Sophisticated Genome Biology in the Tiny Fruit Fly

The fruit fly Drosophila has long been one of the workhorses of genetics and developmental biology. But for many genomic studies, fruit flies have had one big disadvantage: their small size.

As sequencing has become more sophisticated, experiments that were not possible in the fly just a few years ago, such as analyzing gene expression changes in a few cells, are now quite possible, says Don Fox, an Assistant Professor in the Department of Pharmacology and Cancer Biology.

Fox is taking advantage of that new potential to investigate two separate but partially overlapping areas of study. First of all, he wants to know which genes spring into action when tissues get injured and how that changes as flies advance into old age. Second, his lab is preoccupied with cells in the fly gut that are particularly prone to duplicating their genomes, forming genomically unstable polyploid cells similar to those that turn up in many human cancers. Fox wants to know exactly what it is that makes those cells unstable.

He is using sequencing approaches both to characterizethosepolyploidgenomesandto explore gene expression changes over time, with data generated in the IGSPs Genome Sequencing & Analysis Core Resource. Fortunately for Fox who arrived at Duke a year ago well-versed in genetics and cell biology and just beginning to tackle questions on a genomic scale his new lab is positioned right across the hallway from his colleague and long-time IGSP member Dave MacAlpine.

MacAlpine and his team are experts in genome biology,havingplayed animportantrolein modENCODE, an effort to classify all of the regulatory elements in the fly genome. The MacAlpine and Fox labs meet weekly in what is a mutually beneficial collaborative arrangement; Fox gains support in genomics and bioinformatics while MacAlpine gainssupportinmovingfromapproachesin Drosophila cell lines to those in whole fruit flies.

Its allowed my lab to be kind of fearless, Fox says. We can take on these bioinformatics-heavy experiments, which can easily be overwhelming. When I was contemplating where to start a lab, that opportunity for collaboration at Duke was a huge selling point.

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Biology and philosophy combine to form an ideal city

In a bookshelf-lined room of Tribble Hall, Mariska Leunissen from UNC-Chapel Hill began her discussion on the relationship between Aristotles ethics and biology,in front of an audience of students and faculty alike.

Oliver Beck/Old Gold & Black

She began by warning the audience about what was to come in her lecture: foul, racist language and an unexpectedly long hand out. Leunissen then launched into the meat of the lecture. She talked about Aristotles observations on biology, such as his theory of the four humors of the human blood and the idea that humans are a special kind of animal.

Next on the agenda? Aristotles ideal city. Aristotle believed that it was a lawgivers job to help and manipulate nature and create an ideal city. The first step to achieve this ideal city was to select the natural ingredients, i.e. the perfect men who will inhabit the city. Here is where the talk of biology returned: Aristotle believed northern men had blood that made them too spirited and southern men had blood that made them too lazy. Men from Greece however, had the perfect blood balance and were therefore the perfect men to begin the ideal city. However, they wouldnt live forever, so their offspring also had to be perfect.

Aristotle enacted countless rules in his eugenic theory as far as how to produce the perfect offspring. Marriages must be regulated to create perfect pairs, parents had to be at the ideal age when creating children, woman at 18 and men at 37. Whats more, the timing of childbirth had to be at the ideal hour and season, newborns diet and body had to be tweaked carefully and finally, men and women had to stop procreating once the got past their prime age. He also set up many ramifications considering the parental body type that would produce the ideal child. Once the ideal child is produced, they can be the second generation for the continuation of the ideal city.

Aristotles views on biology directly correlate with what he says about politics. He says that nature should not be left up to chance; lawgivers need to step in and make sure things go the way they should. Aristotles theory of reproduction provides facts that the lawgiver can turn into norms for how child-production should be arranged in the ideal city.

Students enjoyed the presentation.Im a more science-y person, I might major in it, so it was interesting seeing the philosophical side of it and how traits are integrated, freshman Tanner Debellis said. It provided more insight into things Im studying even though they might not be the correct way. It was interesting to see things from this point of view.

Freshman Layne Raborn agreed.It was science through reason instead of science through experience, Raborn said. Leunissen was very funny in some parts and presented her topic very well.

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Biology and philosophy combine to form an ideal city

Teen marine-biology buff makes discovery via undersea webcam off B.C. coast

Nice hat, buddy. A bull elephant seal wears a tracking tag glued to its fur. (LiveScience)A Ukrainian teenager is the toast of marine researchers half a world away after apparently witnessing something scientists have never seen an elephant seal devouring a slimy hagfish almost 3,000 feet below the surface of the ocean.

Kirill Dudko, a 14-year-old deep-sea biology nut, lives in the city of Donetsk. He was monitoring a live stream of undersea cameras when he spotted the seal in Barkley Canyon, off the west coast of Vancouver Island, making a meal of the unappetizing hagfish. It's thought to be shunned by predators because of the slimy mucus they exude. The fish, sometimes called slime eels, have existed largely unchanged for 300 million years.

But Dudko spotted the nose of an elephant seal slurping up the hagfish like a fugitive piece of fettuccine.

In a YouTube video of the Jan. 12 incident, Steven Mihaly, a staff scientist with Ocean Networks Canada, said the images confirmed for the first time speculation on how deep an elephant seal could dive.

Dudko emailed Neptune Canada, which links the 800-kilometre network of cameras and instruments to the Internet for Ocean Networks, based at the University of Victoria.

[Related: Seals death sentence in Quebec halted, thanks to outcry from animal lovers ]

Monday morning we had an email from him saying, I saw something strange and weird. Some monster just ate a fish in front of me. What was it? And that sent all of us into a bit of a flurry to back this up," said associate director Kim Juniper.

It was like a horror film, the biology enthusiast wrote in his email, according to the Victoria Times Colonist. This creature wasnt like a fish and I realized it was a mammal because of the nose and moustache.

In a separate email to the Times Colonist, Dudko said he was puzzled because he didn't think any mammal except a whale could dive so deep.

In an interview with CBC News, Kiril's mother, Svetlana, said she was very proud of her son.

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Research and Markets: Cord Blood: Biology, Transplantation, Banking and Regulation Incorporates the Latest …

DUBLIN--(BUSINESS WIRE)--

Research and Markets (http://www.researchandmarkets.com/research/rtrjc4/cord_blood) has announced the addition of the "Cord Blood: Biology, Transplantation, Banking and Regulation" book to their offering.

The relatively new field of cord blood (CB) is still evolving, having seen vast change since the first successful CB transplantation over 20 years ago.

This volume aims to continue advancing the clinical efficacy and relevance of this area by providing a solid understanding of its present status. Representing a significant expansion of previous literature on the topic, this comprehensive resource on CB incorporates the latest developments into 39 chapters by experts in various areas of practice.

Topics:

- CB biology hematopoiesis, stem/progenitor cells and their microenvironment.

- Engraftment preclinical and clinical enhancements such as use of prostaglandin E2, inhibition of cell surface protein CD26, expansion of shortterm

repopulating HSCs, use of fucosylation and intrabone transplantation.

- Regenerative medicine induced pluripotent stem cells, endothelial progenitor cells and other cells.

- Immune cells CB immune cell immaturity, T helper cells, T regulatory cells, neonatal immune tolerance, natural killer cells and T-cell-dependent immune competence.

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Research and Markets: Cord Blood: Biology, Transplantation, Banking and Regulation Incorporates the Latest ...

AP Biology Practice 2 – Using Mathematics Appropriately – Video


AP Biology Practice 2 - Using Mathematics Appropriately
Paul Andersen explains how to use mathematics appropriately. He begins by emphasizing the important role that mathematics plays in the life sciences today and in that the future. He describes important mathematical equations in each of the four big ideas. According to the new AP Biology framework the student can justify the selection of a mathematical routine to solve problems. The student can apply mathematical routines to quantities that describe natural phenomena. Finally the student can estimate numerically quantities that describe natural phenomena. Intro Music Atribution Title: I4dsong_loop_main.wav Artist: CosmicD Link to sound: http://www.freesound.org Creative Commons Atribution License Image Atributions Bayerwald, Mike aus dem. English: Osmosis. Own work. Accessed January 21, 2013. commons.wikimedia.org Johnuniq. English: Hardy--Weinberg Principle for Two Alleles, February 26, 2009. Own work. commons.wikimedia.org Retama. In Vitro Test of Germination of a Dicot; There Are Little Plants and Non Viable Seeds. The Medium Is a Murashige and Skoog Without Any Hormone. Own work. Accessed January 21, 2013. commons.wikimedia.org Sjef. English: DNA Sequencing Trace. Own work. Accessed January 21, 2013. commons.wikimedia.org Trio3D. English: Integrated Micro Solutions/IXMicro IMS 9130 Graphics Processing Unit on a Twin Turbo-128M (4 MB) Video Card. Own work. Accessed January 21, 2013. commons.wikimedia.org "File:Agar Plate with Colonies.jpg." Wikipedia, the Free Encyclopedia ...

By: bozemanbiology

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NU Regents approve center for brain, biology, behavior

The University of Nebraska Board of Regents approved the Center for Brain, Biology and Behavior as an interdisciplinary research center at the University of Nebraska-Lincoln on Friday.

The center is a key component of an emerging collaboration between athletics and research at UNL. Known as CB3, it will be located later this year in half of a 50,000-square-foot research area in the East Stadium addition to Memorial Stadium.

CB3 will house a radiology unit and a state-of-the-art functional magnetic resonance imaging magnet, which will enable faculty and students from a wide spectrum of disciplines to conduct research related to behavior and performance, including the study of concussions.

"CB3 builds on our strengths in concussion research and its strong multidisciplinary emphasis will position UNL as a leader in research on the brain, biology and behavior," said Prem S. Paul, UNL vice chancellor for research and economic development, in a written statement. "This center is at the heart of a unique partnership between our prestigious academic and athletic programs."

The center will occupy space in the south half of the East Stadium addition, while the north half will be dedicated to the Nebraska Athletic Performance Lab. The research facility also will provide shared space, including 48 laboratories and a common area large enough to accommodate 40 to 50 people.

Information provided by the University of Nebraska.

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Trailblazing CLU biology professor leaving classroom after 50 years

Barbara Collins, who is leaving the classroom after 50 years of teaching microbiology and botany at California Lutheran University, has blazed some trails in hertime.

Over the years, leading field trips from local parks to New Zealand, Collins has earned a reputation for charging ahead on the trail, sometimes leaving her students breathlessly trying to catchup.

Collins also has been a trailblazer in her career, working full time as a professor while bringing up fivechildren.

"She's a force of nature," said David Marcey, a biology professor at CLU. "She's maintained an active role in teaching and in field studies, often outpacing her 19-year-old students up the mountain. ... She's reallyirreplaceable."

Collins, 83, has contracted an incurable, progressive lung infection that makes it difficult for her to breathe and left her weighing less than 90 pounds. She will retire this year, a decision she resisted but has reluctantlyaccepted.

"I could teach sitting down, but working in the lab, I wouldn't have the breath to go around and get the work done," she said. "At first, it was really hard, but after the last hospital visit, I realized I really couldn't do it. ... I don't know what the future is, but we just go ahead and do whatwecan."

Collins still shows up at her office most days, working on a project to identify trees and shrubs on campus. She's also planning on writing a book about living life in your80s.

That's typical of Collins.

(View the Trailblazing CLU biology professor slide show.)

When she was pregnant back in the 1960s, her department chairman said Collins would have to stop teaching. Collins would have none of it, telling the chairman that if her students had never seen a pregnant woman, it was about time they did. She went on to receive the President's Award for Teaching Excellence in2007.

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Trailblazing CLU biology professor leaving classroom after 50 years

Research and Markets: The Book 'Cord Blood: Biology, Transplantation, Banking, and Regulation' Incorporates the Latest …

DUBLIN--(BUSINESS WIRE)--

Research and Markets (http://www.researchandmarkets.com/research/r6dd5g/cord_blood) has announced the addition of the "Cord Blood: Biology, Transplantation, Banking, and Regulation" book to their offering.

The relatively new field of cord blood (CB) is still evolving, having seen vast change since the first successful CB transplantation over 20 years ago. This volume aims to continue advancing the clinical efficacy and relevance of this area by providing a solid understanding of its present status. Representing a significant expansion of previous literature on the topic, this comprehensive resource on CB incorporates the latest developments into 39 chapters by experts in various areas of practice.

Topics:

- CB biologyhematopoiesis, stem/progenitor cells and their microenvironment.

- Engraftmentpreclinical and clinical enhancements such as use of prostaglandin E2, inhibition of cell surface protein CD26, expansion of shortterm

repopulating HSCs, use of fucosylation and intrabone transplantation.

- Regenerative medicineinduced pluripotent stem cells, endothelial progenitor cells and other cells.

- Immune cellsCB immune cell immaturity, T helper cells, T regulatory cells, neonatal immune tolerance, natural killer cells and T-cell-dependent

immune competence.

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Research and Markets: The Book 'Cord Blood: Biology, Transplantation, Banking, and Regulation' Incorporates the Latest ...

How can evolutionary biology explain why we get cancer?

Jan. 22, 2013 Over 500 billion cells in our bodies will be replaced daily, yet natural selection has enabled us to develop defenses against the cellular mutations which could cause cancer. It is this relationship between evolution and the body's fight against cancer which is explored in a new special issue of the Open Access journal Evolutionary Applications.

"Cancer is far from a single well-defined disease which we can identify and eradicate," said Dr Athena Aktipis, Director, Human and Social Evolution, Center for Evolution and Cancer at the University of California, San Francisco. "It is highly diverse and evolutionary theory allows us to consider cancer as a highly complex and evolving ecosystem. This approach can improve the understanding, treatment and prevention of a number of different cancer types."

By applying the principles of evolutionary biology papers in the special issue ask: Why do we get cancer, despite the body's powerful cancer suppression mechanisms? How do evolutionary principles like natural selection, mutation, and genetic drift, work in a cancer ecosystem? How can we use evolutionary theory to minimize the rate of cancers worldwide?

"Nowhere is the diversity of cancer better revealed than the many reasons why we remain vulnerable to it," said Dr Aktipis. "Evolutionary medicine allows us to see explanations for traits that leave organisms vulnerable to disease."

These evolutionary explanations include the role of environmental factors, such as the relationship between tobacco availability and lung cancer; co-evolution with fast evolving pathogens; constraints on what selection can do; trade-offs, such as the capacity for tissue repair vs. risk of cancer; reproductive success at the expense of health; defenses with costs as well as benefits, such as inflammation.

"An evolutionary approach can unite and explain the many avenues of cancer research by allowing us to see cancer as an ecosystem," concluded Dr Aktipis. "Just as a forest depends on the individual characteristics of trees as well as the interactions of each tree with its environment; similarly tumors can be [composed of] genetically distinct cells, which depend on both cell-to-cell interactions within the tumor, as well as on the interactions of tumor itself with the body."

This special issue is collaboration between scientists from the Darwinian Evolution of Cancer Consortium in France and the Center for Evolution and Cancer at the University of California, San Francisco. The issue is guest edited by Frederic Thomas, Michael Hochberg, Athena Aktipis, Carlo Maley and Ursula Hibner.

Papers from the Evolution and Cancer Special Issue are all freely available on the Evolutionary Applications website: http://www.evolutionaryapplications.org

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Mersana Therapeutics Expands Senior Leadership Team with Appointments of Peter Park, Ph.D., as VP of Biology and Wayne …

CAMBRIDGE, Mass.--(BUSINESS WIRE)--

Mersana Therapeutics, Inc., a biopharmaceutical company developing its Fleximer antibody-drug conjugate (ADC) platform and pipeline of small molecule Fleximer conjugates, announced today that the company has expanded its senior leadership team. Peter U. Park, Ph.D., has joined the company as Vice President of Biology, and Wayne Foster, CPA, has joined as Vice President of Finance.

The addition of Peter to our senior team reflects Mersanas focus on our next generation Fleximer antibody-drug conjugate (ADC) platform, said Nicholas Bacopoulos, Ph.D., President and Chief Executive Officer of Mersana. Peters extensive and successful experience with ADC discovery and development will be integral to the continued advancement of our Fleximer-based ADC platform and pipeline in oncology. Additionally, as we continue to advance our existing collaborative projects and grow through new strategic alliances, Peters experience with Pharma and Biotech collaborations will be fundamental. Waynes broad and deep expertise on strategic planning, alliance management, financial processes and controls, and fundraising will also serve Mersana very well as we progress to our next stage of growth.

Dr. Park brings to Mersana significant experience in the discovery and development of antibody-drug conjugate therapies. Prior to joining Mersana, he was a co-founder and Chief Executive Officer of Habgen, Inc., a start-up focused on antibody therapeutics. Prior to that, Dr. Park served at ImmunoGen, Inc. for 10 years, most recently as Senior Director of Discovery Research. In this role, he managed the discovery research portfolio for the development of novel monoclonal antibody and antibody-drug conjugates for oncology, advancing two compounds into Phase 1 and several additional projects into late discovery and preclinical development. Additionally, he oversaw ImmunoGens research collaboration with Sanofi. He is the author on many patents and has contributed to numerous scientific publications. Dr. Park earned his Ph.D. and B.S. in Biology from the Massachusetts Institute of Technology.

Mr. Foster has held management positions in several life science and technology companies. Prior to joining Mersana, he served for nine years as Senior Director of Finance at Tolerx, Inc. In this role, he was responsible a wide variety of finance functions as the company grew from early stage through precommercialization. Mr. Foster also served as Senior Manager at Arthur Andersen LLP where he specialized in emerging life science and technology companies. He earned his B.B.A. in Accounting from the University of Massachusetts Amherst.

About Mersana

Mersana engineers novel drug conjugates that maximize the potential of new and established therapeutic classes. Utilizing its proprietary conjugation technology, which is comprised of the Fleximer polymer and a broad array of customizable linker chemistries, Mersana is developing its next-generation antibody-drug conjugate (ADC) platform with superior properties not found with other ADC technologies. Mersana is currently working with a number of top Pharma companies to develop next generation Fleximer-ADCs and most recently announced a $270 million collaboration with Endo Pharmaceuticals in March, 2012. The company is also advancing its own pipeline of next-generation drugs with best-in-class potential to address unmet needs and improve patient outcomes in multiple oncology indications. Mersanas investors include New Enterprise Associates (NEA), Pfizer Venture Investments, Proquest Investments, Fidelity Biosciences, Rho Ventures and Harris and Harris Group. Mersana was founded by PureTech Ventures, LLC and a group of leading academics and clinicians.

For more information, visit http://www.mersana.com.

Fleximeris a trademark of Mersana Therapeutics, Inc.

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Mersana Therapeutics Expands Senior Leadership Team with Appointments of Peter Park, Ph.D., as VP of Biology and Wayne ...

The biology of plague: Systems approach used to investigate strains of Yersinia

Journal cover showing association network inferred from integrated proteomic and transcriptomic data from three different Yersinia strains with varying levels of virulence. Examples of significantly enriched functional clusters are indicated in the figure.

(Phys.org)When is the plague not the plague? When it's a different strain of the same bacteria. In two strains of the bacteria genus Yersinia a highly lethal pathogen and its less-virulent formscientists performed multi-omic analyses to gain insights how they differ. They found that how the genes in both are expressed contribute to the striking difference in the diseases caused by these pathogens. The research team included scientists from Pacific Northwest National Laboratory, the J. Craig Venter Institute, and the University of Texas Medical Branch.

The work, featured on the cover of Molecular BioSystems, is the next step in ongoing research on Yersinia pestis (YP), which causes plague with a high mortality rate, and Yersinia pseudotuberculosis (YPT), an intestinal pathogen with a modest mortality rate. The bacteria are highly similar with some species-specific differences; however, the molecular causes of their distinct outcomes are poorly understood. The team's analysis revealed that gene and protein expression levels of shared or common virulence-related proteins were both higher in YP than in YPT.

This suggests that adaptation in the regulatory architecture of YP, in addition to the presence of unique genetic material, may contribute to its increased pathogenicity," said the study's lead author Dr. Charles Ansong, PNNL.

The availability of genome sequences for several Yersinia strains, including YPT and both epidemic and non-epidemic YP variants, has provided an opportunity to explore mechanisms responsible for the differences in pathogenicity. Scientists already knew that all human pathogenic Yersinia strains, including YP and YPT, share almost identical genes in plasmids that are essential for virulence.

This work highlights the utility of a systems approach incorporating multiple omics measurements and computational analyses to provide novel insights into Yersinia biology; and provides an important resource for the Yersinia research community that should aid the understanding of the markedly different pathogenicities of YP and YPT.

The scientists grew YPT and two forms of YP at temperatures representative of host environments, then sampled them over an 8-hour period. The samples were analyzed using a multi-genome microarray and mass spectrometric methods.

"This experimental design, using multiple omic technologies, was exciting because it allowed us to get a greater grasp of the mechanisms involved in the differences between what have been sometimes called a 'nearly clonal' group of organisms." said PNNL biochemist Dr. Joshua Adkins.

Novel virulence factors predicted from computational analysis of the multi-omics data will be validated in animal models of bubonic plague in follow-on studies. These represent apparent novel therapeutic targets that, with the recent reports of drug-resistant Yersinia strains, are sorely needed.

More information: Ansong, C. et al. A Multi-omic Systems Approach to Elucidating Yersinia Virulence Mechanisms, Molecular BioSystems.DOI: 10.1039/C2MB25287B

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The biology of plague: Systems approach used to investigate strains of Yersinia

Students present research to community at UA Undergraduate Biology Research Program Conference

By ALISON DORF Published January 19, 2013 at 11:05pm Updated January 19, 2013 at 11:05pm

Scientists, mentors, parents and members of the community bustled through the hallways of the Thomas W. Keating building at the UA on Saturday, on their way to listen to students presenting their scientific research and findings.

The Undergraduate Biology Research Program held an annual conference to give students an opportunity to present the results of their projects to members of the general public.

Since UBRP began 24 years ago, it has helped students from many diverse backgrounds advance their science education. Students presented their experiments and research in the form of posters, which are often used at scientific conferences because they can convey a lot of information very quickly, said Carol Bender, director of UBRP and program director of molecular and cellular biology.

The people who are going to be walking around and talking to them, some of them are scientists and they may have suggestions for how they [students] can tweak their experiments or how they can address problems theyve encountered, Bender said.

Other attendees were parents and general members of the public.

Its really important they are able to explain their work in terms that anybody could understand, Bender said.

The presenting students ranged from high school to post-baccalaureate students with diverse majors and interests. A vast majority, 70 percent, are majoring in life sciences, while the rest vary from engineering to social science to psychology majors. The most unusual in UBRP history was a cello performance major, said Bender.

The posters covered topics including black-tailed prairie dogs, and the protein composition of epidemic and non-epidemic strains of clostridium difficile a bacterium that commonly affects hospital patients.

It was quite nerve-wracking because this is my first time presenting data at all scientifically related, besides my lab experiments like during school, UA physiology sophomore Ashwini Kaveti said. Im glad Im getting this experience.

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Cowboy University teaches history, biology and riding skills

HASTINGS -- Ridin' and ropin' are part of the curriculum for one J-term class at Hastings College.

Cowboy University, taught by biology professor John Kuehn, is the name of the class that helped about 14 students learn all about horses, from their history and uses to their biology and equipment. They also got to apply the lessons to actual animals when the students got on real horses last week.

"It teaches the physiology and biomechanics in an applied setting so we give them something to do in terms of riding a horse and observing rodeo," Kuehn said, adding that he hopes the students will get an appreciation for horses.

Shelby Sandford, a sophomore from O'Neill, chose the class because "it looked like it would be ridiculously fun and so far it's proven to be true."

Although she and others in the class said it has been a lot of fun, they have learned a lot as well, even those who have been riding since they were toddlers.

Kuehn, who grew up riding his family's horses, said he felt most people who grow up in Nebraska, whether they come from a farming and ranching background or not, have a fascination with horses and that led many of his students to the class.

"The (riding) was definitely part of the draw," he said. "If I were to just say we were going to have an anatomy or biology course, I doubt as many would have been interested."

The class started Jan. 3 with the other J-term classes, the classes at Hastings College between first and second semester. In the first few weeks of class, students watched a documentary on Mongolian horse racing, learned about the different breeds of horses, studied the biology names for the parts of a horse as well as the proper names for parts of the saddle.

"The first couple days of class we went over basic horsemanship," Sandford said. "We looked at some different areas of horses, different ways people train in different countries and the different ways they use horses."

Holly Bishop, a senior from Beatrice, said learning that first helped the class understand horses better before climbing on the back of one.

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Cowboy University teaches history, biology and riding skills