Category Archives: Microorganisms

Yes, Archaea also have circadian clocks!

ResearchBlogging.orgIf you ever glanced at the circadian literature, you have probably encountered the statement that “circadian rhythms are ubiquitous in living systems”. In all of my formal and informal writing I qualified that statement somewhat, stating something along the lines of “most organisms living on or near the Earth’s surface have circadian rhythms”. Why?
In the earliest days of chronobiology, it made sense to do most of the work on readily available organisms: plants, insects, mammals and birds. During the 20th century, thousands of species of animals, fungi, protists and plants – all living on the planet’s surface – were tested for the possession of the circadian clock, and one was always found. Hence the “ubiquitous” statement seen in so many papers.
But, as it was later discovered, for some marine organisms moon cycles are more important than day-night cycles so they have evolved lunar clocks in addition or instead of circadian clocks (see sponges and cnidaria, for some examples). In the intertidal zone, the tides are more important for survival than the daily rhythms, so the organisms living there have evolved tidal clocks. Animals that live in caves have lost circadian rhythms, at least in behavioral output (a clock may still be operating underneath, driving metabolic or developmental rhythms). In the polar regions, rhythmicity may be seasonal. In subterranean animals, like Blind Naked mole-rats, most individuals are without rhythms, but young males that leave the colony in order to join another one develop rhythmicity during their adventurous journey. In social insects, only the individuals that go outside the hive to forage exhibit daily rhythms.
How does one figure out if an organism has a clock? You need to pick a good output and a way to continuously monitor it. Then you put the organism in constant conditions of light, temperature, air pressure, sound etc., and monitor the output for many days. If you do the statistics on the data at the end of the experiment and see that there is a periodicity in the data (for at least the first 2-3 days)that is reasonably close to 24 hours (between 16 and 32 hours is usually thought to be the limits), you know that your organism of choice has a circadian clock.
In a related experiment, you expose the organism to an environmental periodicity – usually a light-dark cycle, as it is usually the strongest cue, as the evolution of circadian clocks and light-detecting mechanisms is closely intertwined – to see if the rhythmicity of the organism can be synchronized (entrained) to the environmental cycle, indicating that it is a biological function and not the chance quirk in your data. Without these two experiments providing positive data it does not make sense to do any further investigations into mechanisms of entrainment, anatomical location of the clock or the cellular mechanism of the clock.
The trick is to find a good output to monitor. It is easy for rodents – they will run in running wheels (so will cockroaches). Songbirds will jump from perch to perch. Lizards will walk around the cage and tilt the floor from one side to another. And while behavioral output – the general locomotor activity – is not the most reliable (it is very prone to masking effects, so for instance mice will generally not run in wheels in bright light, while rats will), it is usually the easiest and cheapest to monitor and, in most cases (see an example where it failed, while monitoring body temperature worked) will be sufficient.
But what do you do when the organism does not have a measurable behavioral output, especially one that can be continuously monitored by machines? You start thinking very, very hard. And you come up with an alternative. You may be able to implant radiotransmitters and monitor body temperature. Or you may record vocalizations. Or you may take small blood samples several times per day and assay for something like melatonin.
The technological constrains limited our ability to discover circadian clocks in bacteria until the 1990s. Until then, the existence of such clocks was a mystery (one that everyone in the field was eager to see solved). I have written several posts about the discoveries of clocks in bacteria: Circadian Clocks in Microorganisms, Clocks in Bacteria I: Synechococcus elongatus, Clocks in Bacteria II: Adaptive Function of Clocks in Cyanobacteria, Clocks in Bacteria III: Evolution of Clocks in Cyanobacteria, Clocks in Bacteria IV: Clocks in other bacteria, Clocks in Bacteria V: How about E.coli? The understanding of the way bacterial clocks work (more like a relay or a switch than a clock) made us rethink the clock metaphor we have been using for almost a century.
So it appears that most Eukaryotes have clocks and at least some bacteria have them as well. But the other large group – the Third Domain: Archaea – eluded us thus far. After all, Archaea are notoriously difficult to culture in the laboratory and it took some time to figure out how to keep them alive outside of their natural extreme environments.
Do Archaea have clocks? We did not know. Until now. A couple of weeks ago, PLoS ONE published a paper that is the first to demonstrate the daily rhythms in an Archaeon: Diurnally Entrained Anticipatory Behavior in Archaea by Kenia Whitehead, Min Pan, Ken-ichi Masumura, Richard Bonneau and Nitin S. Baliga. Here is the text of the Abstract:

By sensing changes in one or few environmental factors biological systems can anticipate future changes in multiple factors over a wide range of time scales (daily to seasonal). This anticipatory behavior is important to the fitness of diverse species, and in context of the diurnal cycle it is overall typical of eukaryotes and some photoautotrophic bacteria but is yet to be observed in archaea. Here, we report the first observation of light-dark (LD)-entrained diurnal oscillatory transcription in up to 12% of all genes of a halophilic archaeon Halobacterium salinarum NRC-1. Significantly, the diurnally entrained transcription was observed under constant darkness after removal of the LD stimulus (free-running rhythms). The memory of diurnal entrainment was also associated with the synchronization of oxic and anoxic physiologies to the LD cycle. Our results suggest that under nutrient limited conditions halophilic archaea take advantage of the causal influence of sunlight (via temperature) on O2 diffusivity in a closed hypersaline environment to streamline their physiology and operate oxically during nighttime and anoxically during daytime.

What does that mean? What did they do?
First, they picked a good candidate species – Halobacterium salinarum. Why is it a good candidate? Because it lives near the Earth’s surface, in salty lakes and ponds (like this one, in Africa):
salinarium in a lake.gif
Many Archaea live in places where no light ever penetrates: deep inside the rock or ice or the oceanic floor. Some Archaea are exposed to light in cyclical fashion but not a 24-hour cycle – I have written somewhere before that I expect the Archaea living in the waters of the Old Faithful geiser in Yellowstone National Park to have a 45-minute clock instead. But Halobacterium salinarum is exposed to the natural periodicity of the day-night cycle on the surface and is thus a good candidate for an Archaeon that may have evolved a circadian clock. This is how the Halobacterium salinarum look like under the microscope:
salinarium micrograph.gif
There is another reason this is a good candidate. The light-dark cycle has a potential adaptive consequence to the critter. Water that is saturated with salt will have a high variation of its oxygen content and this variation is dependent on the environmental temperature: when it is colder outside, oxygen can more readily disolve in the salty water. When it is warm, it cannot.
The environment where Halobacterium salinarum lives is cold during the night and hot during the day. But the temperature changes are much more gradual and slow than changes in illumination (as well as less dependable: there are colder and warmer days), so being in tune with the light is a better way to synchronize one’s activities than measuring temperature (or oxygen content) directly. By entraining to a ligh-dark cycle, these organisms can make switches in their oxygen-dependent metabolism in a more timely (and thus more energy-efficient) fashion: by predicting instead of reacting to the changes in temperature over the course of 24 hours.
So, Whitehead et al placed some Halobacterium salinarum in light-dark cycles and subsequently released them into constant darkness. But what did they measure? Archaea are known to be lousy wheel-runners!
In bacteria, much of the work is done by measuring bioluminescence coming from the expression of the luciferase gene inserted next to one of the clock gene promoters. But here, we don’t know which if any gene is a clock gene and we do not have the technology ready yet. But, these days microarrays are cheaper and easier to use then some years ago when I started grad school. And remember that Everything Important Cycles!
So they took samples of the organism six times per day and ran them on microarrays, comparing the expression of all the genes between the sampling times, both during entrainment to LD cycles and in the subsequent DD (constant dark) environment:
archaea microarrays.JPG
What they discovered is that about 12% of the genes cycle with the period of 24 hours in LD cycles and continue to cycle in DD with a circadian period of around 21.6 hours:
archaea periods.JPG
What is most interesting is that the genes that cycle are the genes that are involved in oxygen (or oxygen-dependent) metabolism – exactly the kinds of genes that are expected to cycle in this organism. Some of these genes are also know to be directly regulated by oxygen. Now we know they can also be regulated – directly and/or indirectly through a clock – by light, inducing expression in preparation for the changes in oxygen concentration, not just in direct response. In this way, the cell is ready to use oxygen a little bit ahead of time. No time wasted.
I am very excited about this finding. This opens up a whole avenue of future research, something that the authors also realize:

Indeed, further detailed experimentation is necessary to ascertain precise phasing, temperature compensation, adaptability to different periods of entrainment etc. to ascertain the mechanistic underpinnings of this diurnal entrainment and its physiological implications.

Once we know there is a clock in Archaea – and now we do due to this paper – we can start studying it in detail.
Furthermore, this finding has big implications for the study of the evolutionary origins of the circadian clock (and light-reception associated with it). The molecular mechanism of the clock is very different between Bacteria and Eukaryotes, leading the field to conclude that the clock evolved independently in these two groups (and perhaps more – some people think that protist, plant, fungal and animal clocks evolved independently of each other as well). Now we can try to figure out how Archaea measure time. Is their mechanism similar to that in Bacteria? Or in Eukaryotes? Or something completely different, indicating another independent evolutionary origin? Or something in-between Bacteria and Eukaryotes, containing some elements of both, suggesting that perhaps there was only one evolutionary origin for clocks in all the life on Earth. The authors note that this last scenario is a strong contender:

Finally, the discovery of diurnal entrainment of gene expression in an archaeon also raises important questions regarding the origin of light-responsive clock mechanisms. This is because archaeal information processing machinery is assembled from components that share ancestry with eukaryotic (general transcription factors and RNA polymerase) and bacterial (sequence-specific transcription regulators) counterparts [44]. Furthermore, components of both bacterial [45,46] and eukaryotic [47] clocks are encoded in its genome [6,32].

Of course, since this is an Open Access article, you can and should read it yourself to get more details. And post ratings, notes and comments while you are there.
Whitehead, K., Pan, M., Masumura, K., Bonneau, R., & Baliga, N. (2009). Diurnally Entrained Anticipatory Behavior in Archaea PLoS ONE, 4 (5) DOI: 10.1371/journal.pone.0005485
Update: see comment thread for more. Unfortunately, scientists still at this day and age do not report everything and keep data secret. Apparently, this was the case in the question posed by this study. I hear from trusted sources that there is still not evidence for a clock in Archaea beyond the direct effects of light on gene expression and O2 metabolism.

New microbiology aggregator

New microbiology aggregator just went live in Belgrade, built (as always) by Vedran Vucic.

Scarlett Johansson – Bioterrorist?

You may have heard the story that Scarlett Johansson had a cold when she appeared on Jay Leno’s show the other day. And you may have heard that she got the cold from her ‘The Spirit’ co-star Samuel L. Jackson. And you may have heard that she had to blow her nose into a tissue during the show. And you may have heard that this particular tissue is now up for sale on eBay. And you may have heard that all proceeds of this sale will benefit USA Harvest, the charity of Scarlett Johansson’s choice.
What you may not know is that, due to the content of the tissue being regarded as biohazard (or even bioterrorism), you may not be able to have it shipped to you if you live outside of United States.
Update: sold for $5,300

When science bloggers publish, then blog about it ;-)

On Tuesday night, when I posted my personal picks from this week’s crop of articles published in PLoS ONE, I omitted (due to a technical glitch on the site), to point out that a blog-friend of mine John Logsdon published his first PLoS ONE paper on that day:

It’s a updated and detailed report on the ongoing work in my lab to generate and curate an “inventory” of genes involved in meiosis that are present across major eukaryotic lineages. This paper focuses on the protist, Trichomonas vaginalis, an organism not known to have a sexual phase in its life cycle.

Here is the paper (and check John’s post for his experiences publishing in PLoS ONE):
An Expanded Inventory of Conserved Meiotic Genes Provides Evidence for Sex in Trichomonas vaginalis:

Meiosis is a defining feature of eukaryotes but its phylogenetic distribution has not been broadly determined, especially among eukaryotic microorganisms (i.e. protists)–which represent the majority of eukaryotic ‘supergroups’. We surveyed genomes of animals, fungi, plants and protists for meiotic genes, focusing on the evolutionarily divergent parasitic protist Trichomonas vaginalis. We identified homologs of 29 components of the meiotic recombination machinery, as well as the synaptonemal and meiotic sister chromatid cohesion complexes. T. vaginalis has orthologs of 27 of 29 meiotic genes, including eight of nine genes that encode meiosis-specific proteins in model organisms. Although meiosis has not been observed in T. vaginalis, our findings suggest it is either currently sexual or a recent asexual, consistent with observed, albeit unusual, sexual cycles in their distant parabasalid relatives, the hypermastigotes. T. vaginalis may use meiotic gene homologs to mediate homologous recombination and genetic exchange. Overall, this expanded inventory of meiotic genes forms a useful “meiosis detection toolkit”. Our analyses indicate that these meiotic genes arose, or were already present, early in eukaryotic evolution; thus, the eukaryotic cenancestor contained most or all components of this set and was likely capable of performing meiotic recombination using near-universal meiotic machinery.

‘The Hairy Beast’ or ‘Super Virgin’?

Ha! Made you look! Which is exactly the point! Go and add your own ideas in the comments there….

A cellular riddle

It takes 38 minutes for the E.coli genome to replicate. Yet, E.coli can bo coaxed to divide in a much shorter time: 20 minutes. How is this possible?
Larry poses the riddle and provides the solution.
The key is that complex biochemical processes are taught sequentially, one by one, because that is how we think and process information. Yet, unless there is a need for precise timing (in which case there will be a timer triggering the starts and ends of cellular events), most processes occur all the time, simultaneously, in parallel. How do we teach that?

Microbial genomics in PLoS

Considering this I am kinda baffled by this. There is tons of microbial metagenomics and genomics in PLoS journals.

Viruses in the Oceans: join the latest Journal Club

Brendan Bohannan, Richard W. Castenholz, Jessica Green and their students and postdcos at the Center for Ecology and Evolutionary Biology at University of Oregon are currently doing a Journal Club on the PLoS ONE article The Sorcerer II Global Ocean Sampling Expedition: Metagenomic Characterization of Viruses within Aquatic Microbial Samples, which is part of the PLoS Global Ocean Sampling Collection. Please join in the discussion.

International Genetically Engineered Machine competition

My friend Franz, who runs a delightful blog Mikrob(io)log (in Slovenian) alerted me that the team of undergraduates from the University of Ljubljana won the iGEM 2007 at MIT the other day. They did it for the second year in a row (all brand new students, of course). The Ljubljana team won in the Health & Medicine category for their work on HIV-1 virus. One member of the team is Franz’s student. Congratulations to the Slovenian team!

Participate in Journal Clubs on PLoS ONE!

Journal Clubs are a popular feature on PLoS ONE papers. There were several of them in the spring. Now, after a brief summer break, the Journal Clubs are going live again and they will happen on a regular basis, perhaps as frequently as one per week.
What does it mean – a Journal Club? In short, a lab group volunteers to discuss one of the more recent (or even upcoming, not yet published) PLoS ONE papers and to post their discussion as a series of comments, annotations and ratings on the paper itself, triggering a discussion within a broader scientific community.
The first group that will start our Fall series is the Bacterial Metagenomics group led by Dr.Jonathan Eisen at UC-Davis. They chose to discuss last week’s ONE article Metagenomics of the Deep Mediterranean, a Warm Bathypelagic Habitat. It is a good and interesting paper and they have posted their discussion on it already.
If the name Jonathan Eisen rings a bell, it is probably because you are reading his blog. Perhaps you will recognize that one of his students participating in the Journal Club is also familiar to you through her blog as well.
So, what would l really like you to do is to go and read the paper and what the Eisen group wrote about it, then join in the conversation – add your own commentary, including annotations and ratings to the article. If you decide to blog about it at your own site, try to trigger a trackback.
And if you and your group would like to do a Journal Club in the future, let us know – e-mail me at:

Everything You Always Wanted to Know About Pennicillin (and more)

Here is an example of perfect science blogging. It starts seemingly innocuously, with a quiz: Monday’s Molecule #30, where you are supposed to figure out what the compound is.
Then, after a couple of days, there is a post that you may not even realize at first is related to the first one: Bacteria Have Cell Walls
Another day or two, and A and B get connected: How Penicillin Works to Kill Bacteria
But how do we know this? Well, some people figured it out: Nobel Laureates: Sir Alexander Fleming, Ernst Boris Chain, Sir Howard Walter Florey – and now you know how we know.
Finally, putting everything in context of science, society, medicine and history, a two-parter: Penicillin Resistance in Bacteria: Before 1960 and Penecillin Resistance in Bacteria: After 1960
A tour-de-force of science blogging. I wish I could do something like that.

Deinococcus radiodurans – everyone’s favourite Archean Crazy Bacteria

Researchers Uncover Protection Mechanism Of Radiation-resistant Bacterium:

Results of a recent study titled “Protein Oxidation Implicated as the Primary Determinant of Bacterial Radioresistance,” will be published in the March 20 edition of PLoS Biology. The study, headed by Michael J. Daly, Ph.D., associate professor at the Uniformed Services University of the Health Sciences (USU), Department of Pathology, shows that the ability of the bacterium Deinococcus radiodurans to endure and survive enormous levels of ionizing radiation (X-rays and gamma-rays) relies on a powerful mechanism that protects proteins from oxidative damage during irradiation.

I thought it was pretty well established that the original adaptation was against drying out (where on Earth do you get so much radiation except in the nuclear facilities built by humans over the past few decades?). The multi-level DNA repair mechanism evolved to protect DNA from dessication would work quite nicely if DNA is danaged by other causes. So, is this new study right, or the old view?

Aquatic Microbial Diversity

Today is a big day on Plos-Biology for the Oceanic Microbial Diversity Genomics. Last night they published not one, not two, but three big papers chockfull of data.
Accompani\ying them are not one, not two, not three, not even four, but five editorial articles about different aspects of this work.
James has already homed in on one important part of the discovery: the preponderance and diversity of proteorhodopsins – microbial photopigments that are capable of capturing solar energy in a manner different from photosynthesis. As always, light-sensitive molecules are thought to be tightly connected to the evolution of circadian clocks so I expect to see some research on this in the near future.
The biggest challenge of this kind of research is how to take gobs of goo, i.e., the collective DNA from everything collected in the samples, and figure out which sequence belongs to whom. How many microbes have really been captured in the sample? How do those microbes look like? What can we say about their biochemistry, physiology and behavior? What can we say about their ecology and their evolutionary history? What counts as a ‘species’ in the asexual world of microbes?
The methods they use to try to start answering those questions are all genomic – other bloggers may be able to better understand and explain the details which involve various sequence alignments and comparisons to known microbial genomes.
What I’d like to see is a more ecological approach: sampling at different places, at different depths and at different times.
Many aquatic organisms, both unicellular and multicellular, are vertical migrants. They may swim up to the surface during the night and sink down to a greater depth during the day (or vice versa). Sampling at two or more different depths at noon and again at midnight and comparing the sequences can separate the genomes – those sequences that always appear together in the sample will belong to the same organism, those that sequester belong to different organisms.
Likewise, some organisms swim up to the surface only once a month during the full moon. Some never do and are always found only at greater depths. There is likely a seasonal change in the community compposition as well.
Of course, it is expected that different species will be found at different parts of different oceans, in rivers and estuaries, in lakes and streams, which can tell us something about the ecology of the organisms in each of these environments.
Finally, repeated sampling over a number of years at the same place, same depth and same time of day/lunar cycle/year will allow us to track the long terms effects of climate change on the aquatic communities.

Oh, how thoughtful of the Intelligent Designer!

A-ha! Finally! Now I understand the connection between Creationism and the overall anti-sex sentiment of the Fundamentalists!
New reseaarch shows that E.coli swim upstream due to the Design of their flagellum! And where do they swim from and swim to? Yes, you guessed it right! And you can also watch the movie.

Animalcules – call for submissions

Look through your blog’s archives since November 16th. Have you written something about microorganisms? Viruses, Bacteria, Archaea, Protista? Basic biology, medical aspects or ecology of microorganisms? If not, can you write one today or tomorrow? Or perhaps you vividly remember a post written by someone else? Perhaps you know of a new blog that covers microbial topics?
In any case, send the permalinks to those posts to the next host of the Animalcules carnival – Tara of Aetiology.

Ah, why do I like chicken so much?!

The supply in the USA is apparently not very safe.

Scary Stories of Drug Resistance

A brief history of antibiotics and the resistance to them, resistant TB and resistance to Triclosan (antibacterial soap).

New Microbiology Blog

If you are not a North Carolina blogger you may have skipped over this earlier post in which I mention, among else, that a new blog was started right there and then, at the Blogger MeetUp.
Now, the blog is up and running and there is new content there. So, go say Hello to a new science blogger, Lorraine Cramer of Microblogology.

Paramecium is such a cool organism to work with!

Paramecia Adapt Their Swimming To Changing Gravitational Force:

The researchers placed a vial with pond water and live paramecia inside a high-powered electromagnet at the National High Magnetic Field Laboratory in Tallahassee, Fla. The organisms are less susceptible to a magnetic field than plain water is, so the magnetic field generated inside the vial “pulls” harder on the water than on the cells. If the field is pulling down, the cells float. If it’s pulling up, they sink.
Using water alone, Valles and Guevorkian were able to increase the effect of gravity by about 50 percent. To increase the effect even further, they added a compound called Gd-DTPA* to the water. Gd-DPTA is highly susceptible to induced magnetic fields such as those generated in electromagnets. This allowed the researchers to make the water much “heavier” or “lighter,” relative to the paramecia, achieving an effect up to 10 times that of normal gravity. The magnetic field is continuously adjustable, so Valles and Guevorkian were also able to create conditions simulating zero-gravity and inverse-gravity.
By dialing the magnetic field up or down, the researchers could change the swimming behavior of the paramecia dramatically. In high gravity, the organisms swam upward mightily to maintain their place in the water column. In zero gravity, they swam up and down equally. And in reverse gravity, they dove for where the sediments ought to be.
“If you want to make something float more,” said Valles, “you put it in a fluid and you pull the fluid down harder than you pull the thing down. And that’s what we basically do with the magnet. That causes the cell to float more – and that turns gravity upside down for the cell.”
Cranking the field intensity even higher, Valles and Guevorkian could test the limits of protozoan endurance. At about eight times normal gravity, the little swimmers stalled, swimming upward, but making no progress. At this break-even point, the physicists could measure the force needed to counter the gravitational effect: 0.7 nano-Newtons. For comparison, the force required to press a key on a computer keyboard is about 22 Newtons or more than 3 billion times as strong.

Gorgeous Photos of the Cellular Slime Mold

Jenna was having fun with the microscope.

Clocks in Bacteria V: How about E.coli?

Clocks in Bacteria V: How about E.coli?Fifth in the five-part series on clocks in bacteria, covering more politics than biology (from May 17, 2006):

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Clocks in Bacteria IV: Clocks in other bacteria

Blogging on Peer-Reviewed Research

Clocks in Bacteria IV: Clocks in other bacteriaFourth in the five-part series on clocks in bacteria (from April 30, 2006):

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Clocks in Bacteria III: Evolution of Clocks in Cyanobacteria

Blogging on Peer-Reviewed Research

Clocks in Bacteria III: Evolution of Clocks in CyanobacteriaThe third installment in the five-part series on clocks in bacteria (from April 19, 2006):

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Quorum Sensing and the Blogosphere as a Superorganism

Quorum Sensing and the Blogosphere as a SuperorganismA microbiological metaphor for the blogosphere (from November 27, 2005):

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Clocks in Bacteria II: Adaptive Function of Clocks in Cyanobacteria

Blogging on Peer-Reviewed Research

Clocks in Bacteria II: Adaptive Function of Clocks in CyanobacteriaSecond post in a series of five (from April 05, 2006):

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Some hypotheses about a possible connection between malaria and jet-lag

Blogging on Peer-Reviewed Research

Some hypotheses about a possible connection between malaria and jet-lagHypotheses leading to more hypotheses (from March 19, 2006 – the Malaria Day):

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Clocks in Bacteria I: Synechococcus elongatus

Blogging on Peer-Reviewed Research

Clocks in Bacteria I: Synechococcus elongatus
First in a series of five posts on clocks in bacteria (from March 08, 2006)…

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Dr.Love-of-Strange, or How I Learned To Love The Malaria…

Dr.Love-of-Strange, or How I Learned To Love The Malaria...From November 28, 2005, a post about teaching…

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Circadian Clocks in Microorganisms

Circadian Clocks in MicroorganismsThe first in a series of posts on circadian clocks in microorganisms (from February 23, 2006)…

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Another thematic week

This week (Monday to Friday), at least in terms of reposting stuff from my old blogs (but hopefully also a couple of new posts), the theme will be Microorganisms.
In preparation for this, you may want to check my recent posts on biological clocks in Protista, sex life of Paramecium, a virus that made you smart and the ecology of Lyme Disease (oh, I forgot – I also hosted Animalcules #4). I hope you enjoy the series.

Biological Clocks in Protista

Writing 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 that is all fine and well….but, my readers are anthropocentric. They want more posts about humans – both clocks and sleep – something I knew very little about. So, I have learned a lot over the past year and a half by digging through the literature and books on the subject. I was also forced to learn more about the molecular machinery of the circadian clock as most newsworthy (thus bloggable) new papers are on the clock genetics.
I know almost nothing about clocks in plants, fungi or fish, for instance, but I intend to learn – both for my own sake and for the sake of my blog readers. Actually, I started digging through the literature taxon by taxon some while ago, pretty much on two tracks: one covering the Invertebrates (like this and this), the other on microorganisms.
It is interesting to see how much I have regurgitated textbook dogma and conference hallway “truths” in my initial post on the clocks in microorganisms, only to have to contradict myself once I actually delved into the literature and learned for myself (see the series here: one, two, three, four and five).
I bet the same thing is going to happen next, as I am embarking on the literature on the clocks in Protista. I wish I could have a copy of Cellular and Molecular Bases of Biological Clocks: Models and Mechanisms for Circadian Timekeeping by Leland N. Edmunds, an excellent book that contains a lot of infromation on the clocks in protists. However, it is expensive, and although it is on my amazon wish list, I doubt anyone will splurge on it for me.
chlamy5.jpgSo, over the next couple of months, expect a series of posts on the clocks in protists. From the old textbooks and conference lore, I believe that one of the first (if not THE first) circadian mutation was discovered in the Chlamydomonas, belonging to the group of green algae (recently moved into the Kingdom Plantae, but I will treat it as a Protist for the purposes of my series) which was an important laboratory model early in the development of the field.
Euglena.JPGPeople like Leland Edmunds have worked out a lot of cell biology of clocks in the Paramecium (Ciliata) and Euglena (Flagellates).
acetabularia.jpgThe most astonishing results came from some 1950s studies in the Acetabularia, another green alga, in which rhythms persisted in the absence of the cell nucleus. The studies were repeated in early 1990s, yet to this day there is no good explanation of the findings – I am looking forward to reviewing that part!
Starting on my literature search, I discovered that some work was also done on Rhodophyta (red algae), e.g., this and this.
gonyalax.jpegMost of the work in protists, however, was performed on Lingulodinium polyedrum, much better known by its old name Gonyaulax polyedra. It was initially studied by one of the pioneers of chronobiology, J.Woodland Hastings. ‘Woody’, as he is known, had many graduate students who, after leaving his lab, took Gonyaulax with them and did further research for many years. Several very important findings, with implicaitons for the whole field of chronobiology, came out of that research on Gonyaulax.
Unfortunately, the way science funding is going these days, when even fruitfly researchers are complaining, little to no research is currently done on clocks in protista – all those researchers have moved to mice and rats in order to get their work funded. I hope this situation changes in the future. Protists are such a huge and diverse group of organisms, they are bound to keep many cool secrets we should try to uncover.