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Womyn of the Month- June, 2014: Haley Toups

Meet Haley Toups

Building molecular foundations for a mycological future

haley

Haley Toups is a dedicated student at the University of Nevada, Reno pursuing a degree in biochemistry and molecular biology as well as a minor in biophysical organic chemistry, which she will graduate with in the spring of 2015. Although young, she has already started making a difference in the world of mycology by introducing her community to fungi throug the local green house where she teaches the skills of mushroom cultivation and propagation. Periodically, she lectures to the local high school agriculture classes about fungi, biochemistry, and the career options available in science. She works as a laboratory technician at Aloha Medicinals which she recently allied with her university to analyze and identify fungi with DNA sequencing. Haley represents the next generation of mycologists, and only time will tell the advances in the study of fungi her generation will make.

Interview with Haley Toups:

The Telluride Mushroom Festival is proud of its bright and powerful female leaders, and one young woman, who is so diminutive in stature that she could easily be mistaken for a student on break, uses words that are anything but small when she discusses her work analyzing and identifying fungi with DNA sequencing. Meet Haley Toups, a molecular biologist and organic chemist completing her program at the University of Nevada, Reno. She works as a laboratory technician at Aloha Medicinals, a world leader in medicinal mushroom production, but this August, Haley will be part of a mobile laboratory team called the Telluride Institute Voucher Program at the Citizen Science Mushroom Specimen ID Tent in Telluride, Colorado.

“The Telluride Mushroom Festival takes place August 16th – 19th and is a world class mycological event,” explained Haley. “It is said to be the TED Talks of the mushroom world with cooking events, famous authors and mycologists, guided forays into the mountains and more…I can’t wait!” Haley is arriving at the festival a day early, because August 15th is a day of pre-conference workshops that the public can register for. “I plan to take both Tradd Cotter’s mycoremediation class, as well as Alissa Allen’s Mycopigments: Pick Mushrooms and Dye workshop.” Most of the mycology conventions that Haley attends for work are a little stiff, so she’s looking forward to the Telluride Mushroom Festival’s unique Haight-Ashbury feel.

When you see hundreds of festival participants dressed as mushrooms in our epic annual costume parade, you’ll have no idea that serious science is taking place beneath a public tent a few feet away,” said Matt Kostalek, vice-president of Aloha Medicinals. Kostalek and chief-scientific-advisor John Holliday, the internationally renowned mycologist at the helm of Aloha Medicinals, have offered a grant of over $10,000 to fund the Telluride Institute Voucher Program science tent where DNA specimens of mushrooms will be prepared during this year’s Mushroom Festival. One of the best parts of Aloha Medicinal’s generous scientific grant, which made this research possible, is that they’re also providing the staff to conduct the experiments, and Haley Toups is an ace at DNA extraction, public education and maintaining scientific rigor, so her presence in the Citizen Science Tent will prove key.

Haley has become relatively obsessed with fungi, and in addition to a career as a mycologist, her civic involvement also centers around mushrooms. On weekends, she is introducing her community to fungi through the local green house where she teaches the skills of mushroom cultivation and propagation. Her work with the Green House Project has led to hundreds of pounds of mushrooms being donated in less than a year to local food banks and food kitchens, positively impacting the public’s view of fungi. She also lectures to the local high school agriculture classes about fungi, biochemistry, and the career options available in science.

Please come visit Haley this August at the Telluride Mushroom Festival and read the attached interview to learn more about this uniquely talented and passionate woman in mycology:

Female & Fungi: Why do mushrooms captivate your attention?

Haley Toups: Mushrooms captivate my attention because of their mystery. There is so much that is still unknown about fungi. Out of all the kingdoms of organisms on earth, fungi are the least studied, which means they hold the most potential for discovery. Mushrooms have been shown to help cure cancer, fight HIV, eliminate arthritis, they provided the first true antibiotic, and now a species has been found that can digest plastic. It appears fungi can save the world in so many ways, but compared to other fields, few laboratories are dedicated to their study. It baffles me after showing so much potential, how fungi can still be the most cryptic organisms on the planet. Who knows what other applications fungi may hold. The apparent immortality of mycelium in and of itself would make an amazing study that could shed light on our own aging process. Mushrooms have limitless possibilities, and I could study them for a lifetime and never lose my interest in them.

FF: Why is it important to conduct the Telluride Institute Voucher Program during the Telluride Mushroom Festival?

HT: The Telluride Institute Voucher Program is essential for future mushroom identification. As the climate changes, so will local environments like that of Colorado’s western slope where Telluride is located. Without tracking the current species growing in this region and the abundance in which they are present, it will be impossible to track the impact of the climate change and the rate it is affecting fungi. The Telluride Institute Voucher Program provides a fun and easy way for mushrooms to be identified based on similarities that anyone can accurately perform. The Telluride Mushroom Festival is the perfect time to expand the Telluride Institute Voucher Program since so many willing hands are available to do the labor of finding the fungi. This will be a priceless collection holding irreplaceable data for future generations. 

FF: When you’re teaching mycology and microbiology in our citizen scientist specimen tent, what aspects of mycology or basic scientific principles do you plan to discuss with the children and adults who come to meet you?

HT: I am very excited to be working at the Telluride Mushroom Festival this year. Being a student myself, I feel I will be better able to relate to many of the kids who wander into the citizen scientist specimen tent. Much of teaching is passive; students are expected to sit in an uncomfortable desk and retain every word from a dreary lecture, but that is not how learning works. Learning needs to involve hands on experience and fun. I intend to impart what knowledge I have of identifying fungi based on their physical attributes as well as stressing the importance of DNA analysis and other modern techniques. I am sure I will learn just as much from the visitors as they will learn from me because there is always something new to learn about fungi. 

FF: What kind of work do you do? What’s your average day like?

HT: Working at Aloha Medicinals is a very unique experience and an “average” day is usually anything but that. I can honestly say that working at Aloha is unlike anything I have ever experienced.  Not many people get to wake up in the morning and go to work where they visit the company jelly fish and greet the managers’ dogs while having a cup of coffee next to a saber tooth tiger skull before climbing into a cleansuit that could pass for a very convincing ninja outfit to work with mycelium and mushrooms all day. I love my job and what I am able to contribute to scientific knowledge. 

Usually I begin my day with media preparations, which is the base for Aloha’s entire production line. If the plates and tubes I create become contaminated, the product will become exponentially more contaminated at every step down the line, and we will have a lot of unhappy clients on our hands. For this reason it is key to use the world’s most advanced sterile techniques and multiple quality control steps to insure our customers are getting exactly what they paid for. 

I find making media is an undervalued skill in many laboratories, which is a sad fact because you have to think that is what my mycelium will live on for its entire life, and I always ask my students if they think the mycelium has everything it could ever want or need to thrive in its little environment. After explaining the nutritional needs and some toxic compounds that affect fungi, I encourage my students to set out and create their own medium that we can test to see how well they balanced the macro and micro essential nutrients while combining it with a source of protein carbohydrates that induce quick growth. It is important that the substrate allows mycelium to maintain a high production of B-glucans and arabinoxylanes, which are a couple of compounds that provide some of the medicinal benefits of our mushrooms by charging the immune system and acting as antioxidants. As a result, some very interesting media has been created by students ranging from canned peaches and V8 juice to one of my favorites which included avocado peels. Aloha takes its media very seriously, and it is my job to create a multitude of balanced media for our hundreds of species that each have a slightly different metabolism and therefore grow better or worse on different types of media. What you put into your media is what you get out of your mushrooms. Mycelium grown on brown rice is renowned for its arabinoxylane content, and those grown on an insect based medium have faster development of B-D-glucans. It is convenient that all of Aloha’s lab technicians have a different favorite type of medium they think produces the best results because it is essential to vary the type of medium your mycelium grows on every six months to prevent senescence as well as insure nutritional needs are being met. 

After putting my media into the autoclave (so named Roxanne for putting on the red light) and sterilizing it for about an hour at 121oC, my students and I pour it under the hood, allow it to set and then store the plates and tubes for a week before use to prevent any contamination by mold, bacteria, or mites. After media preparations, my day becomes less predictable.  Some days I aid the culture bank manager in refining our new website, which I urge everyone to visit and use to find out about media types, growing conditions and techniques, as well as genetics and about fungi in general (like the common names of all of Aloha’s species in eight languages! It was no easy task to translate Chinese and Italian websites, so if you need to know international names, this is the website for you). Customers are also able to purchase Aloha’s world renowned strains and grow them at home all from this website. 

Other days I reach out to the mycological community on fungi chat-boards and blogs to help solve common propagation problems as well as aid in unraveling some of the deep mysteries surrounding fungi. Most days however, I organize and analyze over 10,000 culture tubes located in Nevada and Hawaii. This is my primary job at Aloha, and it is very time consuming. Twice a year every strain in the culture bank must be transferred to create the next generation to insure the strain will not die out for any reason such as lack of nutrition or even if the building was to burn down (explaining the two storage locations). This process once again requires advanced sterile technique and incredible dexterity. Students also participate in this project, and they create their own culture tubes to take home with them at the end of their internship. Insuring the vitality of the cultures is another part of my work with the culture bank. This is my favorite part of my day at Aloha Medicinals because I get to fruit mushrooms and visit the grow chamber to check up on any ongoing substrate experiments I may have going on. Most recently Aloha has been trying fruiting on coconut coir, which is an incredibly cheap and highly renewable substrate. I am very excited to see the results of this experiment. 

The hardest days at Aloha are inoculation days. These are the days that separate the mushroom enthusiasts from the true mycologists. Standing in a chilly sterile room inoculating upwards of 600 ten pound bags of sorghum for nine hours straight followed by a rigorous two hour cleaning session scrubbing the floor on your hands and knees until it is sterile enough to eat off of is quite an ordeal, but everyone at Aloha helps out, and I have so much respect for my co-workers for what we do and how happily they do it every week. The students also participate in this job, and it shows them just how much hard work is involved in industrial mycology. Morale is very high at Aloha, and it has to be because the work is very hard both physically and mentally. I would never be able to get through production without my co-workers who will spontaneously break into song or tell a hilarious joke when the going gets tough. Working with each other has made us a family. We go on hikes together. We celebrate holidays together. Obviously we go mushroom hunting together, and now we are all going to the Telluride Mushroom Festival together. 

FF: What discoveries do you think may be found in mycology during your lifetime?

HT: Telomeres and their link to aging seem to be a hot topic today, so I bet there will be a discovery linking fungi’s apparent immortality and ability to resist senescence to the ends of their chromosomes. Studying fungi has so many avenues available for study it is nearly impossible to guess what the discovery will be, but there are certain to be many.

FF: What are some of the most important things you’ve learned while working with Aloha Medicinals and John Holliday?

HT: Working at Aloha has given me a very unique view into industrial science that few people are ever able to attain and appreciate. Science is often glorified at as a comfortable job where you sit in a laboratory doing little experiments, but the majority of science takes place in an industrial setting that is loud, messy, and often times repetitive. I feel lucky to be part of a world-class scientific team so early in my career.

The most important skill Dr. Holliday has taught me is trouble shooting and problem solving. If there is a source of contamination, retardation in growth or even if the autoclave is not working properly, it is my job to help remedy these problems.  Understanding and controlling variables underpins all of science and is fundamental to all of my work and research. 

FF: What experience, location or specimen is at the top of your mycology bucket list? 

HT: Aloha Medicinals is famous for its Cordyceps. I would be honored to accompany Dr. Holliday on an expedition to the Tibetan Alps to recover fresh samples and new strains of Cordyceps for Aloha. This experience is definitely at the top of my bucket list. 

FF: If you had a million dollars to design a mycological research study, what would it be? 

HT: This is a very hard question because there is so much I would want to study! It is actually a dream of mine to establish a biochemical research laboratory within Aloha Medicinals. To begin with I would want to identify and further characterize the genes responsible for all of the medicinal benefits of certain fungi like Cordyceps, Ganoderma, and Inonotus obliquus (chaga). Then using simple biochemical techniques I could enhance these genes and study the effects. I would love to sequence other species and using a BLAST program find other potential mushrooms with the same benefit that may be easier or cheaper to produce. Using the sequencing data it would be interesting to attempt to map the evolutionary relatedness of species. It would be incredible to thoroughly map fungi metabolism by finding mutant strains or creating knock outs. I am sure every mycologist including me would want to have side projects figuring out how to fruit truffles and Cordyceps sinensis in the lab. One of the topics that interests me most is stress conditions. Exposing mycelium to different stress whether it is heat, cold, nutrient deficiency, or an invading pathogen (like a bacteria) would show amazing patterns in gene expression that would tell us so much about how they react and adapt to their surroundings. Maybe a new substance like an antibiotic would be discovered. This study could show important insight into the future of fungi with the changing climate. Discovering what hormones regulate fungi would be another interesting study.  Clearly I am all over the board on this question, but that is because there are so many possibilities, and so much is still unknown about fungi. 

FF: While many academics who do not deal with this everyday believe that DNA is a fingerprint that never lies, we, of course, know that this is not the case with fungi. Please discuss the challenges of using molecular methods for species ID. 

HT: The problem with using DNA as a molecular identifier for fungi is the finger printing sites between species in the same genus are too similar to differentiate between (differing only by a few nucleotides). This year I have been aiding a lab at the University of Nevada Reno where we were doing some sequencing of Aloha’s strains. We had already identified the species we were attempting to sequence using morphological characteristics. These were being used as controls before we attempted to sequence unidentified species. Unfortunately, the finger printing site we chose could only narrow down the possibilities to 23 different species of Cordyceps. Another sample was narrowed down to about 50 different possibilities for Ganoderma, and the Morchella strain we sequenced was a lost cause entirely. Narrowing a sample down to its genus is something that can be easily done using morphological techniques, and the money spent was not worth the results we were getting simply because the site we chose to sequence was highly conserved between species.

In 2000, it cost around three billion dollars to sequence a genome. Right now it costs about a thousand dollars, and the price will only continue to drop in the future. Due to the highly conserved nature of DNA between species of the same genus, whole genome sequencing may hold the key to accurate DNA based identification. 

FF: Please explain DNA sequencing and BLASTS for the nonscientist.

HT: Imagine you need to write an email. You would use the alphabet to write the words “Dear friend, today I went to the store.” DNA works much the same way; it is an alphabet, but instead of making words, it makes hooves, leaves, mushrooms, and noses depending on what it says. Just like you would use the same alphabet to write any number of emails to all your different friends, DNA uses the same alphabet to make you, me, monkeys, and asparagus, but instead of having 26 letters, DNA is only made of 4 letters called nucleotides. Again just like the letters of the alphabet make words, the letters of DNA come together to make pieces of an organism. These pieces are called genes. The words you write in an email to your friend come together to make sentences. In DNA, the genes come together to make functional proteins, and in turn these proteins come together to make pieces of an organism like a wing or a scale, just like the sentences of an email come together to make a paragraph. Before you know it your friend has read all the paragraphs that make up your email, and he knows exactly what you mean. When reading DNA, you put together all the pieces of an organism, and you will know exactly what it is. Unfortunately, DNA does not use the same alphabet that we do, so we have solve its message like a puzzle. 

All DNA sequencing is based off the action of a protein called DNA polymerase, which simply adds the next nucleotide (letter) to a gene (word). The ability to read what nucleotide (letter) is added next allows us to figure out what gene (word) the DNA is writing. This is accomplished with dideoxynucleotides, which are essentially a period because they will mark the end of what you are reading and stop it from continuing, but unlike reading an email, scientists can only read the last letter that was added to a word. This essentially means we have to put a period after every letter of a word to be able to read it. For example to read “hello” we would have to read it as “H., HE., HEL. HELL.”, and finally we would see “HELLO.”. 

Early DNA sequencing was terribly rigorous, and my professors joke they all had to get glasses from interpreting the sequences and how lucky us young folk are today a machine does it for us. Back in the day the four types of dideoxynucleotides (one for each nucleotide) would be added to four different tubes all while the polymerase chain reaction (PCR)  was taking place (the writing of the words). The system is set up so the PCR will write the same genes (sentences) over and over again using a template that we want to sequence using primers, which simply tell us where the sentence starts. The writing process is commenced by DNA polymerase, and it even has a sort of spell check function. Remember, DNA is double stranded so only bases that are complementary to the base on the template strand will be incorporated into the strand you are trying to read. After every letter has a period on it. Scientists put it on a gel to read it based on how long the word is. We know the shorter the word is the more incomplete it is. Here is an example of a gel I had laying around.

 Haley Toups mycology woman (1)

The letters at the top represent the four dideoxynucleotides letters incorporated into the sequence and the numbers represent the shortest to longest sequences. Based on this picture we can say my sequence is ACCAGTG. Orientation is a complexity I will not get into depth with. As you can see this is a very short example and sequences are usually thousands of nucleotides long.

Luckily sequencing today has progressed significantly into the second, third and next generations. In the second generation all four dideoxynucleotides were put in one reaction tube and they were differentiated by fluorescent colors a computer could read. One third-generation technique called ion torent involved detecting a pH change from the reaction when a nucleotide was added. And finally the next generation technology, which is still being developed involves DNA being pushed through detector that identifies the nucleotides (much like a one of those new airport security booths that you have to go through and they can detect what is in your pockets). 

BLAST is an acronym for “Basic Local Alignment Search Tool”, and it is a rudimentary application of the data collected from sequencing. After sequencing a scientist is facing a huge line of letters. BLASTing allows a scientist to compare his sequence to all the other sequences that have already been identified in a data base with a simple cut and paste. This process saves a lot of time, and it can be used to identify species as well as figure out if a gene is shared or similar between different species.  NCBI has a great BLAST program that is free. Sequencing DNA is meaningless unless an annotation is applied to the gene and figuring out a species or a function. All a DNA sequence is a long line of letters, so BLASTing is an important follow up step to sequencing.

FF: Oh my gosh, Haley… You’re so smart, and you’re an amazing teacher too! Thank you for explaining that. Do you believe that the public needs to see women in science? Why?

HT: Science tends to be an introverted business, and scientists usually keep to themselves outside of their careers. Scientists are not like movie stars whose faces are plastered on posters and whose every move is documented on social media, but it is crucial for the masses to see and recognize scientists not for who they are dating, what they ate for breakfast, or even who they are as a person; the public needs to see scientists, especially women in science for what they do. A lot of people are afraid of science or they think it is boring simply because they do not understand it. Women of science need to stand up and vouch for what they have done because what they do is important, and the public is not asking. We need to explain science in a way the public can understand. The number one speed bump that impedes the progression of science is ignorance. If people are not sure what is going on they will not support it or worse they will not even talk about, which enables an ongoing lack of awareness. Women shape social media, and it is up to women scientists to use this tool to our advantage to increase scientific literacy. I plan to post to Aloha’s Facebook page about everything we encounter and discover during the Telluride Mushroom Festival.

FF: Haley, you’re an incredible person and role model and I’m very grateful that you’ll be staffing the Citizen Science Mushroom Specimen tent in Elk’s Park at the Telluride Mushroom Festival. Thank you for bringing your talent and energy to share with the TMF community! 

HT: It’s my pleasure, Rebecca. I need all of my friends to hop on the festival’s web page and get their tickets before it sells out, because I want everyone there to mushroom hunt, play, and enjoy it with me. Get your tickets to the Telluride Mushroom Festival here: www.telluridemushroomfest.org 

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