Tag Archives: model organisms

Friday Fellow: C. elegans

by Piter Kehoma Boll

Despite its small size, today’s fellow is one of the most important organisms in current scientific research. Named Caenorhabditis elegans and usually called simply C. elegans, this worms is a nematode and reaches about 1 mm in length and lives in the soil of temperate areas.

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An adult hermaphrodite of C. elegans. Photo by Bob Goldstein.*

There are only four bands of muscles that run along the body of C. elegans and they only alow the worm to bend the body dorsally or ventrally, but not to the sides. Thus, while moving on a horizontal surface, the worms are forced to lie on their left or ride side.

The main food source of C. elegans are bacteria that live on decaying organic matter, although they can also feed on some yeast species. Therefore, they thrive in soils rich in organic matter, where bacteria occur in abundance.

The sex of C. elegans is unusual. An adult organism can be either a male or a hermaphrodite, without a pure female form. Hermaphrodites are the most common form and usually self-fertilize, although they can, and apparently prefer, to mate with males. The larvae pass through four larval stages before reaching the adult stage, but this happens very quickly, since in ideal conditions the lifespan of C. elegans is of about 2 to 3 weeks. However, in conditions of insufficient food, an alternative third larval stage called dauer can be formed. The dauer stage has the body sealed, including the mouth, which doesn’t allow it to take in food, and can remain as such for a few months until the conditions are good again.

As most nematodes, C. elegans presents eutely, i.e., the adult worm has a genetically determined number of cells in the body. This number is fixed and does not change, because cell division ceases in adults. Male C. elegans have 1031 cells and hermaphrodites have 959 cells.

Due to its small size, small and fixed number of cells, transparent body and because it is easy to raise it in the lab, C. elegans became a perfect model organism. It was the first organism to have its genome fully sequenced and up to now it is the only organism with a complete connectome (the map of his neuron connections). It has been used in studies related to ageing, development, apoptosis and all sort of gene expressions.

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References and further reading:

Brenner, S. (1974) The genetics of Caenorhabditis elegans. Genetics 77(1): 71-94.

Klass, M. R. (1977) Aging in the nematode Caenorhabditis elegans: Major biological and environmental factors influencing life span. Mechanisms of Ageing and Development 6: 413–429. https://doi.org/10.1016/0047-6374(77)90043-4

Peden, E.; Killian, D. J.; Xue, D. (2008) Cell death specification in C. elegans. Cell Cycle 7(16): 2479–2484. https://doi.org/10.4161/cc.7.16.6479

Wikipedia. Carnorhabditis elegans. Available at < https://en.wikipedia.org/wiki/Caenorhabditis_elegans >. Access on April 16, 2018.

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You know nothing, humans! A planarian genome challenges our understanding of how life works

by Piter Kehoma Boll

We finally have a rather complete sequencing of a planarian’s genome, more precisely, of the planarian Schmidtea mediterranea, which is an important model organism for the study of stem cells and regeneration.

In case you don’t know, planarians have a remarkable ability of regeneration, so that even tiny pieces are able to regenerate into a whole organism. They are like a real-life Wolverine, but somewhat cooler! This amazing ability is possible due to the presence of a group of stem cells called neoblasts that can differentiate into any cell type found in the planarian’s body. In fact, all differentiated cell types in planarians are unable to undergo mitosis, so that neoblasts are responsible for constantly replacing cells in every tissue. But we are not here to explain the details of planarian regeneration. We are here to talk about Schmidtea mediterranea‘s genome!

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Look at its little cock eyes saying “I will destroy everything you think you know, humans!” Photo by Alejandro Sánchez Alvarado.*

A rather complete genome of S. mediterranea has been recently published and its analysis reveal some astonishing features.

First of all, 61.7% of S. mediterranea‘s genome is formed by repeated elements. Repeated elements are basically DNA strands that occur in multiple copies throught the genome of an organism. They are thought to come from the DNA of virus that was incorporated to the host’s DNA. In humans, about 46% of the genome is formed by repeated elements. Most repeated elements of S. mediterranea belong to unidentified families of retroelements, thus suggesting that they are new undescribed families. Those repeats are very long, having more than 30 thousand base pairs, which are not known to exist in other animals. The only other group of repeated elements with a similar size is found in plants and known as OGRE (Origin G-Rich Repeated Elements). The long repeat found in Schmidtea was therefore called Burro (Big, unknown repeat rivaling Ogre).

But certainly the most surprising thing about S. mediterranea‘s genome is the lack of many highly conserved genes that are found in most eukaryotes and that were thought to be essential for cells to function properly.

Schmidtea mediterranea lacks genes responsible for repairing double-stranded breaks (DSBs) in DNA, which would make them very likely to suffer a lot of mutations and sensitive to anything that induces DSBs. However, planarians are known to have an extraordinary resistance to gamma radiation that induces DSBs. Do they have other repairing mechanisms or is our current understanding about this process flawed?

gene_loss

Several “essential” genes and their presence (in green) or absence (in red) in several animals. Schmidtea mediterranea lacks them all. Image extracted from Grohme et al. (2018).**

Another important gene that was not found in S. mediterranea is the Fatty Acid Synthase (FASN) gene, which is essential for an organism to synthesize new fatty acids. Planarians therefore would have to rely on the lipids acquired from the diet. This gene is also absent in parasitic flatworms and was at first thought to be an adaptation to parasitism but since it is absent in free-living species as well, it does not seem to be the case. Could it be a synapomorphy of flatworms, i.e., a character that identifies this clade of animals?

That is not enough for little Schmidtea, though. More than that, this lovely planarian seems to lack the MAD1 and MAD2 genes, which are found in virtually all eukaryotes. Those genes are responsible for the Spindle Assembly Checkpoint (SAC), an important step during cell division that prevents the two copies of a chromosome to separate from each other before they are all connected to the spindle apparatus. This assures that the chromosomes will be evenly distributed in both daughter cells. Errors in this process lead to aneuploidy (the wrong number of chromosomes in each daughter cell), which is the cause of some genetic disorders such as the Down syndrome in humans. Planarians do not have any trouble in distributing their chromosomes properly, so what is going on? Have they developed a new way to prevent cellular chaos or, again, is our current understanding about this process flawed?

Let’s wait for the next chapters.

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Reference:

Grohme, M. A.; Schloissnig, S.; Rozanski, A.; Pippel, M.; Young, G. R.; Winkler, S.; Brandl, H.; Henry, I.; Dahl, A.; Powell, S.; Hiller, M.; Myers, E.; Rink, J. C. (2018). “The genome of Schmidtea mediterranea and the evolution of core cellular mechanisms”. Nature. doi:10.1038/nature25473

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Friday Fellow: Hay bacillus

by Piter Kehoma Boll

Today we’ll return to the tiny world of the bacteria once more. And I guess it is a good time to introduce another celebrity from the bacterial world, the hay bacillus or grass bacillus, Bacillus subtilis.

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Several colonies of Bacillus subtilis on agar. Photo by Wikimedia user Debivort.*

As any typical Bacillus, the hay bacillus has rod-shaped cells, hence the name. They measure about 4–10 µm in length and 0.25–1.0 µm in diameter and have many flagella, so they can move quickly in a liquid medium. The natural habitat of the hay bacillus is the soil, but it can also be found in the intestine of mammals, including humans.

As it is common among the members of the phylum Firmicutes, the hay bacillus is able to enter in a dormant form called endospore that is able to tolerate extreme environmental conditions. They can survive in this form for decades, centuries, perhaps even millenia, until the conditions are adequate again.

bacillus_subtilis_spore

Microscopic image showing vegetative (red) and endospores (green) of Bacillus subtilis. Photo by Wikimedia user Y tambe.*

The hay bacillus is one of the most studied and cultivated bacterium in the world, being considered a model organism. In East Asia, one of its varieties is used in the production of the Japanese traditional food nattō. Before the introduction of antibiotics, it was common to use cultures of B. subtilis in treatments to improve immunological responses. Currently, it is used in laboratory studies focused on the formation of endospores and the phenomenon of transformation, a process by which a bacterium can capture DNA from the medium in which it is and incorporate it into its own genetic material. Additionally, it is used to produce a variety of substances, including naturally produced antibiotics.

Our fellow is indeed a good friend for us.

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References:

Anagnostopoulos, C.; Spizizen, J. (1961) Requirements for transformation in Bacillus subitilisJournal of Bacteriology81(5): 741–746.

Stein, T. (2005) Bacillus subtilis antibiotics: structures, syntheses and specific functions. Molecular Biology56: 845–857. https://dx.doi.org/10.1111/j.1365-2958.2005.04587.x

Wikipedia. Bacillus subtilis. Available at < https://en.wikipedia.org/wiki/Bacillus_subtilis >. Access on November 9, 2017.

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Friday Fellow: Baker’s Yeast

by Piter Kehoma Boll

Living along humans for centuries, today’s Friday Fellow is certainly one of the most beloved fungi. Scientifically known as Saccharomyces cerevisiae, its common names in English include baker’s yeast, brewer’s yeast or ale’s yeast.

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Saccharomyces cerevisiae under the scanning electron microscope. Photo by Mogana Das Murtey and Patchamuthu Ramasamy.*

Under the microscope, the cells of this single-celled species are ellipsoid or sphere-shaped and usually show small buds from new cells growing from the larger one. But you may have seen this species being sold as tablets or grains in the supermarket, as they are used to make bread and many alcoholic bevarages, such as wine and beer, but the baker’s yeast is much more interesting than just that.

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Grains of dried but yet alive baker’s yeast as it is sold commercially.

The cells of the baker’s yeast occur naturally on ripe fruits, such as grapes, and this was likely the original source of the strains currently cultivated by humans. The yeast reaches the fruits through many wasp species that have it growing in their intestines, an ideal environment for the fungus’ sexual reproduction.

As it is easily cultivated in the lab and has a short generation time, the baker’s yeast has become one of the most important model organisms in current biological studies. It was, in fact, the first eukaryotic organism to have its whole genome sequenced more than 20 years ago.

Saccharomyces_cerevisiae

Saccharomyces cerevisiae growing on solid agar in the lab. Photo by Conor Lawless.**

More than giving us food and drink, this amazing yeast has increased our understanding of gene expression, DNA repair and aging, among many other things. Live long the yeast!

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References:

Giaever, G.; Chu, A. M.; Ni, L.; Connelly, C. et al. (2002) Functional profiling of the Saccharomyces cerevisiae genome. Nature 418 (6896): 387-391.

Herskowitz, I. (1988) Life cycle of the budding yeast Saccharomyces cerevisiae. Microbiological Reviews 52 (4): 536-553.

Wikipedia. Saccharomyces cerevisiae. Available at < https://en.wikipedia.org/wiki/Saccharomyces_cerevisiae >. Access on July 25, 2017.

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Friday Fellow: Giant Amoeba

by Piter Kehoma Boll

The adjective “giant” can be quite relative. When regarding microorganisms, even something with a few milimeters can be considered a giant, and that is the case with the giant amoeba Chaos carolinense (sometimes wrongly written as Chaos carolinensis).

Chaos_carolinense

A chaotic mess as any good amoeba. Photo by Tsukii Yuuji.

Measuring up to 5 mm in length, the giant amoeba is a freshwater organism and is easily seen with the naked eye and, since it is also easily cultivated in the laboratory, it became widely used in laboratory studies.

As with amoebas in general, the giant amoeba has an irregular cell with several pseudopods that can contract and expand. The cell has hundreds of nuclei, as it is common with species of the genus Chaos, this being the main difference between them and the closely related genus Amoeba.

The diet of the giant amoeba is variable and includes bacteria, algae, protozoan and even some small animals. In the lab, they are usually fed with ciliates of the genus Paramecium.

Chaos (Pelomyxa) carolinensisChaos with paramecium prey

A specimen of Chaos carolinense feeding on several individuals of Paramecium. Photo by Carolina Biological Supply Company.*

Wouldn’t the giant amoeba make a nice unicelular pet?

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References:

Tan, O. L. L.; Almsherqi, Z. A. M.; Deng, Y. (2005) A simple mass culture of the amoeba Chaos carolinense: revisit. Protistology, 4(2): 185–190.

Wikipedia. Chaos (genus). Available at: <https://en.wikipedia.org/wiki/Chaos_(genus)&gt;. Access on June 20, 2017.

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Friday Fellow: Field Hornwort

by Piter Kehoma Boll

Three weeks ago our Friday Fellow was a moss, being the third non-vascular plant to be introduced. And before going back to vascular plants, let’s take a look at another non-vascular fellow from the only non-vascular division that was not yet introduced here, the hornworts.

The species I chose to start the participation of hornworts is the field hornwort, Anthoceros agrestis.

Anthoceros_agrestis

A piece of soil with the field hornwort growing on the top. Photo by Wikimedia user BerndH.*

As with other hornworts, the field hornwort has a dominant gametophyte phase which appears as a small flattened plant growing very close to the soil. The sporophyte grows over it and has the form of an elongate vertical horn, hence the name hornwort.

Found in Europe and North America, the field hornwort usually grows in wet places and is often surrounded by  mosses. Its gametophyte has some internal cavities filled with muscilage that are a favorite place for species of cyanobacteria of the genus Nostoc to grow. This association is what makes hornworts acquire their slight bluish tinge.

The field hornwort has the smallest genome of all non-vascular plants studied until the present and because of that it has been cultivated to serve as an interesting model organism.

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ResearchBlogging.orgReferences:

EOL – Encyclopedia of life. Field Hornwort. Available at <http://eol.org/pages/399515/overview&gt;. Access on May 18, 2017.

Szövényi, P., Frangedakis, E., Ricca, M., Quandt, D., Wicke, S., & Langdale, J. (2015). Establishment of Anthoceros agrestis as a model species for studying the biology of hornworts BMC Plant Biology, 15 (1) DOI: 10.1186/s12870-015-0481-x

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Friday Fellow: Spreading Earthmoss

by Piter Kehoma Boll

If you still think mosses are uninteresting lifeforms, perhaps you will change your mind after knowing the spreading earthmoss, Physcomitrella patens.

Found in temperate regions of the world, except for South America, but more commonly recorded in North America and Eurasia, the spreading earthmoss grows near water bodies, being one of the first species to colonize the exposed soil around pools of water. Although widely distributed, it is not a common species.

Physcomitrella_patens

The spreading earthmoss growing on mud. Photo by Hermann Schachner.

Since the beginning of the 1970s, the spreading earthmoss has been used as a model organism, especially regarding gene manipulation. Differently from what occurs in vascular plants, the dominant life phase in mosses is the gametophyte, an haploid organism, meaning it has only one copy of each chromosome in its cells. This is an ideal condition for the study of gene expression, as the activation or inactivation of a gene is not hindered by a second one in another copy of the chromosome in the same cell.

Physcomitrella_patens_ecotypes

Physcomitrella patens growing in the lab. Credits to the Lab of Ralf Reski.*

By controlling gene expression in the spreading earthmoss, researches can track the role of each one of them in the plant’s development. Comparing these data with that known from flowering plants, we can have a better understanding of how the plant kingdom evolved.

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ResearchBlogging.orgReferences:

Cove, D. (2005). The Moss Physcomitrella patens Annual Review of Genetics, 39 (1), 339-358 DOI: 10.1146/annurev.genet.39.073003.110214

Schaefer, D. (2001). The Moss Physcomitrella patens, Now and Then PLANT PHYSIOLOGY, 127 (4), 1430-1438 DOI: 10.1104/pp.127.4.1430

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