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Drowning in Data

New web-based framework helps scientists analyze and integrate data

By Emily Kummerfeld | Bond LSC

Large-scale data analysis on computers is not exactly what comes to mind when thinking about biological research.

But these days, the potential benefit of work done in the lab or the field depends on them. That’s because often research doesn’t focus on a single biological process, but must be viewed within the context of other processes.

Known as multi-omics, this particular field of study seeks to draw a clearer picture of dynamic biological interactions from gigantic amounts of data. But, how exactly can scientists suitably weave multiple streams of information together, especially considering technology limits and other biological variables?

Trupti Joshi and her team are seeking to find a solution to that problem.

Joshi, as part of the Interdisciplinary Plant Group faculty, works on translational bioinformatics to develop a web-based framework that can analyze large multi-omics data sets, appropriately entitled “Knowledge Base Commons” or KBCommons for short. She describes KBCommons as “a universal, comprehensive web resource for studying everything from genomics data including gene and protein expression, all the way to metabolites and phenotypes.”

Her work began about eight years ago with soybeans. Dubbed the Soybean Knowledge Base (SoyKB), her team had developed a lot of their own data analysis tools for soybean research, but they realized the same tools could help research of other organisms. From there sprouted the Knowledge Base Commons, intended for looking at plants, animals, crops or disease datasets without the need to “reinvent the wheel” each time.

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Soybean plants used in research that utilizes Soy KB web-based network. | Emily Kummerfeld, Bond LSC

“Our main focus has been in enabling translational genomics research and applications from a biological user’s perspective, and so our development has been providing graphic visualization tools,” Joshi said.

Those tools provide an array of colorful graphics from basic bar graphs to assorted colored pie charts to help the researcher better analyze the data once data has been added to the KBCommons.

Colorful graphs and comparisons lets many researchers look past the lines of text and tables full of numbers that represent genes, plant traits or other experimental results, and making the interpretation of data much more easier and efficient.

One particular tool allows the researcher to look at the differential genes of four different comparisons or samples at the same time. Differential genes are the genes in a cell responding differently between different experimental conditions. For example, a blood cell and a skin cell both have the same DNA, however, some genes are not expressed in the blood cell that are expressed in the skin cell. With this KBCommons tool, a researcher can examine genes to see “what are the common ones, what are the unique ones to that, and at the same time look at the list of the genes and their functions directly on the website, without having to really go and pull these from different websites or be working with Excel sheets,” Joshi explained.

She envisions KBCommons as a tool to enable translational research as well. Users will be able to compare crops, such as legumes and maize for food security studies, or link research between veterinary medicine and human clinical studies for better therapies.

Intended for a wide range of users, Joshi is keenly aware of its potential users right here at MU.

One current user of the Soybean Knowledge Base (SoyKB) system is Gary Stacey, whose lab at Bond Life Sciences Center studies soybean genomics and to date has been the longest user of the SoyKB resource. Like many researchers, Stacey explained the need for a program like SoyKB that can process enormous amounts of data.

“The reason it’s called “Knowledge Base” is the idea that we’re putting information in, and what we hope to get out is knowledge. Because information is different than knowledge,” he said, “we don’t just want to collect stamps, we want to be able to actually make some sense out of it…By having a place to store the data, and then more importantly have a place to analyze it and integrate it, it allows us to ask better questions.”

This is essential, given that one soybean genome is 1.15 GB in size, and one thousand soybean genome sequences could generate 30 to 50 TB of raw sequencing data and tens of millions of genomic variations (SNPs).

But such numbers are modest compared to the program’s true capabilities.

“The KBCommons system is so powerful that it can allow you to run thousands of genomes at the same time using our XSEDE gateway allocations,” Joshi said. “This whole scalability is a unique feature of KBCommons, which a lot of databases do not provide, and we are happy we have been able to bring that to our MU Faculty collaborators on these projects, so that they can really utilize the remote high performance computing (HPC), cloud storage and new evolving techniques in the field.”

KbCommons.jpg

KB Commons is a new web-based network for biological data analysis and integration developed by students. | Emily Kummerfeld, Bond LSC

Mass data capability and colorful graphs aside, her favorite part is who exactly is designing the program.

“What I like most about KBCommons is that it serves as a training and development ground and is developed by students, undergraduate and graduate students from computer science and our MUII informatics program.”

KBCommons is still under development, but publication and access for all users is planned for the end of this year or early 2018. Users will not only be able to view public data sets, but add their own private data sets and establish collaborative groups to share data.

Dr. Trupti Joshi is an Assistant Professor and faculty in the Department of Health Management Informatics, the Director for Translational Bioinformatics with the School of Medicine, and Core Faculty of the MU Informatics Institute and Department of Computer Science and the Interdisciplinary Plant Group.

 

Beverly Agtuca #IAmScience

IAMSCIENCE Beverly.jpg

Beverly Agtuca was born in New York, but has family in the Philippines, a country that struggles with malnutrition and undernourishment. Her overall goal for her research is to help countries that struggle with undernourishment by increasing the agricultural productivity in those countries.

“When I was little, I went on summer vacation to visit my family, which included my grandmother in the Philippines,” she said. “Everyday my grandmother wanted me to go out to the rice fields from 5 a.m. to 10 p.m. with the other children to get rice for our meals. That was not an easy task and that moment changed my life. That’s when I decided that I wanted to be a plant scientist.”

Agtuca graduated in 2014 with honors in Biotechnology and a minor of Microscopy from the State University of New York College of Environmental Science and Forestry (SUNY ESF) in Syracuse, NY. She’s currently a Ph.D. candidate in plant breeding, genetics, and genomics at MU. She chose to come to Bond LSC because of the community and Dr. Stacey, her supervisor and mentor.

“If you ever need help, there’s always help here,” she said. “Everyone at Bond LSC is so kind, including the staff. I love to make small talk with the custodians and they are always supporting me and say I should never give up when I have a bad day.”

Ever since coming to MU in 2014, Agtuca has been keeping busy. In June, she received a travel award to go to the American Society of Plant Biologists (ASPB) in Hawaii. The International Society for Molecular Plant-Microbe Interactions (IS-MPMI) also awarded her a travel award to attend the 2016 meeting in Portland, Oregon, where she gave an oral and poster presentation. She also has two original research publications under her belt and is currently working in Dr. Gary Stacey’s lab at Bond LSC.

The research for her dissertation is focused on the relationship between rhizobia and soybeans. She collaborates with scientists at George Washington University (GWU) in Washington, D.C. and the Pacific Northwest National Laboratory (PNNL) in Richland, Washington to enhance the capabilities of the 21 Tesla Fourier transform ion cyclotron resonance mass spectrometer (21T FTICR) through application of laser ablation – electrospray ionization mass spectrometry (LAESI-MS) technology that can analyze the contents of single plant cells. This 21T FTICR machine was recently installed at PNNL and represents one of only two such machines in the world.

This is revolutionary because few people do single cell analysis. Usually, scientists deal with the law of averages, which dilutes the final measurements. But this technology gives an in-depth glimpse into a single cell so scientists can obtain a more comprehensive bigger picture.

“After we finish building this technology, we want to spread the technique to different research groups so they can answer these research questions on their own,” said Agtuca. “It can help people outside of plant sciences too, and hopefully will help with cancer treatment and disease prevention.”

Samuel McInturf #IAmScience

Samuel McInturf, Ph.D. candidate

Samuel McInturf, Ph.D. candidate

#IAmScience because it’s fun. You’re paid to work with exotic materials and instruments to solve problems that drive at how life manifests.”

Samuel McInturf’s father is an accountant and his mother is an HR director, but somehow he ended up falling in love with science. By the 4th grade he had already asked his parents to buy him a compound microscope. He completed his undergraduate degree in plant biology at University of Nebraska, Lincoln with a minor in biochemistry. Now, he’s finishing up his fifth year pursuing a Ph.D in plant stress biology and works in Dr. David Mendoza-Cózatl’s lab at Bond LSC.

“I mainly came to Bond LSC to work with Dr. Mendoza,” said McInturf. “The work in his lab was right in line with what I wanted to do and I knew the faculty at Bond LSC was great.”

And he’s enjoyed the last five years he’s spent here.

“Bond LSC has vast resources of knowledge and labs are very friendly towards one another,” he said. “So if you are short up on a reagent, or you need to learn to do an assay, someone is always available to lend a hand.”

McInturf’s thesis deals with understanding the genetic factors that balance the uptake and demand for micronutrients – heavy metals – against their toxicity. He specifically looks are regulators of iron and zinc homeostasis.

In addition to his interest in plant biology, he’s also an engineer of sorts. McInturf helps teach a bioengineering class at Bond LSC with undergraduates. The goal of the class is to build robotics that aid laboratory research, and he has taught three of these classes so far.

“I found the change in scale between building widgets in my bedroom to building full scale devices challenging, but ultimately rewarding,” he said.

For undergraduates interested in continuing a career in science, McInturf advises them not to give up, even when things get tough. He admits that he was intent on dropping out of school up until he was 18, but now he’s almost finished with his Ph.D.

“Ten years ago I was very intimidated by what I saw as the difficulty of science and was wavering on whether I wanted to take the dive into a research-heavy field,” he said. “It took a few years to figure that out, so I guess I would have told myself to get a move on and not be so faint hearted about it.”

McInturf isn’t positive where he’s like to be in 10 years, but he’d enjoy continuing to teach and conduct research at a university like MU.

“I’d love to have Dr. Mendoza’s job one day,” he laughed.

The gall of it

How bossy insects make submissive plants create curious growths

By Samantha Kummerer | Bond LSC

They are bumps on leaves, bulges in stems and almost flower-like growths from plant tissue with a striking amount of variety. They are galls.

These unnatural growths garnered the curiosity of Jack Schulz for years. While he’s spent 40 years studying topics from Insect elicitors to habitat specialization by plants in Amazonian forests, what he’s really wanted to study was galls.

“It’s so weird,” said Schultz, director of the Bond Life Sciences Center. “I’ve always been really curious about how these strange structures form on plants.”

Schultz has spent the last two years trying to answer that question, looking at their development and the underlying genetic changes that make galls possible.

He’s not alone in his fascination.

“I found my very first gall when I was a masters student,” said Melanie Body, a postdoctoral researcher in Schultz’s lab. “I was really excited because it was here the whole time, I just didn’t see it. One of my teachers showed me and it was like a revelation, basically, what I wanted to work on.”

These “strange structures” are often mistaken for fruit or flower buds on a variety of plants from oak trees to grapevines and there’s a good reason why…

“A gall on a plant is actually, at least partly, a flower or a fruit in the wrong place,” Schultz said.

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Galls on a leaf. The leaf’s red bumps are not natural, but caused by tiny insects. Inside each gall is many tiny insects. | photo by Melanie Body

These galls can be the size of a baseball or the size of a small bump depending on the plant. They can also range from just small green bumps on the undersides of leaves to vivid complex growths of color.

Despite the variety, the one thing consist across plants is that the gall is not there by the plant’s choice.

“The insect has a pretty good strategy because it starts feeding on the plant and it will create a kind of huge structure, huge organ, where it can live in, so it’s making it’s own house,” Body said.

The reasoning behind the formation is relatively unknown, however, it is hypothesized that the insect flips a switch within the plant. The insect is not injecting anything new, but rather turning off and on certain genes within the plant.

Schultz explained the galling insect has the power to changes the expression of genes and in some instance disorient the plant’s determination of what is up from down.

 

The Problem

So how does this affect the plant?

Not only is the insect creating the gall against the plant’s nature, it is also using the plant’s energy and materials for the job.

“I think it’s very cool to imagine an insect can hijack the plant pathway to use it for its own advantage,” Body said.

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The view of a gall from under a microscope. The mother insect is the orange figure in the foreground and is surrounded by her eggs. | Photo by Melanie Body

The insect receives protection and a unique food source and in turn, the plant is left with fewer resources.

“From the plant’s point of view that’s all materials that could have gone into growth and reproduction, so you can think of these galling insects as competing with the plant they’re on for the goodies the plant needs to grow and reproduce,” Schultz explained. “That’s not so good for producing grapes.”

Grapevines are just one of the many plants that galls can form on, but also the plant Schultz’s research uses.

“In our case we work on grapes, so it can be a big issue if the fruits are not sweet enough anymore, because if you don’t have sugar in the fruit then it’s not good enough for the wine production, so it’s pretty important,” Body explained.

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Researcher Melanie Body searches the grapevines for galls at Les Bourgeois Vineyards. | Photo by Samantha Kummerer, Bond LSC

In Missouri, the story of grapevines and galls goes back to the 1800’s.

The story goes, the phylloxera insect found its way over to France. Soon it spread throughout the country; wiping out vineyard after vineyard.

“The great wine blight and the world was going to lose all wine production because of this pest,” said Schultz.

Luckily, a small discovery in native Missouri grapevines led to a solution that allowed wine drinkers to rejoice and scientists to puzzle.

“There’s something about the genes in Missouri grapevines that protects them against this insect,” Schultz explained.

While the European wine industry faced extinction, the phylloxera insect, coexisted with native Missouri grapevines. So, now every grapevine in a vineyard is grafted with insect-resistant roots from Missouri grapes.

But, no one really understands what’s so special about grapevine roots in Missouri.

 

The research

These galls aren’t new. They’ve actually existed for up to 120 million years. But, here’s what is:

“When we started this research, we thought this is a really well-studied insect,” Schultz said. “It turns out there is an awful lot we don’t know about them.”

The team collects samples of galls from grapevines at Les Bourgeois. Back in the lab the galls are dissected using very small tools and then examined with a microscope. Under the microscope, a colony of the insects emerges. The otherwise miniscule mother insect and her 200 eggs can be seen alongside other insects just moving around the gall.

Researcher Melanie Body examines a grapevine gall under a microscope. Body is a member of Jack Schultz’s lab that studies galls and the insects that create them. | Photo by Samantha Kummerer, Bond LSC

Body compares the insects’ round textured bodies to oranges but with two black eyes.

Schultz’s team hypothesized that there are specific flower or fruit forming genes that are necessary for the insect to create a gall.

To answer this, the team looks at which genes are turned on when the insect creates the formation of a gall. Those observations by themselves don’t prove which genes are essential. So, next, the researchers manipulate the genes by changing the gene’s expression.

“If we find that Gene A is always on when the insect causes a gall to form, we can stop the expression of Gene A to test the hypothesis that it needs gene A to get the gall to form,” Schultz explained. “We can ask a plant. If you lack Gene A, can our insects still form galls?”

The researchers are still analyzing the results, but the current findings suggest that some genes do reduce the insect’s ability to make a gall.

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A microscopic view of a galling insect in the process of creating a gall. The gall is forming around the insect. | Photo by Melanie Body and David Stalla

Since beginning the research two years ago, Schultz said he has discovered, “all kinds of crazy things”.

Schultz said it was previously believed that the insect was staying in one place when making the circular gall, but actually, the little insect is moving around; something no one realized before.

And that’s not the only myth this research is debunking. For example, many believe there is one insect per gall, but this turns out to be incorrect. The gall can actually become a hospital of sorts where many mother insects flock to move in and lay their eggs.

And although galls sounds like an odd area of study, the research actually falls under basic developmental biology.

Schultz said research on galls could lead to discoveries about flowering and fruiting.

“Finding a situation in which flower or fruit structures are forming in odd places is actually suggesting to us, pathways and signals that are probably not as well studied in developmental – normal flowers and fruits,” Schultz said.

Beyond curiosity, one of the reasons to study the galls is to find a way to reduce the number of pesticides used on grapevines. The small size of the galling-insect causes grape growers to spray a lot of chemicals.

There’s a lot of discoveries, a lot of implications, but also still a lot of unknowns. Schultz doesn’t let that discourage him.

“If we knew everything about all kinds of things in nature, I’d be out of business and we’d have nothing to do,” Schultz reassured.

The curiosity behind the research continues to hold true for both Schultz and Body outside the lab. From collecting galls for each other to photographing the mysterious spheres, the two are always on the look out for the hidden work of the tiny insect.

“They’re everywhere,” Body said.

Pigs pave the way for advancements in IVF treatment

New research makes IVF four times more efficient to create pigs like this for genetics research and breeding in labs like that of Randy Prather at MU. | Photo by Nicholas Benner.

New research makes IVF four times more efficient to create pigs like this for genetics research and breeding in labs like that of Randy Prather at MU. | Photo by Nicholas Benner.

Research quadruples speed and efficiency to develop embryos 

By Samantha Kummerer | Bond LSC

What started as a serendipitous discovery is now opening the door for decreasing the costs and risks involved with in vitro fertilization (IVF).

And it all started with cultured pig cells.

Dr. Michael Roberts’ and Dr. Randall Prather’s laboratories in the University of Missouri work with pigs to research stem cells. During an attempt to improve how they grew these cells, researchers stumbled across a method to improve the success of IVF in pigs.

“Sometimes you start an experiment and come up with up with a side project and it turns out to be really good,” Researcher Ye Yuan said.

Their discovery doubles the number of piglets born and speeds up the entire IVF process by 400 percent, which significantly increases both the efficiency of experiments and their potential application to other species. The journal Proceedings of the National Academy of Sciences published their work July 3 in its online early edition.

 

From the beginning:

The Prather lab in the MU Animal Sciences Research Center uses genetically modified pig embryos to improve pig production for agriculture and also to mimic human disease states, such as cystic fibrosis. Roberts’ team in the Bond Life Sciences Center occasionally collaborates with Prather’s lab to produce genetically modified pigs for this valuable research. However, the efficiency of producing these pigs is very low because it depends on multiple steps.

First, scientists remove oocytes (“eggs”) and the “nurse” cells that surround them from immature female pig ovaries and place the eggs in a chemical environment designed to mature the eggs, allowing them to be fertilized in vitro with sperm from a boar. This process creates zygotes, which are single-celled embryos, that are allowed to develop further until they become hollow balls of cells called blastocysts about six-days later. These tiny embryos are then transferred back into a female pig with the hopes of achieving a successful pregnancy and healthy piglets.

However, Roberts said the chance of generating a successful piglet after all those steps is very low; only 1-2 percent of the original eggs make it that far.

The quality of the premature eggs and the process of maturing them significantly reduces the rate of success.

“In other words, all this depends on having oocytes that are competent, that is they can be fertilized, form blastocysts and initiate a successful pregnancy,” Roberts explained.

Normally, researchers overcome the low success rate by starting out with a very large number of eggs, but this takes lots of time and money.

So, lab researchers, Ye Yuan and Lee Spate, began tinkering with the way the eggs were cultured before they were fertilized, making use of special growth factors they used when culturing pig embryonic stem cells.

Yuan and Spate added two factors called fibroblast growth factor 2 (FGF2) and leukemia inhibitory factor (LIF).

This combination helped more than the use of just a single factor and so they decided to add a third factor, insulin-like growth factor 1 (IGF1).

Together the three compounds create the chemical medium termed “FLI”.

“It improved every aspect of the whole process,” Roberts said. “It almost doubled the efficiency of oocyte maturation in terms of going through meiosis. It appeared to improve fertilization and it improved the production of blastocysts.”

In all, the use of FLI medium doubles the number of piglets born and quadruples the efficiency of the entire process from egg to piglet.

While the researchers are still figuring out why the three factors work together so well, Roberts believes it has to do with the fluid that surrounds the immature eggs while they are still in the ovary.

Roberts explained that unusual metabolic changes happen in the eggs and their nurse cells when the three components are used in combination but not when they are used on their own. These components are also found in the follicular fluid surrounding the egg when it is in the ovary.

However, follicular fluid actually contains factors that hinder egg maturation until the time is right, so it would seem counterintuitive to add the fluid to a chemical environment aimed at maturing the eggs. However, when freed from the other components of follicular fluid, the three growth factors act efficiently to promote maturation.

“It just creates this whole nurse environment for that egg. Once you’ve done that you’ve sort of patterned them to do everything else after that properly — fertilization, development of that fertilized egg to form a blastocyst, and the capability of those blastocysts to give rise to a piglet,” Roberts said.

Researchers hope the FLI medium can be translated beyond genetically modified pigs.

“If we could translate this to other species it could be more meaningful,” Yuan explained.

For the cattle industry, FLI has the potential to decrease the time between generations in highly prized animals.

Currently, if an immature dairy cow has desirable traits, the industry has to wait a year or so for that cow to mature and for its eggs to be collected. Using FLI medium immature eggs could be retrieved when the prized female is still a calf. After fertilizing them with semen from a prized bull, production of more cows with desirable traits could be achieved in a shorter amount of time.

The potential implications of this discovery aren’t just for farm animals.

Yuan said if this treatment could be applied to humans it would be a big help for both the patient and the whole field of human IVF.

Currently, in vitro fertilization for humans comes with high costs and risks.

“You try to generate a lot of eggs from the patients by using super-high doses of expensive hormones, which is not necessarily good for the patient and can, in fact, be risky. ” Roberts explained.

These eggs are then collected, fertilized, and the best-looking embryo transferred back to the patient. As in pigs, this overall process isn’t all that efficient. The hope is that the treatment of the patient with hormones can be minimized if immature eggs are collected directly from the ovary by using an endoscope and matured in FLI medium, allowing them to be just as competent as those retrieved after high hormone treatment.

“The idea is it would be safer for the woman, it would be cheaper, and it might even achieve a better success rate,” Roberts said.

The team still has some time before knowing for sure if FLI medium is applicable in other mammals.

Yuan said the focus is now on understanding the mechanism behind how the three compounds work so well together.

For now, preliminary data are being collected with mice and a patent is awaiting approval. Still, the team has high hopes for this almost accidental finding.

“Whenever you’re doing science, you’d like to think you’re doing something that could be useful,” Roberts said. “I mean when we started this out it wasn’t to improve fertility IVF in women, it was to just get better oocytes in pigs. Now it’s possible that FLI medium could become important in bovine embryo work and possibly even help with human IVF.”

 

Michael Roberts is a Bond LSC scientist and a Curators’ Distinguished Professor of Animal Science, Biochemistry and Veterinary Pathobiology in the College of Agriculture, Food and Natural Resources (CAFNR) and the College of Veterinary Medicine. He is also a member of the National Academy of Sciences.

Randall Prather is a Curators’ Distinguished Professor of Animal Science in the College of Agriculture, Food and Natural Resources (CAFNR) and Director of the National Institutes of Health funded National Swine Resource and Research Center.

#MeetScienceTwitter

How an MU student helped start a Twitter trend and how social media is advancing science.

By Mary Jane Rogers | Bond LSC

In the modern age, science isn’t a solitary endeavor.

You might be a tweet away from connecting with scientists about their work, as one MU student recently proved.

Dalton Ludwick, an MU doctoral student in entomology, helped spur a hashtag trend to connect real scientists with none other than Bill Nye.

If you follow any scientists on Twitter, you may have come across the hashtag #BillMeetScienceTwitter while scrolling through your feed. Thousands of scientists on Twitter introduced themselves to the famous TV host of Bill Nye the Science Guy using the hashtag. By May 22, a mere three days after the hashtag started, more than 27,000 scientists and experts had tweeted at Nye.

#BillMeetScienceTwitter was born from a Twitter discussion between Ludwick, London-based zoologist Dani Rabaiotti and New Zealand-based marine biologist Melissa Marquez.

Bill Nye Saves the World

“Bill Nye Saves the World” is a television show currently streaming on Netflix hosted by Bill Nye. The first season explores topics such as climate change, alternative medicine and video games.

The original sentiment behind the hashtag was something scientists have long been discussing — that Nye’s television show doesn’t include a diverse array of science experts to answer questions outside Nye’s specialty. On Season One of his show, a majority of the experts Nye invited were comedians, supermodels and Hollywood stars, like Karlie Kloss and Zach Braff.

We were curious about the origins of this campaign, so we reached out to Ludwick, one of the creators of the hashtag.

MU Bond LSC Tweet Dalton Ludwick Response

Ludwick regularly uses social media to reach out and connect with other scientists. He meets other scientists on Twitter, shares ideas and often turns that conversation into a real-life, professional relationship on a global scale.

Dalton Ludwick

Dalton Ludwick, a Ph.D candidate in Entomology at MU and one of the creators of #BillMeetScienceTwitter. | Photo by Mary Jane Rogers, Bond LSC

“I talk to people from the UK, Australia and New Zealand on social media,” he said. “It’s a great way to connect with people.”

Social media is a game changer for scientists who once felt walled off from the broader world. It can be a great way to connect with people doing similar research, track grants and jobs, share exciting breakthroughs, and follow conferences.

Jared Decker, an assistant professor in the College of Agriculture, Food and Natural Resources at MU, is another avid social media user on campus. He uses Facebook, Twitter and YouTube accounts to connect with other science professionals and academics, as well as his public — mainly beef and cattle producers and farmers.

Jared Decker

Jared Decker, an assistant professor in the College of Agriculture, Food and Natural Resources at MU. | Photo by Mary Jane Rogers, Bond LSC

“Just the other night I was writing a grant and one of the reviewers had a specific criticism,” he said. “So, I got on Twitter and asked my question. A colleague of mine was online in Australia and was able to respond to make sure we were meeting the guidelines.”

Jared Decker

Scientists used to have to walk down the hall to ask a colleague, or play phone tag with someone abroad.

“You can’t do that at 1 a.m.,” said Decker, “but you can go on Twitter.”

Many scientists believed that Nye’s television show wasn’t utilizing his vast array of science connections to find experts in specific fields of science.

“If you ask me about biology or oncology, I probably shouldn’t answer because that’s not my area of expertise,” said Ludwick.

In response to a tweet by Rabaiotti, Mike Stevenson was the first to ask if anyone had reached out to Nye on Twitter. Ludwick replied to that conversation with the hashtag #BillMeetScienceTwitter, which was meant to show Nye the diversity of scientists on social media.

Dani Rabaiotti original tweet

Rabaiotti – a Ph.D candidate at University College London, who studies the effects of climate change on wild dogs in Africa – was the first to introduce herself to Nye.

First #BillMeetScienceTwitter post

Overall, the tweets and engagement have been overwhelmingly positive.

Maryam Zaringhalam Dr. Solomon David Katherine Crocker Laura Skates Amanda L. Glaze Anne A Madden, Ph.D

We decided to tweet at Nye too!

MU Bond LSC

“What we were actually trying to do was reach out and offer assistance in areas outside the expertise of Bill and Neil,” said Ludwick. “We wanted to show the diversity of people doing science, as well as the diversity of the science that we do. More than 50 percent of the people tweeting on #BillMeetScienceTwitter were women — certainly not just a bunch of nerdy men in lab coats!”

Ludwick adds that the hashtag wasn’t intended as an attack on Bill Nye or Neil deGrasse Tyson, another scientist celebrity with broad reach. Instead, the point was to let them know that fellow scientists exist and can be a great source for accurate scientific information.

Nye responded to the hashtag, and even took the time to retweet and reply to his favorite posts.

Bill Nye Response to Hashtag Bill Nye Response 2 Bill Nye Response 1

Overall, the hashtag was a huge success, brought awareness and engaged scientific topics. But more than that, it shows how responsive and positive the scientific community can be. Some news articles noted that the campaign was “trolling in the politest way possible.”

“The scientific community on Twitter is really welcoming,” Decker said. “It doesn’t matter if you’re a first year science student or an endowed professor. People don’t treat you any differently.”

And an online presence is vital for scientists and their careers. In 2007, BioInformatics LLC conducted a survey of 1,510 scientists with regard to how they used social media. They found:

  • 77% of life scientists participated in some type of social media
  • 50% viewed blogs, discussion groups, online communities, and social networking as beneficial to sharing ideas with colleagues
  • 85% saw social media affecting their decision-making

For junior scientists or researchers who are just getting started, Decker has some advice.

“Tweeting out at conferences is a good way to practice taking in an idea and getting it back out there in written form,” Decker said. “Instead of taking notes, tweet out what you would have written down.”

#BillMeetScienceTwitter also helped bridge the gap between scientists and the public. Ludwick said that this hashtag helped flip the public perception that scientists are only old men in lab coats on its head.

“People were saying, ‘Hey, I’m going to show my daughter this and inspire her,’” Ludwick said.

Ludwick also thinks that, in general, social media makes him better at communicating science to the public.

“Twitter is a great way to break things down and stop using scientific jargon,” he said. “I think it has helped me personally and it’s great practice.”

Decker agrees with Ludwick’s assessment.

“The first few months on the job it felt like I was back in Spanish class,” he joked. “I was taking the science jargon and doing mental gymnastics to translate it into the language a lay person would understand. But, now I’m fluent in both!”

So, think twice the next time you consider social media to be a waste of time. Whether it’s a hashtag that brings issues to the attention of science celebrities, platforms that connect scientists at a global level or posts that make research more accessible, social media has done a pretty cool job of advancing science.

The Necessity of Fungi

Graduate Researcher Sarah Unruh explores the essential role of fungi in orchid germination

By Emily Kummerfeld | Bond LSC

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Graduate Researcher Sarah Unruh | photo by Emily Kummerfeld, Bond LSC

The blooms of orchids are unmistakably beautiful, and how they reproduce has fascinated biologists for centuries.

But, orchids might not even exist if not for the help of fungus. Up to 30,000 species of orchids require the intervention of fungi since their seeds do not contain the necessary nutrients to sprout.

Sarah Unruh, a fifth-year biological sciences PhD student in the lab of Bond LSC’s Chris Pires, seeks to discover and record the specific types of fungi utilized by many orchid species. By studying their specific genetic expressions, she hopes to uncover what allows these fungi to interact with orchids in this way, how these fungi are related to each other and what genes each organism is expressing with and without each other.

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A blooming orchid in the Tucker greenhouse. Although this orchid grows in a pot, like most species of orchid it is an epiphyte and naturally grows on tree branches. | photo by Emily Kummerfeld, Bond LSC

“The main question for me is, what is the nature of this relationship? Is it more mutualistic or parasitic? You don’t often get something for nothing, so why is the fungus participating in this relationship? Most fungi that live in plant roots receive carbon from the plant. Orchid fungi are doing the opposite and that is weird. I want to know how this relationship works,” Unruh says.

Unruh first studied orchid evolution and how each orchid species related to each other genetically. “My assumptions of what a plant was were so violated by orchids and it still fascinates me! So many orchid species grow on trees, many don’t have leaves, some species never even turn green or photosynthesize.”

This focus soon evolved into her interest in the relationship between orchid plants and fungi. Fungi are neither plants nor animals, and have their own branch on the eukaryotic family tree. They are nonetheless essential to plant biology, “eighty percent of plant species have beneficial fungi in their roots,” says Unruh.

Many orchids are technically classified as epiphytes, which means they grow on the surface of another plant and get all their food and water needs from the air, rain and what accumulates nearby. That doesn’t leave a lot of extra nutrients to put into seeds, which typically need the store of food to sprout and grow its first leaves.

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A small mass of fungus is placed in the Petri dish to assist in germination of the recently sprouted orchid seeds seen here. | photo by Emily Kummerfeld, Bond LSC

That’s where fungi come into play. Some types of fungi can even germinate several species of orchids, and studying the DNA sequences of these fungi could be vital in the future for endemic endangered orchids and their associated fungi. “I’ve always been interested in relationships between organisms or symbioses,” says Unruh, “the fact that orchid seeds need fungi to survive was too weird not to research.”

But the process of studying fungi DNA is not a simple one.

Tulasnella calospora, nicknamed the “Super Fungus”. This type of fungus can germinate several species of orchids. | photo by Roger Meissen, Bond LSC

“In order to look at their genomes, I need to grow a lot of fungi and then grind it up and add certain substances to isolate only the DNA. I send this DNA to a facility called the Joint Genome Institute where they send it through a machine that spits out a file with a list of lots of small pieces of the genome – like puzzle pieces. I then use computer programs to put the pieces together and try to assign a function to each gene.”

So, the established relationship between fungus and seed helps the orchid, but it’s not known what the fungus is getting out of this arrangement. One idea, based on recent published research, is the fungi receives a certain form of nitrogen from the orchid seeds. Another experiment Unruh is working on is growing the orchid seeds by themselves through special media, growing the fungus by itself, or growing them together. She then measures the gene expression to see if there are big differences when the plant or fungus is alone or together. “This will help answer my question of how mutually beneficial this association is,” says Unruh.

The data collected from this research will form the bulk of her PhD thesis. However, there remains many questions regarding the relationship between orchids and fungus that Unruh would like to explore in the future, such as which fungi are best for reintroducing endangered orchid species or what other roles fungi play in their environment. “I foresee fungi, especially plant and fungal relationships, becoming the focus of more and more research in the future.”

In 2014, Unruh received a three-year National Science Foundation (NSF) Graduate Research Fellowship. More recently, she has received a grant from the Joint Genome Institute to sequence 15 full genomes of orchid fungi.

A step into summer research

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Jacqueline Ihnat, one of the 12 Cherng Summer Scholars, outside Dr. Cornelison’s lab at the Bond Life Sciences Center. | Photo by Mary Jane Rogers, Bond LSC

Sometimes the most learning occurs outside of the classroom.

For Jacqueline Ihnat, an opportunity to pursue research at the Bond Life Sciences Center this summer will give her that chance. She recently became one of 12 Cherng Summer Scholars, a full-time, ten-week program within the Honors College at MU.

“Doing research helps keep me focused on the bigger picture,” Ihnat said. “Sometimes in class we learn things that don’t seem entirely relevant or useful, but being part of a research lab allows me to apply some of the knowledge that I gain in the classroom.  It’s a daily reminder of why I’m learning what I am.”

Jacqueline Ihnat’s passion for science started in high school. Her high school biology teacher ignited that love by teaching her how to struggle through difficult problems and concepts. Now, Ihnat is an MU pre-med student with a major in business management and a minor in Spanish.

Since Ihnat is fascinated with cells and how our bodies function, she’ll be studying the role of specialized stem cells in muscle regeneration and how they interact with muscle fibers — specifically the role of Eph-A3, a type of cell-surface receptor. This project will take place in the lab of Dawn Cornelison, a Bond LSC biologist who will be mentoring Ihnat this summer.

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Jacqueline Ihnat as she pipettes samples in Dr. Cornelison’s lab in Bond LSC. | photo by Mary Jane Rogers, Bond LSC

Each muscle in the body is unique in its length, fiber organization and fiber type patterning, so Ihnat hopes to explore why two types of muscle — fast and slow twitch muscle — develop and regenerate to maintain each specific muscle fiber-type composition.

When a muscle is damaged from exercise or injury, a muscle’s stem cells, or “satellite cells,” will multiply, move towards the injury and form new muscle, replacing the damaged fiber. There is no research that determines if “fast” satellite cells create fast fibers and if “slow” satellite cells create slow fibers, and Ihnat hopes to tackle that question this summer. This kind of research gives scientists a deeper understanding of degenerative muscle diseases such as ALS, which could lead to more effective treatments and therapies.

The Cherng Summer Scholars program is supported by a gift from Andrew and Peggy Cherng and the Panda Charitable Foundation. The Cherng’s are the founders of Panda Express, a well-known restaurant chain. These scholarships support individually designed theoretical research, applied research or artistry projects under the mentorship of an MU faculty member.

For young scientists who are just starting to conduct research and struggling to feel successful, Ihnat has a few words of motivation.

“My high school biology teacher always said that research is 30 years of frustration and disappointment followed by 30 seconds of elation when you finally make a breakthrough,” she said. “Patience is key.”

From neuroscience to negotiations

Neuroscientist and former Secretary of State science adviser to speak at Life Sciences Week
By Eleanor C. Hasenbeck | Bond Life Sciences

Frances Colon

Frances Colón has spent the past decade representing the United States all over the world on topics ranging from climate change to the advancement of women scientists. She will reflect on that experience in her talk at 3:30 p.m. Monday, April 11 in Monsanto Auditorium. | Photo courtesy of Frances Colón

A career in science doesn’t only mean working in a lab, and no one knows that better than Frances Colón.

Colón, a neuroscientist by training and policy maker by trade, will speak about how scientists can become more involved in policy without abandoning the laboratory bench.

During her Missouri Life Sciences Week lecture “My path to science citizenship,” Colón will talk about her transition from the lab to policy. She’ll speak 3:30 p.m. Monday, April 10, in Monsanto Auditorium.

“I think scientists need to realize that they have a broader set of skills than they give themselves credit for that can be applied to the service of the community and their country in many different ways,” said Colón. “I think we’re living in a time where our country needs scientists to get engaged at every level. That doesn’t mean they need to leave a career in academia to go into policy, but it could certainly mean involvement everywhere from the community level to the national level.”

After receiving a doctoral degree in neuroscience and studying how nerve cells mature at Brandeis University, Colón first got involved in making policy as an American Association for the Advancement of Sciences policy fellow. She then served as science and environment adviser for western hemisphere affairs for more than three years before she became deputy science and technology adviser to the Secretary of State, a position she served in until January.

As deputy science adviser, she led efforts to reengage Cuba in scientific collaboration after U.S. policy regarding Cuba shifted. She also coordinated climate change policy for the Energy and Climate Partnership of the Americas, and she worked to advance women and girls in science, technology, engineering and math. Today, she looks to use platforms outside of the government to accomplish the same missions.

Colón said of her career thus far, she is most proud of the work she’s done to educate women in opportunities in STEM careers.

“A lot of these countries started to realize that they can’t tackle a lot of the biggest challenges they’re confronting, from climate change to energy security, without having all of their best talent at the table. That required providing equal opportunity for women and men to achieve these positions,” Colón said. “We worked a lot on finding opportunities for girls to discover STEM careers and to help countries plan out what their STEM capacity building activities could be.”

These activities included things like the two-week camps for girls in South America and Africa, where they learned about coding and genetics with help from corporate partners.

Colón holds a doctorate from Brandeis University, and a bachelor’s degree in biology from the University of Puerto Rico. She was a delegate to the National Committee on U.S.-China Relations’ Young Leaders Forum, and a graduate of the National Hispana Leadership Institute. Last year, she was named one of the 20 most influential Latinos in technology by CNET en Español.

Colón will speak at 3:30 Monday, April 10 in Monsanto Auditorium as part of Missouri Life Sciences Week.

Hanson to explain why broken metabolites matter at Life Sciences Week

By Jinghong Chen | Bond Life Sciences Center

Andrew Hanson, right, will speak Friday, April 14 in Bond LSC's Monsanto Auditorium as the 2017 Dr. Charles W Gehrke speaker. | Photo by University of Florida, Institute of Food and Agricultural Sciences

Andrew Hanson, right, will speak Friday, April 14 in Bond LSC’s Monsanto Auditorium as the 2017 Dr. Charles W Gehrke speaker. | Photo by University of Florida, Institute of Food and Agricultural Sciences

People often think of metabolism as a perfect network. But that assumption is simply not accurate.

Andrew Hanson, an eminent scholar and professor at the University of Florida, describes the misunderstanding as “the power of a paradigm.” American biochemist Albert Lehninger spread the misunderstanding in his classic textbook “Biochemistry”, in which the message he communicated to generations of students was: metabolism is a beautiful machine that functions flawlessly.

Hanson challenges this “metabolism is perfect” paradigm using illustrations from different kinds of organisms in his lecture. He will speak in Bond LSC’s Monsanto Auditorium at 1 p.m. Friday April 14, during the 33rd annual Missouri Life Sciences Week.

For every living organism, metabolism is the sum of every chemical reaction that occurs to maintain life. This sum contains all the metabolites — small molecules created at each level of cell processes and final products — that share a part in the growth, development, reproduction and running of cells and whole organisms.

However, enzymes can make mistakes; many chemical compounds in cells are unstable and undergo spontaneous reactions. The consequences of enzyme errors and chemical side-reactions are, at best, unwanted and sometimes toxic, so organisms have developed mechanisms – damage-control systems – to deal with the consequences of damage.

Hanson’s lab has studied metabolite damage and the damage-control systems that plants and microorganisms employ to cope. But the impact of metabolic problems also reaches into the human domain, causing disease from failure or mutation of damage repair enzymes. “It matters in aging humans and animals a great deal, because aging is the result of cumulative damage,” Hanson said.

Plants are also afflicted by metabolite damage. Under environmental stress such as high temperature or water loss, the error rate of enzymes and rates of unwanted chemical reactions can go up.

The understanding of metabolite damage could also advance metabolic engineering, which is a purposeful manipulation by combining metabolic pathways and DNA techniques to produce desired products. After creating new pathways in an organism, it may fail to cope with the abnormal reactions produced by the new pathways. To fix the problem, the only solution might be to install the required damage control enzymes.

Hanson’s lab hopes to identify new or unsuspected damage reactions, and enzymes that repair or prevent damage. They also are working to connect with metabolic engineering groups that install modified pathways in plants and microbes to study sources of damage and propose solutions.

Metabolism is not perfect. However, after studying its imperfection for years, Hanson concluded, “life is put together in a very beautiful and even more powerful way than we first realize. It makes a lot of mistakes, but it also fixes them so well that we do not even notice them.”

Hanson’s lecture on “Fixing or safely trashing broken metabolites and why it matters” is this year’s Charles W. Gehrke distinguished lecture. Gehrke, a longtime MU professor of Biochemistry, was selected by NASA to analyze rocks retrieved from the first moon landing for any traces of extraterrestrial life. He died in 2009.

Hanson’s lecture is free and open to the public as part of Missouri Life Sciences Week. It occurs at 1:00 on Friday, April 14 in Bond LSC’s Monsanto Auditorium. See more about events during the week at bondlsc.missouri.edu/life-sciences-week.