I'll confess I'm pretty burned out because I just finished writing and publishing about Cryptomonas borealis (well, that was on 30th May) but I at least wanted to get started on this species. At this point, you might be wondering, "Why this species?" Well, don't overthink it; I didn't either when I chose it. It was supposed to be a simple one, in theory. But the microtubular part was a real headache for a few days. I even almost gave up on continuing these illustrations.
A peaceful screamer reminder: The following illustrations depict Andalucia godoyi E.Lara, Chatzinotas & A.G.B.Simpson 2006, as the name is recorded on AlgaeBase. The images are free to use and are also available on Wikimedia Commons. Of course, commercial use of these images is not permitted, nor is their use without proper attribution. "DOTkamina (2026)" is sufficient. I guess that's it. gng goodbye ʕ•̫͡•ʕ•̫͡
First, some context: Andalucia godoyi belongs to the family Andaluciidae, suborder Andalucina, order Jakobida, class Jakobea.
Damn, I'm already so lazy about having to write this, haha. I have to.
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Hmm, let's see: formally, the class Jakobea only includes the order Jakobida. I suppose that's why these organisms are known as "jakobids," regardless of whether they're referring to the order or the class. Jakobea, along with Malawinonadea, is characterized by having a posterior cilium in a ventral feeding groove, which gives a "scooped-out" appearance, and that's why both taxa were included in the Excavata group (Lewis and Brodie 2007).
The class Jakobea would be included in the subphylum Eolouka, and this in the phylum Loukozoa. According to Mindat, the phylum Loukozoa includes Jakobea along with the subphylum Neolouka, the class Malawimonadea, and the class Tsukubea. Leukozoa would be related to the order Ancyromonadida. Mindat does not consider Eolouka; that's from AlgaeBase.
According to AlgaeBase, the matter is more complicated: Leukozoa would include the subphyla Eolouka, along with Kinetomonada, Metamonada, and Neolouka. The subphylum Eolouka would include the classes Jakobea, Kinetomonadea, and Tsukubea.
In any case, the phylum Loukozoa is included within the infrakingdom Excavata, which is in the kingdom Protozoa, and from there to the domain Eukaryota.
I haven't researched it much, but I would think that the connections between species within these clades are more molecular than morphological. I haven't found much information about what makes jakobids stand out. Wikipedia mentions a number of characteristics, but I don't think they are truly diagnostic enough to distinguish jakobids from the rest. Namely:
Jakobids possess two flagella, inserted at the anterior end of the cell, and, like other organisms in the Excavata group, they have a ventral feeding groove and an associated cytoskeletal support. The posterior flagellum has a dorsal vane and is aligned within the ventral groove, where it generates a current that the cell uses for food intake. The nucleus is generally located anteriorly and has a nucleolus. Most known jakobids have a mitochondrion, also located anteriorly, and different genera have flattened, tubular, or absent cristae. Food vacuoles are located mainly at the back of the cell, and in most jakobids the endoplasmic reticulum is distributed throughout the cell.
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Having said that, I can finally say that the main source I consulted to obtain the information for this blog post, as well as for the creation of the images, was the following: "Andalucia (n. gen.)--the deepest branch within jakobids (Jakobida; Excavata), based on morphological and molecular study of a new flagellate from soil", by Enrique Lara, Antonis Chatzinotas and Alastair G. B. Simpson, 2006. J Eukaryot Microbiol. 53(2):112-120 pp. doi: 10.1111/j.1550-7408.2005.00081.x.
Other sources employed in this text and image construction were:
- "Andalucia godoyi (gen. nov.; sp. nov), a novel jakobid-like flagellate isolated from soil, is a representative of a new excavate clade". by Enrique Lara, 2005. In: Molecular analysis of the biodiversity of protists in hydrocarbon-polluted and pristine soils. Thèse Nº 3211 109-122 pp.
- "Jakobida", by Simpson, A. G. B. 2017. In: Archibald, J., Simpson, A., Slamovits, C. (eds) Handbook of the Protists. Springer, Cham. https://doi.org/10.1007/978-3-319-28149-0_6
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| The "main cell image" or "main illustration", When I use these terms with "main" I will be referring to this image. |
See this sh1t drawing? I have to say, it turned out amazing because it's been a while since I last opened those images, and now I have no idea what it's supposed to show.
Well, I'm back now, and I remember what it's about: you see, the main image is divided into three sections. It's best if you look at it from right to left. Yes, I know it would have made more sense to do it from left to right, but that's just how the sketch came out, and well, I've always been bad at organizing things.
In the right-hand section is the main image of the cell of the organism Andalucia godoyi, in lateral view. In the central part, there's a detail of the flagellar apparatus, which corresponds to the anterior surrounding area, where the basal bodies and the beginning of the ventral groove are located. In that diagram of the flagellar apparatus, you'll notice about four black lines, which correspond to cross-sections. The details of these sections are indicated on the left, under "sections details." Let's discuss each part slowly.
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| Lateral view. |
Right part of the main image: diagram of the organism in lateral view. Specifically, where the ventral side is facing left, and the dorsal side is facing right. It also indicates that the side being viewed is the left, and the opposite side (which is not being viewed) would be the right. Okay, this illustration shows the most representative parts of the Andalucia godoyi cell:
Starting with the ventral groove, whose length I don't know, but in the article by Lara et al. 2006, Figs. 2 and 3, it is indicated as being in the middle of the cell, which leads me to interpret that it occupies more or less almost the entire ventral area of the cell; it must be quite long. I also know that its origin is "at the anterior end" because it mentions that the flagella originate above the ventral groove, and the flagella are correctly positioned at the anterior end.
The single mitochondrion is an elongated structure that runs the length of the cell from the anterior end (near the basal bodies of the flagella) to near the posterior end, after encircling the nucleus from above, either from the left or the right side (according to Lara 2005). The mitochondrion has tubular cristae. I don't know if I'm hallucinating or if I'm really bad at protistology, but in the micrographs, the mitochondrion resembles white bean broth, with whitish spots that give it a trypophobic appearance, and I've decided to represent the mitochondrion that way. You can check the original images yourself if you want.
The nucleus is located in the center of the anterior region of the cell. It has a nucleolus located in the center. One particular feature is the presence of an electron-dense spherical organelle attached to the posterior part of the nucleus, which Lara et al. (2006) refer to it as the "paranuclear body," and that's how I've written it in the illustration.
They also mention the existence of a Golgi apparatus, which for some reason they call the "Golgi apparatus dictyosome," and then say that it has "3 to 5 cisternae" (I've drawn it with 3 cisternae), in the anterior part of the cell, "ventrally and to the right of the flagellar apparatus." I have no problem with that, except that "dictyosome" is supposed to be the name for each of the individual cisternae that make up the Golgi apparatus, and in Lara et al. (2006) they mention it as if it were a synonym for "Golgi apparatus." Well, that's my question; I'll leave you to think about it or discuss it in the comments.
Nothing is mentioned about the endoplasmic reticulum. Fortunately, Simpson (2017) mentions that in jakobids, the endoplasmic reticulum is branched throughout the cell. That's how I've represented it. I've avoided (I think I'll do so in future illustrations) distinguishing between the rough and smooth endoplasmic reticulum as two separate parts (this is for the sake of understanding, as eukaryotic cells are taught in schools and colleges, but it gives the mistaken impression that they are two completely separate sub-parts). In any case, you can still distinguish which part would be the rough endoplasmic reticulum because some branches have a higher concentration of ribosomes (those blue dots). Furthermore, I've drawn more ribosomes more dispersed throughout the cell, as should be the case in any standard eukaryotic cell.
In the posterior half of the Andalucia godoyi cell, there are several food vacuoles with digesting bacteria. I've depicted about four of them. And that's all I have to say about them, really.
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| Flagellar apparatus detail. F2 is the anterior flagellum (and B2 the basal body of F2). F1 is the posterior flagellum (and B1 is... the basal body...... of F1). |
And now for the fun part: the flagellar apparatus. In the main cell image (right side), the basal bodies and their respective flagella are only faintly visible. Both flagella are twice as long as the cell itself, and they have the typical 9+2 flagellar arrangement (9 peripheral microtubular doublets surrounding two central singlets). The microtubular structure of the basal bodies isn't mentioned, but I've decided to represent them with the standard 9+0 arrangement (9 peripheral microtubular triplets surrounding an empty center).
With that brief introduction, let's now describe the central part of the illustration, labeled "flagellar apparatus" in a red box. Before proceeding, I should mention that the representations of microtubules and related structures are very "linear." For some structures, Lara et al. (2006) mention the number of microtubules that compose them, but not for others, and in those I have represented them as a single line or as several, but these are speculative decisions made primarily to avoid confusing the observer. It assumes that in reality they could be wider, more diffuse, more complex, etc. Another point: to avoid double terms and confusion, I have decided to use the same terms employed in Lara et al. (2006), so that it can be compared with the illustrations in that work and the terminology they use.
We can discuss the flagellar apparatus in terms of which structures accompany which of the two basal bodies. But first, let's talk about the basal bodies: both measure approximately 550 nm and are separated by an angle of 135º, with a distance of 170 nm between them. There are two thin, crescent-shaped, electron-dense structures that connect the basal bodies. The first is the StC (striated crescent, striated connecting fibre), which is crescent-shaped. The other is the SmC (thin smooth crescent fibre), and according to Lara et al. (2006), it is associated with the dorsal side of basal body 2. Both structures are shown in Lara et al. (2006) Figure 12, but I couldn't distinguish exactly which one was the SmC. I've represented it as being "below" the StC, because that's how it seems to be indicated in Figure 12 of the article. I'm not entirely sure.
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| Flagellar apparatus detail (right) and sections details (left). |
Now, let's talk about the structures that accompany the basal body of the anterior flagellum (B2). There is a dorsal fan (F) of approximately 12 microtubules, which originates near the anterior side of basal body 2 (B2). The dorsal fan connects to B2 via the fan-associated sheet (FA). And that concludes our discussion of B2.
The structure of the basal body 1 (B1) companions is more complex. There are two main microtubular roots (structures that anchor the basal bodies to the cell): microtubular root 1 (R1) and microtubular root 2 (R2).
R1 "originates against the right edge of basal body 1, is directed posteriorly, and consists of a flat row of microtubules." I understand this to mean that the origin of R1 is on the right side of B1. Along with R1, there is a non-microtubular "I" fiber (denoted simply as the letter "I"), associated with the ventral face of R1. Hence, in my illustration, this I structure is "to the left" of R1, which would be interpreted as it being near the ventral side of R1.
There is also a dense "B" fiber (B), which originates against the right ventral side of B1 and continues along the right side of B1, converging with the external portion of R1. I interpret the "B" fiber as being closer to the "I" fiber first, as can be seen in Lara et al. (2006) Figures 14 to 16, although in those micrographs it appears to be further away. Even so, the order would be with the "B" fiber most ventral, then the "I" fiber, and finally R1.
There is also a non-microtubular "A" fiber (A) that initially originates on the dorsal side of B1 (although in my illustration it is not quite on the dorsal side, but rather at a point between the right dorsal and almost ventral sides of B1, so that it is close to Figures 14 and 15 of Lara et al. (2006)), and then it is located near the dorsal side of R1. The "A" fiber has a striated appearance in some sections, which, in my opinion, gives it the appearance of a line with darkened circular spots on top, and that's how I've represented it.
"A singlet microtubule (S) originates in the 'corner' formed by the dorsal side of R1 and the right side of B1." The "S" microtubule is initially connected to the dorsal side of B1 by a singlet-associated fiber (SA), and then extends downwards (posteriorly). This leads me to believe that the SA fiber only seems to exist when it connects the S microtubule to the dorsal side of B1, and that's why in the illustration it only appears near B1, as if it were on top of the "S" microtubule. I hope it's noticeable, although it's already an eyesore for me. Duh...
In addition to R1, there is microtubular root 2 (R2). It originates near the left side of B1 and extends posteriorly. It is made of 7 microtubules. It is accompanied by the non-microtubular "C" fiber (C), which is on the dorsal side of R2. As I can see in Lara et al. (2006) Figure 13, the C fiber appears to be attached to R2 from its origin. The arrangement of the C fiber consists of two conspicuous dense lamellae that seem to be separated by a thinner lamella in between, like a sandwich. This is what I have tried to represent in my illustration.
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| The sections dude |
I will now pause to discuss the left side of the main illustration: the "Section Details." You will have noticed that in the diagram of the flagellar apparatus, there are 4 lines that refer to the 4 cross-sections indicated in these "Section Details." I will begin by discussing Section 1: "B1 transversal section," where I have attempted to represent a cross-section of B1 and its associated structures according to what I have explained previously: B1 has a 9+0 arrangement (9 peripheral microtubular triplets). On the ventral side is the B fiber (the ventral side in this image would be approximately the lower half of B1). Towards the right (which in this image would be the upper left corner) are R1 along with the I fiber, the A fiber, and the S fiber, which connects to SA on the dorsal side of B1. The dorsal side of B1 in this image would encompass roughly the upper half of B1. The left side would be the lower right corner, where R2 and the C fiber are located.
Returning to the flagellar apparatus, the posterior flagellum (F1) has a particular feature: it possesses a flagellar vane (FVA), located on the dorsal side of F1 and appearing after the origin of the 9+2 axoneme of F1. It's true that in my illustration, the ventral side is, in the image, the orientation towards the left, and the FVA appears to be facing that direction, but the intention is to give the appearance that it's actually "behind the axoneme, on the dorsal side," which would be almost the opposite of the ventral side, which is what we're seeing "from the front" in the drawing. There's also the line for Section 2: "F1 transversal section," where it's clearer: the FVA is in the upper half of F1 (which is the dorsal area), and the lower half of F1 is the ventral side. The truth is, I've made some kind of mistake in representing it there, but honestly, I'm getting sleepy.
Finally, the last tedious thing with which I hope to finish writing this entry: you will notice that in the diagram of the flagellar apparatus, the "tip," or rather, the "beginning" or "anterior end" of the ventral groove (GR) is represented. Lara et al. (2006) suggest that it consists of these parts: a right margin (the edge) (RM), the right wall (RW), the floor of the GR (FL), the left wall (LW), and the left margin (LM). The GR is a groove; understand these parts as if we were talking about a tube cut in half longitudinally, or a semicylindrical water channel, such that the edges where this tube has been cut would be the left and right margins; the non-central curved parts on the sides, the left and right walls; and finally, the curved part that acts as the "base," "center," or "floor" of this cut tube, would be the "ventral groove floor."
These designations are important for what Lara et al. (2006) explain later: the arrangement of the structures adjacent to basal body 1 (B1) changes slightly at the beginning of the ventral groove. R1 divides into two parts: the outer portion (R1o) and the inner portion (R1i). Fiber I, which I mentioned earlier runs alongside the ventral side of R1, once it reaches the beginning of the ventral groove, runs only alongside R1o, presumably also on its ventral side, and they form an R1o/I complex, such that they are assumed to be together.
Fiber B, which is initially located on the right ventral side of B1, somewhat close to R1, once the ventral groove begins, continues only near the R1o/I complex and eventually connects to them.
Fiber A, which is originally on the dorsal side of R1, terminates shortly after the ventral groove begins.
R2, which is initially a compact bundle of 7 microtubules, begins to splay as the ventral groove begins. This also coincides with the termination of the C fiber, shortly after the start of the ventral groove.
The structures that continue alongside the ventral groove provide support for the parts of the ventral groove mentioned earlier. Thus, the B fiber supports the right margin (RM), the R1o/I complex supports the right wall (RW), R1i supports the floor of the ventral groove (FL), and to its left, the singlet (S). This suggests that the S fiber supports the left side of FL, and R1i the right side. The left wall (LW) and the left margin (LM) are supported by the microtubules of R2. This support arrangement can be seen more clearly in Section 4: "Ventral Groove: transverse section (not so proximal part)."
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| The sections but without labels |
The "initial" or "predecessor" states of these structures during the initial (but maximum) stage of the ventral groove are shown in Section 3: "Ventral groove: Proximal start transversal section." The parts of the ventral groove I mentioned earlier are shown, along with how the structures are arranged before reorganizing as described in Section 4. Thus, in Section 3, R1 still exists as a complete structure (without an external or internal part), and the A fiber is still present near R1. Note that the microtubules of R2 are very close together, whereas in Section 4 they are more separated, as Lara et al. (2006) indicate occurs when R2 has already passed the beginning of the ventral groove.
Damn, my fingers and eyes have really hurt having to write all this. It's a mixture of satisfaction at having finished writing and being able to finally release the images on Wikimedia, but also of the hard work of having to thoroughly read about these structures to represent them correctly.
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I guess it's part of the hobby.
