Monthly Archives: January 2018

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?

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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: Timor Black Bamboo

by Piter Kehoma Boll

If there is one important family of flowering plants that hasn’t been featured here yet is the grass family Poaceae. And what would be a better grass to be the first one than a bamboo? So here we have the Timor black bamboo Bambusa lako.

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The beautiful black culms of the Timor black bamboo. Photo by Cas Liber.

As its common name suggests, this species is native from the island of Timor, one of the lesser Sunda Islands in the Indonesian Archipelago. One of the most striking features of the Timor black bamboo is its black stem. As in all bamboos, the stem of the Timor black bamboo is divided into culms. Those are initially green, but become shiny black when mature and may reach 10 cm in diameter. The whole plant can reach a height of 21 m.

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A young and still green branch of the Timor black bamboo. Photo by Mitchell Adams.*

Although still classified in the genus Bambusa, it is known since 2000 that the Timor Black Bamboo is closely related to the genus Gigantochloa, which includes other black bamboos, such as the common black bamboo Gigantochloa atroviolacea.

Currently, the Timor black bamboo is found in many places worldwide and widely used for decoration and landscaping purposes due to its peculiar color.

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References:

Loh, J. P.; Kiew, R.; Set, O.; Gan, L. H.; Gan, Y.-Y. (2000) A Study of Genetic Variation and Relationships within the Bamboo Subtribe Bambusinae using Amplified Fragment Length Polymorphism. Annals of Botany 85: 607–612. https://doi.org/10.1006/anbo.2000.1109

Wikipedia. Bambusa lako. Available at < https://en.wikipedia.org/wiki/Bambusa_lako >. Access on January 22, 2017.

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Xenoturbella, a growing group of weirdoes

by Piter Kehoma Boll

You may never have heard of Xenoturbella, and I wouldn’t blame you. Despite being a fascinating feature of evolution, little is known about it and its magic has been hidden from most of us.

The first Xenoturbella was described in 1949 and named Xenoturbella bocki. At the time, it was considered a strange flatworm, hence its name, from Greek xenos, strange + turbella, from Turbellaria, free-living flatworms. Xenoturbella bocki is a marine animal measuring up to 3 cm in length and looking like a flat worm… a flatworm! Well, actually more like a folded worm, because its body has a series of folds running londitudinally that make it have a W shape in cross section.

Found in the cold waters around northern Europe, its body lacks a centralized nervous system, having only a net of neurons inside the epidermis. There are also no reproductive organs, neither anything similar to a kidney or any other organ beside a mouth and a gut and some structures on its surface.

For decades, X. bocki was the only species of Xenoturbella known to us. A second species was described in 1999 as X. westbladi, but molecular analyses revealed that it was the same species as X. bocki, so we continued having only one species. Thanks to molecular studies, we also figured out that Xenoturbella is not a flatworm at all, but belongs to a group of very primitive bilaterian animals, being closely related to another group of former flatworms, the acoelomorphs. Together, Xenoturbella and the acoelomorphs (a good name for a rock band, right?) form the group called Xenacoelomorpha.

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Xenoturbella churro, “head” to the right. Photo by Greg Rouse.*

Forming its own phylum (or perhaps class if it is grouped in a single phylum with the acoelomorphs) named Xenoturbellida, X. bocki recently discovered that it is not alone in the world. In 2016, four new species were described from the waters of the Pacific Ocean near the coasts of Mexico and the USA, being named Xenoturbella monstrosa, X. churro, X. profunda and X. hollandorum. Considering the small size of X. bocki, some of them were monsters, especially X. monstrosa, which reaches 20 cm in length!

Four new species was quite a finding. The phylum suddenly was five times bigger than before. As someone particularly interested in obscure animal groups, especially those that once were members of the lovely phylum Plathyelminthes, I was very excited by this discovery, but I wasn’t expecting at all what happened after that.

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Photo of the only known specimen of Xenoturbella japonica until now. “Head” to the left. Credits to Nakano et al. (2017).*

In December 2017, one more species was found, this time on the other side of the Pacific, near Japan. Named Xenoturbella japonica, the fifth member of the Xenoturbella genus is very welcome. The new species was based on two specimens, an adult “female” specimen (are they hermaphrodites? I don’t think we can be sure about it yet…) and a juvenile specimen. One more exciting thing is that the juvenile may actually be yet another species! But we need more material to be sure.

You can read the article describing Xenoturbella japonica here.

See also: Acoelomorpha, a phylogenetic headache

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References:

Nakano, H.; MIyazawa, H.; Maeno, A.; Shiroishi, T.; Kakui, K.; Koyanagi, R.; Kanda, M.; Satoh, N.; Omori, A.; Kohtsuka, H. (2017) A new species of Xenoturbella from the western Pacific Ocean and the evolution of XenoturbellaBMC Evolutionary Biology17: 245. https://doi.org/10.1186/s12862-017-1080-2

Rouse, G.W.; Wilson N.G.; Carvajal, J.I.; Vrijenhoek, R.C. (2016) New deep-sea species of Xenoturbella and the position of Xenacoelomorpha. Nature, 530:94–7. doi:10.1038/nature16545.

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Friday Fellow: Deathstalker

by Piter Kehoma Boll

The name of today’s fellow may sound intimidating, and it is for a good reason. Scientifically known as Leiurus quinquestriatus, the deathstalker, which is also known as the Omdurman scorpion, Naqab desert scorpion, Palestine scorpion or Israeli scorpion, is considered one of the most venomous scorpions in the world.

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A deathstalker in Israel. Photo by Wikimedia user מינוזיג.*

The deathstalker is found in arid regions of North Africa and the Middle East. There are two subspecies, L. quinquestriatus quinquestriatus found in Africa from Algeria and Niger to Somalia and Sudan, and L. q. hebraeus found from Turkey to Iran and Yemen. They are relatively large, measuring up to 11 cm in length.

The venom of the deathstalker has been shown to contain a variety of different neurotoxins, including several inhibitors of potassium and chloride channels, which affect the transmission of nervous impulses through the nervous system. Although very painful, the sting of a single scorpion would hardly kill a healthy adult human, but immediate medical treatment with antivenom is always required to avoid any unpleastant consequences. Children, elderly people, or adult people with heart problems or allergies, however, can easily be killed.

One of the toxins, chlorotoxins, which affects chloride channels, has shown potential to be used in the treatment of brain tumors.

Despite its danger, the deathstalker is often raised as a pet. Why? Because humans…

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References:

Castle, N. A.; Strong, P. N. (1986) Identification of two toxins from scorpion (Leiurus quinquestriatus) venom which block distinct classes of calcium-activated potassium channel. FEBS Letters 209(1): 117–121. DOI: 10.1016/0014-5793(86)81095-X

EOL – Encyclopedia of Life. Leiurus quinquestriatus. Available at < http://eol.org/pages/10208954/overview >. Access on January 7, 2018.

Garcia, M. L.; Garcia-Calvo, M.; Hidalgo, P.; Lee, A.; McKinnon, R. (1994) Purification and Characterization of Three Inhibitors of Voltage-Dependent K+ Channels from Leiurus quinquestriatus var. hebraeus Venom. Biochemistry 33(22): 6834–6839. DOI: 10.1021/bi00188a012

Gueron, M.; Ilia, R.; Shahak, E.; Sofer, S. (1992) Renin and aldosterone levels and hypertension following envenomation in humans by the yellow scorpion Leiurus quinquestriatusToxicon 30(7): 765–767. DOI: 10.1016/0041-0101(92)90010-3

Lyons, S. A.; O’Neal, J.; Sontheimer, H. (2002) Chlorotoxin, a scorpion-derived peptide, specifically binds to gliomas and tumors of neuroectodermal origin. GLIA 39(2): 162–173. DOI: 10.1002/glia.10083

Sofer, S.; Gueron, M. (1988) Respiratory failure in children following envenomation by the scorpion Leiurus quinquestriatus: Hemodynamic and neurological aspects. Toxicon 26(10): 931–939. DOI: 10.1016/0041-0101(88)90258-9

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Friday Fellow: Pink Miniacina

by Piter Kehoma Boll

It’s time  for the next foraminifer, which is always a problematic time, but I managed to find a suitable fellow for this Friday. Called Miniacina miniacea in the scientific community, it obviously lacks a common name, so I decided to call it the pink miniacina.

Differently from the previously introduced foraminifers, the pink miniacina is a sessile and colonial species. It usually grows attached to other lifeforms, especially algae and corals. Due to its colonial nature, added to the already bigger-than-average size of foramnifers when compared to other unicellular organisms, the pink miniacina is easily visible to the naked eye and can be seen as a series of small branched organisms with an intense pink color. It is particulary common in the Mediterranean Sea, although it can be found in other places as well.

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Several pink colonies of Miniacina miniacea growing in the Mediterranean Sea. Photo by Stefano Guerrieri.

Due to its habit of living on the surface of other sessile organisms, the pink miniacina competes with many other organisms that have the same behavior. As a result, its abundance tends to increase in deeper water, where many of such organisms find the conditions too unsuitable to live. In a few areas, the abundance of the pink miniacina may be high enough to create a “pink sand” from the shells of dead specimens.

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References:

Di Camillo, C.; Bo, M.; Lavorato, A.; Morigi, C.; Reinach, M. S.; Puce, S.; Bavestrello, G. (2008) Foraminifers epibiontic on Eudendrium (Cnidaria: Hydrozoa) from the Mediterranean Sea. Journal of the Marine Biological Association of the United Kingdom88(3): 485–489. https://doi.org/10.1017/S0025315408001045

Milliman, J. D.(1976) Miniacina miniacea: modern foraminiferal sands on the Outer Moroccan shelf. Sedimentology23: 415–419. https://doi.org/10.1111/j.1365-3091.1976.tb00059.x

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Cat-handedness: can cats be left- or right-handed?

by Piter Kehoma Boll

In humans, as you may know, there is usually a preference for using one side of the body to perform a task, a thing called laterality. And we have a strong tendency to be right-handed, with about 90% of humans using their right side to perform most unilateral tasks. Several studies revealed that many other animals, at least among vertebrates, display laterality as well.

A recent study investigated laterality in the domestic cat during spontaneous behaviors in contrast with the more common experiments using forced behaviors, such as making the cat try to reach food. They looked for a side preference in cats during the behaviors of lying side, stepping down and stepping over.

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Photo by Juan Eduardo de Cristófaro.*

The result indicated that about one third of the cats is left-pawed, one third is right-pawed and one third is ambidextrous while moving up and down, but there is no clear preference for lying on their right or left side. Thus, we can see that, differently from humans, there is no strong bias to use one side of the body in cats, at least not when looking at cats in general.

When we consider sex, though, there was a significant difference: male cats tend to be left-pawed, while female cats are usually right-pawed. That would be very useful if cats danced the waltz.

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References:

McDowell, L. J.; Wells, D. L.; Hepper, P. G. (2018) Lateralization of spontaneous behaviours in the domestic cat, Felis silvestris. Animal Behavior135: 37–43. https://doi.org/10.1016/j.anbehav.2017.11.002

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Friday Fellow: Reishi Mushroom

by Piter Kehoma Boll

The first Friday Fellow of 2018 is here, and it is a beloved parasite from the Far East. This lovely mushroom is scientifically known as Ganoderma lucidum and has no native common name in English, being usually called the reishi mushroom, from its Japanese name 霊芝 (reishi), or lingzhi mushroom, from its Chinese name 靈芝 (língzhī).

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The beautiful and shiny kidney-shaped reishi. Photo by Wikimedia user Mokkie.*

The reishi mushroom, as other species in the genus Ganoderma and in the order Polyporales, grows on tree trunks, usually parasitizing live trees and continuing to grow on them after they die. The mature fruiting body is kidney-shaped and may or may not have a stalk, which is displaced to the side, below the concave side of the cap. The cap has a red-varnished color with a lighter rim. It is easily mistaken for some of its closest relatives, such as Ganoderma tsugae and G. lingzhi.

Traditionally used in Chinese medicine, the reishi mushroom was considered the “mushroom of immortality” and said to improve the heart and the mind. Recently, it has demonstrated, in laboratory studies, to have many potential uses for the treatment of different illnesses. For example, their fruiting bodies release polysaccharides that showed the ability to increase the cytokine production of human white blood cells, which increase anti-tumor activities. Other studies have identified compounds with potential anti-HIV activity and the ability to reduce the levels of blood sugar.

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References:

El-Mekkawy, S.; Meselhy, M. R.; Nakamura, N.; Tezuka, Y.; Hattori, M.; Kakiuchib, N.; Shimotohnob, K.; Kawahatac, T.; Otakec, T. (1998) Anti-HIV-1 and anti-HIV-1-protease substances from Ganoderma Lucidum. Phytochemistry49(6): 1651–1647. https://doi.org/10.1016/S0031-9422(98)00254-4

Wang, S.-Y.; Hsu, M.-L.; Hsu, H.-C., Lee, S.-S.; Shiao, M.-S.; Ho, C.-K. (1997) The anti-tumor effect of Ganoderma Lucidum is mediated by cytokines released from activated macrophages and T lymphocytes. International Journal of Cancer70(6): 699–705. Doi: 10.1002/(SICI)1097-0215(19970317)70:6<699::AID-IJC12>3.0.CO;2-5

Wang, Y.-Y.; Khoo, K.-H.; Chen, S.-T.; Lin, C.-C.; Wong, C.-H.; Lin, C.-H. (2002) Studies on the immuno-Modulating and antitumor activities of Ganoderma lucidum (Reishi) polysaccharides: functional and proteomic analyses of a fucose-Containing glycoprotein fraction responsible for the activities. Bioorganic & Medicinal Chemistry, 10(4): 1057–1062. https://doi.org/10.1016/S0968-0896(01)00377-7

Wikipedia. Lingzhi mushrom. Available at: < https://en.wikipedia.org/wiki/Lingzhi_mushroom >. Access on December 31, 2017.

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