You’ve heard of aquariums and terrariums, but probably not of a vivarium before. These enclosed structures take on a whole new meaning when science is brought into the picture.
And little do people know when they walk across the main floor of Bond LSC, they are walking above a city-like work space where the occupants work to improve our lives.
Vivariums functions as cubicles, condominiums and daycare centers for the rodents that live within them. The 10,000 square-foot lab at Bond LSC uses these transgenic rodents to study muscular dystrophy, diabetes, fertility, and oncology research, among other health research areas.
“These rodents are the living, working team that help us learn more about our health.” said Dana Weir, the facility manager from the Office of Animal Resources. “We want to make sure they are well taken care of so Raye Allen’s team works year-round to make sure they are monitored, well-fed, and comfortable in the vivariums.”
Raye Allen, the lab supervisor for Bond LSC’s vivarium, said cleanliness and care are the top priorities in addition to research. Cleaning, transporting, feeding the rodents all require a carefully detailed process.
The 1,700 clear polycarbonate containers are arranged in rows with single, coupled or a small family of rodents within them. Each shoebox-sized rodent condo, is provided with dry cushioned bedding, large quantities of food and water, as well as their own little hiding space. Clean, filtered air is also pumped through the back of their homes.
“These rodents live a cleaner life than you or I could ever imagine.” Weir said.
Each person who enters the lab must wear closed toe-shoes, two sets of nitrile gloves, a white floor-length, long-sleeved button up lab coat, a face mask and hairnet.
“Raye Allen’s team is mindful of everything they touch when handling the rodents or their homes in the lab. We spray everything with bleach to prevent any outside bacteria from contaminating the lab and only handle our rodents under the biosafety hoods present in each room.”
Several university, state and federal regulations ensure the safety and security of Bond LSC’s transgenic rodents. The National Research Council, USDA’s Animal Welfare Act, and University of Missouri’s Institutional Animal Care and Use Committee work together to monitor animal welfare and set standards for lab research on animals.
The Institutional Animal Care and Use Committee (IACUC) inspects Bond LSC’s vivarium every six months, in order to make sure that containment, handling and safety protocols followed by lab researchers are up-to-date. The IACUC also reviews the purpose of animals being used for each particular research project. A board of faculty members, veterinarians and two non-science community members review justification from lab researchers.
The safety and security of these rodents are the top priority of the researchers working in the labs, but there is also an emotional bond that is formed between them as well.
“Rodents are intelligent and emotional animals, so they learn who their caretakers are very quickly.” said Allen. “They recognize us by the smells we put off and get pretty excited when one of our researchers enters the room to interact with them.”
The researchers like Allen who work with these rodents on a daily basis, care deeply about the rodents as well as the work these furry critters do.
“The bond formed between the animals and their caretakers is equally as important as the research they help us do,” said Weir. “This goes for all of the animal research conducted in Bond as well as other research that is conducted across the Mizzou campus.”
This past weekend not only ushered in Mizzou’s first home game of the season, but the return of Saturday Morning Science. The weekly lecture series connects the Columbia community with MU scientists and their research, from bio-engineering to volcanology to anthropology and linguistics.
Elizabeth G. Loboa, dean of the College of Engineering, kicked off the semester with her talk on tissue engineering in the age of drug-resistant bacteria.
Tissue engineering is about turning cells into tissues and organs, for example, fat-derived stem cells into muscle, bone and cartilage. The tissues take shape on tiny scaffolds that are bio-compatible and biodegradable.
The Loboa lab does this, but they’ve added an extra layer to their research: Loboa’s scaffolds also act as pipelines that deliver wound-healing and anti-bacterial compounds to cells as they grow into tissue. The idea is to reduce infection, inflammation and scarring as the wound heals.
“We’re trying to kill these bacteria while helping these stem cells become the cells we want to create,” Loboa said, about her research at the University of North Carolina-Chapel Hill and North Carolina State University.
Using a process called electrospinning, Loboa’s group makes scaffolds shaped like porous fibers, sheaths, or hollow sheaths. Depending on their structure, these scaffolds act like faucet taps that control the rate and timing at which anti-bacterial compounds are released.
“I look at our fibers as delivery platforms,” Loboa said.
Saturday Morning Science takes place 10:30 a.m. Saturday at the Bond LSC’s Monsanto Auditorium. Coffee and bagels are available preceding the talks. This semester’s schedule is as follows:
9/17: Carolyn Orbann, Assistant Teaching Professor, Department of Health Sciences, “Historical Epidemics, Novel Techniques: Using Historical and Ethnographic Materials to Build Computer Simulation Models”
9/24: Michael Marlo: Associate Professor of English, “Documenting linguistic diversity: a view from the East African Great Lakes”
10/1: Steve Keller, Associate Professor of Chemistry, “The 20 Greatest Hits in Science…In an Hour”
10/8: Manuel Leal, Associate Professor of Biological Sciences, “Are Lizards Smarter Than Those Who Study them?”
10/15: Stephan Kanne: Executive Director and Associate Professor, Thompson Center for Autism & Neurodevelopmental Disorders, “What Do We Look For When We Diagnose Autism?”
10/29: Libby Cowgill, Assistant Professor Anthropology, “Fitness for the Ages: How to Lift Like a Neanderthal?”
11/5: Arianna Soldati, Ph.D. Candidate, Department of Geological Sciences, “Living in a Viscous World: A Volcanologist’s Perspective”
11/12: Frank Schmidt and Gavin Conant, Professor of Biochemistry (Schmidt); Associate Professor of Bioinformatics, Department of Animal Science (Conant), “Networks in Biology and Beyond”
12/3: Elizabeth King, Assistant Professor, Division of Biological Sciences, “What’s the Best Way to Divide up the Pie: The Price of Long Life”
NASA, NIH-funded work seeks to understand bio-chemical mechanisms of life on Earth, and among the stars
By Phillip Sitter | Bond LSC
Any child obsessed with Legos knows the fun of creation bound only by imagination and the size or variety of the blocks within their pile.
For some scientists, that spirit extends into adulthood, but instead of plastic parts they think about arranging blocks of nucleic acids.
Scientists may not be able to create dinosaurs, dragons or mythical sea creatures the way kids with Legos can. Through the manipulation of nucleic acid building blocks though, they may be better able to understand how the processes of life on Earth work, as well as out among the stars.
“I have a lot of fun asking what is possible,” said Donald Burke, a Bond Life Sciences Center investigator who spends his time researching the building blocks of life.
Burke said he has been interested in the origins of life for 40 years, and he has been associated with NASA for about 20 years.
NASA’s interest in understanding the origins of life is pretty straightforward. It wants to know what clues to look for on other worlds to figure out if those planets also support life.
Many of Burke’s previous discoveries at Bond LSC are funded by NASA’s exobiology and evolutionary biology program.
“No, I have not thought of an excuse to fly anything up there. I’ve tried to think ‘which of my experiments would make sense to do in a micro-gravity or zero gravity environment?’” he explained of the prospect of sending some of his work into orbit, with a wry smile.
But, there’s even more to understanding the building blocks of life than looking for bio-chemical signatures out among the stars. Knowing how these parts are put together allows scientists like Burke to understand the origins and processes of Earth’s biology, and, conceivably create chemical and biological processes or even organisms not found in nature in the near future.
A quadrillion arrangements of blocks, one arrangement at a time
“Many of the molecules of life are built from strings of amino acids, or nucleotides or other building blocks,” Burke explained. He also noted that these buildings blocks are not just strings, but fold up into three dimensional shapes.
RNA, or ribonucleic acid, stands out as an essential building blocks in the bio-chemical processes of life.
Put simply, RNA is a kind of molecular structure of nucleic acids similar to DNA (deoxyribonucleic acid) that comes in many combinations. These combinations are at the core of every cell, and play a role in coding, decoding, regulating and expressing the basic operating instructions for each cell — its genes.
The molecules we’re talking about are almost unimaginably small. In one test tube, Burke said there can be one quadrillion of them — that’s a one with 15 zeroes after it. Put another way, that’s roughly equivalent to the estimated number of ants that live on Earth.
Burke’s work focuses on the end goal of being able to artificially create original RNA combinations. In what’s known as experimental evolution, “the population of molecules in the tube is evolving as a result of us imposing experimental constraints upon it.”
This artificial synthesis of RNA molecules looks to create random sequences or variations on natural RNA to create new ones non-existent in nature. A second route aims to selectively choose molecules with certain properties, and use them to build altogether new combinations.
“Their string-like properties allow us to copy them, and make more copies, and make more copies, and make more copies. Their shape-like properties allow us to observe the bio-chemical behaviors they may have,” Burke explained how he and other scientists interact with RNA’s structure in the lab.
“I don’t think we know what those limitations are yet,” he said of the capabilities of RNA.
The motivation for wanting to be able to intentionally design RNA molecules is so that it “can do the things we want it to do under the conditions where we want it to do those things,” he explained of the process of the process of selecting RNA sequences for specific properties.
“I want the ones that will bind a tumor cell. I want the ones that will bind a viral protein. I want the ones that will catalyze useful chemical reactions.”
RNA’s path to the future following in biology’s footsteps
The National Institutes of Health and other organizations recognize that engineered forms of RNA have the potential to fight diseases, and they have funded Burke’s work.
He has studied RNA that instructs human cells on how to defend themselves from HIV and is now looking at other RNA that interferes with the proteins of the Ebola virus.
The expectation is that such therapeutics would work in conjunction with other treatments. In the future, they could be expanded to help fight other viruses, cancers and other diseases.
RNA could also be used to start, or catalyze, chemical reactions. As Burke explained, catalysts remove barriers to chemical reactions — “they don’t make things happen that wouldn’t otherwise happen, but they speed up the process.”
Synthetic RNA could be used to accelerate removal of toxins from soil or to get the bacteria in our guts to recognize cancerous tumor cells and kick-start an immune response.
But, the future of RNA research may soon reveal a few different Holy Grail moments on its horizon.
One such Holy Grail that Burke said will definitely happen will be observations consistent with the presence of life on other worlds, based on evidence like an atmosphere having certain chemical compositions.
Another likelihood could involve construction of a self-replicating, fully-artificial organism, either created from scratch or reverse-engineered from other organisms.
For those of you already anticipating the plot of a low-budget sci-fi thriller, Burke offered to assuage your fears.
“The notion of it escaping out in the world and taking over Los Angeles is [only] good 1950’s B-movie” material, because the conditions under which this artificial organism would survive would probably be difficult to maintain even in the controlled environment of lab, he said.
Instead of B-movie science, Burke explained that “really, I’m thinking about what kinds of chemistries we want to see take place, and then building the enzymes that would make it possible.”
“Biology has had a few billion years to work on this, but we’re just starting to figure it out.”
Donald Burke-Agüero is a professor of molecular microbiology and immunology and joint professor of biochemistry and biological engineering.
Bond LSC scientist internationally recognized for work on salivary glands and autoimmune disorders
By Phillip Sitter | Bond LSC
You might not think too highly of spit, but you would quickly regret not having any.
People with Sjögren’s syndrome suffer chronic dry mouth and eyes from an overzealous immune system that attacks salivary and tear ducts, causing serious health issues.
Gary Weisman’s research might hold the key to understanding and managing this immune response, leading to effective treatment or even prevention of this ailment.
For this, the International Association of Dental Research, or IADR, awarded him the 2016 Distinguished Scientist Award for Salivary Research. Weisman accepted the award in June at the opening ceremonies of the IADR conference in Seoul, Republic of Korea.
“We want the good, but not the bad,” said Weisman, a Bond Life Sciences Center investigator, of what we ideally want from our immune system’s functions.
Mice with un-checked autoimmune disease of their salivary glands have their glands destroyed. The disease can spread to other secretory organs next. An over-reactive immune system on a civil war-path can extend its damage to cause pancreatic failure and death.
The destruction wrought by Sjögren’s syndrome is self-inflicted, caused by an overreaction of our bodies’ defenses against infection and injury. This is what an autoimmune disease is.
But, our bodies’ immune cellular response team is complicated. Weisman said dozens of different cell types have been isolated and identified as part of the immune system, and he likens the immune system to fire, police and construction services in human society all working together.
While firefighters are meant to prevent further damage from an inferno, sometimes our bodies’ first responders start doing the equivalent of using dynamite to stop the spread of a fire.
In chronic inflammation, that autoimmune response can mean a burning, throbbing, constant pain. The key to a healthy immune response is balance. The balance has to be between containment and repair of damage caused by infection or injury and damage caused by chronic inflammation if that emergency response continues unabated.
Weisman has spent almost 30 years studying how to prevent our bodies’ immune system from over-reacting to threats and causing further harm.
Earlier in his career, Weisman studied how extracellular ATP plays a critical role in immune responses, and how too much of it can cause the over-reaction that leads to tissue destruction in autoimmune diseases. ATP, or adenosine 5’-triphosphate, is the main molecule used for energy in cellular activities inside cells. Weisman was one of the first scientists to study how damaged cells release ATP as a distress signal.
The released ATP signals receptors that “send out the alarm to the fire station” — the body’s immune cells, he said.
Once he understood this, Weisman began to manipulate the actions of released ATP to see how that would affect an immune response.
Mice with salivary gland autoimmune disease got healthy when the released ATP was prevented from activating their receptors on the surface of cells. Preventing the ATP receptors from being activated slowed down and even stopped the advance of autimmune disease.
Conversely, if you prevent the activation of the ATP receptors in lab mice with Alzheimer’s disease they die much more rapidly from the disease, Weisman said, suggesting that activation of immune cells by ATP is beneficial in slowing the progression of this disease.
Alzheimer’s disease and autoimmune diseases such as Sjögren’s syndrome are only some of the inflammatory diseases that Weisman has studied. With each of these diseases, the role of ATP receptors has to be investigated individually, suggesting that Weisman’s work may extend beyond salivary glands and the brain to other parts of the body.
“Our [ATP] receptor is also involved in heart disease,” Weisman said, and he added that other diseases like cystic fibrosis, cancer, lupus and arthritis have inflammatory components, too.
For now, we all fight a losing battle when it comes to our bodies’ management of the immune system. As we and our immune system age, it has the potential to destroy more than it protects and “eventually you could slip over to the dark side and die,” Weisman said.
In the meantime, Weisman said that a better understanding of the immune system could lead to more effective, targeted treatments of chronic inflammation and other autoimmune disorders. This could provide a new approach to control undesirable activation of the immune system beyond the use of with anti-histamines, anti-cytokines and ibuprofen.
Weisman is a Curator’s Distinguished Professor of Biochemistry. He began his salivary gland research at MU 27 years ago with Professor John Turner, before Turner’s retirement. Since then, his research has been continuously funded by the National Institutes of Health, where one of his recent grants was well scored and will likely be extended for another five years.
Sweaty scientists put on their full-body, spacesuit-like get-ups to stave off a potentially extinction-level outbreak and at least one scientist invariably gets infected with the deadly agent of disease.
While popular culture propagates this sense of peril, in reality bio-containment labs are designed with safety in mind.
“People tend to think bio-containment facilities are dangerous, mostly from movies I think, but the history is actually spectacular,” said George Stewart, a medical bacteriologist, a Bond Life Sciences Center scientist, McKee Professor of Microbial Pathogenesis and Chair of Veterinary Pathobiology.
For Stewart — whose lab works on the basic science behind anthrax — no one is “under the gun because of big outbreaks, not with the pressure you see in movies.”
But one type of pressure is an important part of bio-containment lab safety. Air pressure differences maintain certain labs at lower pressure compared to the rooms and hallways around them, ensuring that air will only flow in toward a lab and not out, keeping any airborne pathogens trapped inside.
“They know if everything is done properly, it’s perfectly safe for them and even safer for everyone else [outside a lab],” Stewart said of the safety features, procedures and systems of bio-containment lab safety in place at facilities like those at the Bond LSC and elsewhere at MU.
Stewart said he is vaccinated against anthrax. “Whether I have protective immunity or not, I don’t know.”
“Almost like you were working underwater”
The powerful capabilities of anthrax and other lethal pathogens call for particular safety precautions for scientists.
Stewart looks like he’s straight out of the movie Contagion when donning the full-body suit for his more dangerous research in a Bio-Safety Level (BSL) 3 facility at MU’s Laboratory for Infectious Disease Research (LIDR). In the trees on the eastern fringes of campus, the specialized building is where he and other researchers study diseases animals can transmit to humans, including plague, Brucella, tularemia and Q fever, and mosquito-borne diseases like dengue, chikungunya and now Zika virus. The safety protocols and systems at a BSL-3 lab like the LIDR facility Stewart described reflect the likely transmission by aerosols of the human pathogens inside.
After passing through security access to the building and the labs inside, Stewart enters an ante room off of a hallway. The air pressure in this room and the lab beyond it is such that air will only flow in toward the lab, and not out and away.
Anything that goes into the lab only leaves if it is autoclaved, disinfected in a steel machine using pressurized steam that “essentially kills everything, even heat-resistant spores,” so that means Stewart changes clothes, removes his watch, phone and any other personal items.
Next come layered scrubs and a water-proof Tyvek suit with booties and a hood that cover everything but his hands and face. Two layers of gloves take care of his hands, but shielding his face is a bit more technical.
A plastic face cover with a Tyvek hood shrouds over Stewart’s shoulders. Inside, a pump fills the hood with positively-pressured filtered air – this has the inverse effect of the negative pressure of the rooms and keeps air flowing out away from his face and not toward it.
Everything inside the lab and the building is about redundancies like that. A final safety measure is that all work on pathogens take place in bio-safety hoods – HEPA-filtered cabinets.
Stewart said it can be difficult to hear with the air filter systems blowing, so every move by researchers is calculated and announced. Colleagues take their time in handing off equipment to one another, so as to avoid torn gloves.
It’s “almost like you were working underwater as two divers,” Stewart said about working in the BSL-3 lab with a colleague.
“Everything is orchestrated in a very intentional way.”
Only dangerous when dry
Anthrax isn’t always lethal, so the scene is quite different inside a BSL-2 lab at Bond LSC where Stewart studies non-virulent strains.
BSL-2 labs study infectious agents that can cause disease in humans, but are usually treatable. Researchers only need lab coats, gloves and eye protection in these labs and all waste must be autoclaved. Here anthrax and other colonies of organisms are stacked in covered Petri dishes and handled without any Tyvek or air pumps.
The Anthrax bacterium researched here is missing a specific plasmid, a DNA molecule essential for virulence that protects the anthrax bacteria from white blood cells that attack them.
On top of that, all samples in this lab are wet, and anthrax spores are only dangerous as aerosols when dry. Before 2001, Stewart said virulent strains of anthrax were only labeled BSL-2 agents for this reason.
The anthrax letter attacks that year not only changed some of the organism’s lab classifications, but also interest in it. Prior to 2001, Stewart said there was not a lot of funding available for anthrax-focused researchers, a small and tight-knit community. Even though the attacks did spur an increased investment of government money into the field at the time for defense against anthrax as a bio-weapon agent, almost 15 years later Stewart said that funding is more or less back at pre-2001 levels, “perhaps marginally better.”
There are now only a handful of anthrax-dedicated labs in the U.S., Stewart said, trying to name them off as he counted his fingers. The Bond LSC has not had any lab higher than a BSL-2 plus for years now, not since the BSL-3 research moved to LIDR, Stewart said.
Several local residents called when LIDR was under construction and asked questions and voiced concerns about the facility and the work to be done there, Stewart recalled. However, Stewart said he and his colleagues gave the callers honest answers, and he has not heard of any pushback since.
Stewart sees bio-containment labs as positive technological achievements in the study of disease – without them, many advances in treatment would never have been possible. In terms of the work done at facilities at MU and in the Bond LSC, Stewart said “we have the facilities, we have the equipment, we have the training,” to ensure the safety of researchers inside the labs, and even more so everyone else on the outside.
Anthrax is not contagious and responds well to antibiotics, despite concerns in the scientific community Stewart shared that there is a possibility antibiotic resistance could be intentionally engineered into anthrax.
Stewart could only think of a couple of cases when lab workers got infected with the organism through mishaps, and those were at USAMRIID – the United States Army Medical Research Institute for Infectious Disease at Fort Detrick, Maryland – when anthrax was produced there in very large quantities for research of it as a bio-weapon during the Cold War.
When you spend a lot of your time working with potentially lethal pathogens though, what do you tell your doctor when you come in with flu-like symptoms? Stewart said that not only does he and any of his colleagues disclose to their doctor the organisms that they work with, but doctors at MU already know exactly what organisms are being researched inside the LIDR labs. As a precautionary measure for their own well-being in case accidental infection did occur in a lab after all, Stewart or another colleague working with anthrax who turned up sick would receive antibiotics just to be safe – “there are standard operating procedures for everything.”
He does not want to make light of the dangerous organisms he works with, but inside the BSL-3 facility at LIDR, Stewart said that breathing in HEPA-filtered air all day there does do wonders for his hay fever.
Stewart couldn’t help but share a chuckle with that one. Laughter might be the most un-containable thing in nature.
Naomi Oreskes is a professor of the history of science at Harvard University and a geologist by training.
At a time when global warming was framed by the media as a debate, her 2004 paper in the journal Science showed that climate change was a settled fact among climate scientists. Of the 928 papers she sampled in her literature search, not a single author denied the reality of climate change. Digging further, Oreskes explored in her book, Merchants of Doubt, co-authored with Eric Conway, the people, organizations, and motivations behind climate science misinformation. From cigarettes and acid rain to global warming and the ozone hole, Oreskes and Conway uncovered how industries such as Big Tobacco and Big Oil employed a core group of ideologically-motivated scientists to fabricate doubt and stymie government regulations.
Naomi Oreskes speaks on Saturday,3:30 pm as part of the LSSP Symposium, “Combatting Climate Change,” held at the Bond Life Sciences Center.
What has been the response of people who, through reading Merchants of Doubt or watching the documentary, have changed their minds about climate change?
Many people have written to me and Erik Conway to thank us for writing the book. I’d say the most common response was that the book helped them to understand why there was so much opposition to accepting the scientific evidence. I can’t say that I know for sure that thousands of people changed their minds after reading the book, but I do know that among those who did, the link to the tobacco industry was most compelling. Our research showed that the opposition was not rooted in problems with or deficiencies in the science.
You said in an interview with Mongabay, “In our society, knowledge resides in one place, and for the most part, power resides somewhere else.” How can we hold accountable oil and gas companies which have quietly known since the early 1980s that burning fossil fuels contributes to global warming, but used their power to impede actions that would combat climate change?
I’m not a lawyer, so I cannot answer the legal aspects of this question, but state attorneys around the country are now looking into that question. As a citizen and a consumer, I can say this: One way we can hold companies accountable by not investing in them, and this is why I support the divestment movement. We can also boycott their products. In the current world, that is very difficult to do, but we can make a start. I installed an 8-watt solar PV system in my house, and we are now just about net-zero for electricity.
Is it possible to make up for 30 years of squandered time?
No of course not. Lost time is lost time. But knowing how much time has been lost, we should have a sense of urgency now, try not to lose any more.
Which strategies are being proposed for immediate climate action? Are environmental scientists and economists in agreement over which courses of action make the most sense?
Yes I think so. Nearly everyone who has studied the issue agrees that the most effective immediate action that is available to us is to put a price on carbon. This will immediately make renewables and energy efficiency more economically attractive, and it will send a signal to investors that fossil fuels will no longer be given a free pass for their external costs. This means that future returns will be greater in the non-carbon based energy sector. Anyone interested in this should read Nicolas Stern’s very informative book, Why are we Waiting?
How might the nomination of Merrick Garland to the Supreme Court and the results of the 2016 presidential elections affect the role that the US will play in combating climate change? Best case and worse case scenarios.
Best case: Republicans in Congress come to their senses, and listen to fellow Republicans like Bob Inglis, Hank Paulson, and George Schultz who have made the conservative case for putting a price on carbon. They can do this pretty much any way they want— through a tax, thru tradeable permits, or whatever. it’s clear Democrats would support either, and we know from experience that either approach can work, so long as the price is real (i.e., not just symbolic.) Right now Alberta is talking about $20—that is probably a bit low. BC is at $30
Of all the important issues out there, what motivates you to devote your time and energy to fighting climate change?
Oh that’s a good question. I didn’t decide to work on climate change, I fell into it when Erik Conway and I tripped over the merchants of Doubt story. Then, as I learned more and more about the issue, I came to appreciate scientists’ sense of urgency about it.
Nineteen colorful foam flowers decorate the walls of Marc Johnson’s office, a memento from his lab members when they “redecorated” while he was out of town.
Each flower is labeled in bold Sharpie with the names of viruses and viral proteins that his lab studies—MLV, RSV, Gag, Pol, to name a few.
One flower stands out, marked in capital letters: H-I-V.
Johnson, an associate professor of molecular microbiology and immunology, is one of four researchers at Bond LSC who studies HIV, the virus that leads to AIDS. His research focuses on understanding how HIV assembles copies of itself with help from the cells it infects.
Like most viruses, HIV hijacks cellular functions for its own purposes.
“It has this tiny itty bitty little genome and yet it can infect 30 million people,” Johnson said. “It doesn’t do it by itself.”
To understand how viruses reprogram the proteins in our bodies to work against us, he said, you have to understand the cells they infect. If cells were a chamber, then viruses are the keyhole.
For example, cells use a protein called TSG101 to dispose of unwanted surface macromolecules by bending a patch of cellular membrane around the macromolecule until it is surrounded inside a membrane bubble. The process, like trapping a bug inside a sheet of tissue paper, is called budding.
The cell sweeps all the pinched-off bubbles into a larger receptacle, or multivesicular body. These bodies, Johnson said, act as the cell’s garbage collection system. To dispose of the trash, the compartments become acidic enough to disintegrate everything inside or fuse with the cell membrane so that the trash gets dumped outside the cell.
It’s like in the second Star Wars movie, “The Empire Strikes Back,” Johnson said. “They just drop all their garbage before they go into hyperspace, and that’s how the Millennium Falcon got out.”
HIV uses the same housekeeping mechanism to break out of infected cells and infect more cells, but it remains unclear which other host proteins HIV commandeers.
“It’s all part of the puzzle,” Johnson said.
THE GAME CHANGER
On his desk, Johnson keeps a white legal pad with a list of 16 projects written in blue ink.
“Things make it off the list or they’ll get added,” Johnson said. “Or they’ll spend years on the back burner. I have a lot of projects.”
One of the biggest projects involves using CRISPR/Cas9 — a precision gene-editing tool — to identify genes that make a cell resistant to viral infections.
“It’s a game changer. It really is,” Johnson said. “It’s so cool.”
The technology uses a missile-like strand of guide RNA to target specific sites in the genome for deletion. Before CRISPR, scientists had to suppress gene expression using methods that were neither permanent nor absolute.
But because CRISPR manipulates the genome itself, Johnson said, there’s less doubt about what is happening.
Using the CRISPR library, the Johnson lab can scan the effects of 20,000 unique gene deletions in a population of cells. When these cells, each of which contains a different deleted gene, are exposed to HIV, not all of them die. Those that survive can cue researchers in to which genes might be important for blocking HIV infection.
And if another researcher has doubts that a gene is truly knocked out, Johnson said, you can tell them, “I’ll just send you the cell line. You try it and see for yourself.”
A DAY IN THE LIFE
The Johnson lab is a tight-knit group that consists of a lab manager, two grad students, a postdoc and four undergrads.
Dan Cyburt — a third year grad student — studies molecules that interact with proteins that keep HIV from infecting the cell, such as TRIM5α. TRIM5α, a restriction factor, blocks replication of the viral genome.
Fourth year grad student Yuleum Song focuses on how the viral envelope protein, Env, is packaged into viruses before they break free from cells. While Env isn’t necessary for viral assembly and release, she said, it’s critical for the infection of new cells.
Undergrads work in a tag team, picking up where the other left off, to generate a collection of new viral clones.
And lab manager Terri Lyddon keeps day-to-day experiments on task.
Lyddon, who has been with the Johnson lab for ten years, spends much of her day working with cells inside the biosafety level 2 hood. The area is specifically designated for work with moderately hazardous biological agents such as the measles virus, Samonella bacteria, and a less potent version of HIV.
Normally, HIV contains instructions in its genome for making accessory proteins that help the virus replicate, but the HIV strains used in the Johnson lab lack the genes for some of these proteins. That means the handicapped viruses can infect exactly one round of cells and spread no further.
Lyddon also ensures quality control for the lab by making sure students’ work is reproducible.
As a pet project, Johnson also independently confirms new findings reported in academic journals about HIV. Sometimes, Johnson says, the phenotypes that get published are not wrong, but they tend to represent the best outcomes, which might only exist in very specific scenarios.
“They’re only right by the last light of Durin’s day,” Johnson said, making a Lord of the Rings reference to a phenomenon in The Hobbit that reveals the secret entrance to a dwarven kingdom only once a year.
Because scientists base their work on the research of other scientists, he said, it’s always important to check.
A RECONSIDERED POSITION
According to the World Health Organization, 37 million people worldwide in 2014 have HIV or AIDS. The virus infects approximately two million new individuals every year. Breakthroughs in treatment have turned the autoimmune disease from a highly feared death sentence into a chronic and manageable condition.
For the longest time, HIV researchers scrambled to find better therapies against HIV why trying to develop a vaccine that could prevent AIDS.
But in the past five years, Johnson says he’s noticed a shift: researchers are gaining confidence in the possibility of finding a cure, something he once thought was impossible.
“Now it’s been demonstrated that it’s possible to cure a person,” Johnson said, referring to the Berlin patient. “So it’s only going to get easier.”
However, Johnson pointed out, most people would never undergo the kind of high-risk treatment that Timothy Ray Brown, the Berlin patient, received. Brown underwent a bone marrow transplant to treat his leukemia, and his new bone marrow, which came from an HIV-resistant donor, cured him of AIDS.
A “full blown cure” will be hard to attain, but Johnson believes there may be ways for HIV patients to live their lives without having to constantly take medication.
As an example, he points to certain “elite controllers” who are HIV positive but never progress further to show symptoms of AIDS. If scientists can figure out what’s different about their immune systems, Johnson said, then researchers could train the immune response in AIDS patients to resist HIV or keep it in check.
That’s a project for the immunologists. As a basic scientist, Johnson says he adds to the knowledge of how HIV works.
“I am not thinking about a therapy,” Johnson said, “but I’m also acutely aware that some of the best solutions come from basic science. “
Even though scientists haven’t discovered all the mechanisms behind cellular and viral function yet, Johnson said, the rules do exist.
“The sculpture is already there in the stone,” he said.
Johnson’s job is to chip away at the marble until the rules are found.
The next time you slather mustard on your hotdog or horseradish on your bun, thank caterpillars and brassica for that extra flavor.
While these condiments might be tasty to you, the mustard oils that create their flavors are the result of millions of years of plants playing defense against pests. But at the same time, clever insects like cabbage butterflies worked to counter these defenses, which then started an arms race between the plants and insects.
An international research team led by University of Missouri Bond Life Sciences Center researchers recently gained insight into a genetic basis for this co-evolution between butterflies and plants in Brassicales, an order of plants in the mustard family that includes cabbage, broccoli and kale.
“We found the genetic evidence for an arms race between plants like mustards, cabbage and broccoli and insects like cabbage butterflies,” said Chris Pires, an MU Bond Life Sciences Center researcher and associate professor of biological sciences in the College of Arts and Sciences. “These plants duplicated their genome and those multiple copies of genes evolved new traits like these chemical defenses and then cabbage butterflies responded by evolving new ways to fight against them.”
A biting taste
While you might like the zing in mustard, insects don’t.
Compounds, called glucosinolates, create these sharp flavors in plants to defend against caterpillars, butterflies and other pests. Brassicales species first evolved glucosinolate defenses around the KT Boundary — when dinosaurs went extinct — and eventually diversified to synthesize more than 120 different types of this compound.
For most insects, these glucosinolates prove toxic, but certain ones like the cabbage butterfly evolved ways to detoxify the compounds.
“Seeing the variation in the detoxification mechanisms among species and their gene copies gave us important evolutionary insights,” said Hanna Heidel-Fischer, a lead author on the study based at the Max Plank Institute for Chemical Ecology in Germany.
To look at these genetic differences, the team used 9 existing Brassicales genomes and also generated transcriptomes — the set of all RNA in a cell — across 14 Brassicales families. This allowed the team to map an evolutionary family tree of sorts over the millennia, seeing where major defense changes occurred. This family tree was compared with the family tree of 9 key species of Pieridae butterflies, which includes the cabbage butterfly.
Pires and his colleagues identified three significant evolutionary waves over 80 million years, where plants developed defenses and insects evolved counter tactics.
“We found that the origin of brand-new chemicals in the plant arose through gene duplications that encode novel functions rather than single mutations,” said Pat Edger, a former MU post doc and lead author on the study. “Given sufficient amounts of time the insects repeatedly developed counter defenses and adaptations to these new plant defenses.”
This back-and-forth pressure resulted in the evolution of many more species of plants and butterflies than in other groups without glucosinolate pressures.
Proving an old concept
Co-evolution is not a new idea.
About 50 years ago two now-renowned biologists, Peter Raven and Paul Erhlich, introduced the idea of co-evolution to science. Using cabbage butterflies and Brassica plants as a prime example, the two published a landmark study in 1964 advancing the idea that two species can mutually influence the development and evolution of each other.
“Using Ehrlich and Raven’s principles and models, we looked at the evolutionary histories of these plants and butterflies side-by-side and discovered that major advances in the chemical defenses of the plants were followed by butterflies evolving counter-tactics that allowed them to keep eating these plants,” Wheat said.
This research provides striking support for the ideas of Ehrlich and Raven published 50 years ago.
“We looked at the patterns 50 years ago, and found conclusions that proved correct,” said Peter Raven, professor emeritus of the Missouri Botanical Garden and a former University of Missouri Curator. “The wonderful array of molecular and other analytical tools applied now under leadership of people like Chris Pires, provide verification and new insights that couldn’t even have been imagined then.”
Understanding more about how plants and insects co-evolve could one day lead to advances in crops.
“If we can harness the power of genetics and determine what causes these copies of genes, we could produce plants that are more pest-resistant to insects that are co-evolving with them—it could open different avenues for creating plants and food that are more efficiently grown,” said Pires.
Proceedings of the National Academy of Sciences (PNAS) published the study, “The butterfly plant arms-race escalated by gene and genome duplications,” in June. The National Science Foundation (PGRP 1202793), the Knut and Alice Wallenberg Foundation and the Academy of Finland provided the funding for this research.
Endocrine disruptors alter parent behavior in California mice
By Roger Meissen | MU Bond Life Sciences Center
What if a chemical changes the way an animal parents?
That could happen due to endocrine disruptors like bisphenol A (BPA).
A recent study of California mice exposed to BPA showed parents spend less time feeding, grooming and interacting with their babies, according to University of Missouri research. Even mother mice not exposed to the chemical parented differently if their male partner was exposed during development.
Most studies only use laboratory mice and rats — where the mother is the sole parental provider — so how early contact to BPA may affect the father and his partner remained a critical gap in existing research.
“The nature and extent of care received by an infant is important because it can affect social, emotional and cognitive development,” said Cheryl Rosenfeld, a researcher in MU’s Bond Life Sciences Center and associate professor of biomedical sciences in the College of Veterinary Medicine. “We found that females who were exposed early on to BPA spent less time nursing, so the pups likely did not receive the normal health benefits ascribed to nursing. Likewise, we found that developmental exposure of males and females resulted in them spending more time out of the nest and away from their pups, further suggesting that biparental care was reduced.”
BPA and other endocrine disrupting chemicals like ethinyl estradiol (EE) — found in birth control — concern scientists because they build up in the environment and mimic natural hormones produced by animals, including humans. Everyday exposure to these chemicals can impact offspring development and now have been found to alter adult behavior in test animals.
California mice have special significance for studying parental behavior. Unlike most lab mice, Californian mice pair up to mate and care for offspring. This monogamous behavior could give researchers insight into child rearing behavior found in most human societies and other biparental animals that would be impossible to measure in lab mice and rats.
MU graduate student and primary author Sarah Johnson worked with Rosenfeld to design the study to look at both sexes. Female and male mice were fed one of three diets — food supplemented with BPA or ethinyl estradiol or endocrine-free (control) food — two weeks before breeding. The mice were then randomly paired with the same mate for the entire study. The behavior of both sexes was then tracked for activities like time spent grooming pups, time spent in the nest and time mothers spent nursing.
But how do you measure the behavior of parents?
Rosenfeld’s team depended on hundreds of hours of video footage, taken at particular times of day and night for seven days, starting two days prior to birth. By using infrared cameras they tracked all 56 litters of mice, logging the number of and duration of activities mothers and fathers completed. During this time, the body weight and temperature of the F2 pups, who were not directly or fetally exposed to any chemicals, was logged to monitor their development.
While results showed reduced pup attention from BPA/EE exposed mother mice, the most intriguing result showed that unexposed moms mated with exposed fathers reduced the time they groomed and cared for offspring.
“These female mice have not been exposed here, but if you can see they are still reducing parental care when paired with the BPA/EE-exposed males,” Rosenfeld said. “And what’s even more interesting is that if a mother and father are both exposed, that parental care diminishes further, and becomes even more statistically significant.”
Researchers hope these results will spur others to look at long-term effects of endocrine disruptors on parenting behavior from generation to generation in animal models and, more importantly, in humans, to see if these chemicals can disrupt parental behavior of mothers and fathers, and if so, whether these effects can be transmitted to subsequent generations.