Field of Science

Turve = Peat in Finnish

A postdoc pal recently came back from visiting family in Finland and brought me this gift for managing the postdoc seminar series here at UC Davis while she was away. 

I love the hand-build soap dish. I have been a potter for the last 8 years, so I don't by pottery very often, especially if it is something I can make myself. So getting some as a gift is quite the treat. And best of all the soap is made from peat moss! I can't see any stems of Sphagnum mixed in the soap, but it does smell a bit like peat moss. I will definitely enjoy using this mossy-filled soap! 

Translation of the first four lines.
Domestic, Hand-made
Rapeseed Oil Soap

Mosses on the Walls

Many species of mosses grow on vertical surfaces. Rock walls, brick walls, trees. Unfortunately mosses on vertical surfaces are pretty scarce here in the central valley of California. Despite the scarcity, I now have some new mosses hanging on my wall at home.

From the Yale Peabody Museum
This is not a wall hanging but is a moss covered dishtowel! I decided to hang it in the kitchen instead of using it as a towel. Now that I see it up on the wall I think it could use a bit of ironing. 

The images on the towel are probably from an old German text illustrating the different parts of the mosses.

Above are sporophytes attached to some leafy gametophytes. But what is the moss species? The light pink and green circle in the middle left is the top of the capsule and looks like a moss in the Polytrichaceae. Nematodontous teeth with an epiphragm. Basically those are teeth around the opening of the capsule attached to a disc that combine to form a salt-shaker dispersal mechanism. However, the gametophyte leaves don't look like Polytrichaceae. The leaves are typically covered in lamellae and are significantly longer than wide. Anyone else have a guess about this species? There wasn't a reference for the images on the towel. It would have been super nerdy and helpful if they had included a citation. 

Some beautiful peristome teeth.
A Dicranum-type on the left and a Bryum-type on the right.
Thanks Rachel for this awesome present! A great combination of my love of mosses and my midwestern abundance of dishtowels!

Build-Your-Own Microscope

The microscope that I built with my aunt.
Continuing my pursuit of home microscopy, I came upon these instructions for building a microscope and had to try it out. As a microscope, it is bulkier than the small lens I discussed in my last post, but one of the major advantages is stability. Both the phone and the sample can be held still making focusing much easier. 

I tackled this project when I was in Ohio visiting my family. My aunt is a prolific woodworker and I raided her shed for supplies and power tools. The only component I ended up purchasing was a laser pointer that I disassembled for the small, plastic focusing lens inside. My first thought was to head to an office supply store for a laser pointer, but then a cat-lover in my family mentioned that laser pointers for cats can be found in many pet sections. Three dollars later, I had a laser pointer to tear apart. The online instructions mention a site where small lenses can be ordered, so that less destruction is necessary. 
A view of the adjustable stage and light source.

The project took an afternoon. Cutting wood and plexiglass, drilling holes for the bolts, and then putting it all together. I think it took me longer to hunt up all the supplies in the metal chest of drawers full of an odd assortment of bolts, nuts, and washers, along with the trip to the store for the laser pointer, than the actually assembly.

Some challenges with the microscope. The stage is a bit unsteady and can be challenging to adjust both washers in sync to the same height. In the comments of the online instructions several people came up with solutions that enable just one wheel to turn and the height of both sides to be adjusted. I didn't try any of these modifications, but I think they would be a nice addition. My solution to the unsteady stage was to use very large washers on top of the smaller ones. The stage still wobbles a bit when adjusting up and down, but the large washers were a significant improvement. 

Another issue is the light source that I am using. It was hanging out in the shed so I just grabbed it to use. However the light has a bank of bulbs that make the background illumination uneven. A quick fix was putting a piece of paper over the top to diffuse the light, but in the long term I will need to hunt up a replacement. 

A quarter for a focusing test.
Here are some photos that I took using this microscopy setup. 

A zoomed in shot of pollen on a lily anther.
I think this one came out a bit better than the one
from my previous post. It was also a bit easier to
focus using the microscope stand.

I then mounted some of the pollen on a slide topped
by a coverslip. The edges of the grains were not a crisp
as I would have liked, but maybe that is just the limit
of this microscope's magnification range. 
And now to try this microscope out on some mosses! I had a Grimmiaceae sample hanging around in my desk and thought that it would be a good test for the microscope. 

It works pretty well as a dissecting microscope.
We can see the long white hair tips at the apex
of each leaf. 
The moss leaves came out a bit better than
the pollen grains. I think practicing with the microscope
improved my focusing and skill lining up the camera
with the lens to get a better photo. 

Overall I really like the setup and think that it is a good alternative for having a home microscope. After the test run, I think that I could use a more powerful lens, or I think some of the instructions mention stacking lenses. It has plenty of magnification to function as a dissecting microscope, but needs a bit more power to work well as a compound microscope, at least for things as small as mosses. 

If you end up building one of your own it would be great to hear about your experiences in the comments section!

July 2014 Desktop Calendar

July Desktop Calendar
1 - Single click on the image to open it up in a new window. (If you use the image directly from the blog post you will lose a lot of resolution.)

2 - Right-click (or ctrl-click) on the image, and chose the option that says, "Set as Desktop Background" or "Use as Desktop Picture". The wording may vary.

3 - If the image does not fit your desktop neatly, you may have to adjust the image (Mac: System Preferences - Desktop and Screen Saver - Desktop; Windows: Control Panel - Display - Desktop) and choose "Fill screen" as the display mode of your background image.

Cell Phone Microscopy

micro phone lens packaging
and case
In my pursuit of portable microscopy I came across this product initially funded through Kickstarter. The micro phone lens is a small plastic disc that sticks to a cell phone's camera lens, turning it into a 15X microscope. I had to try it out and I thought it would be worth the $15 experiment. 

Case with lens in the
lower lefthand corner.
The lens comes in a small container with an eye-catching black and white design on the top. It is great that the whole setup is so portable, but I am in a constant state of nearly loosing it. I have set my phone down, forgetting to have the lens facing up, only to have the lens come off as I picked up my phone. I have dropped it on the floor covering it in dust. And last night I completely forgot to take the lens off when I was finished and found it stuck on the kitchen table when I went to eat my cereal and read my morning dose of The Economist. Maybe it was just a forgetful and slightly klutzy episode of microscopy, but you get the idea. Beware of loosing this small disc that is slightly larger than the O on your keyboard! Fortunately the lens is also quite resilient. It is bendable and can be easily cleaned with water. 

Let me show you what this little lens can do. I pulled out a dried lichen that I collected on a drive into the California coast range. It is the lace lichen, Ramalina menziesii, aptly named for the lacy filaments that increase the surface area of this lichen, enabling it to better absorb moisture and nutrients from the air. 

Ramalina menziesii the lace lichen

I took the photos below with the micro phone lens stuck to my Nokia Lumina 928 cell phone. The lens requires a camera with at least a 5 megapixel camera and mine is 8.7 megapixels. The center of the photos is in crisp focus, but I was disappointed that the field of view is so small and that parts of the lichen near the edge of the image are thus out of focus. The demo on the website has the entire field of view in focus. That video was taken with a tablet whereas mine were with a phone, so it could be that the interaction between the lens and my phone optics are the issue. 

An even closer view of the lace lichen
Up close with the lace lichen

The other issue I had was stabilizing the camera and taking a photo at the same time. The instructions online recommend using the lens case as a platform for the phone when taking photos. This works pretty well, but I ended up needing to tip my phone to adjust the distance to the sample I was looking at since it wasn't sitting flush against the table.

This company is also in the process of developing a 150X lens and just had another successful Kickstarter project to fund it. After my experience with the 15X lens I think I will hold off on purchasing the higher magnification one. More magnification means a smaller depth of field and I think that the 15X lens is reasonably challenging to focus. I bet that the 150X will be even more difficult. I will wait until some reviews come out before jumping on that one. 

Lily flower
Another plant I examined was a lily that I got in a bouquet from the farmer's market on Saturday. Specifically I zoomed in to take a look at the the pollen-covered anthers.


The 15X lens gets us significantly closer to the pollen than my cell phone camera can without assistance. Still a small field of view, but all-in-all reasonably good for a 15 dollar addition to my magnification arsenal.  
The pollen up close and personal. 

Microscopy for the Masses

Microscopes are amazing tools! I had a small plastic one as a kid and I loved exploring items I collected outdoors. Parts of plants, a scoop of soil, basically anything I could get my hands on I mounted up on a slide and looked at under my microscope. That is one aspect that drew me to study mosses. Microscopes are an essential tool to identify moss species and the closer you look at mosses the more amazing features you uncover!  

My family is well aware of my love of microscopes and my sister recently sent me a link to this TED talk about a microscope made almost entirely of paper that costs around 50 cents to produce. It is a really inspirational talk and I think that these scopes are going to revolutionize microscopy. 

I completely agree with the assessment that traditional microscopes are much too bulky for the field. When I head out to collect mosses I don't take my microscopes with me. I bring the mosses back to my microscopes, which stay at home or in the lab. I think that foldscopes would be a great way to take moss identification into the field and enable identification to species without bulky microscopes or having to wait until returning to the laboratory. 

I thought about submitting an application for the 10,000 Microscope Project, focusing on outreach to the public and exploring mosses in the field, but life became busy and it slipped off my priority list. I will definitely have to get a proposal put together for the next round of testing. I think that these scopes would be a great way to introduce people to mosses and enable exploration and identification without a costly setup. 

June 2014 Desktop Calendar

Some mosses with a friendly fungi : )

June Desktop Calendar

1 - Single click on the image to open it up in a new window. (If you use the image directly from the blog post you will lose a lot of resolution.)

2 - Right-click (or ctrl-click) on the image, and chose the option that says, "Set as Desktop Background" or "Use as Desktop Picture". The wording may vary.

3 - If the image does not fit your desktop neatly, you may have to adjust the image (Mac: System Preferences - Desktop and Screen Saver - Desktop; Windows: Control Panel - Display - Desktop) and choose "Fill screen" as the display mode of your background image.

Art and Plant Evolution

Check out this beautiful art project telling the tale of sporophyte evolution in plants. 
They use wonderful finger drawings in sand to illustrate the the story. 

HatTip to Dr. Bernard Goffinet for sending me this lovely video.

May 2014 Desktop Calendar

This is another moss from my March trip to Yosemite National Park. Since I found it in a park, I don't have collection to help with the identification and it doesn't look like a species I encountered on the SOBEFREE foray. Thus I don't have an identification for this spectacular little plant. 

Does it look familiar to anyone? A pleurocarpous moss growing on granite in the Sierra Nevada mountains. If you have a guess please share it in the comments section. Thanks!

May Desktop Calendar

1 - Single click on the image to open it up in a new window. (If you use the image directly from the blog post you will lose a lot of resolution.)

2 - Right-click (or ctrl-click) on the image, and chose the option that says, "Set as Desktop Background" or "Use as Desktop Picture". The wording may vary.

3 - If the image does not fit your desktop neatly, you may have to adjust the image (Mac: System Preferences - Desktop and Screen Saver - Desktop; Windows: Control Panel - Display - Desktop) and choose "Fill screen" as the display mode of your background image.

The Color of Light

Sunshine, to our human eyes the light appears white, but buried within are all the colors of the rainbow. In order for you or I to detect the colors that compose white light we need help. Shining light through a prism is one way I know to separate light into its many colorful components. Plants, on the other hand, need no such help. They have proteins called photoreceptors that enable them to detect different wavelengths of light. There are several different types of photoreceptors. Phototropins sense blue light, phytochromes sense red light, and neochrome is a chimeric protein that has the ability to sense both blue and red light. 

Light, especially the blue and red portions, are the main types plants use to run their photosynthesis machinery. When taller plants shade out shorter plants they alter both the quantity and quality of the light that reaches the plants below. Thus it is important that plants can detect the light quality in order to respond appropriately, by either growing away from shady spots or altering how they develop. 

A few ferns hanging out with their mossy pals.
A recent study was published that literally sheds some light on the evolution of these light sensing photoreceptors. Neochromes, the light sensing proteins with dual abilities, are present in only two groups of plants, the green algae and the ferns. Previously, scientists thought that these two groups independently evolved neochromes. But this new research proposes a different explanation. They found that the hornworts, a small group of bryophytes, also have neochromes and their proteins are closely related to those in ferns. They are so similar in fact that they were most likely transferred from hornworts to ferns. 

Horizontal gene transfer is a pretty wild thing that can happen in biology. One organism, potentially distantly related to another, can transfer some of its genetic code to another organism. If it is helpful the organism will keep the new piece of DNA, use it, and pass it on to its offspring. Scientists think that neochromes were very useful for ferns. Growing in the shadows of taller flowering plants, neochromes enabled ferns to take full advantage of low light conditions, thrive, and diversify. I think the ferns should send a thank you note to the hornworts for that super useful gift. The transfer of neochromes from one to the other happened over 150 million years ago, but you know what they say, better late than never.

Fay-Wei Li, Juan Carlos Villarreal, Steven Kelly, Carl J. Rothfels, Michael Melkonian, Eftychios Frangedakis, Markus Ruhsam, Erin M. Sigel, Joshua P. Der, Jarmila Pittermann, Dylan O. Burge, Lisa Pokorny, Anders Larsson, Tao Chen, Stina Weststrand, Philip Thomas, Eric Carpenter, Yong Zhang, Zhijian Tian, Li Chen, Zhixiang Yan, Ying Zhu, Xiao Sun, Jun Wang, Dennis W. Stevenson, Barbara J. Crandall-Stotler, A. Jonathan Shaw, Michael K. Deyholos, Douglas E. Soltis, Sean W. Graham, Michael D. Windham, Jane A. Langdale, Gane Ka-Shu Wong, Sarah Mathews, and Kathleen M. Pryer. Horizontal transfer of an adaptive chimeric photoreceptor from bryophytes to ferns. PNAS, published ahead of print April 14, 2014, doi:10.1073/pnas.1319929111

Additional coverage of this research can be found at these links: National Geographic, ScienceDaily, and The Economist

For more on plant colors, check out Johnna's April edition of the Berry Go Round plant carnival. My favorite is the post about the iridescent fruits of Pollia condensate. Pretty cool that they are the shiniest living things on Earth!

A Video on the Moss Life Cycle

Take a break from your regularly scheduled program to check out this video on the moss life cycle. I would definitely recommend this video to students learning about mosses or bryophytes in class or for anyone who wants to brush up on their plant life cycles.

Overall I think that it is a nice video with accurate information. There was only one typo that I saw. The maternal gametophyte cap covering the sporophyte apex during its development is called the calyptra. No e after the t. 

Hat tip to Dr. Juan Carlos Villarreal for sending me this video from YouTube. 

Learning mosses at SOBEFREE

At the end of March I attended the SOBEFREE foray with amateur and professional bryologists from across California and beyond. I highly recommend attending this foray, especially if you live in California. This year we went to some really great locations in Santa Cruz county and I learned tons of California mosses. The days are spent hiking and collecting mosses with our permits in hand. Then the evenings we all gather around our microscopes to look at the plants and to identify them to species.

With my new skills in hand, I decided to take a look at some of my older photos to see if I could make any identifications. I looked at my desktop calendar from January and now recognize the species. It is Dendroalsia abietina! It is a super common moss on trees in California. When dry the leaves curl downward and may remind you of a clenched fist. When wet, the fronds are splayed out and form an array of small shelves across the trunk. Peek beneath the fronds to find the short sporophytes hiding on the undersides in clusters. I love learning the names of new plants, especially mosses. I often think of it as making new botanical friends.

Being out in the field and looking at plants was such a great change of pace from being in the laboratory. I am hoping that I can make it to the Schofield Bryophyte and Lichen foray up in British Columbia this fall. I don't think the time and location have been announced yet. As soon as I hear I will share it here on the blog.

It would also be nice to stop by the University of British Columbia while up in Canada to meet the chemists I am collaborating with. I have only interacted with them through email and skype. It would be great to see them and their lab setup in person. 

Keep your eyes peeled for the announcement about SOBEFREE 2015, which will be held in March somewhere in California. I will most certainly be there next year!