on the way to UConn

I am on the way to University of Connecticut for invited seminar. I am going to talk about chromodomains in plant retrotransposons and how we can use these tiny sequences in out attempts to figure out evolutionary history of plant genomes.

Plant chromodomains

I was working in this area for a few years now and have published  four papers :} Two pet-projects are on there way, but now I am very slow since my primary projects have nothing to do with neither plants or retrotransposons. Oh, well… I will come back to you guys [waiving to the mosses and ferns] one day! I will…

New Terrariums

Several new terrariums for bright light environment…

New Terrariums September 2012

Terrarium with three mushrooms

This is very temporary terrarium. It has three small mushrooms. I do not think they will live long, maybe other couple days. I plan to put something different as substitution, more permanent :]

Terrarium – 3 Small Mushrooms :]

vacations are over…

… back to work

My terrariums

The Flora Universalis: Proof-Prints Study

Some of the scans from possible proof-prints of The Flora Universalis to support my point that they are indeed pre-pocessed botanical prints ‘in work’. I wish I could see the finals, but because the work is very rare I could not find any of my prints as final version.

Ficinia contexta whole [almost] print with drawings and legends. [The size of the prints is not standard, they are larger than A4 and Letter – that is why the bottom is cut off]

Hand writing with pencil and small additional drawings appear on quite a few of the prints. Another example:

Fragment from Fuirena coerulescens print. The picture drawn with pencil and hand colored plus hand writing are very remarkable on this piece.

Many of the prints are only partially colored which most probably indicates color study.

Passiflora print only half colored – probably color study.

Not quite mosses

… or! To be more accurate, not mosses anymore, but not ferns yet. Who are they?

The are Lycopodiophyta: Club Mosses, Spikemosses and Quillworts.

They might look like mosses and still use spores for propagation but they already posses some features of the higher or vascular plants such as true roots and vascular system. It is not surprising, that the modern evolutionary systems put Club Mosses (and others) between mosses and ferns.

Figure 1. The image (on the left) belongs to BioLib. The evolutionary tree (on the right) is represented according to Bowman et al., 2007 [1] and Berbee and Taylor, 2001 [2] with minor modifications. Divergence times (Mya – million years ago) are indicated according to Hedges, 2002 [3].

My interest to this particular group of plants emerged from my graduate study of the genomic content of mosses [4]. At some point I realized that if I would like to understand what had really happened and is really happening in mosses genomes evolution I have to take steps back and forward: one step back – towards green algae as the most primitive green plants, and one step forward – towards club mosses and their relatives.  Luckily for me one of the spikemosses, Selaginella moellendorffii, was already in the list of species for whole genome sequencing and even some progress was already made towards decoding its genome [5]. While the genomic sequence is still a first draft, it offers terrific opportunity for comparative analysis and evolutionary studies. After genomic sequence became available to researchers Selaginella moellendorffiiis conquering scientific world. More and more scientific papers published include studies of these fascinating plants.

The Selaginella moellendorffii is not only spikemoss which is getting all the attention. A few years ago the beautiful movie about Selaginella apoda life cycle was published on Vimeo by Ciaran Moloney.

Club mosses and spikemosses are between the most popular plant for terrariums not only because they are truly wet-legs+shade lovers but also for their ‘exotic’ appearance and, for some species, stunning foliage. Selaginella uncinata is called ‘Blue spikemoss’ or ‘Peacock moss’. Blue spikemoss got such name for its metallic blue iridescent foliage. From certain angles the leaves of Selaginella uncinata are unbelievably brilliant blue, changing with the slightest movement of view point. There are two types of color – chemical and structural. Iridescence is a form of structural color where the observer experiences a change in hue according to the angle from the iridescent structure is viewed [for review, 6]. Structural color has been well characterized in animals, but very little studied in plants. Blue spikemoss (as well as Selaginella willdenowii [7]) became one of the model species for plant iridescence studies [8].

Figure 2. Selaginella uncinata. From: Vukusic P, Sambles JR. Photonic structures in biology. Nature. 424:852-855 [8].

[Dr. Heather Whitney is a molecular biologist by training, but now uses ideas from across the scientific spectrum (from optical physics to beekeeping) to study plant-animal interactions. As both a researcher and speaker, she hopes to show that plants are much more sneaky than is usually suspected — they have to do everything that animals do (from finding a mate to coping with predators) but manage it without moving.]

Another beautiful species Selaginella erythropus is highly prized for it’s blood red underside and called ‘Ruby Red’. Its bright red stems accent the upright leaflets and dark green tops. Under cold temperatures, the foliage will turn red on the top but under normal growing conditions it is green on top and stems and underside to be the ruby red color. Thanks to this unusual foliage, like many other common Selaginella species, Selaginella erythropus was introduced in the horticulture. However, beware if [gardening/terrarium] on-line shop page informs that selaginellas are easy to grow. Majority of the selaginellas are very picky. Selaginella erythropus, for example, should be in shade (at least 50%!) and very high humidity [it will enjoy even dripping water!]. Other selaginellas are not SO hydro-lovers but almost all species available on the market need high humidity of their habitat. The soil should be rich and well drained, never allowed to dry. Majority do well in a soil mix consisting of 2 part peat moss to 1 part loam to 1 part small pine bark. The light fertilizer (the regular fertilizer significantly diluted) is recommended weekly during the period of active grows.

References:

1. Bowman JL, Floyd SK, Sakakibara K . Green genes-comparative genomics of the green branch of life. Cell. 2007 129: 229-234.

2. Berbee ML, Taylor JW.  Fungal Molecular Evolution: Gene Trees and Geologic Time. In: McLaughlin DJ, McLaughlin EG, Lemke PA, editors. The Mycota: a comprehensive treatise on fungi as experimental systems for basic and applied research. Volume VII: Systematics and Evolution, Part B. New York: Springer-Verlag. 2001 pp. 229-246.

3. Hedges SB. The origin and evolution of model organisms. Nat Rev Genet. 2002 3: 838-849.

4. Novikova O, Mayorov V, Smyshlyaev G, Fursov M, Adkison L, Pisarenko O, Blinov A. Novel clades of chromodomain-containing Gypsy LTR retrotransposons from mosses (Bryophyta). Plant J. 2008 Nov;56(4):562-74.

5. Banks JA, Nishiyama T, Hasebe M, Bowman JL, Gribskov M, et al. The Selaginella genome identifies genetic changes associated with the evolution of vascular plants. Science. 2011 332:960-963.

6. Doucet SM, Meadows MG. Iridescence: a functional perspective. J R Soc Interface. 2009 Suppl 2:S115-S132.

7. Thomas KR, Kolle M, Whitney HM, Glover BJ, Steiner U. Function of blue iridescence in tropical understorey plants. J R Soc Interface. 2010 7:1699-1707.

8. Vukusic P, Sambles JR. Photonic structures in biology. Nature. 424:852-855.

BTW, BioLib is very good library of historic and modern biology books. Many antique books are in pdf format.