Category Archives: Biology

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.

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,”

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!

 

 

Science Café

 

Here’s a great chance to learn about Oklahoma’s amazing raptors. Oklahoma State University and the Stillwater Public Library are teaming up for what they’re calling Science Café OSU.

They have two programs planned for the coming weeks, both will be talking about red-tailed hawks and golden eagles.

Golden Eagle

Golden Eagle  

 

Red-tailed Hawk

Red-tailed Hawk

OSU associate professor Jim Lish and doctorate candidate Megan Judkins will be giving the presentations. They’ll also be bringing along birds as guests.

Lish has been researching red-tail hawks for more than 40 years. He holds three degrees in wildlife ecology including a Master of Science and a doctorate degree from OSU. Judkins is a Choctaw tribal member and assistant manager at the Grey Snow Eagle House. She is currently pursuing a doctorate degree in integrative biology at OSU. Her research focuses on the genomics of bald and golden eagles.

“The Payne County Audubon Society will have copies of Dr. Lish’s new book ‘Winter’s Hawk: Red-tails on the Southern Plains’ available for purchase and signing at both programs,” said Karen Neurohr, OSU Library professor and Science Café coordinator. “Ms. Judkins is bringing Ann, a red-tail hawk and RB, a golden eagle to the programs.”

The first program is Nov. 12 at 6:30 p.m. in the Stillwater Public Library Auditorium. The program will be repeated Nov. 17 at 6:30 p.m. in the Peggy V. Helmerich Browsing Room of the Oklahoma State University Library.

Everyone is welcome, you don’t need to have a science background to attend.

Digging for Dinos

Who doesn’t like digging for dinos? I had the chance this summer to go on a real-life, honest to goodness dinosaur dig in the Oklahoma Panhandle. It was in Black Mesa near Kenton, OK. That’s about thisclose to the New Mexico and Colorado state lines.

I was a guest of Dr. Anne Weil of the OSU Center for Health Sciences. (She’s been featured before here, here, and here.) The dig was part of the ExplorOlogy program run through the Sam Noble Museum in Norman. ExplorOlogy is all about helping Oklahoma students and teachers get a hands on look at the wonderful world of science. The kids spend the night in the Sam Noble Museum, they get an up close look at the OKC Zoo, and they go work in the field on actual science expeditions.

The dinosaur dig in Black Mesa is an example. The students were helping dig up some Apatosaurus bones. That was a huge dinosaur most of us grew up calling a Brontosaurus.

In addition to digging up the dinosaurs the students went hiking and took a census of the local insects in Black Mesa (video to come!!).

I can’t thank Dr. Weil and the staff at the Sam Noble Museum enough for letting me tag along.

If you know a student who is interested on going next summer click here to learn more about the program and how you can register.

 

This Scientist is OK- Dr. J.P. Masly

Dr. J.P. Masly is an assistant professor of biology at the University of Oklahoma. He studies how genes evolve over time to form complex organisms (like you and me!!).

He recently received an award from the National Science Foundation that will allow him to continue with his research and build educational outreach programs in the community.

He talks, in this video, about why he studies the genes of fruit flies (here’s a hint, we’re a lot a like) and at the 2:15 mark about why he thinks science and religion do not have to conflict.

Using Radar to Track Bird Migration

Two University of Oklahoma students have discovered a way to use weather radar to track bird migrations. Kyle Horton is a biology student and Phillip Stepanian is studying meteorology and electrical engineering. They recently found a way learn how birds migrate using the country’s weather radar network. Below the pics is a news release from OU. I think this is a fantastic way to use an already existing system (the weather radar network) for an entirely different field than it was built.

Phillip M. Stepanian- Doctoral student in Meteorology and Electrical Engineering at the University of Oklahoma

   Phillip M. Stepanian- Doctoral student in Meteorology and Electrical Engineering at the University of Oklahoma

Kyle G. Horton- Doctoral student in Biology at the University of Oklahoma

Kyle G. Horton- Doctoral student in Biology at the University of Oklahoma

OU Students Use Nation’s Weather Radar Network to Track Bird Migration at Night

Norman, Okla.—Using the nation’s weather radar network, two University of Oklahoma doctoral students have developed a technique for forecasting something other than the weather: the orientation behavior of birds as they migrate through the atmosphere at night.  The students have discovered a way to use the latest dual-polarization radar upgrade to measure broad-scale flight orientation of nocturnal migrant birds—a promising development for biologists and bird enthusiasts.

The approach to the problem paired Phillip M. Stepanian, a meteorology and electrical engineering student, and Kyle G. Horton, a biology student, on the study that demonstrates how the upgraded national weather radar network contributed to the understanding of animal flight orientation behavior at a large spatial scale. Stepanian and Horton may be the first to develop a practical application of polarimetric radar data for tracking migrant birds during nighttime flight.

“This is an important advance because we can now measure how migrants compensate for wind speed and direction to achieve a particular migration track direction; essentially extracting a large-scale measure of bird behavior.  We are already involved in several follow-on studies that look at the behavioral variation in flight orientation at large spatial scales,” says Jeffrey F. Kelly, Oklahoma Biological Survey.

Horton, who is interested in bird strategies and orientation as they migrate from one place to another at night, will use the methodology to track migrant birds on the east coast and weather events that may disrupt flight patterns of the birds.  Stepanian is interested in the method for collecting the data using the nation’s upgraded weather radar network.  He wants to apply measurements to bird migration in ways not done before, which is a new application of the radar.

The ability to forecast migrant bird patterns will provide biologists and birders with an important tool for tracking nighttime flight of migrants.  Horton hopes to answer some big biological questions with this methodology, while Stepanian values the importance of the radar in tracking migrants and applying the data in new and innovative ways.

An article on this study has been published in the Institute of Electrical and Electronics Engineering’s Geoscience and Remote Sensing online early edition.  The National Science Foundation and the U.S. Department of Agriculture funded this research project.

Ancient Dental Plaque

A University of Oklahoma scientist is perfecting the art (and by art I mean science) of studying ancient dental plaque. We’ve highlighted Dr. Christina Warinner before when her research gained national recognition. Now she’s featured in a fantastic video produced by Illumina. The company describes itself as, “a leading developer, manufacturer, and marketer of life science tools and integrated systems for large-scale analysis of genetic variation and function.” 

Dr. Warinner likes to say she’s an “archaeologist of the invisible”. She studies the dental plaque from teeth that are thousands of years old. Bacteria covers that dental plaque, from that she’s able to learn all kinds of things about the person who once used that tooth. Where they lived, what they ate, whether they were healthy or not, etc…

This video is an amazing look inside the process.