Final Blog Post

Throughout my whole experience, I really got a strong feel for what working professionally in a laboratory is like.  It is an experience way different than the labs we do in school.  I learned the first steps to developing a good aseptic technique in the lab.  If I want to work in more research labs, this is an important technique to develop.  This is one of my goals I had hoped to accomplish at the beginning of the year.

I also found the opportunity to design my own experiments.  While in sciences classes, we have designed experiments as a class, it is not the same when it comes down to yourself and the word document.  I did have my mentors there to help me, but I was faced with numerous questions that needed answers before further steps could be taken.  Questions such as what tools were needed and what precise measurements were needed.  These details are just details, but in the end they make a big difference in your results.  

Furthermore, I learned so much about mushrooms and fungi.  I never really understood how complicated this whole kingdom is.  In my mind, they were mostly just a food group.  What I knew about mushrooms could be summed up in two or three sentences.  Now, while I don't know as much about mushrooms as my mentors do, I have a small understanding of how mushrooms are structurally and how those components can help make improvements and advancements in science and technology.  

Reading scientific papers was challenging experience.  In the beginning, I had to learn how to read the papers and understand them.  Even now, there are a bunch of papers that are harder to read.  This was because there were a lot of terms and concepts I weren't familiar with.  Measurement notation was even strange to read.  Ways a tackled this problem included using Wikipedia and a dictionary.  However, the more papers I read, the more familiar I became with many of the terms.

While learning to read papers was difficult, the end result of learning new things was the most pleasant.  Learning about mycoremediation to different mushroom species to how a mushroom can regenerate nerve ends was all rewarding, even if getting through papers was difficult.  

Suggestions:

I can't really think of any suggestions.  Knowing presentation/poster dates a little sooner would be nice. 

Some advice for next year's interns...

If you are reading a scientific paper last minute, read the introduction and then the conclusion.  

When you begin to first work in a laboratory, its ok to be paranoid about contaminating everything.  Actually, you should be paranoid about contaminating anything.  That way you'll develop good aseptic techniques.

Never hesitate to ask questions.  When you are stuck or especially when you are curious. 

April 23 and 30, College Visit and Last Day :(

April 23, I was unable to make my internship due to a college visit that weekend.  However, I worked on my presentation over the weekend with Caroline.  We sent the presentation to our mentors for review.  The following Wednesday, Caroline was able to get more pictures for our presentation.

April 30 was my last day!  Courtney was unable to make it that day, however I was able to see her once more when she came to watch my presentation with Caroline.  Sarah and I took a few last minute pictures, one of her and a few of some nice, fresh looking mushrooms to replace the dry mushroom pictures.  Then we proceeded to practice my presentation.  We went to the old building to do this.  The old building is now really the engineer's building, so we went by a lot of building projects.
I asked Sarah a bit more about the types of engineers that worked at Ecovative and she told me they were primarily mechanical engineers.  Of course, I had to ask how many were women and not too surprisingly, there were none.  Even for a company such as Ecovative, there are just too few women mechanical engineers.  Sarah did say though, that the type of mechanical engineer they wanted at Ecovative were ones who could easily apply their skills physically.  Most engineers are able to design and build things with programming, but the ones at Ecovative not only programmed but built things themselves.

After practicing the presentation, for which Sarah gave a bunch of good tips, I left with an Ecovative t-shirt!

April 9,

Today was spent helping Sarah with a variety of tasks from making regrind to checking up on mushroom BTTR blocks.  They give me a lot of independents tasks now because I've been fully trained!  Before I left, Sarah encouraged me to apply for the paid summer internship position at Ecovative, which I will most definitely try.
After I finished all the task, we started talking about mushroom topics I could look into more.  One thing we briefly discussed was fungi taxonomy.  I found it interesting how fungi categorization has changed over time.  Fungi classification has been based off of spore prints and physical characteristics, but these methods soon proved ineffective with the discovery of more and more species.  These new species would hold similar but different physical traits so they had to classify species differently.  From my understanding, the phyla are classified by their methods of reproduction.  After that, fungi are classified by morphology, molecular techniques, and several other ways.  However, due to the fact that the classification changed several times, there are mushrooms with several names such as the following example:

Agaricus nidiformis 1844 Pleurotus nidfiformis 1887 Omphalotus nidiformis 1994 - current name

Images taken from http://www.anbg.gov.au/fungi/classification-names-identification.html

April 2

I spent the day in the lab, making regrind of P. ostreatus for my current experiment.  It turns out the P. citrinopileatus  (golden) didn't grow well enough in the grain bag to continue with the experiment.  We have to now order the two oyster species, the pink and golden oysters.  The two mushroom species probably failed to grow properly due to the way the strains were packaged.  Hopefully our next order will work.
Also, we decided that we wouldn't perform the experiment I designed dealing with the black mold and mycoremediation.  With the mold, it is possible to contaminate the lab, even using proper aseptic tools.  We don't want to risk that, and the main idea was to gain experience in designing an experiment.  I also learned a lot from this experiment I designed.  Not only how to design experiments but how to research information effectively, on top of learning about other peoples' research.  I found a lot of unexpected information that improved my understanding of mushrooms in the bigger health picture.  
I really liked this method of learning, so I am going to continue doing outside research to perform a smaller experiment.  I'm interested in maybe reading up more about hormones and more structural components of mushrooms.

Beneath is also a picture of a block Sarah gave me to grow.  This block has to examples of contamination on it.  The obvious one being in the very center is mold.  At the far right corner you see Rhizopus which is a type of parasitic fungi.  It can be deceiving at first because it is white and fluffy like regular mycelium.  However, as it grows you begin to see dark specks in the white, fluffiness.  
Surprisingly, this block did produce some fruiting bodies, but their wet weights were small.

March 12, Inoculation Day

Today, I spent most of the time inoculating grain bags with the mushrooms for the experiment with different oyster species.  Sadly, we are not going to be able to use Pleurotus djamor because the mushroom did not spawn enough on the plate.  You can see this on the picture below.  The very left plate is the normal Pleurotus ostreatus that we have been using for the other experiments.  In the middle is Pleurotus citrinopileatus which did not spread as much as P. ostreatus but enough for us to continue the experiment. The very right plate is P. djamor which clearly did not grow on the plate.

Inoculating the grain bags was another good review of aseptic techniques.  Furthermore, since I had only inoculated grain bags with Courtney before, it was a good experience to be doing it with Sarah.  I was able to see more ways of handling contamination.  This is good for me because it allows me to pick and choose methods that work best for me.

Over break, I am to finish the conclusion for the light vs. dark experiment.  The average of the total wet weight (the weight from the first flush added to the second flush) was greater for the light set than the dark set, not as we had predicted.  For both sets, the second flush yielded smaller oysters.  I don't believe much error came from contamination, as only three blocks were contaminated and two of those were from the light set.

March 5, Bio-future!

Today, I got to sit in on a meeting with Courtney for the Bio-future group at Ecovative.  This is just a small group of people working on projects that are not meant to be developed into products in the near future, but for further down the road.  The purpose of the meeting was for a few members part of this group to share what they were working on.  It was difficult to completely understand everything discussed, but as someone told me at the meeting, it only matters that I understood 10% of the material.  So long as I learn something new.  Among the topics included creating a new material for ice packs, something about a car engine, crystallization in the mushroom, and strength of mycelium blocks.

The project with the different oyster mushroom species didn't need any work this week.  We just let the plates containing the mushrooms grow, so that we can use them to innoculate grain bags next week.
I have been researching other mushrooms to use for the antibacterial experiment I want to do.  The three I will pick from are Hericium erinacus (Lion's Mane, Bearded Tooth Mushroom), Ganoderma lucidem (Lingzhi Mushroom), and Trametes versicolor (Turkey Tail).  All three have really amazing healing properties.

The Lingzhi mushroom has been traditionally used in Chinese medicine.  It has anti-tumor and immunotherapeutic (modifying an immune response--whether by making it stronger, restraining it, or instigating it--to treat a disease) properties.  I think this mushroom looks disgusting, but it is healthy!
http://commons.wikimedia.org/wiki/File:Ganoderma_lucidum_01.jpg

This is the Turkey Tail mushroom.  Its very fitting.  This mushroom contains something called Polysaccharide K (PSK) which can boost the immune system and be used to treat cancer.  PSK has shown to be beneficial in treating gastric, esophaegal, colorectal, breast and lung cancer.  This too is a Chinese medicinal mushroom.
http://en.wikipedia.org/wiki/File:Stumpfungus.jpg

I think this mushroom is a winner for my project.  The Lion's Mane (also called the Bearded Tooth) mushroom has crazy properties!  It is also a traditional Chinese medicine and has been proven to have antioxidant effects.  It can also be used to treat gastric ulcers.  Currently their are lots of studies going into the anti-dimentia compounds of this specific mushroom.  This mushroom has been determined to stimulate animal nerve cell growth.  In my research I found a paper that experimented with this on rats.  Here is a link if you are interested: http://www.dl.begellhouse.com/pt/journals/708ae68d64b17c52,03ea8c440cfbb276,23c2fd3840f4e0c9.html
This is also an edible mushroom.  I believe I've eaten myself at some point.  I've known it as the Monkey Head mushroom.  Pretty yummy :)

http://www.mykoweb.com/CAF/photos/Hericium_erinaceus(nw-01).jpg

February 26, Solo Work!

I am still figuring out specific but important technicalities to my experiment.  As part of my method and procedure, I am going to dehydrate the fruiting body.  However with C. cinereus, once they release their spores, they turn goop and obviously it becomes impossible to dehydrate them.  So I am looking for another species of mushroom I can test on.
Despite still figuring out the small details, I was able to begin collecting A. niger, the black mold, by placing agar plates in contaminated areas.  This might not be the most efficient way of getting the mold, but it is convenient with the tools we have.  The plates will not be purely A. niger.  While working on this project, I am also starting another experiment with Sarah for her oyster mushroom kit experiments.  This time, we are looking into different species of oyster mushrooms and seeing how they can grow on the grow-it-yourself kits.  Along with Pleurotus ostreatus I will be testing Pleurotus djamor,and Pleurotus citrinopileatus.  They are both edible mushrooms.

Pleurotus citrinopileatus

Pleurotus djamor

                                   

Other than discussing upcoming projects, I spent the majority of this time helping prepare substrate for Caroline's straw experiment.  I was let loose to make the substrate by myself and boy was it intimidating at first.  I made substrate once or twice with Courtney and Sarah, so I had to recall the procedure.  It was a good thing that making substrate does not require aseptic techniques.  Straw was everywhere but after making a bag or two though, I got the hang of it and now I can confidently make substrate bags myself.

February 19

One of my flow charts

Today, I was supposed to work with Sarah, but she was at an appointment.  So, I learned how to sort corn substrate.  The substrate is sorted by size, and it was done so by a vibrating machine of sorts.  There were holes of different sizes in the machine so that when the substrate passed by, the different sized particles would fall through the holes accordingly.

After sorting corn, I went to work on designing the procedure of my experiment.  From my research, I knew the general outline that I had to follow, but the details were vague.  I didn't know what equipment was available to me, and since I want to work with a pathogen, how was I going to do this without contaminating the whole lab?  Courtney clarified many of these details and suggested that I utilize a flow chart to help organize my thoughts and details.  The flow chart especially helps with figuring out the timing.  What else could I be doing when the mushrooms are drying or how long does it take to centrifuge?  Since I have limited time, this is crucial.

My final experiment will be comparing the antibacterial properties of Pleurotus ostreatus and Coprinus cinereus on Aspergiillus niger.  

My first DoE, the one looking to compare light and dark reactions came out with data.  Based off of the data for the fruiting bodies wet weight, the light mushrooms had the greatest average wet weight.  This is not what we predicted but it is helpful to know nonetheless.

February 12, C. cinereus

I worked with Courtney this time, and we spent time transferring plates (the first thing I did way back in October).  It was a good review of lab skills, especially involving contamination!  I had to remember not to open the pipette outside of the hood or let my hand pass over open containers (even if it is gloved and sprayed with alcohol).
I also made observations for the DoE on lighting regimes.  Here are some of the things I saw:

LIGHT SET
All 8 sets are fruiting
5 are in the beginning stages of fruiting
1 in the medium stage
1 in the middle/end stage, not quite ready for harvest
all 8 blocks fully colonized

DARK SET
All 8 sets are fruiting
Five are still in the early stages of fruiting
Two in the middle stages of fruiting
One nearly ready to be harvested

Next week the mushrooms should be ready to harvest.  Then I'll be able to weigh them for my data and write the rest of my DoE.

For my final experiment, I think I'm going to simplify my experiment by just comparing the antimicrobial effects of two mushrooms for the mold Aspergiillus niger.  One of these mushrooms for sure will be oyster mushrooms as we have a lot of them coming from Sarah's experiments for the self-growing mushroom product she is helping to develop.  The other mushroom might be one called Coprinus cinereus, also called the gray shag.  It is an edible mushroom.  This mushrooms short life cycle (two weeks in a lab) and easy cultivation makes it a useful organism to study and analyze genetics and molecular studies.  It has also been proven that this mushroom has antimicrobial properties against A. niger.

C. cinereus before spores are released.

C. cinereus after spores are released.

February 5!

Today was spent working with Sarah.  I helped out with preparing regrind and rehydrating blocks for other experiments apart of Sarah's coffee grind product for Back to the Roots Company.
My own experiment on lighting regimes for oyster mushrooms has come a long way.  I believe in a few weeks we will be able to harvest them.  Here are some pictures that summarize my experiment.

These are all part of the dark treatment.  A few blocks did not colonize, at least on the outside, such as the one in the middle.  However they did still grow mushrooms such as the one below.  From observation, the dark treatment blocks that did colonize seemed to colonize more. 

Dark Treatment, the largest of the oysters.  To answer a question Peggy asked during our meeting, we know when to harvest to mushrooms when they begin to produce spores.  This you can see, and it looks like fine dust.  Then we'll cut and weigh the mushrooms.

Dark treatment.  These mushrooms are nice.  

A light treatment.

These are baby mushrooms growing on the sides of the block that has no hole cut in it.  Since there is no air hole, these mushrooms will not last long, but as of this picture, they are trying to grow along the edge of the ziploc bag and up.
  

For my next experiment I'm still looking for possibilities.  Since this is really the first experiment I am designing myself, I don't want to complicate it too much.  Still thinking along the lines of mycofiltration, but I'm looking up pathogens.  Many of the pathogens in my book however were really dangerous, they trigger tuberculosis and cholera, but there was one that I might really be able to work with.  It is called Aspergillus niger.  This microbe causes black molds which is commonly found everywhere in the world.  Aspergillus niger has proven to be helpful in biotechnology and waste treatment but it can be harmful to human health if not treated carefully.  My mentors said they can also easily obtain this pathogen.

January 22 and 28: Dehydration, Rehydration, and Mycorestoration

On these two days, I alternated between working with Sarah and Courtney.  Both days I performed a variety of tasks.  Those that involved my project included dehydration and rehydration.  After these two processes, the mushrooms will begin to fruit and I will be able to collect wet weight data.  According to Sarah, all my mushrooms are doing well!  A handful of the light experiment blocks are contaminated with a mucor called Rhizopus which is also known as bread mold.  Luckily, this contamination is not too severe and  all my mushrooms are growing, healthy white.  Look forward to pictures in the next post!
When I was not working on my experiment, I helped perform other tasks such as making regrind for other projects (including one for Courtney involving engineered wood) and hydrating blocks for Sarah.

Both Sarah and Courtney gave me readings to begin looking at ideas for my own experiment.
In a book called Mycelium Running: How Mushrooms Can Help Save the World by Paul Stamets, I was introduced to the idea of mycorestoration.  This is a process by which fungi repair or restore the environment.

The following is a quick summary of four practices of mycorestoration:
Mycofiltration: filtering water, where the mushroom can act as a net to capture or digest toxins and contamination
Mycoforestry:  sustaining forest environments through an understanding of the mushroom's role in an ecosystem.
Mycoremediation: using mushrooms to break apart toxins and even heavy metals from the land.
Mycopesticides: Creating biopesticides from mushrooms

It would be interesting to pursue one of these topics, especially mycofiltration.  However, since these practices are new and much more needs to be discovered in these areas, this could make for a challenging experiment for me.  This just depends on what I want to focus on and the experiment purpose and design.

Here are some awesome mushrooms I discovered from the book Mushrooms of Northeast North America by George Barron for your viewing pleasure.

Panellus stipticus,a mushroom that looks ordinary by day but glows at night.

Marasmiellus candidus, they look like flowers.

Lycoperdon perlatum, Gem-Studded Puffball

January 15, Starting My Experiment!

Today, I worked with Courtney to begin the process for my first experiment!
To extremely summarize my DoE, I am looking to see if a dark treatment on the grow-it-yourself oyster mushroom kits Sarah is helping to develop will affect the wet weight of mushrooms.  Many commercial growers colonize oyster mushrooms with a 24 hour dark treatment.  We want to see if this will specifically work on this product.  Through data of the mushroom wet weight, we will be able to determine if a dark treatment is better than a light treatment.  Who doesn't want bigger mushrooms?
Courtney and Sarah already prepared substrate which they inoculated so I was able to dive into the regrind and packing parts.  This step creates the shape of the final product, a block, and allows for the mycelium to settle into this shape.  While I worked on packing parts, Courtney told me some more about her research.  One project she is currently working on is finding a way to quantify mycelium.  To do so, she is working closely with chemicals such as hormones, and their effect on the organisms.

These are bags of inoculation that Sarah and Courtney helped me make.  These bags were given the light treatment.  

I packed what was in the bags into parts like this.  This is from a bag that is undergoing the dark treatment.

This contraption (rack, black pod cover, and duct tape) is where the dark treatment takes place.  

After packing the parts, Courtney and I began discussing possibilities for an experiments that I myself would be interested in pursuing.  She gave me ideas that involved topics from micro-nutrients to agar or liquid inoculation.  While I am not working on this light treatment experiment, I will begin to research and find topics for my experiment.  Ecovative has several mushroom publications which I am allowed to borrow and my mentors are helping me to find science articles to broaden my understanding of mushrooms.