Hello ✌️ 😄
A new species of salamander from Costa Rica, Bolitoglossa chirripoensis, has been described!
KLANK, JEREMY, et al. "A new species of salamander of the genus Bolitoglossa (Caudata: Plethodontidae) from the highest massif of the Cordillera de Talamanca, Costa Rica." Zootaxa 5642.5 (2025): 427-450.
Not sure how I managed to never hit this species with UV. I would describe the colour as a bright, hot, lipstick pink. I am unsure if this lichen is actually fluorescing or if something else to do with how the pigments show up under UV light - maybe @[email protected] would know. Picture doesn’t quite do it justice.
You are pointing a UV lamp at it which probably sends out 365 nm or 395 nm photons. The lichen is shooting back photons with a broad range of wavelengths, and a lot of ~600 - 750 nm ones (red). So, the UV photons had to be "captured" by some molecular system, the system dissipated some energy, and then re-radiated some of these longer-wavelength photons.
The general term that covers the many different possibilities is "photoluminescence". In this case we can say for sure that the lichen exhibits "UV-induced photoluminescence", because it is re-emitting lower energy (longer-wavelength) photons. It is common to make the connection "photoluminescence" = "fluorescence", but technically fluorescence makes specific claims about how the light is re-emitted (singlet -> singlet emission), and it is not the only luminescence process. Other examples of luminescence are phosphorescence from a triplet state and luminescence via charge-recombination. So, to call it "fluorescence" in the strict sense we need know what the exact pathway is.
That said, when it comes to biological pigments fluorescence is generally the most common pathway. Triplets that live long enough to produce light are generally undesirable as they can react indiscriminately with molecules inside of the cell as well as produce reactive oxygen species, and good phosphorescent materials often combine metals and heavy atoms that are not as abundant in living tissue.
So, knowing nothing else, and seeing that red light comes out when you shine UV/blue light on a lichen, it is generally fair to call it "fluorescence".
Now, if we discuss this specific lichen... I have looked it up and it does get interesting! Do you have it with you? I suspect that its fluorescence might be different during the day than during the night.
I can find online two significant fluorescent components: parietin, which produces the fluorescent yellow pigment, and Chlorophyll a/b, which produces red fluorescence. There is an interesting paper exploring the idea that one functional purpose of parietin's fluorescence is that it can transfer energy to the algae to boost their photosynthesis. Their conclusions in the paper is that the idea is not supported by the evidence, so, a "negative result". It is a fun example of the type of research that is performed in photobiology and also an example to show that even negative results can be interesting enough to be published!
As for the difference between day and night - if what you see is a combination of the fluorescence of parietin and chlorophyll, then the color might change with the day/night cycle. Photosynthetic organisms regulate the flow of excess photon energy towards a safe non-radiative dissipation pathway in response to light. This is called the non-photochemical quenching pathway, and during the day this pathway tends to be active. During the night there is little light, and so this protective pathway shuts-off. This allows more of the absorbed photon energy to flow into the radiative fluorescence pathway, increasing the red fluorescence. You can actually see this easily with plants - you can dark adapt a leaf and then compare its fluorescence with that of a leaf that is being exposed to a bright light. The dark-adapted one will usually show significantly more red fluorescence.
This time you did ask, so I won't apologize for my essay 😆 But I am a bit sorry I didn't have the time to make it shorter.
No. I think they both lose more than they gain here. It doesn't make sense as a strategy. Ego clash is a simple explanation.
Too bad you don't get to bring your equipment, but at least you will get to see them :D Good luck finding some wild ancestors!
Great find, congratulations!!
Enjoy your holidays!! 🕊️
Hi! I’ve looked through /r/shittyaskscience and I think it leans too far into jokes with very little actual science content. The idea behind mander is to support specific, niche science-related communities, so a general joke-focused community doesn't really fit.
For 'science_memes', the mod is a very capable superstar and I agree with their vision of memes as a laid-back way to connect people to science. It’s plausible that a community like 'shittyaskscience' could achieve something similar, but honestly I think science_memes already covers that space well.
As for !askscience - it simply hasn’t been created yet. It would be more fitting than 'shittyaskscience', but I still prefer encouraging people to ask lichen questions in the lichen community, mushroom questions in the mushroom community, chemistry questions in the chemistry community, and so on. I support content flowing toward niche communities rather than having a centralized place for general questions. A general community would be more popular, but popularity isn’t a goal, and it works against the underlying philosophy. Niche spaces may be smaller, but they offer much better signal-to-noise for building meaningful connections.
Unfortunately the article is behind a paywall... But I am curious, does this mean there won't be any new Cortex-Mxs microprocessors?
The summary says that Arm wants to "enter the chip design space". They weren't doing this already?
And, is the prospect of a proprietary chip an exciting tease when pitted against an open standard one? I am excited about RISC-V microprocessors precisely because they rely on an open standard, so I am curious to see what their angle here is. I tried to find a non-paywalled source but I couldn't find one.
Wow, that is spectacular!
I bought a National Instrument's data acquisition card (PCIe-6535B) not knowing that National Instruments is not very Linux-friendly and I was not able to get it working. At least it was a used card so I did not pay to much for it, but I learned my lesson not to assume compatibility.
Once I also used 'rm -rvf *' from my home directory while SSH'd into a supercomputer (I made a syntax error when trying to cd into the folder that I actually wanted to delete). I was able to get my data restored from a backup, but sending that e-mail was a bit embarrassing 😆
cross-posted from: https://mander.xyz/post/31227704
This weekend I did some experiments with turmeric powder. Here are some images of the results, and the description of how to create these microscopic chemical landscapes is given below.
Turmeric powder is a fantastic material to play with. The powder has a high concentration of colored and fluorescent curcuminoids and volatile turmerone oils.
When you use a polar solvent to extract these compounds, what you get is a kind of fluorescent oily resin called a turmeric 'oleoresin'.
The curcuminoids are yellow at acidic and neutral pH, but they become bright red at high pH due to keto-enol tautomerization. There is a lot of cool things you can do with the curcuminoids in terms of photo/electrochemistry.
I have been playing with very simple chemistry under the microscope, and I have noticed that you can create some cool-looking micro-landscapes. During this process you can also see different types of physico-chemical processes happening in real time.
Procedure to do this:
- Place a few grams of turmeric powder into a glass container
- Add enough isopropanol to cover the material, and a bit more
- Mix
- Wait for the solids to settle
- Collect a bit of the isopropanol liquid from the top and place on a glass coverslip
- Wait for the isopropanol to evaporate.
At this time, you can see under the microscope that golden oil droplets have been deposited, and that the surroundings are also yellow. The drops are oleoresins, which consist of curcuminoids suspended in turmerones and other oily compounds. Thin curcuminoid films might also be forming in between these droplets.
Add a sprinkle of baking soda crystals (sodium bicarbonate) on top of the coverslip. You can blow on the coverslip if you accidentally add too much.
Add a small drop of water, and wait a bit.
At this time you can see that the crystals are dissolving under the microscope, but the colors are not changing. The water and oils are not mixing, and so you get this film of alkaline water surrounding the oil droplets, but nothing is yet really changing.
- After waiting a few minutes, add a drop of isopropanol.
Now the isopropanol will re-dissolve the oleoresin and mix with the alkaline water. The carbonate ions are now able to react with the curcuminoids, and when they do, they go into the ketone form and instantly turn red. Under the microscope you can see quite dramatic movements of yellow and rad streaking as well as turbulent movements of the baking soda crystals.
Wait some time for the liquids to evaporate again
You will end up with a landscape that combines yellow resins, red resins, sodium bicarbonate crystals, and several different patterns.
You can vary the parameters - the amount of sodium bicarbonate, the position and size of the drops, you can pre-mix the water and isopropanol, etc. Small changes can drastically affect the resulting landscape.
This weekend I did some experiments with turmeric powder. Here are some images of the results, and the description of how to create these microscopic chemical landscapes is given below.
Turmeric powder is a fantastic material to play with. The powder has a high concentration of colored and fluorescent curcuminoids and volatile turmerone oils.
When you use a polar solvent to extract these compounds, what you get is a kind of fluorescent oily resin called a turmeric 'oleoresin'.
The curcuminoids are yellow at acidic and neutral pH, but they become bright red at high pH due to keto-enol tautomerization. There is a lot of cool things you can do with the curcuminoids in terms of photo/electrochemistry.
I have been playing with very simple chemistry under the microscope, and I have noticed that you can create some cool-looking micro-landscapes. During this process you can also see different types of physico-chemical processes happening in real time.
Procedure to do this:
At this time, you can see under the microscope that golden oil droplets have been deposited, and that the surroundings are also yellow. The drops are oleoresins, which consist of curcuminoids suspended in turmerones and other oily compounds. Thin curcuminoid films might also be forming in between these droplets.
Add a sprinkle of baking soda crystals (sodium bicarbonate) on top of the coverslip. You can blow on the coverslip if you accidentally add too much.
Add a small drop of water, and wait a bit.
At this time you can see that the crystals are dissolving under the microscope, but the colors are not changing. The water and oils are not mixing, and so you get this film of alkaline water surrounding the oil droplets, but nothing is yet really changing.
Now the isopropanol will re-dissolve the oleoresin and mix with the alkaline water. The carbonate ions are now able to react with the curcuminoids, and when they do, they go into the ketone form and instantly turn red. Under the microscope you can see quite dramatic movements of yellow and rad streaking as well as turbulent movements of the baking soda crystals.
Wait some time for the liquids to evaporate again
You will end up with a landscape that combines yellow resins, red resins, sodium bicarbonate crystals, and several different patterns.
You can vary the parameters - the amount of sodium bicarbonate, the position and size of the drops, you can pre-mix the water and isopropanol, etc. Small changes can drastically affect the resulting landscape.
This is a stack of 7 images, you can click on the image to see the full resolution and guess what the subject is :D
The photos were taken using a Nikon D7500 camera connected through a T2 adapter tube with 2X magnification (NDPL-1(2X)). Microscope is the Swift SW380T. The objective is a 4x Plan objective.
For stacking the images together I use three tools: ImageMagick's mogrify to transform from the raw NEF files to .tif, Hugin's align_image_stack function to align the images, and enfuse to blend the images together.
The output .tif file was post-processed using rawtherapee in order to increase local contrast and tune some other parameters.
The process of focus stacking a set of images is rather simple in Linux. The programs above can be installed via the package manager. Then, you copy the raw files to focus-stack into a folder, and run the following sequence of commands:
(1) Convert from RAW to TIF:
mogrify -format tif *NEF
(2) Align images
align_image_stack -a aligned_ -v -m -g 10 -C *.tif
(3) Focus stack
enfuse -o result.tiff --exposure-weight=0 --saturation-weight=0 --contrast-weight=1 --hard-mask aligned_*
Below are the images used for the stack after alignment, for reference:
This specimen came from a slimy film of algae that grew in one of my algal cultures. I think that it is a Nostoc. Objective is 40x/0.65
This image was taken through the 100x oil objective and a 2x camera adapter projecting the image into a Nikon D7500. The sample is a leaf from one of my plants (Dioscorea elephantipes, but I don't think this picture would look very different for other plant species)
The edges of he leaf were already yellowish brown. Here is a photo of that area with much less chlorophyll:
And here is a photo through the 40x objective using oblique illumination:
If you want to see some really fantastic photos of plant stomata I recommend having a look at Rolf Vossen's photographs here: https://microscopyofnature.com/stomata
I am looking through his documentation trying to understand how he managed to get those images. They are spectacular.
This is a photograph of a small trichome on the surface of a seedling through the 40x objective. Not sure if it is a happy trichome looking up at what it will become or a sad trichome looking down 😆 I liked the colors and the scene, reminds me of a painting.
Here is a photo through the 10x:
I prepared a 1:200 dilution of red blood cells using a ~1% NaCl solution. The imaged region contains 4 nano liters of the diluted sample. This image was taken using a 40x objective.
A count is performed by counting the number of red blood cells in a few of these sections, averaging the result, and then converting back to red blood cells per microliter by multiplying times 200 (dilution) and dividing by 0.004 (sampled volume in micoliters).
For this particular sample I estimated 3.8 million red blood cells per micro liter of blood.
I tested a few different types of hemocytometer/Neubauer chambers from China and I can recommend this specific one:
There are some even cheaper alternatives but the lines are very difficult to see.
I followed the Gram Staining tutorial from this video to prepare a sample of my cheek cells: https://www.youtube.com/watch?v=lMoT-FmhS6A
For preparing the staining solutions I purchased crystal violet, ethanol, potassium iodide, iodine, and an already prepared safranin solution from laboratorium discounter.
The slight 3D effect is achieved by displacing the filter holder to block the light coming from one direction and achieve oblique illumination to cast a shadow (https://www.youtube.com/watch?v=9btIpf5mjyA).
The image is post-processed using Rawtherapee to increase the contrast.
Here is another photo without using the oblique illumination trick, also post-processed with rawtherapee:
In trying to isolate Trebouxia from an Evernia lichen. I found that some of the cultures are contaminated by a what I think are rotifers. I am not sure of what kind of rotifer (or other organism) is the one pictured, so if anyone has some idea please let me know.
I also recorded a video of what I think are belloid rotifers feeding on the same lichen culture:
https://peertube.uno/w/uoSCNagVVmbuMcgXdVfPGR
I don't have much hope that the algae will survive this attack, but I might turn those jars into rotifer cultures.
Thanks for the idea! That looks very nice, I like how the collection is organized in those storage containers. They look very well preserved so far so your well water + sun protocol seems to be working well. Perhaps I will too start a lichen collection!