was going to be the title of this post. I got the paper and was ready to write the post when I noticed that Peter scooped me and posted about the same paper today (yup, there is just not that many cool papers on Charismatic Marine Megavertebrates to spread around this week). I have nothing to add, so just go and see his post:
The results demonstrated that a free-ranging whale shark displays ultradian, diel and circa-lunar rhythmicity of diving behaviour. Whale sharks dive to over 979.5 m, making primarily diurnal deep dives and remaining in relatively shallow waters at night.
clock | April 18, 2007It is Marine Megavertebrate Week right now, so why not take a look at one of the most Mega of the Megaverts - the grey whale (Eschrichtius robustus):
Do whales sleep? You may have heard that dolphins do - one hemisphere at the time, while swimming, and not for very long periods at a time. A combined Russian/US team of researchers published a study in 2000 - to my knowledge the best to date - on sleep-wake and activity patterns of the grey whale: Rest and activity states in a gray whale (pdf) by Lyamin, Manger, Mukhametov, Siegel and Shpak.
The whale in the experiment rested in two…
clock | April 12, 2007I made only a brief mention of the study when the press release first came out, but the actual paper (which is excellent) is out now. It is on PLoS so it is free for all to see: Mania-like behavior induced by disruption of CLOCK:
Circadian rhythms and the genes that make up the molecular clock have long been implicated in bipolar disorder. Genetic evidence in bipolar patients suggests that the central transcriptional activator of molecular rhythms, CLOCK, may be particularly important. However, the exact role of this gene in the development of this disorder remains unclear. Here we show that…
clock | April 2, 2007
One of the big questions in circadian research is how does the transcription/translation feedback loop manage to get stretched to such a long time-frame: 24 hours. If one took into account the normal dynamics of transcription and translation, the cycle would last a couple of hours at best. The usual answer is that, probably, interactions with a variety of other cellular components slows down the cycle. And this may be correct in Eukaryotes, but a paper came out a couple of years ago showing that placing three cyanobacterial clock genes and some ATP into a test-tube results in a 24-hour…
clock | March 23, 2007Apparently, in Denmark, the 'larks' (early-risers) are called 'A-people' while 'owls' (late-risers) are 'B-people'. We all know how important language is for eliciting frames, so it must feel doubly insulting for the Danish night owls.
Today, in the age of the internets, telecommuting and fast-increasing knowledge about our rhythms and sleep, retaining the feudal/early capitalism work schedules really does not make sense.
And owls are by no means minority. Among kids and adults, they comprise about 25% of the population (another 25% are larks and the rest are in between). But among the…