Clock Zoo
clock | August 10, 2007Writing a chronobiology blog for a year and a half now has been quite a learning experience for me. I did not know how much I did not know (I am aware that most of my readers know even less, but still....). Thus, when I wrote about clocks in birds I was on my territory - this is the stuff I know first-hand and have probably read every paper in the field. The same goes for topics touching on seasonality and photoperiodism as my MS Thesis was on this topic. I feel equally at home when discussing evolution of clocks. I am also familiar with the clocks in some, but not all, arthropods. And…
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 | 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 different…
clock | March 21, 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 | February 13, 2007Last week I had lunch with a good old friend of mine, Jim Green. He got his degree in Zoology, then a law degree (patent law) and is now coming back for yet another degree in biological and chemical engineering. He did his research on snakes, so we reminisced and laughed about the time several years ago (that was before Kevin joined the lab, which is why I was recruited for this study in the first place) when we were taking blood samples from copperheads.
What we wanted to do is see if snakes have melatonin and if so, if it shows a diurnal rhythm in concentration like it does in other…
clock | February 10, 2007There are several journals dedicated to biological rhythms or sleep. Of those I regularly check only two or three of the best, so I often miss interesting papers that occur in lower-tier journals. Here is one from December 2006 that caught my eye the other day:
Mammalian activity - rest rhythms in Arctic continuous daylight:
Activity - rest (circadian) rhythms were studied in two species of Arctic mammals living in Arctic continuous daylight with all human-induced regular environmental cues (zeitgebers) removed. The two Arctic species (porcupine and ground squirrel) lived outdoors in large…
clock | December 5, 2006
No other aspect of behavioral biology is as well understood at the molecular level as the mechanism that generates and sustains circadian rhythms. If you are following science in general, or this blog in particular, you are probably familiar with the names of circadian clock genes like per, tim, clk, frq, wc, cry, Bmal, kai, toc, doubletime, rev-erb etc.
The deep and detailed knowledge of the genes involved in circadian clock function has one unintended side-effect, especially for people outside the field. If one does not stop and think for a second, it is easy to fall under the impression…
clock | November 13, 2006
This post is a relatively recent (May 24, 2006) critique of a PLoS paper.
----------------------------------------------------There is a new study on PLoS - Biology that is getting some traction in the media and which caught my attention because it was supposed to be about circadian rhythms. So, I downloaded the paper and read it through to see what it is really about.
Well, it is a decent study, but, unfortunately, it has nothing to do with circadian rhythms. Many examples of tritrophic relationships involve parasitoids (usually small wasps) being attracted by plant volatiles which are…
clock | November 6, 2006
Making connections (from January 22, 2006)...
---------------------------------------------------I love Miss Frizzle from the cartoon "The Magic School Bus". She always says "Make connections, kids, make connections!" Here I'll try to make some tentative connections between two recent papers, both concerning health issues in humans.
The first paper, brought to my attention by Corpus Callosum, a blog I belatedly placed on my blogroll here only today, is titled Commonly Used Antidepressants May Also Affect Human Immune System, which is a high-hype way of presenting a finding that some types…
clock | October 26, 2006
There is nothing easier than taking a bad paper - or a worse press release - and fisking it with gusto on a blog. If you happen also to know the author and keep him in contempt, the pleasure of destroying the article is even greater.
It is much, much harder to write (and to excite readers with) a blog post about an excellent paper published by your dear friends. But I'll try to do this now anyway (after the cut).
Paul Shaw is a friend, and Indrani Ganguli is a good, good, good friend. Faculty and graduate students in biology are usually a pretty smart lot. A subset of those, as self-…
clock | October 23, 2006How birds know when and where to migrate (from April 03, 2006)
I've never ever expected to see the word "Zugunruhe" in New York Times! But here it is. It is one of my most favourite words of all times (right after "elusive"), and is even described pretty accurately:
Zugunruhe brooks no confusion. It has a Germanic certainty, and there can be no doubt what it means, once you know what it means. I confess that I only learned the word this week. If I understand the paper about it by Barbara Helm of the Max Planck Institute for Ornithology in Andechs, Germany, and the late Eberhard Gwinner in…
clock | October 19, 2006Randy Nelson is a wonderful person, an engaging speaker and the author of the best textbook on Behavioral Endocrinology. I heard that he is also a great teacher which does not surprise me and he has a talent for attracting some of the best students and postdocs to work in his lab. Oh, by the way, he also does some great research.
For decades, the study of seasonality and photoperiodism was a hustling bustling field, until everyone jumped on the clock-gene bandwagon. Randy Nelson is one of the rare birds to remain in the photoperiodism field, coming out every year with more and more…
clock | October 9, 2006
A January 20, 2006 post placing a cool physiological/behavioral study into an evolutionary context.
There are two main hypotheses - not mutually exclusive - for the adaptive value of having a circadian clock. One is the Internal Synchronization hypothesis, stating that the circadian clock serves to synchronize biochemical and physiological processes within the body. The second is the External Synchronization hypothesis, stating that the circadian clock serves to syncronize the physiology and behavior to the natural environment.
The prediction from the Internal Hypothesis is that circadian…
clock | October 6, 2006Considering that circadian clocks were first discovered in plants, and studied almost exclusively in plants for almost a century before people started looking at animals in the early 20th century, it is somewhat surprising that the molecular aspects of the circadian rhythm generation mechanisms have lagged behind those in insects, vertebrates, fungi and bacteria. It is always nice to see a paper reporting a discovery of a new plant clock gene:
New function for protein links plant s circadian rhythm to its light-detection mechanism:
Plants set their clocks by detecting the light cycle, and…
clock | October 2, 2006
From January 20, 2006, on the need to check the model-derived findings in non-model organisms.
There are pros and cons to the prevalent use of just a dozen or so species as standard laboratory models. On one hand, when a large chunk of the scientific community focuses its energies on a single animal, techniques get standardized, suppliers produce affordable equipment and reagents, experiments are more likely to get replicated by other labs, it is much easier to get funding, and the result is speedy increase in knowledge.
On the other hand, there are drawbacks. One is narrow focus which can…
clock | September 18, 2006In this post from April 06, 2006, I present some unpublished data that you may find interesting.
Understanding the role of serotonin in depression has led to development of anti-depressant drugs, like Prozac. Much of the research in this area has been performed in Crustaceans: lobsters and crayfish. The opposite behavioral state of depression, something considered a normal state, could possibly best be described as self-confidence.
Self-confidence is expressed differently in different species, but seems to always be tied to high status in a social hierarchy. In crayfish, self-confidence is…
clock | September 8, 2006Fifth in the five-part series on clocks in bacteria, covering more politics than biology (from May 17, 2006):
In the previous posts in this series, I covered the circadian clocks in Synechococcus, potential circadian clocks in a couple of other bacteria, and the presence of clock genes (thus potentially clocks) in a number of other bacteria. But what happened to the microbiological workhorse, the Escherichia coli? Does it have a clock? Hasn't anyone checked?
Believe it or not, this question is colored by politics. But I have to give you a little background first. Latter half of the 19th…
clock | September 8, 2006
Fourth in the five-part series on clocks in bacteria (from April 30, 2006):
For decades, it was thought that prokaryotes did not have circadian clocks. Then, a clock was discovered in a unicellular cyanobacterium, Synechococcus (later also in Synechocystis [1] and Trichodesmium [2]) which quickly became an important model in the study of circadian rhythms in general. Still, it was thought, for ten years or so, that no other prokaryotes had a circadian clock. Recently, the clock genes were found in filamentous (chain-forming) cyanobacteria, as well as a whole host of other bacteria and…
clock | September 7, 2006
The third installment in the five-part series on clocks in bacteria (from April 19, 2006):
As you probably know, my specialty are birds, so writing this series on clocks in microorganisms was quite an eye-opener for me and I have learned a lot. The previous two posts cover the clocks in the cyanobacterium Synechococcus elongatus, the first bacterium in which circadian rhythms were discovered and, thus, the species most studied to date.
The work in Synechococcus has uncovered a cluster of three genes - kaiA, kaiB and kaiC - that are essential for circadian rhytmicity in this species. kaiA…