Tag Archives: biology

From A(lgorithms) to Z(O-1 proteins): A Computer Scientist’s Journey into the Lab

By Grace Deitzler

Improvements in DNA sequencing technology have allowed scientists to dig deeper than ever before into the intricacies of the microbes that inhabit our gut, also called the gut microbiome. Massive amounts of data – on the scale of pentabytes – have been accumulated as labs and institutes across the globe sequence the gut microbiome in an effort to learn more about its inhabitants and how they contribute to human health. But now that we have all of this data (and more accumulating all the time), the challenge becomes making sense of it.

This is a challenge that Christine Tataru, a rising fifth year PhD student in the Department of Microbiology, is tackling head-on. “My research is trying to understand what a ‘healthy’ gut microbiome actually looks like, how it ‘should’ look, and to do so in a way that is integrative,” she explains. 

A woman with long hair in a red and white striped shirt sits at a computer.
Christine Tataru, fifth year PhD student in Maude David’s lab.

An integrative approach looks at all of the processes and relationships that are occurring between all of the trillions of microorganisms in our gut, and the cells within our body. Previous microbiology dogma focused on the behavior and impact of singular species such as pathogens, but as we learn more about microbiomes, this approach becomes limiting. There are a vast number of relationships that can occur between microbes and human cells. And there are many different lenses through which we can look at this system: taking a census of what microbes are present; tracking the genes that are present rather than just the microbes (this tells us about the functions that might be carried out); and what proteins or metabolites are actually present, whether those are created by the bacteria or the host. Each piece of the puzzle allows us a glimpse of the massively complex system that is the gut microbiome.

“It’s difficult for a human brain to keep track of these relationships and sources of variations, so I use computer algorithms to try to get a picture of what is happening, and what that might mean for health.” 

It’s an approach that makes sense for the Stanford-trained computer-scientist-turned-biologist. Christine recalls a deep learning class in college in which a natural language processing algorithm on the whiteboard struck her with inspiration: what if instead of being applied to words, this algorithm could be applied to gut microbiomes? The thought stuck with her and when she came to OSU to pursue her PhD, she already had a clear goal in mind for what she wanted to do.

The natural language processing and interpretation algorithm treats words in a document as discrete entities, and looks for patterns and relationships between words to gain context and “understand” the contents. A computer can’t really understand what words mean linguistically and with the complex nuances that natural language presents, but they are really good at looking for patterns. It can look at what words occur together frequently, what words never occur together, and what words share a ‘social network’ — words that don’t appear together, but appear with the same other words. Christine has developed a way to apply this algorithm to large gut microbiome datasets: using this approach to identify what microbes frequently appear together, which don’t, and which share ‘social networks’. This produces clusters of microbes, or what she refers to as ‘topics’, which can then be interpreted by humans to try to understand how these clusters relate to certain aspects of health. You can read more about this method in her recent PLOS Computational Biology publication here.

It’s quite the challenging undertaking: no one has done this type of approach before, and even when the clusters are generated, we still need to be able to interpret what it means – why is it interesting or important that these microbes occur with each other and also correlate with these genes or metabolites? Biologically, what does it actually mean?

The question of biological meaning prompted Christine to pivot to a more traditional ‘wet lab’ biology approach. “Who gave this computer scientist a pipette,” she jokes. But to be perfectly honest, it makes a lot of sense: who better to investigate the hypotheses that can be generated by computers than the scientist who wrote the code?

Taking the ‘integrative approach’ to the next level, she now works on recapitulating the environment of the gut microbiome on a chip in the lab. The organ-on-a-chip system is a fairly new approach to studying biological mechanisms in a way that better mimics the naturally occurring environment. In Christine’s case, she is using a ‘gut on a chip’, which is made of a thin piece of silicone with input and output channels. The silicone is split by a microporous membrane in such a way that two different kinds of cells can be grown, one on the top layer and one on the bottom. What makes this system unique as compared to traditional cell culture is that the channels and membrane allow for constant flow of growth media, which physically simulates the flow of blood over the cells. It can also mimic peristalsis, which is the stretching and relaxing of intestinal cells that helps push food and nutrients through the digestive tract. It’s a sophisticated system, and one that allows her a high degree of control over the environment. She can use this system to mimic Inflammatory Bowel Disease, and then add in specific microbes or combinations of microbes to see how the gut cells respond, using findings from her algorithm results to inform what kinds of additions might have anti-inflammatory effects.

Christine in a biosafety hood, preparing gut-chips for experiments.

This innovative approach provides Christine another lens through which to view the relationship between the gut microbiome and health. Though she will be finishing her doctorate at the end of the year, the curiosity doesn’t end there – “Broadly, my life goal to some extent has always been to make ways for people to help people.” Whether that’s pipeline and methods development or building the infrastructure to study complex biological relationships, Christine’s innovation-driven approach is sure to lead to huge strides in our understanding of how the tiny living things in our gut influence our health, behavior, and mood.

Tune in at 7 PM this Sunday evening on KBVR 88.7 or stream online to hear more about her research and how she ended up here at OSU!

Core Strategies for Conservation of Greater Sage-Grouse

Greater sage-grouse (GRSG) is a North American bird species that nests exclusively in sagebrush habitat. In the last century, natural populations of this species have significantly declined largely due to human influenced habitat loss and fragmentation. This has prompted multiple petitions to the U.S. Fish and Wildlife Service (USFWS) to list GRSG under the Endangered Species Act (ESA), which would require mandatory restrictions on critical sagebrush habitat. This means that land managers of sagebrush areas would face land use restrictions for natural resource extraction and development, the bulk of the economy in Wyoming.

Wyoming Basin study site with associated GRSG Core Areas in blue. These Core Areas were designated as part of the GRSG Core Area Protection Act, Wyoming’s GRSG conservation policy aimed at protecting at least 67% of male GRSG attending leks. This policy is focused on directing development outside of these areas by setting strict conservation measures inside the Core Areas. Overall, the policy has remained effective in protecting at least 2/3 of GRSG habitat and has been identified as having the highest conservation value to maintaining sustainable GRSG populations.

 

Scent station and associated trail camera set-up in Natrona County, WY. Scent stations were randomly placed throughout the study site along roads and stratified between Core and Non-Core Areas. Mammalian predators are known to use roads for easy travel. These scent stations will help gather occupancy data of mammalian predators (Photo Credit: Eliana Moustakas).

Wyoming is a stronghold for GRSG, with the most birds, the most leks (male mating display grounds), and the largest contiguous sagebrush habitat in North America. Since GRSG declines have led to its possible endangered listing, Wyoming Governor Dave Freudenthal launched an effort in 2007 to develop stronger policies for GRSG that would protect the species and its habitat while also sustaining the state’s economy. A public forum followed, including representatives from state and federal agencies, non-governmental organizations, and industries, and in 2008 a conservation policy called the Greater Sage-Grouse Core Area Protection Strategy was developed to maintain and restore suitable habitat and active breeding GRSG pairs. The plan aims to protect at least 67% of male GRSG attending leks, and is focused on directing development outside of Core Areas by setting strict conservation measures inside Core Areas. By protecting sagebrush habitat and allowing development and mining in Non-Core Areas, Wyoming can continue to expand its natural resource economy and play a critical role in GRSG conservation.

In 2010, the USFWS concluded that GRSG were warranted protection but left them off the ESA list because threats were moderate and did not occur equally across their range. The status of GRSG was reevaluated in 2015 and the USFWS determined that GRSG did not warrant protection, claiming that the Core Area Strategy was sound framework for a policy by which to conserve GRSG in WY. However, recent monitoring of GRSG has shown that populations are still in decline in some Core Areas and in populations across their range. Our guest this week, Claire Revekant, a second year Master’s student in the Department of Animal and Rangeland Science, is trying to understand if avian and mammalian predator abundance differs between Core and Non-Core Areas.

Golden eagle using a utility pole to perch. Raptors and corvids are known to use  structures to perch and nest.

 

Working under Dr. Jonathan Dinkins, Claire estimates associations between human influence areas and habitat variables on the abundance of predatory birds and occupancy of mammalian predators. For example, raptors and corvids have been documented to perch and nest on fences and other human structures, and roads have been found to be used as travel paths for mammalian predators. Claire’s hypothesis is that predatory animals will be higher in Non-Core Areas where human-influenced environments serves as areas of food subsidies. Identifying areas of predator abundance and relating those areas to human features and habitat variables may help policy makers prioritize plans to mitigate human influence and protect sagebrush habitat.

Badger captured by trail camera at scent station in Lincoln County.

While her research is focused on predators of GRSG, Claire’s work for GRSG conservation contributes to the conservation of other sagebrush-obligate species (species that relay on sagebrush for all or some parts of their life cycle). By protecting the ecosystem for one “umbrella” species, other species may also benefit. Throughout her career as a wildlife biologist, Claire has been involved with numerous projects where she has handled and monitored several species. From learning to band raptors as a child to monitoring seabird productivity as an intern at the Monomoy National Wildlife Refuge, Claire has developed a passion for research. She told us that she can’t remember a time when she had a different dream job. Tune in tonight Sunday November, 11 at 7 to hear more about Claire’s research and her journey to graduate school on 88.7 FM KBVR Corvallis, or stream the show live.

The Mold That Keeps On Giving

All around us, plants, fungi, and bacteria are waging chemical warfare against one another to deter grazing, prevent against infection, or reduce the viability of competitor species. Us humans benefit from this. We use many of these compounds, called secondary metabolites, as antibiotics, medicines, painkillers, toxins, pigments, food additives, and more. We are nowhere close to finding all of these potentially useful compounds, particularly in marine environments where organisms can make very different types of chemicals. Could something as ordinary as a fungus from the sea provide us with the next big cancer breakthrough?

Paige Mandelare with one of the many marine bacteria she works with

Paige Mandelare thinks so. As a fourth-year PhD student working for Dr. Sandra Loesgen in OSU’s Chemistry department, she has extracted and characterized a class of secondary metabolites from a marine fungus, Aspergillus alliaceus, isolated from the tissues of an algae in the Mediterranean Sea. After growing the fungus in the laboratory and preparing an extract from it, she tested the extract on colon cancer and melanoma cell lines. It turned out to be cytotoxic to these cancer cells. Further purification of this mixture revealed three very similar forms of these new compounds they called allianthrones. Once Paige and her research group narrowed down their structures, they published their findings in the Journal of Natural Products.

Next, she grew the fungus on a different salt media, replacing bromine for chlorine. This forced the fungus to produce brominated allianthrones, which have a slightly different activity than the original chlorinated ones. Her lab then sent two of these compounds to the National Cancer Institute, where they were tested on 60 cell lines and found to work most effectively on breast cancers.

The recent publication of Paige in her story of the allianthrones from this marine-derived fungus, Aspergillus alliaceus.Like many organisms that produce them, this wonder mold only makes secondary metabolites when it has to. By stressing it with several different types of media in the lab, Paige is using a technique called metabolomics to see what other useful compounds it could produce. This will also give insight into how the fungus can be engineered to produce particular compounds of interest.

A native Rhode Islander who moved to Florida at the age of ten, Paige has always been fascinated with the ocean and as a child dreamed of becoming a marine biologist and working with marine mammals. She studied biology with a pre-med track as an undergraduate at the University of North Florida before becoming fascinated with chemistry. Not only did this allow her to better appreciate her father’s chemistry PhD better, she joined a natural products research lab where she first learned to conduct fungal chemical assays. Instead of placing her on a pre-med career path, her mentors in the UNF Chemistry department fostered her interest in natural products and quickly put her in touch with Dr. Loesgen here at OSU.

Paige enjoying her time at the Oregon Coast, when she is not in the research lab

After finishing her PhD, Paige hopes to move back east to pursue a career in industry at a pharmaceutical company or startup. In the meantime, when she’s not discovering anticancer agents from marine fungi, she participates in a master swimming class for OSU faculty, trains for triathlons, and is an avid baker.

To hear more about Paige and her research, tune in to KBVR Corvallis 88.7 FM this Sunday July 15th at 7 pm. You can also stream the live interview at kbvr.com/listen, or find it on our podcast next week on Apple Podcasts.

Beetle-Seq: Inferring the Phylogeny of Clivinini

We humans are far outnumbered by organisms that are much smaller and “less complex” than ourselves. The cartoon above depicts representatives of major groups of organisms, and each organism is drawn such that its size reflects the number of species contained within its group. The bird, the fish, and the trees look as expected, but you may notice the enormous beetle. No, beetles are not generally larger than trees or elephants, but there are more species of beetles than any other group of organisms. Beetles are a wonderful representative of the biodiversity of the earth because they can be found in almost every terrestrial and non-marine aquatic environment!

Examples of carabid beetles of the tribe Clivinini (top row; photos with ‘HG’ – Henri Goulet, otherwise – David Maddison). Male genitalia of a clivinine species, Ardistomis obliquata, with possible ‘copulatory weapons’ (right) and several examples of clivinine female genitalia (bottom row) modified from Zookeys 2012;(210):19-67 shared under CC BY 3.0.

Our guest this week, Antonio Gomez from the Department of Integrative Biology, studies a group of beetles called clivinines (pronounced kliv-i-nīnz) which has 1,200 species, and potentially more that have yet to be discovered. Antonio is also particularly interested in the morphological diversity and evolution of clivinine beetle sperm. Antonio wants to know: What is the evolutionary history of clivinine beetles? What is the pattern of morphological diversity of sperm in clivinine beetles, and how are sperm traits evolving? The objective is to collect beetles, study their form, sequence their DNA, and understand their diversification.

Several examples of sperm conjugates (cases where two or more sperm are physically joined and travel together) in carabid beetles. Conjugation is considered rare, but in carabid beetles, it’s the rule and not the exception to it. In many carabids, sperm leave the testis but do not individualize. Instead, they remain together and swim as a team.

This is no small task, but Antonio is well equipped with microscopes to dissect and describe beetle anatomy, a brain geared to pattern recognition, and some fresh tools for genome sequencing. All of this is used to build an evolutionary tree for beetles. This is kind of like a family tree, but with species instead of siblings or cousins. Antonio and other students in the lab of David Maddison are adding knowledge to the vastness of the beetle unknown, bit by bit, antenna by antenna, gene by gene.

Antonio Gomez collecting beetles near a really bright light (a mercury vapor light trap) near Patagonia, Arizona.

Like many of our graduate students at Oregon State, a group of great mentors can make all the difference. Before working with Dr. Kelly Miller at University of New Mexico, he never knew beetle phylogenetics meant exploring exotic locations around the world to collect and potentially discover new species. As an undergraduate, Antonio even named a species of water beetle, Prionohydrus marc, after the undergraduate research program that go him started as a beetle systematist, the Minority Access to Research Careers (MARC) program. Pretty amazing. That was not his first or last research project with insects before he joined ranks at Oregon State, he also was participated in a Research Experience for Undergraduate program at the California Academy of Sciences and completed a Master’s at University of Arizona. Now he has ample experience working with beetles and is maybe a little overwhelmed but still excited by the unknown beetle tree of life. Next on his list of questions: did the ancestor of all clivinines likely have sperm conjugation?

You’ll have to tune in on Sunday April, 16 at 7 pm to hear more about that evolutionary arms race!
Not in Corvallis? No sweat! Stream the show live.

Can’t get enough? Follow this link to learn about Stygoprous oregonensis, a blind subterranean diving beetle that had not been seen in 30 years. Recently, a team of researchers that included Antonio Gomez reported the discovery of more specimens, which allowed them to place Stygoporus in an evolutionary tree.

Just keep swimming or don’t! Curiously following Zebrafish

People often think of science as focusing on very specific questions or rigorous hypothesis testing. However, some of the most exciting advancements were the result of general curiosity of seemingly disparate ideas, and a sprinkle of creativity. For example, the beginnings of how electricity was discovered started by poking frog legs with different types of metals. The modern zero-calorie sugar (saccharin) was discovered by playing creative-chef with coal tar products in the 1870’s when the chemist accidentally tasted his chemical concoction.

Sarah Alto

Our guest this week is using young zebrafish to investigate how environmental factors affect their behavior, and whether behavioral changes can be attributed to specific brain activity. Why zebrafish you may ask? They are a model organisms or they tend to be well studied, relatively easy to breed and maintain in lab settings, and as vertebrates, they share some characteristics with humans. The more we know about zebrafish, the more clues we may have into our own neurobiology. Sarah Alto is exposing these model organisms to different levels of oxygen and carbon dioxide stress. She monitors their swimming with infrared cameras and examines their brain to get an idea of how they respond to stress physically and mentally. This is no easy task because the young zebrafish are only a few millimeters long!

Oxygen, nitrogen, and carbon dioxide gas is bubbled into the tank holding the larvae.
The entire set-up is enclosed in a light-tight box so the larval behavior is more connected to the environment changes and not human interaction.

Curious Sarah is asking: Are low oxygen or high carbon dioxide concentrations changing the swimming behavior of zebrafish? What happens in the brain of a zebrafish when it experiences environmental stress? What can we learn about how environmental factors shape the brain’s connections and influence behavior? Sarah has a long road ahead of her, one that is unpaved with many junctions, but she is performing the exploratory work that may inspire future investigations into the affects of stress on the brain.

The second part of Sarah’s research will be investigating the neural activity when the larvae are exposed to the same gas concentrations as studied in the behavioral experiments.
Image courtesy of Ahrens et al. (2013)

Prior to Sara’s interest in biology, she was always drawn to art as an escape and a method of expression. When choosing which colleges to attend, she didn’t want to choose between art and science. So she chose to pursue both! Sarah enrolled at UC Berkeley as double major including Molecular and Cellular Biology, as well as Practice of Art. The San Francisco art scene was highly accessible, and Berkeley is a top-flight university for the sciences. Needless to say she flourished in this environment and her love of science grew but her love of art continues to this day. Finishing her schooling she began working at UC San Francisco, a premier medical research university, investigating the role of stem cells in facial development to for possible medical treatments for facial reconstruction. She was involved in a variety of projects but her gut feeling led her to continue schooling at Oregon State.

Sarah is now a part of Dr. James Strother’s lab in the College of Science within the department of Integrative Biology focusing the behavioral neurobiology of zebrafish. Be sure to tune in Sunday April 9th at 7PM PST on 88.7FM or listen live.