Collisions during DNA replication and transcription contribute to mutagenesis

Wednesday, June 29th, 2016

When a cell makes copies of DNA and translates its genetic code into proteins at the same time, the molecular machinery that carries on replication and the one that transcribes the DNA to the mRNA code move along the same DNA double strand as their respective processes take place. Sometimes replication and transcription proceed on the same direction, but sometimes the processes are in a collision course. Researchers at Baylor College of Medicine and the University of Wisconsin-Madison have determined that these collisions can significantly contribute to mutagenesis. Their results appear today (June 29) in Nature.

Jue Wang

Jue D. Wang

“We first developed a laboratory assay that would allow us to detect a wide range of mutations in a specific gene in the bacteria Bacillus subtilis,” said corresponding author Jue D. Wang, who was an associate professor of molecular & human genetics at Baylor when a portion of the work was completed. She is currently an associate professor of bacteriology at the University of Wisconsin-Madison. “In some bacteria, we introduced the gene so the processes of replication and transcription would proceed on the same direction. In other bacteria the gene was engineered so the processes would collide head-on.”

The researchers discovered that when replication and transcription were oriented toward a head-on collision path the mutation rate was higher than when their paths followed the same direction. Furthermore, most of the mutations caused by replication transcription conflicts were either insertions/deletions or substitutions in the promoter region of the gene, the region that controls gene expression.

“People have mostly been looking at mutations in the DNA sequence that codes for protein, but in this paper we found that the promoter, the regulatory element of gene expression, is very susceptible to mutagenesis,” said Wang, “and this susceptibility is facilitated by head-on transcription and DNA replication.”

Promoters control how much of a gene is transcribed, for instance, particular mutations in promoters may enhance or reduce the production of proteins, or silence them completely. These genetic changes in gene expression may affect an organism’s health.

“The mutation mechanism we identified is not just applicable to our experimental system, but can potentially contribute to mutations that alter gene expression in a genome-wide scale, from bacteria to human,” said Wang.

Other contributors to this work include T. Sabari Sankar, Brigitta Wastuwidyaningtyas, Yuexin Dong, and Sarah Lewis.

This work was supported by the National Institutes of Health Director’s New Innovator Award DP20D004433.

UW-Madison seeks to capitalize on push to harness helpful microbes

Tuesday, June 14th, 2016
Microbiome bacteria

In this scanning electron microscope image, the bacteria (Acetobacter xylinum) is producing cellulose nanofibers, which are incredibly strong for how light they are. Engineers use the nanofibers to create materials that have a wide range of uses, from strong composites to tissue engineering. Photo: Thomas Ellingham, UW-Madison mechanical engineering graduate student

Since the 17th century, when Antonie van  Leeuwenhoek first observed microorganisms through the lens of a rudimentary microscope, humans have slowly come to appreciate that ours is a germy world.

Through the ages with van Leeuwenhoek, Louis Pasteur and Robert Koch, the 19th century scientist who found that microorganisms could cause disease, human awareness of the microbial world and its importance has expanded to help underpin critical medical and agricultural discoveries, such as antibiotics and nitrogen-fixing bacteria, as well as to make us masters of the organisms that enrich our lives and diets through ordinary bread and wine.

In more recent years, microbes have proved their worth through things like polymerase chain reaction, a now common method to amplify DNA in the lab, in forensics and in medicine. The process depends on an enzyme from a bacterium retrieved from a hot spring in Yellowstone National Park in the 1960s and fuels billions of dollars in economic activity annually. In addition, the re-tasking of a natural microbial immune system, CRISPR, has enabled precise genome editing from microbes to plants and animals.

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Timothy Donohue. Photo: Great Lakes Bioenergy Research Center

Now, seeking to further harness microbes’ many uses, the federal government has launched the National Microbiome Initiative (NMI) to “foster the integrated study of microbiomes across different ecosystems.”

Microbiomes are defined as communities of microorganisms that live on or in people (and other animals), plants, soil, oceans and the atmosphere.

The initiative will put us in a position to better understand microbes in context and how they work, explains University of Wisconsin—Madison bacteriology Professor Timothy Donohue. Its resources will depend much on the next federal budget, but various funding agencies as well as private organizations have committed to finding new support to enhance budgets for work related to the initiative.

“It is a scientific fact that ‘microbes touch everything,’ from the food we eat, the air we breathe and the water we drink,” says Donohue. “They are the master chemists of the universe, responsible for the world around us, and are intimately linked to the future health and evolution of the planet and its inhabitants.”

UW-Madison, Donohue argues, has both strengths and challenges in terms of capitalizing on the initiative. “Wisconsin has a history of and currently benefits by having many of the global thought leaders in microbiology,” he says. “However, to realize the potential of the NMI, we can benefit from leaders from disciplines who traditionally have not worked in the microbial sciences.”

Trina McMahon

Trina McMahon. Photo: Bryce Richter

In addition to strong programs in microbiology, he lists Wisconsin’s disciplinary breadth and long history of interdisciplinary research as assets. Researchers in fields such as chemistry, engineering, business and ethics will work to demystify microbiomes, how they function and how they might be exploited for the benefit of human health, food and energy production, environmental remediation and basic discovery.

A challenge, he says, will be aligning the technologies necessary to be successful in what is sure to be a competitive market for both capital and intellectual resources.

“There are major technology areas of need in this arena, including data analysis, modeling, imaging, technology development, biodesign, materials science, biomanufacturing and others,” Donohue says. “Some of these are common to this initiative and others, so there is intense national and international competition for leaders in these emerging areas.”

Trina McMahon, a UW–Madison professor of bacteriology and civil and environmental engineering, is cautiously optimistic about the national microbiome push, if for no other reason than it puts a spotlight on a corner of biology that is only now wending its way into public consciousness.

“The buzz is awesome,” she says. “Bringing the spotlight to the microbiome generally lets people know it’s not just about the gut microbiome,” an area that has received notoriety due mostly to its implications for human health.

McMahon studies microbial ecology in freshwater systems such as Lake Mendota and in the sludge processed at wastewater treatment plants. Her group is particularly interested in organisms that store phosphorus, a chemical nutrient and pollutant that helps spur the lake’s epic algae blooms.

Federico_Rey

Federico Rey

At UW–Madison, exploration of the microbiome is occurring in many different labs and contexts, ranging from surveys of the microbiomes of the bat wing, copepods and Lake Michigan algae to the gut microbiomes of the Wisconsin high school class of 1957 as part of the Wisconsin Longitudinal Study (WLS).

Bacteriologist Federico Rey, who helps lead the WLS microbiome effort, is excited about the national push, but is naturally concerned about the competition. “I think it is really exciting to see how much interest there is in this field. Funding for this kind of research is going up, but it is nerve-wracking to see how much money other universities are putting into it. How is the University of Wisconsin going to compete?”

Wisconsin’s strengths, he says, reside in breadth of expertise, “a collaborative spirit and fantastic students.” But to be successful in a big way will require bringing all of those things and associated technologies — rapid gene sequencing, bioinformatics, computational resources and biologists — together to solve big problems.

Melissa-Christopherson

Melissa Christopherson

The microbiome can also be a powerful teaching opportunity. Melissa Christopherson, a faculty associate in the Department of Bacteriology, took her microbiology capstone students on a tour of the microbiome of the human mouth this past semester, comparing the oral microbiomes of student athletes to see if there were differences in the microbial communities in elite athletes compared to others and if diet had an influence on the microbial cast of characters. The project’s findings are now being prepared for publication.

“One of the aims of this initiative is education,” says Christopherson, who was on hand for the May 13 White House summit where the initiative was announced by Jo Handelsman, a former UW–Madison professor of bacteriology and now associate director for science in the White House Office of Science and Technology Policy.

“There are only one or two examples of a course like this around the country,” Christopherson notes. “The students in this course got their money’s worth. They worked their butts off. A project like this is a way to summarize a lot of the things they’ve learned.”

The initiative rests on the growing array of technologies that make the sequencing and analysis of genetic material cheap and easy, says civil and environmental engineering Professor Dan Noguera. Most microorganisms can’t be cultured in the lab, but they can be cracked open and their genetic material can be plumbed with growing speed and accuracy.

U.W. Madison College of Engineering Dept of Civil & Environmental Engineering Portraits of faculty & staff

Dan Noguera

“We’re able to do things we weren’t able to do 10 or 12 years ago,” says Noguera, who uses a Madison sewage treatment plant as a laboratory. “There are some very sophisticated tools and models, but only a few people are good at using them and interpreting them, so the hope is there will be some synergy.”

One potential upshot of the initiative, he observes, is the opportunity for the development of centers on the scale of the Department of Energy’s Great Lakes Bioenergy Research Center, a collaboration of UW–Madison and Michigan State University whose mission is to develop the next generation of biofuels.

This story was originally published on the UW-Madison News site.

Chemistry lessons from bacteria may improve biofuel production

Thursday, June 9th, 2016

If you’re made of carbon, precious few things are as important to life as death.

A dead tree may represent a literal windfall of the building blocks necessary for making new plants and animals and the energy to sustain them.

“The recycling of plant carbon is fundamental to the function of our ecosystems,” says Cameron Currie, professor of bacteriology at the University of Wisconsin–Madison. “We get food, water, air, energy — almost everything — through those ecosystem services. It’s how our planet operates.”

But the component parts of a dead tree were carefully assembled in the first place, and don’t just fall apart for easy recycling.

In the case of cellulose — a key structural component in plant cell walls and the most abundant organic compound in life on land — a world of specialized microbes handles this careful deconstruction. Much of that work is done by fungi growing on decaying plants, but bacteria in the soil, in the guts of animals like cows and working alongside insects, get the job done, too.

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Researchers tried to grow different strains of Streptomyces bacteria on dead plant material (filter paper). Successful cellulose processing strains tapped special genes to produce enzymes that break down cellulose. Photo: Currie Lab/UW-Madison.

A new analysis of a group of bacteria called Streptomyces reveals the way some strains of the microbe developed advanced abilities to tear up cellulose, and points out more efficient ways we might mimic those abilities to make fuel from otherwise unusable plant material.

Streptomyces were long thought to be prominent contributors at work in breaking down cellulose, and to be equally active in the cause across hundreds or thousands of strains of the bacteria.

“That assumption — which is based on a very good, old study of one type of Streptomyces — is not right on the mark,” says Brian Fox, a UW–Madison biochemistry professor and co-author of the study published today in the journal PLOS Biology. “What we see now is that there’s a relatively small group of types of Streptomyces that is far more effective at breaking down cellulose, and a much larger group that is far less effective.”

The UW–Madison researchers measured the relative abilities of more than 200 types of Streptomyces bacteria by growing them on simple sugar and on a good source of cellulose: filter paper (which is made of dead trees).

They were able to collect the genomes of more than 120 of those strains, and identify the genes — and the ways key genes were expressed — that set strong cellulose degraders apart from poor ones.

“The strains that aren’t good at degrading cellulose mostly express the same genes whether we grow them on glucose or on plant material,” says Gina Lewin, a bacteriology graduate student and study co-author. “The strains that are really good at degrading cellulose totally change their gene expression when we grow them on plant material.”

The successful Streptomyces strains — which were typically those found living in communities with insects — ramp up production of certain enzymes, the proteins that do the cleaving and dissolving and picking apart of cellulose.

celluloseStreptomyces

Counter to long-held belief about the bacteria Streptomyces, seen growing here in a petri dish, the ability to break down a stubborn molecule in plant cell walls called cellulose may be limited to just a few gifted strains. Photo: Adam Book/UW-Madison

“There are families — six or eight or maybe 10 of these enzymes — that all of the active Streptomyces have,” Fox says. “And this paper shows that the most abundant one of them has to be there or the whole thing collapses.”

It’s the particular combinations of enzymes that makes the research useful to scientists working on biofuels.

Biofuels are typically made from the sugars easily extracted from the same parts of plants we eat.

“We eat the kernels off the corn cob,” Currie says. “But most of the energy in that corn plant is in the part which is not digestible to us. It’s not in the cob. It’s in the green parts, like the stalk and the leaves.”

Evolving microbes like Streptomyces have been sharpening the way they make use of those parts of plants almost as long as the plants themselves have been growing on land. That’s hundreds of millions of years. On the other hand, the Department of Energy’s UW–Madison-based Great Lakes Bioenergy Research Center, which funded the Streptomyces study, was established in 2007.

“The natural world is responding to the same kind of things that humans are,” Fox says. “We need to get food. We need to get energy. And different types of organisms are achieving their needs in different ways. It’s worth looking at how they do it.”

The new study identifies important enzymes, and new groups of enzymes, produced when Streptomyces flex particular genes. If they represent an improvement over current industrial processes, the microbes’ tricks could make for a great boon to bioenergy production.

“For a cellulosic biofuel plant, enzymes are one of the most expensive parts of making biofuels,” Lewin says. “So, if you can identify enzymes that work even just slightly better, that could mean a difference of millions of dollars in costs and cheaper energy.”

Banner photo: The ability to break down the cellulose in plant material is rare in Streptomyces bacteria, except in strains that live alongside insects — honeybees, leaf-cutter ants (above), some beetles —that eat or make use of the woody parts of plants. Photo: Don Parsons/UW-Madison.

This story was originally published on the UW-Madison News site.

Xylome’s quest to lower the cost of cellulosic ethanol

Monday, May 23rd, 2016

In their lab on a 20-acre prairie in Madison, Wisconsin, Xylome scientists are busy tinkering with the yeasts that live in the bellies of wood-boring beetles. A spin-off from the Great Lakes Bioenergy Research Center (GLBRC), Xylome is lowering the cost of making ethanol by creating new yeast strains that more efficiently convert cellulosic biomass to fuel.

While the early stages of biofuel manufacturing focused on fermenting corn grain to ethanol, corn is not the only available feedstock for making biofuel. Cellulosic biomass – i.e., wood, perennial grasses, and the non-food portion of plants – offers another, arguably more sustainable feedstock for fuels.

GLBRC-Tom-Jeffries

Tom Jeffries (L) and Tom Kelleher (R) conduct R&D and provide research services from Xylome’s labs at University Research Park, Madison, WI.

And yet developing an economically viable cellulosic biofuel pipeline remains a technically challenging endeavor. Compared to corn, the sugars in cellulosic biomass are much more difficult to access and convert to fuel. The sugar xylose, in particular, which accounts for up to 20 –30% of the dry weight of non-food plants, is notoriously difficult to ferment.

“In order to make ethanol out of cellulosic biomass economically,” says Tom Jeffries, Xylome founder and UW–Madison professor emeritus of microbiology and bacteriology, “the technical problem of how to ferment xylose needed to be solved. It’s a problem I’ve worked on for decades.”

It’s also a problem that got a lift in 2006, when Louisiana State University biologist Meredith Blackwell discovered xylose-fermenting yeasts in the guts of wood-boring beetles. Well-acquainted with Jeffries’ research, Blackwell sent him samples of a particularly interesting yeast species she named Spathaspora passalidarum, and it has been the focus of his work ever since.

“These yeasts inhabit the mid-gut,” says Jeffries, “where they consume the sugars the beetles chew on. They have a huge capacity for degrading not only xylose and other complex sugars, but also cellulose.”

Engineering S. passalidarum to even more effectively ferment xylose and other plant sugars is the work that defines Xylome.

Sequencing the S. passalidarum genome and deepening their understanding of the yeasts’ physiology and biochemistry has allowed Xylome scientists to increase the rate and efficiency of the yeast’s ability to ferment sugars, including xylose, to ethanol.

“We don’t introduce any extraneous genes in this process,” says Jeffries. “We take a native organism with a desirable capability, modify the organism’s genes in useful ways, and put them back into the cell. And it’s working! They’re hardy organisms – it’s not difficult to scale up the process.”

GLBRC-yeast

A microscopic image of one of Jeffries’ yeast strains.

Jeffries emphasizes that Xylome is not focused on establishing new biofuel facilities. Existing ethanol plants, he says, are already built just where they need to be – in the middle of fields, adjacent to railroad tracks, and on rivers.

“Ethanol plants have easy access to feedstocks, transport, and towns that can provide labor. They’ve obtained air and water permits and have community acceptance and support – all very important things!” Jeffries says. “And none of these things has to change when a plant shifts from processing grain to processing cellulosic feedstocks if you have the right fermentation capability.”

Xylome’s first-generation product, a cellulose- and xylose-fermenting yeast strain developed with GLBRC support, will debut at the International Fuel Ethanol Workshop & Expo in June 2016. And Jeffries is confident that Xylome’s product will go a long way in helping grain ethanol producers enter the market for second-generation, cellulosic fuels and chemicals.

GLBRC is one of three Department of Energy Bioenergy Research Centers created to make transformational breakthroughs and build the foundation of new cellulosic biofuels technology. For more information on GLBRC, visit www.glbrc.org or visit us on twitter @glbioenergy.

This story was originally published on the Great Lakes Bioenergy Research Center News site.

Panda poop study provides insights into microbiome, reproductive troubles

Wednesday, May 18th, 2016

A stomachache can put a real damper on your love life — especially if you’re a giant panda.

One minute it’s breeding season and you’re happily dining on fresh bamboo leaves, the next you’re left clutching your stomach while your gastrointestinal lining passes through your system. It exits your body as a thick, gooey, gelatinous mass.

Le Le stalk

Le Le, a male giant panda at the Memphis Zoo, feeds on a bamboo stalk. Researchers analyzed the percentage of feeding time Le Le and his female zoo mate, Ya Ya, spent feeding on bamboo leaves relative to stalks. Photo: Candace Williams

This is exactly what seems to happen to captive giant pandas, and the researchers behind a new study published in Frontiers in Microbiology are beginning to suspect it may play a role in their struggles to reproduce.

“We think they are sloughing off the internal mucous membrane of their gastrointestinal tract and because of this, they get really sick, which coincides with gestation,” says Garret Suen, a University of Wisconsin–Madison professor of bacteriology and co-author of the panda poop and feeding behavior study. “The pandas stop eating and they produce these painful, membranous fecal pellets.”

No one quite understands why these gelatinous masses, called mucoids, happen but Suen and his co-authors believe bamboo may be a factor. Evolutionarily speaking, giant pandas are not built to eat a sole diet of bamboo. As bears, their digestive systems are designed to break down meat and small amounts of plant material, yet in the wild and in captivity these bears are exclusively herbivorous. The study suggests this may lead to digestive troubles that could negatively affect panda pregnancy. It motivated the researchers to take a closer look at the gut bacteria involved.

“Gastrointestinal diseases are a major cause of mortality in wild and captive pandas but scientists understand very little about their digestive process,” says co-author Ashli Brown Johnson, state chemist and Mississippi State University associate professor of biochemistry, molecular biology, entomology and plant pathology. “By studying the microbial community in the panda’s gastrointestinal tract, we gain a better understanding of panda nutrition, which could help improve the health and reproduction of the endangered species.”

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Garret Suen

Suen, an Alfred Toepfer Faculty Fellow, also has other motivations. A renaissance man of the microbiome, his lab studies the gut bacteria of everything from cows to sloths to pandas. His interests are both fundamental and applied. For example, understanding how animals and their microbes break down fibrous plant materials could aid in more efficient production of biofuels. It could also lend insights into human digestive diseases.

For the study, Suen, Brown Johnson and co-first authors Candace Williams and Kim Dill-McFarland enlisted help from the Memphis Zoo, which has collected feeding behavior on its two giant pandas — Le Le (male) and Ya Ya (female) — since 2003. Williams, who conducted the work as a Ph.D. student in Brown Johnson’s lab, had also performed her master’s degree work at the zoo, watching the pandas feed for 12 hours a day.

Using data recorded by trained zoo docents, the research team analyzed how much time Ya Ya and Le Le spent feeding on both bamboo stalks and leaves. They saw dramatic shifts in eating behavior: The pandas ate leaves less than one percent of the time in winter and spring, but by August — when mucoids became more prevalent — nearly 60 percent of their feeding time was spent eating leaves.

Every summer, in captivity and in the wild, pandas switch from eating primarily the woody stalks of bamboo to the leaves. It is at this transition — which also coincides with when most female pandas become pregnant — that their digestion appears to go awry. In July and August, pandas pass more mucoids, cease eating, become lethargic, and express their discomfort and pain.

“If it’s happening every three to four days, and the pandas stop eating for half to a whole day — when they normally spend their whole day eating — that’s a lot,” says Dill-McFarland, a Ph.D. student in Suen’s lab.

leaf and culm

A fecal sample from a giant panda, showing a mix of bamboo stalk and leaves. Pandas eat up to a third of their body weight in bamboo every day. Photo: Candace Williams

The researchers studied bowel movements the pandas made in February 2013, during the season when pandas don’t normally have mucosal poop, and between June 29 and Aug. 22, 2014, when they more frequently pass mucoids. During this time, zookeepers collected the mucoids as well as the regular feces the bears produced immediately prior to and immediately after these events.

The team studied five normal fecal samples from Ya Ya and one mucoid, and 13 regular bowel movements from Le Le and five mucoids. The samples arrived from the zoo like “chicken breasts wrapped in foil,” says Dill-McFarland.

Williams traveled to Madison to learn from Suen and Dill-McFarland how to analyze the microbial composition of panda poop. Regular panda poop resembles shredded bamboo stalks and was a challenge for the researchers to process. The mucoids were gooey, smelled “ghastly” (says Williams) and presented their own challenges.

The team found the panda poop had unusually low bacterial diversity relative to other herbivores, though the mix of bacteria changed day to day. The diversity dropped even lower right before mucoids, but then spiked in the mucoids themselves, which contained a different population of microbes than regular poop. In particular, they were made up of bacteria typically found in the gut lining.

They also found bacteria in the mucoids associated with dysfunctional digestion in humans, called Actinobacteria.

“What we think might be happening is that their diet is causing a strong internal reaction, leading to an inflammatory response,” says Suen. “Pandas are basically shedding their gastrointestinal lining to allow for the replacement of those microbes. It’s kind of like resetting the microbiome.”

While researchers can’t be certain why pandas experience this resetting, it is clear their diet is rough on the animals. At 220 to 275 pounds, pandas eat up to a third of their body weight in bamboo every day. It passes quickly through their digestive systems, which does not give the microbes in their guts much time to break things down. This is entirely different from other animals adapted to consuming plant matter, like cows, whose rumen microbes take up to 24 hours digesting the complex carbohydrates found in plants.

“I’m very interested in animals that eat way more than should be necessary to maintain their body size, and on the flip side, in animals that eat way less than should be required to maintain their body size,” says Suen.

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tubes of feces from badgers, porcupines, lemurs and more sit on top of a lab freezer. Photo: Kelly Tyrrell, UW-Madison

The study does not provide solutions to prevent the gastrointestinal distress pandas experience, which Williams says is very hard to watch. Whether pandas feed on stalks or leaves appears related to chemical changes in the bamboo leaves themselves, a strategy some plants use to prevent herbivores from munching on them. And meat is out of the question.

“It’s gotten to the point where if you try to feed them meat, they get violently ill,” says Suen.

But the study does give scientists a place to start.

“Until recently, the gut microbiome hasn’t really played a role in the management of animals,” says Williams. “Having a balanced gut is important, and it’s also important that we know these things, especially about such unique animals. I strive to let people know how important the gut microbiome really is and the impact it has on reproduction, health and even immune function.”

That Ya Ya produced just a single mucoid is one limitation of the analysis, as is her unusual breeding cycle. However, pandas are incredibly difficult to study, the researchers say, and data of this kind are rare.

Additional researchers from Mississippi State University and the Memphis Zoological Society contributed to the study, which was funded by the United States Forest Service’s International Programs, the Memphis Zoological Society, the United States Department of Agriculture’s National Institute of Food and Agriculture, the Mississippi Agricultural and Forestry Experiment Station, and the Leo Seal Family Foundation.

This story was originally published on the UW-Madison News site.

UW expert at White House summit

Thursday, May 12th, 2016

On Friday, May 13, the White House Office of Science and Technology Policy will host an event on microbiomes – communities of microorganisms that live on and in people, plants, soil, oceans and the atmosphere. Microbiomes maintain healthy function of these ecosystems, influencing diverse features of the planet – human health, climate change and food security.

During the event, the administration will announce steps to advance the understanding of microbiome behavior and enable protection and restoration of healthy microbiome function, including by investigating fundamental principles that govern microbiomes across diverse ecosystems, and developing new tools to study microbiomes.

Lending expertise to the summit will be UW-Madison bacteriology Professor Timothy Donohue. Donohue directs the Department of Energy-supported Great Lakes Bioenergy Research Center and is an expert on biofuels and bio-based renewable energy technologies. Donohue can talk about microbiome research in general and, more specifically, how it might inform strategies for devising alternative fuel technologies. He can be reached at (608) 770-1283.

For Theo Loo, an unintimidated, humble approach to solving global problems

Tuesday, May 10th, 2016

mt-st-helensBig problems don’t intimidate UW-Madison senior Theo Loo.

And big ideas, it seems, come naturally.

One of eight undergraduate Wisconsin Idea Fellows at the Morgridge Center for Public Service this year, Loo is wrapping up the latest stage in his multi-year community-based study on water quality and access in rural South Africa.

And when he’s not on the ground in South Africa, you can find him back in Madison hard at work developing a potentially revolutionary approach to HIV diagnostic testing —one that would cost perhaps just 1% of current tests.

Loo, humble in sharing credit at every step, says his persistence comes from his passion for the work.

“I truly enjoy research,” Loo says. “It would definitely be a chore to go into lab or write grants and papers if I did not enjoy my workplace and research subject.”

Loo credits Global Health Institute Director Dr. Jonathan Patz’s Health Impact Assessment of Global Environmental Change course for changing his perspective on research back in 2013.

When Loo took the class, his assessment group paired with Dr. Michael Bell, director of the Center for Integrated Agricultural Systems, studying waterborne disease and land use in the eastern rural South Africa village of KuManzimdaka.

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Sunrise on the rural eastern cape of South Africa

But when the class ended, Loo didn’t feel like his work was done.

“There were definitely long-term opportunities that transcended the class,” Loo said. “It kind of seemed like a shame that we had put a whole semester into doing this project, and I knew we hadn’t really produced a solution to the problem.”

Loo’s friend and 2014-15 Wisconsin Idea Fellow Kayla Sippl suggested he should apply for the fellowship. He did, partnering with Dr. Bell as his faculty mentor and South Africa-based Indwe Trust NPC as his community partner. His waterborne disease community-based research project was accepted as one of six 2015-16 Wisconsin Idea Fellowship projects.

But Loo knew to be successful, his project needed strong community input.

Recognizing what you don’t know

Valerie Stull, a PhD student in the Nelson Institute and a teaching assistant for Dr. Patz’s health impact assessment course, says Loo’s humble approach to community-based research has been critical to the project.

“One of the weaknesses I see in many undergraduates is the inability to recognize what they don’t know,” said Stull. “Theo recognized what he didn’t know right away, and he took special care to consult the appropriate people before his research trip.”

And when Loo landed in South Africa last summer, he took special care to talk with everyone. Literally.

“I actually went to every single household,” said Loo. “I went to every single child, mother and father and asked them what they thought their primary problem was in the village.”

KuManzimdaka’s residents face health issues directly tied to decades of apartheid in South Africa. Loo says the community was pushed into the foothills of a rocky mountain range that’s not conducive to livestock management or grazing or farming. And their water sources are springs contaminated by animal waste that are often kilometers away.

Some people walk up to six hours to collect water.

rocky hillside

A contaminated spring at the bottom of a rocky hillside

In addition to community dialogues, Loo performed water quality tests (confirming that the water was, in fact, badly contaminated) and conducted extensive mapping that helped identify infrastructure and terrain. The data and experiences he gathered told him the village needed a serious long-term solution. But Loo said it didn’t feel right to abandon the village with just a data set and a few distant solutions.

“Yeah, it would be hard to go,” said Loo. “I feel so morally conflicted and wrong if I went to the community and said, ‘You have this problem. You have this water issue problem. We’re going to give this data to the South African government and just kind of leave.’”

So with his partners in South Africa, Loo is proposing a series of “water plazas” that will help collect and store rain water within the community for the near term. A crowdfunding campaign has been established for the project.

“We’re hoping that can mitigate the situation until they have a more permanent solution,” said Loo. “I think I have a big responsibility in that. I think I have to help them out somehow until the longer-term issue gets resolved.”

A novel mechanism

“The goal for all of us should be to live a life of consequence. And he’s making that happen,” said Dr. Bell. Theo Loo, in fact, is making that happen a couple times over.

Two years ago, Loo and his friend Nico set off on a road trip from Madison for Colorado. “We were stuck in the car together for 14 hours. We needed to make it productive.”

By the time they reached the Rockies, the pair had developed a rough idea to revolutionize HIV diagnostic testing. “We just kind of played in back and forth until we had something tangible.”

When they returned to Madison, the pair approached Dr. David Beebe and Dr. Scott Berry at the Wisconsin Institutes for Medical Research, who funded the idea with seed money.

Here’s the issue: Patients with HIV need regular testing to determine the amount of the virus in their blood. A sudden increase in virus loads can indicate that the patient needs a change in treatment. But according to Loo, only 25 percent of patients living in low-resource settings have access to the test, which usually cost $24-44 per test. On top of that, the test requires complex equipment that can cost hundreds of thousands of dollars, involves intensive training and requires steady electricity.

The new simpler test costs just one dollar.

“It’s just as good as the other ones,” said Loo. “And it’s also really rapid. So fast, cheap, reliable and accurate.”

So how does it work?

“The chemicals you use for HIV diagnostic testing are really expensive,” Loo said. “We’re cutting down the re-agents and the materials used by 95 percent. So it’s nano-scale.”

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A homemade incubator Theo Loo used for his research in South Africa

“It’s certainly exciting that no one is looking at the approaches that we’re looking at.”

A cheaper test, along with a cheaper and simplified quantification device in development, could very likely mean better HIV treatment for potentially millions around the world. And that’s exactly what Loo has in mind.

“It’s a novel mechanism. So we’re going to try to patent that and try to bring this product widespread throughout the world.”

In April, Loo traveled to Berkeley, Cal., to share his work at the Clinton Global Initiative -University—an annual summit showcasing top research and global solutions from university students. Loo said the event inspired him to keep pushing further.

“The main takeaway for me was not a business card, funding, or tidbit of knowledge, but the urge to do more,” said Loo of the event. “It inspired me to further my research and apply my skills to improve global health.”

The very best sense of the Wisconsin Idea

Loo is heading back to northern California for a longer stay in the fall—he’ll be attending graduate school at the University of California-Berkeley where he plans to continue his work. In fact, he wants to combine his water quality work with the HIV diagnostic research.

“I didn’t want to just be there for a few weeks, leave and never see them again,” said Loo of his time in South Africa. “I wanted to make it into a long-term project.”

Loo knows it’s ambitious, but he hopes his water project can establish a replicable blueprint for water quality and access solutions across all of rural South Africa—covering nearly 20 million people.

Theo Loo’s unintimidated, humble persistence to fight some of the world’s most pressing challenges is both inspiring and motivating.

“He just has such a passion for really doing something good,” said Dr. Bell. “Really the very best sense of the Wisconsin idea.”

This story was originally published on the Morgridge Center News site.

Microbiomes new research frontier – Audio

Friday, March 4th, 2016

Microbiomes new research frontier

Garret Suen, Assistant Professor
Department of Bacteriology
UW-Madison College of Agricultural and Life Sciences
gsuen@wisc.edu
(608) 890-3971

3:03 – Total Time
0:14 – What is a microbiome
0:30 – Microbiomes large and small
0:41 – Life driven by microbiomes
1:10 – Cow rumen a microbiome
1:50 – Powerful new technology
2:29 – Will touch medicine and agriculture
2:55 – Lead out

TRANSCRIPT

 Sevie Kenyon: The new frontier of microbiomes. We are visiting today with Garret Suen, department of Bacteriology, University of Wisconsin-Madison in the College of Agricultural and Life Sciences and I’m Sevie Kenyon. Garret, start out by defining for us, what is a microbiome?

Garret Suen: A microbiome is the collection of all microbes that lives within a given environment. So what we are talking about, are all the bacteria, all the archaea, all the fungi, and all of the viruses that live within any type of community. Continue reading

Tim Donohue, the power of microbes and the pull of Rockaway Beach

Monday, February 1st, 2016
Tim-Donohue-Lab_0_1

Tim Donohue, director of the Great Lakes Bioenergy Research Center (GLBRC) and UW-Madison professor of bacteriology, says microbiology is enjoying a renaissance period: “Innovation in biology and microbiology can help provide food, health, and energy for a growing population while also ensuring that future generations have access to resources they need to thrive on the planet. That prospect really excites me.”

Long before Tim Donohue became a bacteriology professor and the director of the Great Lakes Bioenergy Research Center (GLBRC), he was a teenage beach cleaner and would-be biologist growing up on the boardwalk of New York City’s Rockaway Beach.

“I was fascinated by the change in the seasons, the tides, the weather, the wildlife,” Donohue says of those early years. “Exposure to the ocean really led me to biology.”

Rockaway, the largest urban beach in the U.S., fed Donohue’s interest in science but it also gave him the cash he needed for college. As a young man, Donohue held two summer jobs, performing routine vehicle maintenance for the National Park Service during the day and emptying Rockaway’s trashcans as the sun set every night.

“I was the first child in our family to go to college,” Donohue says. “My mother had a sixth grade education, my father had an eighth grade education. I think there was probably an implicit expectation that I would go to college, but the idea of me becoming a scientist, getting a Ph.D., that was not really on the table.”

As a college student at the Polytechnic Institute of Brooklyn in the early 1970s, Donohue  met Professor Ron Melnick, who introduced him to the world of microbes. The most ancient form of life on earth, microbes are microscopic, single-cell organisms such as bacteria, fungi, and viruses. Donohue’s love of all things biology had found a tiny new focus.

“I was just fascinated by the power of microbes,” Donohue says, “and by their global impact on our everyday lives. They shaped this planet’s history, they’re central to many of the foods we eat, and they have a huge impact – sometimes positive, sometimes negative – on our bodies and agriculture.”

Melnick also encouraged Donohue to begin working in his lab or, as Donohue puts it, “to drive the car instead of just reading the driver’s manual.” Donohue definitely drove that car, heading to the Pennsylvania State University to pursue a doctorate in microbiology and then on to the University of Illinois at Urbana-Champaign for a post-doctoral research fellowship.

Now a professor of bacteriology at the University of Wisconsin–Madison, Donohue likes to describe his research as “unlocking the secrets” of microbes.

“Microbes have been doing interesting chemistry on this planet for billions of years,” Donohue says. “We can learn a lot from studying how they do what they do.”

Individual bacteria use different strategies to obtain the energy and nutrients they need to live. Some microbes harvest sun light, others have a sweet tooth and prefer to eat sugars. Some digest aromatics, while still others grow by using energy from splitting hydrogen.

“We knew about many of these different processes when I was a student”, Donohue says, “but now, with genomics tools such as DNA sequencing, we can see the actual blueprints of these processes.”

Possessing these exact blueprints gives scientists the information they need to design new pathways that coax bacteria to perform new and desirable tasks.

“In our GLBRC projects, we’re trying to re-task native pathways and engineer next-generation microbial factories that can manufacture valuable fuels and chemicals from renewable wastes.”

While biofuel production is one area of research that will continue to gain from advances in microbiology, the field of microbiology is exceptionally wide-ranging, and enjoying what Donohue calls a “renaissance period.”

Donohue was recently among a group of leading scientists who published a call for a new, government-led “Unified Microbiome Initiative” in the scientific journals Science andNature. A more coordinated research effort, the authors argue, would go a long way toward harnessing the power of microbes to benefit agriculture and energy production and help address issues such as climate change and disease.

“We’re really at an inflection point,” Donohue says. “Innovation in biology and microbiology can help provide food, health, and energy for a growing population while also ensuring that future generations have access to resources they need to thrive on the planet. That prospect really excites me.”

Donohue, who has published in collaboration with other researchers for much of his career, is a firm believer in coordinated, cross-disciplinary research. As director of the GLBRC, he oversees a team representing a wide array of disciplines and specialties collaborating to overcome a major energy challenge: developing a robust and environmentally sustainable pipeline for biofuels.

“It’s been eye-opening for me to see how GLBRC’s team approach has allowed us to make advances much faster than I ever imagined,” Donohue says. “I never thought we would’ve accumulated the body of knowledge, produced the number of papers, and generated the amount of intellectual property that we have.”

In early 2015, GLBRC reported the filing of its 100th patent application. And to date, the Center has published approximately 850 papers, many of which represent collaborations with researchers from over 32 U.S. states and 24 countries.

Tim Donohue, son of New York City’s so-called Irish Riviera, now occupies an office with a view of the west end of UW–Madison’s campus and is candid about drawing inspiration from the Wisconsin Idea, or the notion that the university should improve people’s lives well beyond the classroom.

“GLBRC really is a proud contributor to the Wisconsin Idea,” Donohue says. “We are doing relevant research that will benefit the state, the region, and the country. It’s been an honor to be a part of this work.”

The GLBRC is one of three Department of Energy Bioenergy Research Centers created to make transformational breakthroughs and build the foundation of new cellulosic biofuels technology. For more information on the GLBRC, visit www.glbrc.org or visit us on twitter @glbioenergy.

This story was originally published on the Great Lakes Bioenergy Research Center news page.

Researchers collaborate to break down lignin and advance biofuels

Thursday, January 14th, 2016

To tackle what many consider the next frontier in biofuels research, the Great Lakes Bioenergy Research Center (GLBRC) recently joined forces with the Joint BioEnergy Institute (JBEI) in Emeryville, California. The focus of their collaboration? Lignin, a glue-like compound in the cell wall of most living plants that gives them their sturdiness.

While lignin accounts for up to one third of plant carbon, it’s also the most difficult part to break down and remains a formidable obstacle to accessing the valuable sugars contained within biomass. As a result, the biofuels and paper industries mostly treat it as a waste product, isolating it to be burned or discarded.

GLBRC lignin Kate Helmich

Kate Helmich analyzes bacterial enzymes called LigF and LigE that break particular chemical bonds within larger lignin molecules.

But GLBRC and JBEI researchers hope to change all that by bringing their collective expertise to the challenge of unraveling lignin’s strong and unique molecular bonds. With two new studies already complete, the payoff for their effort could be significant.

“If we can convert lignin from an undesirable byproduct into a starting material for advanced biofuels and other lucrative chemicals,” says Tim Donohue, GLBRC director and UW–Madison professor of bacteriology, “we would dramatically change the economics of tomorrow’s biorefineries.”

The researchers began by studying bacterial enzymes that cleave specific chemical bonds inside larger lignin molecules with the idea of creating a single new enzyme to break down lignin. That turned out to be a difficult task, however, because lignin molecules are similar to snowflakes: they have a multitude of spatial configurations, even within a single plant, and each of them requires a different approach to deconstruction.

“Making a single enzyme would be like trying to make a glove that’s designed for your left hand fit on your right hand,” explains Kate Helmich, co-first author of one of the studies and a recent PhD graduate of UW–Madison’s biochemistry department. “Our two hands are different configurations of the same fingers, and lignin is like a chain of many different hands. Degrading that entire chain would require an enzyme, or glove, that can attach to both the left and the right hands within it.”

Nature has instead evolved multiple, highly specialized bacterial enzymes that work in concert to break down lignin, each of them cleaving different sets of chemical bonds in the complex molecule.

Though a single lignin-cracking “master hybrid enzyme” remains elusive, the study informs future enzyme engineering efforts and sets the stage for more GLBRC and JBEI collaborations to convert lignin and other parts of plant biomass into biofuels and valuable chemicals.

GLBRC’s Helmich and Daniel Gall share first authorship, ​with JBEI’s Jose Henrique Pereira, on a paper recently published in the Journal of Biological Chemistry; and former GLBRC researcher and Rice University professor George Phillips, Jr. is senior author. In a sister study led by JBEI (currently slated for publication), the team reports new insights into bacterial enzymes that could someday help produce aromatic compounds of great interest to the chemical industry from lignin.

“It is exciting to see that our collaboration has resulted in the simultaneous publication of these two important papers,” Donohue says. “Collaboration is at the center of everything we do at GLBRC. We look forward to doing more of this mutually beneficial work with JBEI and other academic and industrial partners to advance the growing biofuels industry.”

GLBRC is one of three Department of Energy-funded Bioenergy Research Centers created to make transformational breakthroughs that will form the foundation of new cellulosic biofuels technology. For more information on the GLBRC, visit www.glbrc.org.

This story was originally published on the Great Lakes Bioenergy Research Center website.