Biology@memphis

by Kate Parsley
Ph.D. candidate

For those who don't know, plant awareness disparity (or PAD) used to be called "plant blindness," and is defined as the tendency not to notice plants in the environment around you. It's split into four different characteristics: attention (not noticing plants), attitude (not liking or caring about plants), knowledge (recognizing the importance of plants...or not), and relative interest
(how interesting you find plants in comparison to other organisms, like animals). It's a complex situation, and a big problem.

Plant awareness disparity might seem like it's harmless until you think about how much we benefit from plants (and what they do) on a daily basis. Plants are sources of food, medicine, clothing, shelter, and even oxygen. We benefit from their existence and use in many different ways. But what happens when we rely on plants, but don't acknowledge their importance or even notice that they're around?

We can (and often do) become very disconnected from the ecosystem around us if we become disconnected from plants in this way. We start to take them for granted, and just when we do, they start to disappear. Plant conservation is an issue not just because plants are disappearing faster than we can identify them, but also because we aren't the only ones who rely on plants... other animals do too. In fact, the vast majority of animals on the endangered species list are there because their habitats are disappearing. These habitats are mostly comprised of (you guessed it) plants.

Plants become even more important when we consider their implications for climate change. Plants absorb carbon dioxide and release oxygen as a by-product of photosynthesis (the purpose of which is to create glucose, a type of sugar that is a source of food for the plant). We need oxygen to live, and on top of that, we need plants to absorb carbon dioxide from the atmosphere. This need is especially pronounced because humans are responsible for a lot of extra carbon dioxide, so there's much more in the atmosphere than what could ever be considered, "normal." Unfortunately, we keep tearing down forests to use for our own purposes, or to make room for agricultural efforts, effectively ruining our carbon sinks.

We seem to have conflicting interests where plants are concerned. We rely on them for so many things (paper, food, etc.), which often requires us to tear them down. But we also rely on them for more general purposes (absorbing carbon dioxide, producing oxygen) which means we can't cut them all down or we won't be able to survive (not to mention the millions of other species on the planet that depend upon them too). Like I said, it's a complicated issue, and we have no chance of solving it if we continue to be unaware of plants and ignore that it's happening.

Some of you might be thinking: well how do we fix it? I'm a Ph.D. candidate here in the biology department, and I study botany education, meaning that my dissertation is about trying to answer that question. I've spent a lot of time thinking about the topic and I can safely say this: I don't know — yet. I do have some ideas, but it's a complicated question with a complicated answer.

Speaking of education: something we do know is that students who don't have good experiences with plants and plant mentors early in life often develop plant awareness disparity beginning in grade school and continue this trend all the way through college. A plant mentor is anyone who takes you under their wing and teaches you about plants in a context outside of school. These people are often family members, but can be scout masters, teachers, friends, or anyone! So, if you're concerned about a student in your life developing plant awareness disparity, here is one thing you can do to help: take them outside! Go to a botanical garden, go hiking, start a garden, anything that gets them outside and around plants can help ensure they recognize plants in their environment, and later on, they'll be more likely to retain related information from their teachers.

Plant awareness disparity isn't doing us any favors. Not only does it hurt us for the reasons above, but it reduces our capacity to do research and find ways to support plants (and, by extension, ourselves and the rest of the planet). If students are unaware of plants, they're less likely to learn about them (or even want to learn about them) which means they don't go to graduate school, learn how to do plant research, and find the next big plant-related innovation. We're cheating ourselves out of some very important and exciting scientific innovations, especially when you add in the fact that plant research gets funded less often than many other kinds of research!

For more information about plant awareness disparity, you can check out this new publication I wrote where I develop the term and explain it in more detail: https://nph.onlinelibrary.wiley.com/doi/10.1002/ppp3.10153

You can also check out my blog (which this post is modified from): https://plantawarenessdisparity.wordpress.com/

Or follow me on Twitter:
@KateParsley_
#PADisBAD
#PlantAwarenessDisparity

-Kate Parsley (Ph.D. Candidate, Sabel Lab)

Dr. Emily Puckett, Assistant Professor of Biological Sciences, attended the 2nd International Sun Bear Symposium in Kota Kinabalu, Malaysia on Sept 25-26, 2019. The symposium focused on developing a 10 year action plan for the species that included setting conservation goals, stakeholder engagement strategies, and research priorities. Dr. Puckett contributed knowledge about integrating population genomics of bears to support conservation.

Sun bears (Ursus malayanus) are the world's smallest bear species and classified as Vulnerable to extinction by the IUCN. They range across Southeast Asia, and on the islands of Sumatra and Borneo. Habitat removal and conversion of forest to agriculture has resulted in both declining area and habitat fragmentation across their range. Further, sun bears are legally and illegally hunted for Traditional Asian Medicine products (gall bladder, bile, claws, teeth), meat, and due to bear-human conflict particularly on plantations. Further, cubs may be captured and kept as pets.

Dr. Puckett noted significant challenges researching sun bear ecology and evolution. "Like all bears, sun bears are a solitary species where males have largely non-overlapping ranges. That means you have to cover a lot of area if you set up hair snag corals or barrel traps. For American black bears we work in lots of temperate forests with low understory; but sun bears live in jungle habitats, which makes setting traps to obtain genetic samples much harder." The sun bear community works around this challenge by studying the bears in ex situ conservation care. These animals provide information on diet, behavior, and hopefully in the future a better understanding of their evolutionary history.

When asked about the highlight of the symposium, Dr. Puckett said, "meeting Dr. Wong Siew Te! He's a giant in the bear conservation community and approaches his work with unending enthusiasm." Dr. Wong is the founder of the Bornean Sun Bear Conservation Center.

Dr. Puckett's trip was supported by a seed grant from the University of Memphis Center for Biodiversity Research.

by Cheryl A. Goudie, Program Director
Meeman Biological Station

It was a chance encounter at a meeting that started the research (isn’t it always?). Dr. Christopher Vanags (a geology professor at Vanderbilt) asked if I had mentioned “Meeman?”. He was stunned to hear that name because his father, aunt and uncle, grandmother and great-grandfather, all WWII refugees from Latvia, had worked and lived on “Meeman Farm”. Surprised to have made this amazing connection with the past and not having known about this part of Meeman Biological Station (MBS) history, I made my way to the 4th floor “Special Collections” archives of the University library to research Edward J. Meeman’s donated papers. Among his meticulous records were several items that mentioned different members of the Vanags family.

After sharing some of the findings with Chris and his family (and all of us wanting to know more!), he set up a meeting with one of the few living persons who could provide a first-hand account of life on Meeman Farm as it was in the 1950’s – his 99-year-old grandmother, Mrs. Dzidra Vanags Berzins. Her family and friends call her “Laima”. Before the meeting, I consulted with Dr. Charles Crawford, Director of the Office of Oral History Research, for tips on how to conduct and record an oral history, as I knew this would be no ordinary conversation.

We talked outdoors on a beautiful western Pennsylvania day for about 2.5-hours. Laima first recounted harrowing stories of near-misses and close to death encounters as she and several family members (including her father and three
young children) endured the First Soviet Invasion of Latvia, then the German Invasion (where German soldiers commandeered parts of her home and barn for use during their occupation), and then finally their escape to the Baltic Sea during the Second Soviet Invasion. They went from there to Berlin, Germany and spent three years in a Displaced Persons Camp in the zone occupied by the Americans. While there, she tried to find the whereabouts of her husband, who had been forcibly conscripted into the German army, but learned later he had died. After securing paperwork and haggling with authorities about which family members would be allowed to leave, they were finally approved to relocate in the United States. They arrived in New Orleans, along with about 800 other Latvians, on a returning troop transport ship (not the most luxurious accommodations!) and
about 200 of them travelled by train to a refugee settlement in Senatobia, Mississippi. Senatobia was the childhood home of US Army commander, Col. A.T. Callicott, who owned a cotton plantation and who personally sponsored many Latvians for relocation to rural Mississippi to work on local farms.

Mr. Meeman had previously employed Latvians on his “forest farm”, so he knew they were honest and hard-working people. When Laima landed an interview with Mr. Meeman, she and her father (Peter Sauleskalns, an educator who had earlier founded an agricultural college in Latvia) were both hired. They worked at Meeman Farm for about nine years (~1950-1959). Laima worked around the house, cleaning and preparing meals for Mr. Meeman, his sister Gertrude and his brother Benjamin while her father tended the cattle and improved the fields for grazing. Laima told about the many guests that came to the house, individually and to Mr. Meeman’s parties, to curry favor or trade opinions with the editor of the Memphis Press-Scimitar, including such notables as Tennessee Senators Estes Kefauver and Albert Gore, Sr. Mr. Meeman told Laima to keep the doors to the kitchen open and to listen closely to what was being said by the guests, as she was trying to learn English and he thought the conversations would help. Her children, Intis, Peter and Anna, became part of the Meeman “family” and were welcomed and participated in events at their home, at work on the farm and during parties. Mr. Meeman helped with their education at the nearby E.E. Geeter School and later paid for college tuition. Among many other snippets she told during our conversation, Laima said the music of Beethoven and Bach were often playing when Mr. Meeman was home, she twice encountered (and escaped!) what she thought was a mountain lion on the trails around the farm, and that Kudzu was present, even back then!

Mr. Meeman left quite a legacy, not only of his tangible gifts (Meeman Biological Station and Meeman Journalism Building at The University of Memphis and The Center for Lifelong Learning at Rhodes College), but in his philanthropy that included helping Latvian refugees return to a normal life. A monument was erected in 2004 (left) to recognize and commemorate the contributions the Latvian refugees made to the culture and society of Senatobia, Mississippi. Mr. Meeman is equally deserving of such a tribute and the recently completed Conceptual Master Plan for Development of Meeman Biological Station includes a River Center and Meeman Museum to illustrate his significant contributions to the region. His relationship with the Latvian refugees who worked on “forest farm” will certainly be part of that story.

Meeman Biological Station is the University’s 623-acre natural resource asset on the 3rd Chickasaw Bluff in northwest Shelby County. MBS was bequeathed to the University in 1967 following the death of Edward J. Meeman, newspaper editor and avid conservationist, who was instrumental in development of Great Smokey Mountains National Park and Meeman-Shelby Forest State Park. The Deed of Conveyance designated Mr. Meeman’s home as the Edward J. Meeman Conference Center (to be used for small meetings and conferences and as a get-away from our urban campus) and the farm and forested lands were to be used for education and research. MBS is a center in the Department of Biological Sciences and its faculty and students are the Station’s primary users. To learn more visit Meeman Biological Station.

My sincere thanks to Chris Vanags, Sandra Vanags (Peter’s wife), Leva Berzins (Laima’s daughter), and Laima Berzins for adding content and context to this history. The audiotape and transcript of our conversation will be added to the MBS website and reposited in the Office of Oral History Research.

 

 

Giving Students Hands-on Lab Experience: In a science department like Biological Sciences, undergraduates often ask faculty members for the opportunity to do a research project in their lab.  While faculty members do what they can to offer those opportunities, none have room in their labs for every student who asks.  If the department had a way to provide more research opportunities for our students, they would have a better chance of landing a job with a bachelor’s degree in biology.  Enter CURE courses!

What is a CURE course? In a CURE course, students identify a research question they’d like to answer, and then design, perform, and analyze experiments where the outcomes are unknown.  Along the way they develop technical skills, learn to trouble-shoot their experimental designs, and problem-solve when experiments don’t work or produce unexpected data. Finally, they learn how to communicate their findings to their instructors, their departments, or at scientific meetings.

Why are CURE courses useful?  CUREs can give our students marketable skills for employment in the Memphis biotech industry or research institutes like St. Jude Children’s Research Hospital and the University of Tennessee Health Science Center.  Research experience is also important for resume-building for professional schools and new findings could lead to a scientific publication.  Seeing concepts discussed in class put into practice in the lab reinforces what they’ve learned.

The Department’s first CURE: BIOL 4090 Synthetic Biology:   Drs. Jaime Sabel and Judy Cole, along with graduate assistant Malle Carassaco-Harris, began offering the department’s first CURE course, Synthetic Biology, in the fall of 2018.  In this lab, students design and construct a novel biological device using the International Genetically Engineered Machine (iGEM) registry of standardized “parts” (DNA sequences that encode a biological function).   They then use these devices to answer a specific scientific question.   In the pilot run of the course, three groups of students learned to how to make bacteria express plasmids containing a specific part, how to harvest the plasmid from the bacteria, isolate each part, and join the parts together.  In Figure 1 a DNA ligase is used to join the LacI V5 promoter (a region of DNA where converting DNA into RNA starts) to a composite part consisting of a ribosomal binding site (a nucleotide sequence that recruits a ribosome to start protein translation) and a green fluorescent protein reporter gene used to indicate that the device is being expressed. If bacteria glow green, they are making the device.  In the first running of the class the all three groups of students chose to ask questions about the ability of a cobalt-sensitive promoter to (1) drive the expression of a super yellow fluorescent protein, (2) examine the cobalt promoter's sensitivity to nickel activation and (3) ask if cobalt-induced activation could overcome the effects of a weak terminator.  Although we discovered later that the promoter had a mutation that made it insensitive to cobalt (drat!), everyone managed to ligate three parts to make a three-part device.
Figure 2: Images from the first Synthetic Biology lab: (1) bacteria expressing the three-part device on an antibiotic-selective agar plate (2) groups updating their notebooks, (3) prepping DNA for ligation (4) setting up DNA to run an agarose gel, (5) running agarose gels, and (6) Look!  Restriction digests shows three parts!

Synthetic Biology Part Deux: At the end of last year's lab, students and faculty had a trouble-shooting session where they all exchanged ideas for improving the student experience.  Based on those suggestions, and their own observations on what did and didn't work,  Drs. Sabel and Cole are looking forward to a new group of students getting a hands-on experience synthesizing biology.

 

 

 

By Jennifer R. Mandel
listen to Dr. Mandel discuss her recent paper

Making up one in every ten flowering plants on Earth, members of the daisy, or sunflower, family have fascinated scientists for hundreds of years. Many species of plants that you might not expect belong to this family: Gerber Daisies and the iconic sunflower of course, but lettuce, artichoke, wormwood (think absinthe), and dandelions. Sunflower relatives aren't all herbaceous either--there are trees, vines, and shrubs. The oldest fossil of a sunflower-like flower head is roughly 40 million years (MY) old and was discovered in Southern South America in Patagonia. From 40 MY onward, the fossil record for sunflowers picks up with evidence showing up around the globe. In large part due to these findings, the sunflower family was thought to have originated in the Eocene (56 to 33.9 MY) by most scientists making it a (relatively) young family in evolution's time frame.

However, with the advent of molecular dating techniques and the rapid advances made in sequencing technologies and genomics, the data began to hint that the family could be older--possibly even twice as old. Two small studies in the family described a sunflower scenario with a much older origin that was prior to the mass extinction event that corresponded to the extinction of dinosaurs about 66 MY. Adding to this, a fossil pollen grain ascribed to the family was discovered in Antarctica and dated to 72 MY in the very late Cretaceous. The Antarctica of today was not the Antarctica of the Cretaceous, the climate was cool temperate, and no ice existed. At this time, Southern South America, Antarctica, and Australia were much closer to one another and possibly even connected. This land connection describes how many of the plant and animal distributions that are now separated may have originated including the closest family relatives of sunflowers.

The Mandel Lab along with collaborators at the Smithsonian Institute and Oklahoma State University have been investigating the origins of the family in both space and time making use of the new sequencing technologies and fossil evidence. We sequenced nearly 1000 genes in 250 species and used molecular dating, biogeographical analyses, and diversification tests to ask where, how, and when did the sunflower family originate. Our data show that the family probably originated in Southern South America though Antarctica cannot be ruled out (my money would be on the latter). And we further confirm a pre-mass extinction origin for daisies when dinosaurs still walked the Earth! We also showed that the family tremendously increased in species number during the Eocene connecting our work with the extensive fossil record from that time. Finally, we link this explosion of diversity with a global change in climate that likely transformed many of the habitats to those that were most suitable for sunflowers and their relatives to thrive. This study is only the beginning of our investigations into understanding how sunflowers have become the largest and most diverse family of flowering plants on Earth. We aim to use this new information to continue to understand how climate, habitats, and genomic diversity influence plant biodiversity and distributions.

The full story published June 2019 in PNAS can be read here.

The Department of Biological Sciences is part of the University of Memphis - an urban university. You might think that limits our ability to give students the opportunity to study plants and animals in their native habitats, but that's not the case.  We have a number of classes with a field study component and in this blog entry, we're going to talk about a class that takes students into the field to observe frogs, salamanders, and snakes in the wild.

Dr. Matthew Parris teaches BIOL 4744 Herpetology (the study of amphibians like frogs, toads, and salamanders, as well as reptiles such as snakes, lizards, and turtles) which introduces students to the classification, distribution, life histories, techniques of collection and preservation, and natural habitats of North American reptiles and amphibians. According to Dr. Parris, herpetology is one of the most rapidly expanding branches of zoological study. There are number of reasons for the increased interest, including the importance of amphibians and reptiles in many ecological communities, and because they have been experiencing extraordinary population declines over the last few decades. These declines herald a global deterioration of ecosystem quality, which negatively affects both wildlife and human populations. Dr. Parris’ class provides a contemporary assessment of amphibian and reptile conservation, ecology, and evolution and he emphasizes three fundamental biological components: evolutionary history, form and function, and ecology and conservation.

Dr. Parris’ class reflects the kind of research he conducts in primarily two settings: a temperature-controlled laboratory with access to a wet lab, and an outdoor array of pond mesocosms (any outdoor experimental system that examines the natural environment under controlled conditions) located at the Meeman Biological Field Station. Access to both the lab and a more natural outdoor experimental system allows him to conduct experiments with individual animals and at the population or community level. His primary focus is determining how natural and human influence impact amphibian life history and fitness. These pressures include predation, pesticide exposure, and infection by the chytrid fungus Batrachochytrium dendrobatidis. The work in his lab seeks to describe the effects of these pressures, both independently and interactively, on amphibians and aquatic communities. Read more about Dr. Parris’ research.

 

Pictured are members of this spring’s class who collected snakes, frogs, and toads from T.O. Fuller State Park and from the Department’s Meeman Biological Station

 

 

The Ins and Outs of Requesting a Letter of Reference
by Communications Committee

You're thinking about medical or dental school or perhaps graduate school and you notice that most of them require one or more “letters of reference” to go with your application. Generally, the application instructions will indicate whether the letters should come from an instructor, a professor or a supervisor of your work. What should you do? The first thing you need to do is decide who to ask.  This should be a person who knows you fairly well (no, don’t ask your mom) and yet is an authority figure, for example the professor in charge of the lab you worked in rather than a technician or post doc. Once you’ve identified who you want to write a letter, ask them, preferably in person. This is why having some prior contact and interaction with the individual will help immensely in soliciting their help and giving them more detailed information to add in their letter. You should also provide the referee a release that allows them to discuss your performance in school. The form is found on the Biology website: click on the undergraduate menu on the left side or click on this link: https://www.memphis.edu/biology/undergraduate/pdfs/letter_recommendation.pdf

Many students use electronic application services such as PharmCAS or AMCAS.  These provide websites for the transfer of electronic letters of reference and make the process fairly easy, especially if you plan to apply to multiple schools or programs. If you are applying directly to a program or for a particular job be sure to provide the snail-mail address or email of the person that should get the letter. Letters need to be sent either by the services such as AMCAS or directly from the referee to the admissions committee. Generally, letters forwarded from the applicant are not very useful; if you are concerned whether a letter has been sent, it is perfectly acceptable to email the referee to inquire, especially if there is an application deadline. Most letter writers understand the deadline dilemma.

That brings up when you should solicit letters. It never hurts to ask well in advance if an individual would be amenable to supporting your application with a letter. Usually the program application instructions will indicate the deadline and that needs to be passed along to your referees. Do not expect a very helpful letter if you ask to have  it sent tomorrow! Give the referee some time measured in weeks rather than hours to write your letter. A general rule would be to give the letter writer at least a month before the deadline to submit the letter. It helps enormously if you provide them with your resume or curriculum vitae, outlining not only your schoolwork but also jobs, hobbies, sports and other activities such as volunteering. Remember that crusty old prof had to ask for lots of letters of reference to get where they are now. Good luck with your applications and with attaining your future goals.

Students ask me about career choices and how best to attain their dream job. I tell them my experiences, both personal and professional, indicate that motivation and interest are key. Ask yourself this question: what do you truly enjoy doing? For example, is it an outdoors activity (useful for ecotech, environmental work), is it talking and being with people (needed for teaching, biotech reps, medicine), is it doing some type of fine handcraft (useful for surgeon assistants, cell biologists), is it working with animals or plants (labtech, vet techs, agriculture)? Binge watching Netflix probably is not going to get you far in terms of job prospects even though it may be a favorite pastime. Motivation plays a major role: This must last long-term, in other words lots of things motivate us at first, but can quickly get old, mundane and we lose interest. Will your chosen profession/career give you motivation to wake up in the morning and get at it?

Another key to this puzzle is your experiences. At the bachelor degree level, starting jobs often eventually lead to other doors opening, in other words the first job after the BS may not be “it”, your dream job. That starting job may be because you happened to take an extra chemistry, biology lab or math course not directly needed for the major. It may be because of a summer job at a lab testing service, or volunteering at a research lab. So not only are your goal-directed courses important, other tangential experiences will likely also determine your success. Every experience may be important to an employer and you may not know what single factor got you the job. It is the aggregate and diversity of experience that win the day. Well, OK, maybe even binge watching would be important to some employers! Best of luck in your search.

Dr. Amy Abell is promoted to Associate Professor with Tenure

As of September 1st, the Department of Biological Sciences has a new Associate Professor!  Dr. Amy Abell was promoted to Associate Professor with tenure.  Dr. Abell began her research career as graduate student studying the structure and function of G protein coupled receptors that are essential for reproduction. During her post-doctoral training, she created a mouse model with defects related to perturbations in epithelial to mesenchymal transition (EMT), a biological process controlling the conversion of stationary epithelial stem cells to motile mesenchymal cells. Importantly, EMT is essential for normal development, but it is reactivated in several pathologies including organ fibrosis and cancer metastasis.  Dr. Abell teaches undergraduate courses on the Biology of Stem Cells, and Molecular Biology of the Gene as well as a graduate course entitled Stem Cells: Culture/Application. Dr. Abell's lab uses stem cells that she has isolated from mice with EMT-related defects to define the signaling/gene expression networks regulating EMT. One goal of her research is to identify novel master regulators of EMT and the reverse process MET. This information will be used in designing new strategies for regenerative medicine and the treatment of EMT related pathologies. Projects in the lab use molecular, cellular and embryological tools to identify regulators of EMT.  Read more about Dr. Abell's lab

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Dr. Duane McKenna receives The William Hill Professorship in Biology

At the Fall College of Arts and Sciences Faculty meeting, Dr. Duane McKenna was presented with The William Hill Professorship in Biology for his consistent and extraordinarily high level performance in terms of research and external funding, teaching, and service to his department and the university. This endowed professorship will be indefinitely renewable every five years, based upon his continued excellence in research, teaching, and service. Dr. McKenna’s research interests include the phylogeny and evolution of insects, the genomic basis of plant-feeding in beetles, and interactions between beetles and plants on ecological and evolutionary time scales. Dr. McKenna, who joined the Department of Biological Sciences at the University of Memphis in 2010, received his a BS in Biology and Chemistry from Western Michigan University, an MS in Entomology from the University of Illinois (Urbana-Champaign) and his PhD in Organismal and Evolutionary Biology from Harvard University.  Dr. McKenna teaches a number of course including Evolution, Entomology, and new course this year - Biodiversity.

The William Hill Professorship in Biology is named for the late William D. (“Billy”) Hill and was established using a gift to the college from the Hill-Clayton Trust. Mr. Hill lived in Memphis for most of his life and attended Memphis Public Schools, worked for Buckeye Cellulose Corp, and was a sergeant in the Army Air Force during WWII. Congratulations Dr. McKenna! Read more about Dr. McKenna's work