Category Archives: Wisconsin Stem Cells

Photo collage: S.V. Medaris

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Whether a close-up of a leafcutter ant, or a micrograph of the neurons derived from marmoset stem cells, or an MRI of the hidden pathways in the human brain, submissions to UW-Madisons 2015 Cool Science Image Contest continue to put science and nature on eye-catching display.

Sorting through a record number of entries, judges for the contest selected 11 still images and one video as winners of the annual competition. The judges representing broad expertise in scientific imaging, art and science communication worked through 115 submissions to arrive at this years winning entries.

Submissions overall and winning submissions represent a wide segment of the UW-Madison community, including faculty, staff and students and a range of disciplines from art to zoology.

This years contributions were among the strongest weve had and reflect the diversity and creativity of the UW-Madison scientific imaging community, says Kevin Eliceiri, a contest judge and director of UW-Madisons Laboratory for Optical and Computational Instrumentation. I was struck in particular by the broad number of disciplines and range of techniques represented.

Winning images depended on techniques ranging from MRI to a cell phone camera.

2015 CSI Contest winners are:

Zoology graduate student Hilary Bultman for her micrograph of thyme plant floral trichromes.

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Science meets art: 2015 Cool Science Images unveiled

This Saturday when the University of Kentucky basketball team faces off with the University of Wisconsin in the NCAA tournament semi-finals, die-hard Kentucky fan Scott Logdon may think twice about rooting against the Wisconsin Badgers.

Nearly two years ago, Logdon was given a life-saving donation of stem cells that helped combat his acute myeloid leukemia. The donor of those cells turned out to be 22-year-old Chris Wirz, a student at the University of Wisconsin.

Logdon, 44, learned the identity of his donor last April, more than a year after the stem cell treatment and just days after the University of Kentucky squeaked past the University of Wisconsin at the NCAA semi-finals with a score of 74 to 73.

Logdon remembers feeling mixed emotions when the Kentucky wildcats won. Later, when he found out about his donor, he joked, That must have been the Badger blood in me.

Courtesy Angela Logdon

PHOTO: Chris Wirz gave life saving stem cells to Scott Logdon, who was suffering from leukemia.

Logdons ordeal started in the fall of 2012, when he was diagnosed with acute myeloid leukemia after mistaking early symptoms for strep throat. Logdon said his doctors told him chemotherapy could only keep the cancer at bay. A full stem cell transplant would be needed to cure him of the deadly disease.

Logdons doctors hoped one of his two siblings might be a match, but neither was able to donate. Longons family and community rallied in the small town of Saldasia, Kentucky, and registered over 120 people who would be willing to donate stem cells or bone marrow.

But no one who registered was a good match for Logdon.

[The doctors] went to the national bone marrow registry to try and find the match, the father of four said. I had to go back to the hospital every 30 days [for] maintenance chemo; it was a very long wait.

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Kentucky Fan Gets Life-Saving Stem Cell Donation From Univ. of Wisconsin Student

Scott Logdon is a die-hard University of Kentucky basketball fan, but he can't deny he's got some Wisconsin blood in him -- literally.

When the father of four was being treated for high-risk leukemia at UK in 2013, 20-year-old University of Wisconsin student Chris Wirz anonymously donated bone marrow stem cells to him. The two men first spoke just after the Wildcats bested the Badgers during last year's NCAA Final Four, and basketball was a frequent topic of conversation as their friendship grew.

While each will be rooting for his own team during this Saturday's Final Four rematch, both say they have a soft spot for the other team.

"I've stayed true to UK," said Logdon, 44, of Salvisa, Ky. "But when I talked to Chris for the first time I told him, 'That's why I felt so bad when we beat you: I've got Badger blood in me!"'

Wirz, who lives three blocks from where the Badgers play, hopes Wisconsin wins this year, and has even predicted an upset in his basketball bracket. "Who doesn't want to root for the underdog?" he said.

But he plans to send a text of congratulations if Logdon's team wins -- since their connection is much deeper than basketball rivalry.

"We're literally working off the same immune system," said Wirz, now 22 and a University of Wisconsin senior. "This has been one of the most emotionally overwhelming experiences of my life, realizing how important he is to his family and his community and seeing the hole that would've been left by him."

A dire diagnosis

Logdon, chief deputy at Woodford County Detention Center in Versailles, Ky., and a youth minister in his church, recalled playing basketball with teenagers just a few nights before going to the doctor for what his wife, Angela, initially thought was strep.

But tests showed he had acute myeloid leukemia, a blood cancer estimated by the American Cancer Society to have stricken 18,860 Americans last year and killed about 10,460, mostly adults.

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Blood ties: Ky. basketball fan gets Wisconsin assist

The Wisconsin Stem Cell Roundtable (WiSCR) was founded in 2009 by a group of junior stem cell researchers at the University of WisconsinMadison (UWMadison). The goals of WiSCR are to provide a casual scientific forum to foster interaction, collaboration, dialogue, and support for graduate students and postdoctoral fellows at UWMadison and also provide outreach to educate the public about stem cells and current research in the field.

WiSCR holds monthly meetings during which we either discuss current stem cell literature or have a member present their research. WiSCR also organizes and participates in various science outreach events in order to engage and educate both children and adults in Wisconsin about stem cell research.

If youre interested in being added to the WiSCR mailing list, please send an email to uwstemcellroundtable@gmail.com. This way you can receive notifications about upcoming meetings and outreach opportunities.

Where would stem cell research and outreach be today without Ka Yi Ling? Check it out here on the UW Graduate School website and learn more about the past President of WiSCR.

Summer Undergraduate Research Fellowship (SURF) program, which aims to introduce talented undergraduate students to stem cell research with the help of a graduate student or postdoc mentor. To learn more about this exciting opportunity please see information for undergraduates [trainee application] or graduate students/post-doctorate fellows [mentoring application]. It will continue in the summer of 2014 but no details are available yet. Please keep watching this space for more information as we get it.

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Wisconsin Stem Cell Roundtable (WiSCR) - Welcome to Stem ...

Two NIH Roadmap Epigenomics studies answer longstanding questions about the differences between chromosome pairs and how chromosome folding influences gene expression

While genomics is the study of all of the genes in a cell or organism, epigenomics is the study of all the genomic add-ons and changes that influence gene expression but aren't encoded in the DNA sequence. A variety of new epigenomic information is now available in a collection of studies published Feb. 19 in Nature by the National Institutes of Health (NIH) Roadmap Epigenomics Program. This information provides a valuable baseline for future studies of the epigenome's role in human development and disease.

Two of these studies, led by researchers at University of California, San Diego School of Medicine and Ludwig Cancer Research, address the differences between chromosome pairs (one inherited from mom, the other from dad) and how chromosome folding influences gene expression.

"Both of these studies provide important considerations for clinicians and researchers who are developing personalized medicines based on a patient's genomic information," said Bing Ren, PhD, professor of cellular and molecular medicine at UC San Diego, Ludwig Cancer Research member and senior author of both studies.

The first paper by Ren's group takes a look at differences in our chromosome pairs. Each of us inherits one set from our mother and the other from our father. Chromosome pairs are often thought to be identical, one just a backup for the other. But this study found widespread differences in how genes are regulated (turned on and off) between the two chromosomes in a pair. It turns out that we all have "biases" in our chromosomes. In other words, different traits have a stronger contribution from one parent than the other. The study also suggests that these biases are rooted in inherited sequence variations and that they are not randomly distributed. These findings help explain why, for example, all kids in a family may have their father's hair but their mother's eyes.

The second paper by Ren's group tackles how the genome is organized and how it changes as stem cells differentiate (specialize). DNA strands in every cell are tightly wound and folded into chromosomes. Yet chromosomal structures, and how they influence gene expression, are not well understood. In this study, Ren and team mapped chromosomal structures in stem cells and several different differentiated cell types derived from stem cells. First, they induced differentiation in the stem cells. Then they used molecular tools to examine how the structure of the cells' chromosomes changed and how that change is associated with gene activity. The team found that chromosomes are partitioned into relatively stable structural units known as topologically associating domains (TADs), and that TAD boundaries remain constant in different cell types. What's more, the researchers found that the changes in chromosomal architecture mostly take place within the TADs in a way that correlates with changes in the epigenome.

"The epigenome -- chemical modifications to chromosomes and 3D chromosomal structure -- is not just a linear object," Ren said. "The epigenome is a 3D object, folded in a hierarchical way, and that should affect how we think about many aspects of human development, health and disease."

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Co-authors on the paper "Integrative Analysis of Haplotype-Resolved Epigenomes Across Human Tissues" include Danny Leung, Inkyung Jung, Nisha Rajagopal, Anthony Schmitt, Siddarth Selvaraj, Ah Young Lee, Chia-An Yen, Yunjiang Qiu, Samantha Kuan, Lee Edsall, Ludwig Cancer Research; Shin Lin, Yiing Lin, Stanford University and Washington University School of Medicine; Wei Xie, formerly at Ludwig Cancer Research and now at Tsinghua University; Feng Yue, formerly at Ludwig Cancer Research and now at Pennsylvania State University; Manoj Hariharan, Joseph R. Ecker, Howard Hughes Medical Institute and Salk Institute for Biological Studies; Pradipta Ray, University of Texas; Hongbo Yang, Neil C. Chi, UC San Diego; and Michael Q. Zhang, University of Texas, Dallas and Tsinghua University.

Co-authors on the paper "Chromatin Architecture Reorganization during Stem Cell Differentiation" include Jesse R. Dixon, Siddarth Selvaraj, Ludwig Cancer Research and UC San Diego; Inkyung Jung, Yin Shen, Ah Young Lee, Zhen Ye, Audrey Kim, Nisha Rajagopal, Yarui Diao, Ludwig Cancer Research; Jessica E. Antosiewicz-Bourget, Morgridge Institute for Research; Wei Xie, Tsinghua University; Jing Liang, Huimin Zhao, University of Illinois at Urbana-Champaign; Victor V. Lobanenkov, National Institute of Allergy and Infectious Diseases; Joseph R. Ecker, Howard Hughes Medical Institute and Salk Institute for Biological Studies; James Thomson, Morgridge Institute for Research, University of Wisconsin and University of California, Santa Barbara.

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New insights into 3-D genome organization and genetic variability

Madison, Wisconsin A team led by a University of Wisconsin School of Medicine and Public Health stem-cell scientist and ophthalmologist is beginning work on a patch made of induced pluripotent stem cells (iPSCs) to help restore vision to people whose retinas have been damaged by conditions such as retinitis pigmentosa and age-related macular degeneration.

Dr. David Gamm, director of the McPherson Eye Research Institute and associate professor of ophthalmology and visual sciences at the UW School of Medicine and Public Health, and collaborators will begin developing the stem-cell therapy, thanks to a $900,000 grant from the Foundation Fighting Blindness.

Gamm, a pioneer in retinal stem-cell research, says that a two-layered patch of cells to replace damaged retinal tissue could be the best strategy for reconstructing the outer retina when multiple cell types have succumbed to disease. Gamms lab has succeeded in using stem-cell technology to turn skin and blood cells into retinal cells.

The continuing challenge has been to get the transplanted cells to survive the hostile conditions of the diseased retina, arrange themselves appropriately, and make the necessary connections to restore vision, says Gamm. I believe we have a plan that will make progress toward that goal.

Video: Learn more about how David Gamm is using stem cells to treat retinal diseases.

Gamms collaborators include Dr. James Thomson of the Morgridge Institute for Research, Dr. Derek Hei of the UW-Madison Waisman Center and Dr. Dennis Clegg of the University of California-Santa Barbara.

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UW Stem Cell Researchers Building a 'Retinal Patch' to ...

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Newswise While genomics is the study of all of the genes in a cell or organism, epigenomics is the study of all the genomic add-ons and changes that influence gene expression but arent encoded in the DNA sequence. A variety of new epigenomic information is now available in a collection of studies published Feb. 19 in Nature by the National Institutes of Health (NIH) Roadmap Epigenomics Program. This information provides a valuable baseline for future studies of the epigenomes role in human development and disease.

Two of these studies, led by researchers at University of California, San Diego School of Medicine and Ludwig Cancer Research, address the differences between chromosome pairs (one inherited from mom, the other from dad) and how chromosome folding influences gene expression.

Both of these studies provide important considerations for clinicians and researchers who are developing personalized medicines based on a patients genomic information, said Bing Ren, PhD, professor of cellular and molecular medicine at UC San Diego, Ludwig Cancer Research member and senior author of both studies.

The first paper by Rens group takes a look at differences in our chromosome pairs. Each of us inherits one set from our mother and the other from our father. Chromosome pairs are often thought to be identical, one just a backup for the other. But this study found widespread differences in how genes are regulated (turned on and off) between the two chromosomes in a pair. It turns out that we all have biases in our chromosomes. In other words, different traits have a stronger contribution from one parent than the other. The study also suggests that these biases are rooted in inherited sequence variations and that they are not randomly distributed. These findings help explain why, for example, all kids in a family may have their fathers hair but their mothers eyes.

The second paper by Rens group tackles how the genome is organized and how it changes as stem cells differentiate (specialize). DNA strands in every cell are tightly wound and folded into chromosomes. Yet chromosomal structures, and how they influence gene expression, are not well understood. In this study, Ren and team mapped chromosomal structures in stem cells and several different differentiated cell types derived from stem cells. First, they induced differentiation in the stem cells. Then they used molecular tools to examine how the structure of the cells chromosomes changed and how that change is associated with gene activity. The team found that chromosomes are partitioned into relatively stable structural units known as topologically associating domains (TADs), and that TAD boundaries remain constant in different cell types. Whats more, the researchers found that the changes in chromosomal architecture mostly take place within the TADs in a way that correlates with changes in the epigenome.

The epigenome chemical modifications to chromosomes and 3D chromosomal structure is not just a linear object, Ren said. The epigenome is a 3D object, folded in a hierarchical way, and that should affect how we think about many aspects of human development, health and disease.

Co-authors on the paper Integrative Analysis of Haplotype-Resolved Epigenomes Across Human Tissues include Danny Leung, Inkyung Jung, Nisha Rajagopal, Anthony Schmitt, Siddarth Selvaraj, Ah Young Lee, Chia-An Yen, Yunjiang Qiu, Samantha Kuan, Lee Edsall, Ludwig Cancer Research; Shin Lin, Yiing Lin, Stanford University and Washington University School of Medicine; Wei Xie, formerly at Ludwig Cancer Research and now at Tsinghua University; Feng Yue, formerly at Ludwig Cancer Research and now at Pennsylvania State University; Manoj Hariharan, Joseph R. Ecker, Howard Hughes Medical Institute and Salk Institute for Biological Studies; Pradipta Ray, University of Texas; Hongbo Yang, Neil C. Chi, UC San Diego; and Michael Q. Zhang, University of Texas, Dallas and Tsinghua University.

Co-authors on the paper Chromatin Architecture Reorganization during Stem Cell Differentiation include Jesse R. Dixon, Siddarth Selvaraj, Ludwig Cancer Research and UC San Diego; Inkyung Jung, Yin Shen, Ah Young Lee, Zhen Ye, Audrey Kim, Nisha Rajagopal, Yarui Diao, Ludwig Cancer Research; Jessica E. Antosiewicz-Bourget, Morgridge Institute for Research; Wei Xie, Tsinghua University; Jing Liang, Huimin Zhao, University of Illinois at Urbana-Champaign; Victor V. Lobanenkov, National Institute of Allergy and Infectious Diseases; Joseph R. Ecker, Howard Hughes Medical Institute and Salk Institute for Biological Studies; James Thomson, Morgridge Institute for Research, University of Wisconsin and University of California, Santa Barbara.

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New Insights into 3D Genome Organization and Genetic Variability

12 hours ago by Ken Kingery A microscopic view of lab-grown human muscle bundles stained to show patterns made by basic muscle units and their associated proteins (red), which are a hallmark of human muscle. Credit: Nenad Bursac, Duke University

In a laboratory first, Duke researchers have grown human skeletal muscle that contracts and responds just like native tissue to external stimuli such as electrical pulses, biochemical signals and pharmaceuticals.

The lab-grown tissue should soon allow researchers to test new drugs and study diseases in functioning human muscle outside of the human body.

The study was led by Nenad Bursac, associate professor of biomedical engineering at Duke University, and Lauran Madden, a postdoctoral researcher in Bursac's laboratory. It appears January 13 in the open-access journal eLife

"The beauty of this work is that it can serve as a test bed for clinical trials in a dish," said Bursac. "We are working to test drugs' efficacy and safety without jeopardizing a patient's health and also to reproduce the functional and biochemical signals of diseasesespecially rare ones and those that make taking muscle biopsies difficult."

Bursac and Madden started with a small sample of human cells that had already progressed beyond stem cells but hadn't yet become muscle tissue. They expanded these "myogenic precursors" by more than a 1000-fold, and then put them into a supportive, 3D scaffolding filled with a nourishing gel that allowed them to form aligned and functioning muscle fibers.

"We have a lot of experience making bioartifical muscles from animal cells in the laboratory, and it still took us a year of adjusting variables like cell and gel density and optimizing the culture matrix and media to make this work with human muscle cells," said Madden.

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Madden subjected the new muscle to a barrage of tests to determine how closely it resembled native tissue inside a human body. She found that the muscles robustly contracted in response to electrical stimulia first for human muscle grown in a laboratory. She also showed that the signaling pathways allowing nerves to activate the muscle were intact and functional.

To see if the muscle could be used as a proxy for medical tests, Bursac and Madden studied its response to a variety of drugs, including statins used to lower cholesterol and clenbuterol, a drug known to be used off-label as a performance enhancer for athletes.

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First contracting human muscle grown in laboratory

Madison, Wisconsin - A team of researchers based at the University of Wisconsin-Madison will receive a four-year, $250,000 Catalyst Award grant from Research to Prevent Blindness (RPB), in partnership with the International Retinal Research Foundation, to advance stem cell research to treat vision loss from age-related macular degeneration (AMD).

Dr. David M. Gamm, the director of the McPherson Eye Research Institute at the UW School of Medicine and Public Health, will lead the consortium investigating stem-cell approaches for age-related macular degeneration (AMD), which affects more than two million Americans 50 and older.

Dr. Aparna Lakkaraju, also in the UW School of Medicine and Public Health's Department of Ophthalmology and Visual Sciences with Gamm, and Dr. Janis Eells, a professor at the University of Wisconsin-Milwaukee, are the other members of the research team.

The goal is to study how to improve and maintain the health and function of retinal cells - created from induced pluripotent stem cells - before and after they are put into a diseased eye. These donor cells are placed into a hostile environment, where they need to survive and thrive in order to offer hope of a long-term benefit for patients with AMD. To accomplish this goal, they want to maximize the function of mitochondria, the cells energy-producing powerhouses.

There are three key pieces to this study for which we all have important roles, says Gamm. My lab can create unlimited supplies of the needed retinal cells, called retinal pigment epithelium (RPE), from human induced pluripotent stem cells. Dr. Eells is a mitochondria expert and Dr. Lakkaraju is an expert in the study of RPE cells. In addition, we all have expertise in AMD. Its great to be able to work with such world-class collaborators here in Wisconsin.

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Eye Researchers Awarded Grant for Stem-Cell Research in ...

Our Stem Cell Learning Lab was made possible through a grant from the Ira and Ineva Reilly Baldwin Wisconsin Idea Endowment. Through this effort, we seek to build a greater understanding of stem cell research and regenerative medicine into school and community science outreach programs in Wisconsin. Our UW-Madison stem cell outreach labs are among the very few in the country and continue to place Madison at the forefront of stem cell research education and science education. We hope teachers will be able to take advantage of our opportunities and provide more of these unique experiences to their students.

Through this hands-on experience, either in our lab at the Biotechnology Center or at schools and science fairs, learners use the same equipment and methods stem cell researchers use to prepare and grow their cells. Our participants, however, use realistic cell and media substitutes due to biosafety and contamination concerns in public settings. To help your visit run smoothly, please provide us information by filling in this form, then mail it to us.

Our outreach programs are also part of many existing UW-Madison science programs, including Science Expeditions, Science Olympiad, the Wisconsin Science Festival, Grandparents University and UW Day at the Wisconsin State Fair. Our Stem Cell Learning Lab is a collaboration among the Stem Cell and Regenerative Medicine Center, Biotechnology Center,WiCell, Wisconsin National Primate Research Center, Student Society for Stem Cell Research(SSSCR), the Wisconsin Stem Cell Roundtable(WiSCR), and Morgridge Outreach Experiences.

Since 2009, our stem cell outreach programs have reached more than 16,000 learners.

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UW-Madison Stem Cell & Regenerative Medicine Center