romunov’s blog et al

Biology students’ society has organized a "field weekend" in Budanje in Vipavska dolina valley. I was attending the buttefly group. We visited Goriško (famous for its fine assortment of wines) and Mlake. Goriško was, from butterflies point of view, totally devestated. Only two habitat types that we noticed were vinyards and fragmented forest. The only viable habitats were along the roads, but they had only grasses, not suitable for adult butterflies. We found only a few species of butterflies - and not even the most common ones one would expect. We took a trip to Mlake, a marsh area recently turned into highway and military shooting range. According to older biologists, they destroyed the most valuable part of the marshy grassland that sheltered innumerable vulnerable species of plants and animals. All three pictures are from this location.

Mellicta britomartis (I hope that’s the species - I’m waiting confirmation from a senior lepidopterologist). It’s Mellicta athalia, one of the most common ones. My bad.

Euphydryas aurinia

A cerambicid beetle. My guess would be Aromia moschata. Have to check with the experts though, as I’m very short on coleopterid literature.

I took the oportunity and went for a photographing spree around the local meadows and woods. A bunch of pictures under the fold. It’s 11 p.m. and I still have some work to do, so I’ll be attaching names at a later date. I know most of them, but I need to identify a few of them.

(more…)

One of the main and most recognizable characteristics delineating arthropods (and some other animals - see Ecdysozoa) from other animals is its ability to moult. Contrary to our body plan, they have a hard exoskeleton and attached muscles on the inside, where we have exactly the opposite. We have an endoskeleton and muscles attached outside. Both types have their own advantages. Having a hard shell makes it a bit harder to grow, but, you do have a hard shell for potential impacts.

Moulting is a critical time for all animals. This is the time where they shed part of their old skin (a lot of it reabsorbs and is used again to build the new shell) and expose their soft sides. This is the ideal time for predators to strike and hence, animals tend to hide. They also lose their usual coloration (see pictures) which usually makes them more visible. This is also the time where interspecific "confrontations" often take place. If you are growing crickets and it’s too crowded and/or limited supply of food and water, the animals will tend to eat each other during moults, less frequently when fully armorned (personal observation).

Luckily for me, there are also weirdos out there, and here is one of them. I keep a tiny grass stem in the terrarium where I keep the crickets, and one thought this would be a great spot to moult. In the pictures below, you can see the (pale) coloration (or the lack of), the exuvium (moult) and a fully grown cricket. It takes at least 10-20 minutes for them to attain their full coloration. I don’t know how long it takes for the shell to reach terminal hardness (I’m not fond of poking animals). Perhaps it correlates with the color?

Adult males and females have wing, and males use them to produce a high pitch sounds, also audible to us, but especially to their females. The females (not pictured) have a long hard ovipositor protruding from the terminal end of their abdomen. They use it to deposit eggs deep into the soil, where they have more favorable constant conditions (temperature, humidity) to develop.

Scientists found potential new species at the Ross sea (between Antarctica and New Zealand). Cruises to destination of remote locations often yield similar result. It’s still common belief that the wonder of science is discovering new species. There must be something majestic (self-centered?) to the fact that your name is attached everywhere the species is mentioned (in print)? But this is far from the truth, and has been for quite some time. The erra of describing species is over, at least for now. While molecular techniques offer a fesh new look at the species concept and recognition, it’s far from applicaple on a massive and field scale. A lot of the morphological identification has been done in the past century. Today, a lot of people are not pursuing to find new species, but work with ecology (interaction of species with other species and environment), physiology and recently most pronunced, genetics, instead. Which is just a step forward in the race for knowledge.

A lot of new species awaits us in the ocean deeps, the forrest darks and mountain colds, but even more new knowledge is stored within and between them.

Yesterday, about a month long project has been launched in Ljubljana - Dvoživke na Večni poti. A project of translocating amphibians across the road will try to minimize the roadkill that results when frogs, toads, newts and salamanders migrate to their "nesting" sites.

A small fence has been erected yesterday that will prevent animals from crossing the road. Volunteers will be picking moving them across the road daily. The project is also about identifying and counting individuals, which will give us a clearer picture of which sections are "hot spots" for crossing animals.

L’oreal and UNESCO are awarding their international "For women in science" scholarship to dr. Maja Zagmajster, one of the junior scientists at "my" faculty. We are all very happy and pleased that she received the award. She has been recognized for her work in researching the biodiversity of subterranean fauna in western karst region. She is the first Slovenian junior scientist to receive the scholarship. She will be receiveng her award in Paris. Read the story here (in Slovene) or here (official page). On the other hand, some of our research facilities and institutions are "overstaffed" with women, and missing technical people for heavier and more technical work. .. Or so I hear.

I’ve managed to get a temporary job at the National institute of biology. I’m going through a bucket load of samples (a few 1000 vials), identifying animals, grouping them into size clusters and finally, count them. The work is done routinely, a perfect job for a graduate student like me. Behold my work place, my sanctuary where I spend my time lurking down the EtOH-ed insects (mostly), fighting off the janitors in the late evening hours. The only thing I could wish for is a good radio station. Radio Ekspres has gotten really boring, really fast.

Found this roadkill (Lepus europaeus) on Thursday morning. I cleared it off the road and placed it on a meadow about 15 steps from the road (yes, I counted so I could locate it later). This was around 7 am in the morning. As I grabbed it by the legs and carried it to the meadow, a common buzzard (Buteo buteo = kanja) fllew away from a near-by tree, sounding very upset. When I was returning home around 11 pm, the poor wittle bunny wabbit was already 1/3 eaten (posterior end and eyes). I of course ran out of battery juice  to document that, so I was forced to return in the morning. About 8 hours were enough for *something* to locate it and drag it off somewhere else. I suspect a dog, or perhaps a fox. Note my foot (number 39) for size reference.

To keep the homosexuals and Sting on one side, I’d like to point out a site called http://www.europe-aliens.org. I was at a DAISIE conference yesterday, and was listening to the results from various authors from around the EU (and even New Zealand). An interesting page giving you some basic information about (truly) alien species to Europe. This page and its information is a result of three years of work done by about 1700 scientists.

Stephan Gollasch, who had, in my view, the best presentations, especially because he was talking about aquatic invasions, also mentioned e-journal called Aquatic invasions. The journal isn’t indexed to get points for publishing. Too bad. On the bright side, it’s totally free to read!

Zooxanthellae and their cnidarian (all (little) beasts with stinging cells) hosts live in mutualism, meaning they live in close contact and both reaping benefit from the association.

By defining the group, we must realize that this is a paraphyletic group. Various algae and other organisms have been grouped in this group “for convenience”. The word xanthos is Greek for yellow, you add zoo and with some degree of imagination, you have a working word. This describes the color that is characteristic for some “algae”, the dinoflagellates, from where the soon to be famous Symbiodinium comes from. I will use the term algae from now on, but I realize these are not algae per se.
These algae can be found in various groups of animals. Predominantly in cnidarians (corals, sea anemones, gorgonians…), but also in foraminiferans, radiolarians, ciliates, sponges, bristle worms, flat worms, mollusks (the famous giant Tridacna clams) and tunicates.

Zooxanthellae can get transferred to the host by at least two means – horizontal transfer, where they’re ingested from the water column or vertical, where the zooxanthellae are passed on from parents to their offspring.
Zooxanthellae live inside the host cells in special vacuoles. Exchange of gases and molecules is done by diffusion. Zooxanthellae are exposed to light, which powers their photosynthetic apparatus (made from chlorphyll) and form simple sugars. They pass at least some of these sugars to their host, and, in return, get some of the juicy metabolites that were meant to be thrown away (talk about one man’s garbage…). This is a source of carbon and other nutrients for the zooxanthellae.

Photosynthesis is very important for algae as well for the coral. When photosynthesis is running, major part of calcification of coral skeleton is taking place. The mechanism of calcification is far from certain, and various authors have introduced different models based on their results. A lot of work on transporters across the cells are done pharmacologically by various poisons. A lot of stuff in science is done by disfunction. To put it another way, you kill “something” (usually the target molecules of the poison is known) and see what happens.

Corals can form various pigments to protect their and algal cells from harmful sunlight (think UV light). This results in sometimes breath taking colors on coral reefs. Some pigments can be used for harnessing the light energy at different wavelengths, which gives corals another edge, because it enables them to colonize deeper waters.

When things become unfavorable, a host can expel some (all?) of the algae. This is probably because the algae are more sensitive to damage (by light, for example), and the process of dying forces the coral to dump the algae before they can cause any more damage to their cells. Coral bleaching has become a real problem in the past few decades. Most scientists contribute this “plague” to the elevated sea water temperatures (global warming, El Niño…). Animals losing the algae can recover, but the prognosis for such animals is dire. Dying corals mean direct shift in composition on coral reefs, which can have unforeseeable consequences on local, regional and, eventually, global scale.

Some light reading on this subject can be accessed in Eric Borneman’s book Corals. The author can be reached at MarineDepot forums here.

Blessed thy who understands slovene, for you can see:

Light pollution is light emitted into the sky with no clear target to be illuminated. Some call us “Las Vegas” of Europe. On average, we waste almost 100 kWh/year/person, which is well above that of Europe (this costs us about 10 million euros). It effects animals, traffic safety, us and of course, our wallets.

More information at http://www.temnonebo.org/

As you might have noticed (see below), Katja (my school mate) and I are writing a seminar for a class called Interaction of organisms, a seminar on alga-animal (more specifically zooxanthella-animal) relationship. During my search I’ve come across an article that talks about fatty acids and their role in thermal stress (Berkelmans & van Oppen 2006). A certain paragraph reads like this:

Thermal tolerance among different zooxanthella types is in large part due to thermal stability of the thylakoid lipid membranes of the chloroplasts, with sensitive types having lower concentrations of saturated polyunsaturated fatty acids and greater susceptibility to attack by reactive oxygen molecules which ultimately damages host cells.

Authors basically re-wrote verbatim with, what seems at first sight, no critical thinking. I’m not sure weather or not they’ve contacted the original author, but given that the fact reads the same as in the original, I would wage a guess that they haven’t.

The original work by Tchernov et al. (2004):

“Specifically, thermally tolerant, cultures Symbiodinium clones and zooxanthellae freshly isolated from corals that did not bleach after experimental thermal stress have a markedly lower concentration of the major polyunsaturated fatty acid, (delta)6,9,12,15-cis-octadecatetraenoic acid (18:4), in relation to (delta)9-cis-octadecatetraeonic (18:1) acid, independent of the experimental temperature. The differences in the lipid profile are statistically significant at the 0,001 level (ANOVA). The higher relative concentration of the saturated polyunsaturated fatty acid enhances thermal stability in eukaryotic thylakoid membranes and simultaneously reduces the susceptibility of the membrane lipid to attack by ROS.”

I have contacted the author and he confirmed my suspicion, that what was actually meant was the RATIO between saturated and polyunsaturated fatty acids. Looks like a : or / somehow got left out. I hear it happens (too) often!

Cited works:
Berkelmans, R. van Oppen, M. J. H. 2006. The role of zooxanthellae in the thermal tolerance of corals: a ‘nugget of hope’ for coral reefs in an era of climate change. Proc. R. Soc. B. 273, 2305-2312.

Tchernov, D., Gorbunov, M. Y., de Vargas. C., Narayan Yadav. S., Milligan, A. J., Häggblom, M., Falkowski, P. G. 2004. Membrane lipids of symbiotic algae are diagnostic of sensitivity to thermal bleaching in corals. Proc. Natl. Acad. Sci.. 101, 13531-13535 (doi:10.101073/pnas.0402907101).

I’ve been doing a lot of reading lately. I’m preparing a seminar on zooxanthella-animal symbiosis interactions, and I’ve downloaded (god bless remote access) a great deal of article.
I usually read the whole article, but due to time constraints, I had to abbreviate my task. I chose to cut out Materials and methods and Results, which left me only with Introduction and Discussion. While you may get good info - Introduction for writing ideas and Discussion for actual data - I’ve learned that passing the Results section may have set me back a bit. Especially, if one is searching or re-checking some facts found in another article. Once you’re “into” the business of a certain topic, reading the results, from what I’ve gathered, should give you enough information to set your arguments, latter reinforced in the Discussion section.

Along this work, I’ve found that reviews are not that good source for direct information, especially if you want to do things right. Reading a review is especially frustrating, because almost every information is cited, and you have to check the original article - which takes time, and I don’t have access to them all. I have been thinking of how to get around this, but haven’t found a sensible solution -yet. Keep in mind that I’m writing a <10 page seminar for internal purposes and not publicly available synthesis.
I really started to enjoy short works. Not as much for their brevity but because they usually yield the most information. Jumping to results usually gives you a pretty good idea of what they were doing, what their goal was and of course - the results. If I manage to pursue my publishing career, this is the type of work I’ll be doing, for sure!

Linking through LiLoLe this really neat page called DiKUL. It has the ability to search up to 20 sources at once. For natural sciences, it searches databases such as Wiley InterScience, Sciencedirect, Highwire Press, Nature… Give it a try!

The official part of the Conference (see page here) is now behind us. Almost 100 participants attended. The conference was in my view very well organized. While the whole ceremony started on Wednesday (registration, opening ceremony and so on), I attended the first lectures of Orange section on Thursday afternoon. I really liked the lecture on bacterial toluene degradation by Manuel Alejandro Sarrión Perdigones, who also won first place for his presentation in his section. Congrats!

Field trips were organized on Friday to three different parts of Slovenia - Karst, Štajerska (beer) and Dolenjska (wine). I said I’m not picky, so they put me where there was a photographer missing - to Kostanjevica nad Dolenjska we went! The trip was interesting, we saw castle Otočec, city Kostanjevica with the monastery and a wine cellar. I was recruited as a translator there, which was a bit awkward for me, since I have never thought about that sort of vocabulary. None the less, we managed to communicate, even in Polish-Slovenian.
The real deal started on Saturday, where I would be participating as a “technician”, who changes the presentations between lectures. I was also giving my talk on buckwheat in the Green section. At this point, I would like to congratulate all the participants, especially those from the Balkans who, in most part, gave kick ass presentations.

The conference wasn’t all about talks. It was interesting to meet people from all over Europe. I liked the facts that everybody I talked to knew English very well. What surprised me (in a very good way) is the way Serbs approached me. Everybody who started talking with me, even after they knew I’m from Slovenia, used English. At some point I commented that we can use our own languages, but most insisted on using English, which suited me just fine. It also helped other people join the conversation.

We closed the conference with the final ceremony on Saturday, followed by a party.
I’ll put on some pics as soon as I manage to sort them out.

Kevin from The other 95% has out-done himself and produced this video. I’m reproducing the lyrics, in shame, here:

Thats Why the Spineless Are Atheist

Now listen here my good ole friends
And let me tell me you how this all ends
There ain’t no afterlife out there
Just a dead carcass with worms out the ears

For you it may come as a surprise
A great big scam, years of lies
But even more surprising to me
All we had to do was listen you see

It may have started fore the Precambrian
A little spark in earth’s great ocean
With a little time you’ll plainly see
Differential reproduction is the key

The critters have known since the end of time
Death and decay is all you’ll find
An endless cycle land, air and sea
But that don’t make some folk happy

Our spineless buddies have been trying to scream
There ain’t no God, its all dream
But we shunned them good and spit on their face
Now the jokes on us to our disgrace

If you ever sit and listen at the beach
You might just hear the crabs start preach
We’ve been changing for millions of years
Our diversity is high so listen here

If I were such an intelligent design
Why can’t I walk forward in a straight line
And perhaps if you take a close look you’ll see
Some crustaceans have asymmetry

If you ever walk through a tall forest
You might here spiders sing out in chorus
We’ve had millions of years to adapt
To cover this here entire map!

If I were but a special creation
Why should I die when I’m matin’
And if in our form there was no match
Why do some of us look like ants

Invertebrates as you can plainly see
Have tried to tell us for centuries
There can’t be no god you creationist
That’s why the spineless are atheist

Just ordered four more books for my collection. I’ve been working all week to earn the privilege that comes with this line of work.

I’ll be digging into Ecology (Krebs), Das leben im Wassertropfen (Streble), Oceanography (Gross & Gross) and Fishes of the sea (Lythgoe & Lythgoe). And now to find the time to read them all. :/

Many people has probably heard of the two lobed Ginkgo (Ginkgo bioloba, the famous living fossil and how hard it is to pronounce it. Supposedly someone messed up y and wrote g, as the name was suppose to be, long long time ago, Ginkyo. I was just reading something about dugongs (Dugong dugon) (I’m preparing a seminar on sea grasses) and came upon this flower.

The word “dugong” derives from the Malay “duyung” meaning “lady of the sea”.

Notice that the y got turned into g as well. Perhaps the work of the same dyslexic transcriber?

Back from a three day field trip to the mountains. We went to (near) Krn (see below), a mountain in Julian alps. Our mission was to collect samples from three mountain lakes. My job was to filter the samples and carry some of the instruments. We had luck with weather. We did have snow just under Krn (~ 1800 m) - and thank good as well. Far better than rain. We slept in a cottage very near one of the lakes we sampled. Some pictures just bellow the fold.

(more…)

Recently, a critique paper on methodology of evaluating long term coral reef decline by Ridd came out, and was later succeeded by Bruno & Selig’s PlosOne article (see here). The first claims that GBR (Great barrier reef) is the most pristine coral reef on Earth, and Bruno & Selig take the matter a step further:

The general absence of quantitative data on reef health has led to several misconceptions about the causes, patterns, and best remedies for global coral decline. For example, in 2003, coral cover on the Great Barrier Reef (GBR), considered the “best-managed” [25] and “one of the most ‘pristine’ coral reefs in the world” [21], was not significantly greater than on reefs in the Philippines and other subregions that are often thought to be highly threatened and poorly managed [13]. Additionally, based on the impression that Hawaiian reefs were “far further down the trajectory of decline” [than reefs in the Caribbean and Australia] a recent essay [25] argued for a total overhaul of U.S. coral reef management policy. But our analysis suggests that coral cover in the main Hawaiian islands, including frequently visited reefs close to urban and tourism centers, appears to have been as high as GBR cover over the last two decades (Fig. 2A; also see Fig. S5).

Kudos to coral bones.