OSU Scientist Reconstructs Four-billion year old (yes, 4-billion) Genetic Code

The following is a news release from Oklahoma State University

(STILLWATER, Okla., August 9, 2016) – An Oklahoma State University microbiologist and a colleague have reported progress in understanding the evolutionary origin of the genetic code used by all known cells. The scientists reconstructed the genetic code of the last universal common ancestor (LUCA), believed by some scientists to be the origin of all life on Earth.

Wouter Hoff, with OSU’s Department of Microbiology and Molecular Genetics, and Peter van der Gulik, with CWI, the Netherland’s national research institute for mathematics and computer science, published their findings in the journal PLoS ONE. The evolutionary origin of the genetic code has remained a scientific puzzle since its original discovery in the 1960s, which was a seminal breakthrough in understanding the molecular basis of life.

OSU Microbiologist Dr. Wouter Hoff

OSU Microbiologist Dr. Wouter Hoff

LUCA is the proposed single-cell organism that gave rise to the current three domains of life: Archaea, Bacteria, and Eucarya that includes plants and animals. It is believed LUCA lived four billion years ago and may have developed in the extreme conditions surrounding deep sea vents where magma rises to the surface. The properties of LUCA and its possible resemblance to present day organisms are currently attracting intense scientific attention and mainstream news coverage. An influential, but hotly debated, notion is that modern Archaea living in extreme environments most resemble LUCA.

“Our reconstruction of LUCA’s genetic code reveals that the evolution of the set of transfer RNA molecules that are at the center of the genetic code was already almost complete in LUCA,” said Hoff. “Our work reveals that the set of transfer RNA molecules in LUCA closely resembles that in present day Archaea. In this respect, the primordial character referred to in the name of Archaea seems very appropriate.”

To obtain their results, Hoff and van der Gulik used recent genomic and biochemical data in combination with a largely ignored but central biochemical regularity in the genetic code.

“While many questions regarding the origin of the genetic code remain to be addressed, this publication makes a clear step in elucidating part of the evolutionary development of this process that is so important for all living organisms,” Hoff said.

Want more? Click here to read the article Hoff published.

Evolution and the Human Body

Signs of evolution can easily be found in the human body. Vox recently put together this AMAZING video explaining how you can see evidence of evolution in your own body. From babies born with tails to why you get goosebumps.

I can’t recommend this enough to get a better understanding of how evolution has affected the human body.

Keystone Ancient Forest

The Keystone Ancient Forest is one of the gems of northeastern Oklahoma. The forest is located in Sand Springs and is home to trees that are hundreds of years old. It’s made up of cross timbers which are some of the toughest trees in existence which is why it’s never been developed.

The forest shows what Oklahoma (or at least the Sand Springs area) looked like well before civilization began exploring it.

It’s a great place to go for a walk and take a step back in time but it does have limited hours and pets are not allowed.

It’s only open on select days throughout the month. For more information on the Forest click here for the city of Sand Springs.


Climate Change Guide

Earth is getting hotter. There’s really no doubt about it. This past January, for example, “was the planet’s most unusually warm month since we started measuring temperature in 1880.”

The misinformation out there about climate change is maddening and time consuming to go against. Thankfully there’s a great resource available to help sift through the BS.

It’s a YouTube channel called Scientists on Climate Change. You’ll find a number of videos there with interviews from actually climate scientists. These are the people who know what they’re talking about. These are not politicians or wishful thinkers. I highly recommend it if for no other reason than to see what real-life scientists are studying.

Citizen Scientist

Here’s a great chance for anyone, specifically teachers and students, to be citizen scientists and be part of a real-life, real-world science test.

The Cameron Siler lab at the University of Oklahoma and the Sam Noble Oklahoma Museum of Natural History is launching the Oklahoma Infectious Disease Citizen Science Project. Basically you would gather information from the state’s reptiles and amphibians. Researchers are specifically looking to track cases of chytridiomycosis or chytrid fungus. It’s a deadly disease in amphibians.

Jessa Watters is the collections manager for herpetology at the Sam Noble Museum, she says “The project is important because we know so little about this life-threatening disease for amphibians in Oklahoma. Understanding where it occurs in the state can help us track its progress and work with state officials to protect amphibians that may be particularly at risk due to already low population sizes within the state. In other parts of the United States and globally, chytrid fungus has been blamed for local extinctions.”

The lab is looking for help from teachers and students (or really anyone who wants to do a little science). All you need is access to a pond or stream. You’ll get a kit with all the equipment you need, teachers will get a packet, and you’ll be given resources online to to show how to collect the data and work in the field. “By having students help us collect the data, they will gain an appreciation for ponds and amphibians, and how things in their own neighborhoods are at risk. They will also learn how to correctly swab frogs in order to collect accurate and relevant scientific data” added Watters.

SIO has profiled Jessa Watters before. Below are the two stories we’ve produced showing what it’s like to do science in the field and why she likes herpetology.


Microbes and You

(Note: The following is a news release from the University of Oklahoma)

Norman, Okla.—University of Oklahoma anthropologists are studying the ancient and modern human microbiome and the role it plays in human health and disease.  By applying genomic and proteomic sequencing technologies to ancient human microbiomes, such as coprolites and dental calculus, as well as to contemporary microbiomes in traditional and industrialized societies, OU researchers are advancing the understanding of the evolutionary history of our microbial self and its impact on human health today.

Dr. Christina Warinner

Dr. Christina Warinner

Christina Warinner, professor in the Department of Anthropology, OU College of Arts and Sciences, will present, “The Evolution and Ecology of Our Microbial Self,” during the American Association for the Advancement of Science panel on Evolutionary Biology Impacts on Medicine and Public Health, at 1:30 pm, Sunday, Feb. 14, in the Marriott Marshall Ballroom West, Washington, DC.  Warinner will discuss how major events, such as the invention of agriculture and the advent of industrialization, have affected the human microbiome.

“We don’t have a complete picture of the microbiome,” Warinner said. “OU research indicates human behavior over the past 2000 years has impacted the gut microbiome.  Microbial communities have become disturbed, but before we can improve our health, we have to understand our ancestral microbiome.  We cannot make targeted or informed interventions until we know that.  Ancient samples allow us to directly measure changes in the human microbiome at specific times and places in the past.”

Warinner and colleague, Cecil M. Lewis, Jr., co-direct OU’s Laboratories of Molecular Anthropology and Microbiome Research and the research focused on reconstructing the ancestral human oral and gut microbiome, addressing questions concerning how the relationship between humans and microbes has changed through time and how our microbiomes influence health and disease in diverse populations, both today and in the past.  Warinner and Lewis are leaders in the field of paleogenomics, and the OU laboratories house the largest ancient DNA laboratory in the United States.

Warinner is pioneering the study of ancient human microbiomes, and in 2014 she published the first detailed metagenomics and metaproteomic characterization of the ancient oral microbiome in the journal Nature Genetics.  In 2015, she published a study on the identification of milk proteins in ancient dental calculus and the reconstruction of prehistoric European dairying practices.  In the same year, she was part of an international team that published the first South American hunter-gatherer gut microbiome and identified Treponema as a key missing ancestral microbe in industrialized societies.

Warinner has published 17 peer-reviewed journal articles, 2 books, and 5 book chapters, and she serves on the Editorial Board of Scientific Reports.  Her research earned an Honorable Mention for the Omenn Prize, an annual prize for best article published on evolution, medicine and public health; and her ancient microbiome findings were named among the top 100 scientific discoveries of 2014 by Discover Magazine.

Warinner’s research has been featured in more than 75 news articles, including stories in Science, Cell, Scientific American, The New Scientist, Archaeology Magazine, the LA Times, the Guardian, WIRED UK, MSNBC, FOX News, and CNN, among others.  She has presented before the Royal Society of London and on behalf of the Leakey Foundation, and in 2015 she was invited to participate in a White House microbiome innovation forum sponsored by the Office of Science and Technology Policy.  She has been featured in two documentaries, and her current work on ancient Nepal appears in the award-winning children’s book, Secrets of the Sky Caves.

Warinner was named a U.S. National Academy of Sciences Kavli Fellow in 2014, and she was awarded a TED Fellowship in 2012.  Her TED Talks on ancient dental calculus and the evolution of the human diet have been viewed more than 1.5 million times.  For more information on Warinner’s AAAS presentation on the “Evolution and the Ecology of the Microbial Self,”

Earthquake Test

Make plans Monday February 8th at 8am to watch a University of Oklahoma professor conduct a unique earthquake test.

Dr. Amy Cerato- courtesy The OU Daily

Dr. Amy Cerato- courtesy The OU Daily

Dr. Amy Cerato is an assistant professor in the School of Civil Engineering and Environmental Science. On Monday she’ll be conducting a one-of-a-kind shake test that could help people living in places where there are lots of earthquakes (aka, Oklahoma).

She’ll be looking at how helical piles shake during an earthquake. Helical piles are deep foundation elements that look like and are installed like a large steel soil screw to support the structure they hold. Helical piles are used in seismic areas, such as New Zealand and Japan, but they have not been widely used in the United States.

Here’s a story from Oklahoma City’s News 9 where Dr. Cerato explained what she’ll be doing.

The test could help engineers develop and build safer structures for those living in seismic zones.

Dr. Cerato will be conducting the test  on helical piles in seismic conditions at the University of California-San Diego’s Shake Table site beginning at 8 a.m. Oklahoma time this Monday, Feb. 8.

You can watch it live from this link.


courtesy: Oklahoma State University

Geology Students Study Tectonic Rifts

note: the following is a news release from Oklahoma State University

Four Oklahoma State University geology students traveled to Malawi in Africa to study tectonic rifts last summer thanks to a 2014 grant from the National Science Foundation.

courtesy: Oklahoma State University: Sam Dawson, from Davidson, North Carolina; Tiara Johnson, from Midwest City, Oklahoma; Courtney Hall, from Broken Arrow, Oklahoma, and Bryan Clappe, from Chelsea, Oklahoma.

courtesy: Oklahoma State University

courtesy: Oklahoma State University: Bryan Clappe, from Chelsea, Oklahoma; Tiara Johnson, from Midwest City, Oklahoma, and Dr. Estella Atekwana study tectonic rifts in Malawi.

Dr. Estella Atekwana, geology department head, and Dr. Daniel Laó-Dávila, a geology professor, took four students to Karonga, Malawi, to explore the East African Rift that extends for thousands of miles along the continent’s edge bounded by the Indian Ocean.

“People don’t know what rifts are,” Atekwana said. “There used to be one big continent, called Pangea; it’s because of rifts that the continents broke apart. Malawi has a young rift system and is the go-to place to study the entire rift process.”

The grant allowed the Boone Pickens School of Geology to create an international program for its students, sending a total of 12 students in groups of four for three years. The trips allow the students to collect geological data and gain cultural experience outside of the university.

“The last thing I was expecting was a culture shock,” said Sam Dawson, a graduate student from Davidson, North Carolina. “Seeing what life was like in a developing country was eye-opening. The people are so happy. I saw some kids playing with simple toys for hours on end.”

courtesy: Oklahoma State University

courtesy: Oklahoma State University: Landscape view of Karonga, Malawi, where the students studied tectonic rifts.

courtesy: Oklahoma State University

courtesy: Oklahoma State University

Other students included undergraduates Tiara Johnson, from Midwest City, Oklahoma; Bryan Clappe, from Chelsea, Oklahoma; and Courtney Hall, from Broken Arrow, Oklahoma. Clappe has since enrolled in the graduate program. The trip lasted from July 14 to Aug. 11, with students working five or six days a week from 8 a.m. to 8 p.m. This international opportunity will help make the students more competitive for job opportunities after graduation, according to Atekwana.

“It was a win-win experience,” she said. “Students can do research from the beginning of a rift and learn a lot. They don’t just learn about the science, but what it takes to collect it, to learn new cultures, meet new people. Students need to be competitive in the global economy. This gives them the advantage because they’ve now been there and done that.”

Karonga is a small town in northern Malawi, with a population similar to Stillwater. In 2009, there was a major earthquake in the town. Atekwana said the earthquake meant the rift was still active, so they needed to find the earthquake zone and image it.

“It’s sort of like a CT scan but of the underground,” she said.

In previous years, the geology department has led trips to Zambia and is looking into more places in the future, including Uganda and Ethiopia. But Laó-Dávila says there are other places in the U.S. that can be explored as well.

“There’s an ancient rift in Oklahoma not many people know about,” he said. “It’s in the southwest part of the state by the Wichita Mountains. Other places we can explore are the Rio Grande Rift, in New Mexico, and the Mid Continent Rift System that spans across Kansas, Iowa, Minnesota and Michigan. It’s one of the oldest examples of a rift, at about 1.1 billion years old.”

But the trip wasn’t all work and no play. The group took trips to see different national parks in Malawi, including the Nyika National Park, a major tourist destination for the country. The group also toured the Cultural and Museum Center Karonga as well as going on safari rides.

“I woke up the next morning to see zebras out of my window,” Dawson said. “So that was pretty cool. I enjoyed getting to learn more about the geologic and cultural history at the museum as well. And there were so many beautiful sites to see.”

Some of the struggles the group had throughout the trip included living conditions and Internet connectivity. The hotel they stayed at cost $6 a night. Dawson said sometimes he didn’t have a shower, and if he did, there was only cold water available. Other problems included the electricity going on and off and waiting days to get Internet connectivity.

“That made it difficult for us to record our data or get connected to our resources on campus when we needed to.”

In the end, the experience was one that Atekwana believes changed the students’ lives. She said it showed them how people get by with a tenth of what Americans have and to learn how to get good scientific data from it.

“I recommend people not being closed minded as far as interacting with the culture goes,” Dawson said. “I did not expect to become such great friends with our driver, Kennedy. He taught us some of the language, including some pick up lines for us to use. We paid him $30 a day for a month, and he said that money would pay for his entire living expenses for six months. If I go back, I’d definitely try to find him again.”

The students reported on their trip at the American Geophysical Union’s 2015 Fall Meeting December 14-18, where 24,000 attendees met to present research and discover more about the latest happenings in their fields. For more about the Boone Pickens School of Geology, visit geology.okstate.edu.

courtesy: Oklahoma State University

courtesy: Oklahoma State University: Tiara Johnson, from Midwest City, Oklahoma; Sam Dawson, from Davidson, North Carolina; Courtney Hall, from Broken Arrow, Oklahoma, and Bryan Clappe, from Chelsea, Oklahoma.

Science Research in Oklahoma

There is so much science happening right under our noses here in eastern Oklahoma. The OSU Center for Health Sciences is just one example. You’ll find research into biomedical and forensic science, healthcare, medicine, and ,my personal favorite, paleontology.

The cool thing is OSU-CHS has a fantastic resource to help you stay on top of what they’re doing. They call it the Research Spotlight. There are videos and information all on kinds of topics. The video below is one example of the research taking place right here in Tulsa!



OU Scientist Named a National Academy of Inventors Fellow

A note from Dan- The following is a news release from the University of Oklahoma

Dr. Heloise Anne Pereira, courtesy University of Oklahoma

Dr. Heloise Anne Pereira, courtesy University of Oklahoma

Norman, Okla.—University of Oklahoma Health Sciences Center Professor Heloise Anne Pereira has been named a 2016 National Academy of Inventors Fellow, a high professional distinction awarded to academic inventors who have demonstrated a prolific spirit of innovation in creating or facilitating outstanding inventions that have made a tangible impact on quality of life, economic development and the welfare of society.

Pereira has been on the OU Health Sciences Center faculty for the past 23 years.  Throughout her career, she has been a leader in promoting entrepreneurship and collaboration between academia and the biotechnology industry.  Her research has resulted in numerous patents, and she has transitioned innovative technology from her academic research laboratory into a successful company for commercialization.

In her academic role, Pereira serves as associate dean of research in the OU College of Pharmacy, dean of the Graduate College, professor in the Department of Pharmaceutical Sciences and adjunct professor in cell biology and pathology.  She was awarded the Henry Zarrow Presidential Professorship for Excellence in Scholarship and Teaching from 2008-2012.  Pereira has published 34 manuscripts in peer-reviewed journals and has contributed to six book chapters.

Pereira is known internationally for her expertise on the naturally occurring protein CAP37 and has been invited to make numerous presentations on her research and commercialization experiences around CAP37-derived antimicrobial peptides.  She has received numerous awards, including the distinction of Fellow to both the American Association for Advancement of Science and American Association of College Pharmacy Academic Research Program.

Pereira has been studying the naturally occurring CAP37 protein for over 25 years.  Through her research, she identified and developed novel CAP37-derived antimicrobial peptides that have the ability to kill bacteria that are resistant to standard antibiotics.  Currently, she has 14 U.S. patents, 4 foreign patents and numerous pending U.S. and foreign applications directed to these novel peptides and their therapeutic uses in infections.

In 2005, Pereira founded the company Biolytx Pharmaceutical Corp., and she currently serves as Chief Scientific Officer for the company.  In the last 10 years, antibiotic-resistant infections have risen around the world, and new therapeutic strategies for treating antibiotic-resistant infections are urgently needed.  Biolytx is working to meet this unmet need and is in pre-clinical development of antibiotic peptides for use in treatment of ocular, topical and serious hospital-acquired infections.

Pereira has been awarded over $7 million in grants to support the commercialization of new antimicrobial therapeutics.  Two basic research grants totaling $3.7 million were awarded to Pereira for basic research on the naturally occurring CAP37 and CAP-37-derived peptides.  An additional $3 million from state-supported funds has been awarded to Pereira and to Biolytx for applied and translational research.  Recently, Biolytx received $1 million in private seed money for continued commercialization efforts.

Pereira will be inducted on April 15, 2016, as part of the Fifth Annual Conference of the National Academy of Inventors at the United States Patent and Trademark Office in Alexander, Va.  Commissioner for Patents Andrew Hirschfeld will provide the keynote address for the induction ceremony.  Fellows will be presented with a special trophy, medal and rosette pin in honor of their outstanding accomplishments.