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  <title>Pfrender Lab | News</title>
  <updated>2026-06-04T09:42:00-04:00</updated>
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  <subtitle>Explore evolutionary and ecological genomics research with Notre Dame's Evolutionary &amp; Ecological Genomics Lab, which investigates the adaptation in changing environments.</subtitle>
  <entry>
    <id>tag:pfrenderlab.nd.edu,2005:News/182296</id>
    <published>2026-06-04T09:42:00-04:00</published>
    <updated>2026-06-04T09:42:11-04:00</updated>
    <link rel="alternate" type="text/html" href="https://pfrenderlab.nd.edu/news/pfrender-named-as-interim-chair-of-department-of-biological-scienc/"/>
    <title>Pfrender named as interim chair of Department of Biological Sciences</title>
    <summary type="text">
      <![CDATA[Michael Pfrender, professor and associate chair in the Department of Biological Sciences at the University of Notre Dame, has been named interim department chair, effective July 1. Pfrender, who is also the director of the Genomics…]]>
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      <![CDATA[<p><a href="https://biology.nd.edu/people/michael-pfrender/">Michael Pfrender,</a> professor and associate chair in the Department of Biological Sciences at the University of Notre Dame, has been named interim department chair, effective July 1.</p>
<p>Pfrender, who is also the director of the <a href="https://genomics.nd.edu/">Genomics and Bioinformatics Core Facility</a> (GBCF) at Notre Dame, replaces <a href="https://biology.nd.edu/people/jason-rohr/">Jason Rohr,</a> the Ludmilla F., Stephen J., and Robert T. Galla College Professor, who served as director of the department for six years.</p>
<p>"Having worked closely with Mike over the past six years while he served as associate chair, I’ve seen firsthand his thoughtful, collaborative leadership style and his deep commitment to both faculty and students,” Rohr said. “He is exceptionally well qualified to step into the chair role, and I’m excited to see the department continue to build momentum under his guidance. I’m confident he’ll do an extraordinary job leading the department."</p>
<p>Pfrender was hired at Notre Dame in 2009 as an associate professor, after working as an assistant and associate professor at Utah State University. His research centers around evolutionary and ecological genomics, which is the study of an organism’s entire set of genetic material, including how genes interact with each other. Pfrender studies everything from how specific genes help animals adapt to new environments to how genetic variety keeps entire ecosystems healthy.</p>
<p>In his role as the director of the GBCF, Pfrender assists researchers across disciplines using next-generation sequencing and spatial genomics to solve a variety of complex problems.</p>
<p>"I get to interact with a wide variety of colleagues in my role as GBCF director, and I've really enjoyed that, because it exposes me to cutting-edge research that is well outside my specific area," said Pfrender.</p>
<p>As he takes on the role of department chair, he has identified several priorities. One is ensuring strong collaboration and communication across the department, which is housed in three buildings: Galvin Life Sciences, McCourtney Hall, and Jordan Hall of Science. He is committed to keeping the department well connected and operating seamlessly across these locations.</p>
<p>He sees the modern, shared space in McCourtney as a benefit to student and researcher collaboration. “For students especially, it’s a great environment because they’re completely integrated with students from widely different research areas,” he said.</p>
<p>Pfrender also plans to continue the foundation laid by Rohr, whose leadership resulted in a significant increase in the global research profile.</p>
<p>"I think Jason's been a tremendous chair. The faculty hires we made under his leadership have significantly enhanced our expertise and elevated our national and international reputation," Pfrender said. “Jason leaves us with a well-organized department that is on a great trajectory to contribute to the growth and development of research and education in the life sciences at the University.”</p>
<p>Pfrender earned his bachelor’s and master’s degrees from the University of Michigan and his doctorate in biology at the University of Oregon, and then worked as a postdoctoral research associate at Oregon State University.</p>
<p>As he steps into his new role, Pfrender said he is excited to influence the next generation of scientists.</p>
<p>"I think the ability to foster our up-and-coming, early career faculty is really exciting,” he said. “I look forward to playing a role in shaping the future of the department by contributing to the hiring process.”</p>
<p class="attribution">Originally published by <span class="rel-author">Deanna Csomo Ferrell</span> at <span class="rel-source"><a href="https://science.nd.edu/news-and-media/news/pfrender-named-as-interim-chair-of-department-of-biological-scienc/">science.nd.edu</a></span> on <span class="rel-pubdate">June 03, 2026</span>.</p>]]>
    </content>
    <link rel="enclosure" type="image/jpeg" href="https://pfrenderlab.nd.edu/assets/661659/michaelpfrenderjpg.jpg" title="Portrait of Michael Pfrender"/>
    <author>
      <name>Deanna Csomo Ferrell</name>
    </author>
  </entry>
  <entry>
    <id>tag:pfrenderlab.nd.edu,2005:News/163486</id>
    <published>2022-01-25T10:50:00-05:00</published>
    <updated>2026-08-05T15:29:10-04:00</updated>
    <link rel="alternate" type="text/html" href="https://pfrenderlab.nd.edu/news/faculty-in-chemistry-biological-sciences-psychology-named-aaas-fellows/"/>
    <title>Faculty in chemistry, biological sciences, psychology named  AAAS fellows</title>
    <summary type="text">
      <![CDATA[Patricia L. Clark, Darcia Narvaez and Michael Pfrender have been named fellows of the American Association for the Advancement of Science (AAAS).]]>
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      <![CDATA[<figure class="image-right"><img src="https://news.nd.edu/assets/457937/patricia_clark_1_300x.jpg" alt="Patricia L. Clark" width="300" height="400">
<figcaption>Patricia L. Clark</figcaption>
</figure>
<p>Three faculty members at the University of Notre Dame have been named fellows of the American Association for the Advancement of Science (AAAS).</p>
<p><a href="https://chemistry.nd.edu/people/patricia-l-clark/">Patricia L. Clark</a>, the Rev. John Cardinal O’Hara, C.S.C., Professor of <a href="https://chemistry.nd.edu/">Chemistry and Biochemistry</a>, associate vice president for research and director of the <a href="https://research.nd.edu/our-research/facilities-and-resources/biophysics-instrumentation-core-facility/">Biophysics Instrumentation Core Facility</a> at Notre Dame, is being honored for her seminal contributions in characterizing the biology and biochemistry of unfolded proteins, and for her pioneering work in the consequences of synonymous substitutions on fitness. Clark studies how proteins — the powerhouses of human cells — fold or misfold into three-dimensional shapes as they are synthesized and secreted across cell membranes. Misfolded proteins can lead to a variety of diseases, from cancer to Alzheimer’s disease</p>
<figure class="image-left"><img src="https://news.nd.edu/assets/457940/darcia_narvaez_300.jpg" alt="Darcia Narvaez portrait">
<figcaption>Darcia Narvaez</figcaption>
</figure>
<p><a href="https://psychology.nd.edu/people/darcia-narvaez/">Darcia Narvaez</a>, professor emerita of <a href="https://psychology.nd.edu/">psychology</a>, is being honored for her distinguished contributions illuminating typical and atypical development in terms of well-being, morality and sustainable wisdom. Narvaez examines how early life experience, the “evolved nest,” influences moral functioning and well-being in children and adults and integrates evolutionary, anthropological, neurobiological, clinical, developmental and education sciences in her work. Narvaez received the William James Book Award from the American Psychological Association and the inaugural Expanded Reason Award for research for her book “Neurobiology and the Development of Human Morality: Evolution, Culture, and Wisdom.”</p>

<figure class="image-right"><img src="https://news.nd.edu/assets/457946/bj_3.5.19_michael_pfrender_3551_300x.jpg" alt="Michael Pfrender" width="300" height="400">
<figcaption>Michael Pfrender</figcaption>
</figure>
<p><a href="https://biology.nd.edu/people/michael-pfrender/">Michael Pfrender</a>, professor of evolutionary and ecological genomics and director of Notre Dame’s <a href="https://genomics.nd.edu/">Genomics and Bioinformatics Core Facility</a>, is being honored for his distinguished contributions to the field of ecological and environmental genomics, and in particular for work developing the genomics of the species Daphnia, often referred to as a water flea, as a model evolutionary system. Pfrender’s work connects genome structure, quantitative genetic architecture, patterns of gene expression and gene evolution with the process of, and limits to, adaptation in changing environments. </p>
<p>The election of AAAS fellows is an honor bestowed upon members by their peers.</p>
<p class="attribution">Originally published by <span class="rel-author">Notre Dame News</span> at <span class="rel-source"><a href="https://news.nd.edu/news/faculty-in-chemistry-biological-sciences-psychology-named-aaas-fellows/">news.nd.edu</a></span> on <span class="rel-pubdate">January 26, 2022</span>.</p>]]>
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    <link rel="enclosure" type="image/jpeg" href="https://pfrenderlab.nd.edu/assets/571931/bj_9.27.16_golden_dome_sunset_10075.jpg" title="Notre Dame's Main Building and Golden Dome under a pink and blue sunset sky, partially visible through green trees."/>
    <author>
      <name>Notre Dame News</name>
    </author>
  </entry>
  <entry>
    <id>tag:pfrenderlab.nd.edu,2005:News/163488</id>
    <published>2019-12-24T10:51:00-05:00</published>
    <updated>2024-06-19T10:55:54-04:00</updated>
    <link rel="alternate" type="text/html" href="https://pfrenderlab.nd.edu/news/scientists-tackle-potential-drug-resistance-by-using-new-single-cell-genetic-method/"/>
    <title>Scientists tackle potential drug resistance by using new single-cell genetic method</title>
    <summary type="text">
      <![CDATA[Using a new technique that can identify genetic profiles of individual cells, University of Notre Dame researchers modeled a breast cancer tumor’s potential resistance to a drug, and then identified a drug combination that reversed that resistance.]]>
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    <content type="html">
      <![CDATA[<p>Using a new technique that can identify genetic profiles of individual cells, University of Notre Dame researchers modeled a breast cancer tumor’s potential resistance to a drug, and then identified a drug combination that reversed that resistance.</p>
<p><a href="https://biology.nd.edu/people/siyuan-zhang/">Siyuan Zhang</a>, the Dee Associate Professor of <a href="https://biology.nd.edu/">Biological Sciences</a> at Notre Dame, and his team used a new profiling process to make the discovery, published in <a href="https://www.nature.com/articles/s41467-019-11729-1">Nature Communications</a>.</p>
<p>“The new technology allows us to do sequencing on each individual cell,” Zhang said, adding that his lab worked with Notre Dame’s <a href="https://genomics.nd.edu/">Genomics and Bioinformatics Core Facility</a> to apply the new technology, called high-throughput single-cell profiling, on campus.</p>
<p>Until recently, finding patterns of gene expression for cancer tissue has been performed using whole tumor tissue, a process called bulk sequencing. Unfortunately, cancer cells are embedded in a matrix of other cells, making it difficult to distinguish the true signatures of individual cells. The new single-cell profiling technique makes the task of discerning the nature of each cell possible.</p>
<p>In this study, researchers observed how a particular new drug works for shrinking tumors in an aggressive type of cancer, HER2-positive breast cancer. The drug, called a CDK 4/6 inhibitor — used to block a specific type of enzyme — works rapidly. But most drugs start out working well, before the tumor eventually changes and becomes resistant to the treatment. Researchers then look at the resistant tumors and start to develop new drugs to overcome resistance, but by then it’s too late. “By the time we find a new drug, the tumor has shifted into something different,” said Zhang.</p>
<p class="image-right"><img src="https://news.nd.edu/assets/336014/siyuan_zhang_crop.jpg" alt="Siyuan Zhang">Siyuan Zhang</p>
<p>Zhang decided to investigate predicting the potential for drug resistance. Running tests in tandem with the clinical trial for the CDK 4/6 drug, and using the single-cell profiling technology, his team discovered a type of tumor-infiltrating immune-suppressive cells that led to resistance. The team then added another already-FDA-approved drug to target the immune-suppressive cells. The combination reversed the resistance.</p>
<p>“The new combination of drugs shows that the resistant tumor can be treated, and can maintain and control the tumor size for a pretty long period of time,” Zhang said. Given the effectiveness of the additional drug, clinicians could begin the combination therapy even before resistance occurs, Zhang noted. Because the drug is already FDA-approved, clinicians may choose to try the protocol now.</p>
<p>Single-cell profiling could lead to additional discoveries, said <a href="https://biology.nd.edu/people/michael-pfrender/">Michael Pfrender</a>, director of the Genomics and Bioinformatics Core Facility and professor in the Department of Biological Sciences.</p>
<p>“The applications of single-cell approaches to human disease and development are profound,” he said. “This technology is rapidly becoming an essential feature in the biomedical research tool kit.”</p>
<p>In addition to Zhang, other researchers include Qingfei Wang, Ian H. Guldner, Samantha M. Golomb, Longhua Sun, Jack A. Harris and Xin Lu, all of Notre Dame and the <a href="https://harpercancer.nd.edu/">Mike and Josie Harper Cancer Research Institute</a>. Lu and Zhang also are affiliated with the Indiana University Melvin and Bren Simon Cancer Center.</p>
<p>The study was funded by the National Institutes of Health, Notre Dame’s Boler-Parseghian Center for Rare and Neglected Diseases Catalyst Award and a grant from the Notre Dame Advanced Diagnostics and Therapeutics initiative.</p>
<p><strong><em>Contact:</em></strong><em> Jessica Sieff, assistant director of media relations, 574-631-3933, <a href="mailto:jsieff@nd.edu">jsieff@nd.edu</a></em></p>
<p class="attribution">Originally published by <span class="rel-author">Deanna Csomo McCool</span> at <span class="rel-source"><a href="https://news.nd.edu/news/scientists-tackle-potential-drug-resistance-by-using-new-single-cell-genetic-method/">news.nd.edu</a></span> on <span class="rel-pubdate">September 25, 2019</span>.</p>]]>
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    <link rel="enclosure" type="image/jpeg" href="https://pfrenderlab.nd.edu/assets/571933/mc_2.20.18_microscope_feature.jpg" title="Close-up of a person's hazel eye looking intently through clear glasses at a Zeiss microscope."/>
    <author>
      <name>Deanna Csomo McCool</name>
    </author>
  </entry>
  <entry>
    <id>tag:pfrenderlab.nd.edu,2005:News/163490</id>
    <published>2018-02-19T10:52:00-05:00</published>
    <updated>2024-06-19T10:56:24-04:00</updated>
    <link rel="alternate" type="text/html" href="https://pfrenderlab.nd.edu/news/as-climate-changes-so-could-the-genes-of-the-eastern-tiger-swallowtail-butterfly/"/>
    <title>As climate changes, so could the genes of the Eastern tiger swallowtail butterfly</title>
    <summary type="text">
      <![CDATA[Researchers warn climate change can not only influence the geographic distribution of a species in response to changing conditions — it could also affect the evolutionary trajectories of interbreeding species.]]>
    </summary>
    <content type="html">
      <![CDATA[<p style="margin: 0in 0in 10pt 0in;">The reality of climate change poses a significant threat to global biodiversity. As temperatures rise, the survival of individual species will ultimately depend on their ability to adapt to changes in habitat and their interactions with other species.</p>
<p style="margin: 0in 0in 10pt 0in;">A new study published in the <a href="http://www.pnas.org/content/early/2018/02/13/1714950115">Proceedings of the National Academy of Sciences</a> examines movement of the Eastern (<em>Papilio glaucus</em>) and Canadian (<em>Papilio Canadensis</em>) tiger swallowtail butterfly over a 32-year period within the geographic region where the two species mate, called the hybrid zone. The findings highlight the impact of changing climates and provide critical information for the protection and management of biodiversity.</p>
<p style="margin: 0in 0in 10pt 0in;">Researchers from the <a href="https://environmentalchange.nd.edu/">Environmental Change Initiative</a> at the University of Notre Dame, Michigan State University and the University of Minnesota warn climate change can not only influence the geographic distribution of a species in response to changing conditions — it could also affect the evolutionary trajectories of interbreeding species.</p>
<p style="margin: 0in 0in 10pt 0in;">“Climate change can alter the patterns of gene flow and change the interaction between species,” said <a href="https://biology.nd.edu/people/michael-pfrender/">Michael Pfrender</a>, a co-author on the study, director of the <a href="http://genomics.nd.edu/">Genomics and Bioinformatics Core Facility</a> at Notre Dame and associate professor in the <a href="https://biology.nd.edu/">Department of Biological Sciences</a>. “Changes in gene flow not only impact the fitness and survival of each species individually, but it can alter their genetic composition — what makes them distinct in the first place. If climate change results in a decrease of connectivity between the two species, they may become more distinct, and potentially useful genetic material will not move across the species boundaries.”</p>
<p style="margin: 0in 0in 10pt 0in;">Researchers focused on documented warming over a 32-year period within the hybrid zone and measured movement over the same period, using molecular and morphological markers. They found the center of the hybrid zone had moved north nearly 40 kilometers (24.85 miles) at a rate of 1.25 km (0.77 miles) per year.</p>
<p style="margin: 0in 0in 10pt 0in;"> “Temperature is a key variable in determining how quickly individuals grow and how likely they are to survive to the next life stage,” explained <a href="https://biology.nd.edu/people/stuart-e-jones/">Stuart Jones</a>, associate professor of biological sciences at Notre Dame and co-author of the study. Through a sampling of historical specimens, detailed modeling and genetic data, the team was able to explore how climate variation interacts with reproduction, tracking development of a complete life cycle, from egg to butterfly, as well as growth at specific temperatures to estimate how many generations would develop under different climate conditions.</p>
<p style="margin: 0in 0in 10pt 0in;">“We also made predictions for how the location of hybridization would continue to move northward and up mountainsides as the region’s climate continues to warm in the future,” Jones said. According to the study, researchers have predicted that the movement could range from 55-144 km (33-89 miles) per degree Celsius increase in temperature.</p>
<p style="margin: 0in 0in 10pt 0in;">“Variability in how climate warms, the effects on those hybrid zones, and how the two species respond to those changes will determine the potential for gene flow,” Pfrender said. “Reductions in gene flow could lead of a loss of genetic variation, and as a result, one or both species could experience a reduction in population size and become threatened in its native range. Alternatively, a dramatic increase in gene flow could lead to the loss of unique qualities of each species as they merge together.”</p>
<p style="margin: 0in 0in 10pt 0in;">The study’s results should encourage local conservation and management organizations to consider the influence of climate change on similar hybrid zones and the potential ecological and evolutionary impact.</p>
<p style="margin: 0in 0in 10pt 0in;">“These results provide a roadmap for understanding and predicting gene flow and hybrid zones for species of concern under future climate change,” said <a href="https://biology.nd.edu/people/jennifer-tank/">Jennifer Tank</a>, director of the Environmental Change Initiative at Notre Dame. “Successful prediction will require a powerful toolbox that combines understanding of ecology and evolution along with cutting-edge molecular and genomics techniques.”</p>
<p style="margin: 0in 0in 10pt 0in;">The study was led by Sean F. Ryan, a graduate student in the Department of Biological Sciences at Notre Dame, who’s currently at North Carolina State University, and Jessica J. Hellmann, now at the University of Minnesota. Other co-authors include <a href="https://engineering.nd.edu/profiles/semrich">Scott Emrich</a> at Notre Dame, Jillian M. Deines and J. Mark Scriber at Michigan State University.</p>
<p style="margin: 0in 0in 10pt 0in;">Research was funded by the Notre Dame Environmental Change Initiative, the National Science Foundation and the University of Wisconsin-Madison Agricultural Experiment Station.</p>
<p style="margin: 0in 0in 10pt 0in;"><strong><em>Contact:</em></strong><em> Jessica Sieff, assistant director, media relations, 574-631-3933, <a href="mailto:jsieff@nd.edu">jsieff@nd.edu</a></em></p>
<p class="attribution">Originally published by <span class="rel-author">Jessica Sieff</span> at <span class="rel-source"><a href="https://news.nd.edu/news/as-climate-changes-so-could-the-genes-of-the-eastern-tiger-swallowtail-butterfly/">news.nd.edu</a></span> on <span class="rel-pubdate">February 20, 2018</span>.</p>]]>
    </content>
    <link rel="enclosure" type="image/jpeg" href="https://pfrenderlab.nd.edu/assets/571935/eastern_tiger_swallowtail_butterfly_feature.jpg" title="Yellow and black swallowtail butterfly with blue and orange markings resting on a person's hand, wings spread."/>
    <author>
      <name>Jessica Sieff</name>
    </author>
  </entry>
  <entry>
    <id>tag:pfrenderlab.nd.edu,2005:News/163492</id>
    <published>2017-12-19T10:53:00-05:00</published>
    <updated>2024-06-19T10:54:51-04:00</updated>
    <link rel="alternate" type="text/html" href="https://pfrenderlab.nd.edu/news/researchers-isolate-biting-non-biting-genes-in-pitcher-plant-mosquitoes/"/>
    <title>Researchers isolate biting, non-biting genes in pitcher plant mosquitoes</title>
    <summary type="text">
      <![CDATA[Understanding that divergence, researchers say, is a starting point to determining whether there are non-biting genes in other species that could be manipulated in order to reduce transmission of vector-borne diseases.]]>
    </summary>
    <content type="html">
      <![CDATA[<p style="margin: 0in 0in 10pt 0in;">Mosquito bites can be an itchy nuisance but they can also be deadly. Diseases such as malaria, Dengue fever and West Nile virus can spread with a single bite.</p>
<p style="margin: 0in 0in 10pt 0in;">Understanding the genetic variation — identifying those genes that differentiate biters from non-biters — is the first step toward discovering new approaches to mitigating a mosquito’s tendency to bite, while still allowing populations to reproduce and survive in their environments.</p>
<p style="margin: 0in 0in 10pt 0in;">According to a new study in the <a href="http://www.pnas.org/content/early/2017/12/14/1717502115.full?sid=4df7c013-5be7-407d-bda2-38debe219697">Proceedings of the National Academy of Sciences</a>, researchers have taken a first step in identifying gene variation in biting and non-biting mosquitoes.</p>
<p style="margin: 0in 0in 10pt 0in;">“Populations of some mosquitos vary in their propensity to bite,” said <a href="http://biology.nd.edu/people/michael-pfrender/">Michael Pfrender</a>, director of the <a href="http://genomics.nd.edu/">Genomics &amp; Bioinformatics Core Facility</a> at the University of Notre Dame, which processed the genetic data for the study, and a professor in the <a href="http://biology.nd.edu/">Department of Biological Sciences</a> and at the <a href="https://globalhealth.nd.edu/">Eck Institute for Global Health</a>. “As soon as you have that variation you can exaggerate it through selection experiments.”</p>
<p style="margin: 0in 0in 10pt 0in;">Experiments led by researchers at the University of Oregon, focused on Wyeomyia smithii, known as the pitcher plant mosquito. Out of 21,618 genes, the team isolated 1,380 which they found to be directly related to biting and non-biting. Of those genes, 902 were identified as relating to biting and blood-feeding, and 478 were linked to non-biters.</p>
<p style="margin: 0in 0in 10pt 0in;">“By leveraging variation in the tendency to bite within and between populations of this mosquito, we are able to identify a set of genetic pathways associated with non-biting,” Pfrender said. “This study lays the groundwork to identify key regulators to these pathways that may ultimately provide tractable solutions.”</p>
<p style="margin: 0in 0in 10pt 0in;">The pitcher plant mosquito has been of particular interest to researchers for some time. It is unique in that it is the only species to have both biters and non-biters — in southern populations of the species, the females bite while northern populations are non-biters.</p>
<p style="margin: 0in 0in 10pt 0in;">Other mosquito populations consist of only biters or only non-biters. By focusing on W. smithii, scientists can study the genetic variation for biting and non-biting within a single species.</p>
<p style="margin: 0in 0in 10pt 0in;">Understanding that divergence, researchers say, is a starting point to determining whether there are non-biting genes in other species that could be manipulated in order to reduce transmission of vector-borne diseases.</p>
<p style="margin: 0in 0in 10pt 0in;">While studying W. smithii, researchers found that biters tend to rely on olfactory cues, while non-biters rely more on visual cues. Researchers also found that both biters and non-biters activate metabolic pathways necessary for taking a blood meal — but something stops the non-biters from taking the bite. Key proteins involved in metabolic processes like fatty acid synthesis and energy production are being produced in both biters and non-biters, but the linking enzymes that determine which metabolic pathways are turned on are missing in the non-biters. “The car is gassed up and running at the intersection but the light is red,” Pfrender said.</p>
<p style="margin: 0in 0in 10pt 0in;">Stopping at this flexible point in the metabolic pathways is unusual and Pfrender said he hasn’t seen this in any other study. Researchers plan to study additional species including common house mosquitoes, which can spread encephalitis, West Nile and heartworm; Asian tiger mosquitoes, known to carry Dengue fever, Zika and yellow fever among other viruses; and Anopheles gambiae, which carry malaria.</p>
<p style="margin: 0in 0in 10pt 0in;">Pfrender and Jacqueline Lopez, a senior research technician in the Genomics &amp; Bioinformatics Core Facility, co-authored the study led by William E. Bradshaw and Christina M. Holzapfel at the University of Oregon. Other co-authors include Joshua Burkhart, at Oregon Health and Science University; John K. Colbourne, at the University of Birmingham in the United Kingdom; Rudyard Borowczak, at the University of Oregon’s Institute of Ecology and Evolution; and David L. Denlinger and Julie A. Reynolds of The Ohio State University.</p>
<p style="margin: 0in 0in 10pt 0in;">Research was funded through grants from the National Science Foundation.</p>
<p style="margin: 0in 0in 10pt 0in;"> </p>
<p class="MsoNoSpacing" style="margin: 0in 0in 0.0001pt 0in;"><strong><em>Contact:</em></strong><em> Jessica Sieff, assistant director, Media Relations, 574-631-3933, <a href="mailto:jsieff@nd.edu">jsieff@nd.edu</a></em></p>
<p class="attribution">Originally published by <span class="rel-author">Jessica Sieff</span> at <span class="rel-source"><a href="https://news.nd.edu/news/researchers-isolate-biting-non-biting-genes-in-pitcher-plant-mosquitoes/">news.nd.edu</a></span> on <span class="rel-pubdate">December 19, 2017</span>.</p>]]>
    </content>
    <link rel="enclosure" type="image/jpeg" href="https://pfrenderlab.nd.edu/assets/571937/2015_genomics_10_feature.jpg" title="Two scientists, one with a beard and glasses, intently view a laptop in a lab with centrifuges and other equipment."/>
    <author>
      <name>Jessica Sieff</name>
    </author>
  </entry>
  <entry>
    <id>tag:pfrenderlab.nd.edu,2005:News/183333</id>
    <published>2017-10-25T08:25:00-04:00</published>
    <updated>2026-07-24T08:28:44-04:00</updated>
    <link rel="alternate" type="text/html" href="https://pfrenderlab.nd.edu/news/little-giants-a-closer-look-at-a-tiny-bug-with-a-big-role-to-play/"/>
    <title>Little Giants: A closer look at a tiny bug with a big role to play</title>
    <summary type="text">
      <![CDATA[Michael Pfrender sits facing a whiteboard in his lab at the Galvin Life Science Center.…]]>
    </summary>
    <content type="html">
      <![CDATA[<figure class="image image-right"><img src="https://pfrenderlab.nd.edu/assets/667654/pregnant.webp" alt="Translucent Daphnia with visible internal organs and several white, spherical eggs inside its body." width="545" height="874"></figure>
<p>Michael Pfrender sits facing a whiteboard in his lab at the Galvin Life Science Center. He’s discussing the genomics of <em>Daphnia</em> – water fleas, found in every standing body of water in the world – and has a tendency to sketch when he speaks.</p>
<p>“You want to see some of them?” he asks. “That’s the fun part, right?”</p>
<p>At the back of the lab, two beakers sit on a table near a microscope. There isn’t much to see at first glance. Even leaning in, <em>Daphnia</em> are so small they look like bouncing flecks in the water, frantically trying to keep afloat.</p>
<p>Pfrender dips an eyedropper into one of the beakers, releases a drop of water onto a slide and slips it under the microscope for a closer look.</p>
<p>There she is.</p>
<p>Portly with a round, neckless head and antennae sprouting from either side, she is translucent – her organs visible within the razor-thin outline of her body. She also happens to be pregnant, her eggs equally visible, and encased in little pouches.</p>
<p><a href="https://stories.nd.edu/stories/little-giants/" class="btn">Read the full story</a></p>]]>
    </content>
    <link rel="enclosure" type="image/webp" href="https://pfrenderlab.nd.edu/assets/667655/lead.webp" title="Two translucent daphnia under a microscope. Left has a reddish interior; right has a pale orange interior with eggs."/>
    <author>
      <name>Jessica Sieff</name>
    </author>
  </entry>
  <entry>
    <id>tag:pfrenderlab.nd.edu,2005:News/181271</id>
    <published>2017-07-17T15:59:00-04:00</published>
    <updated>2026-08-05T15:20:14-04:00</updated>
    <link rel="alternate" type="text/html" href="https://pfrenderlab.nd.edu/news/researchers-improve-method-to-identify-aquatic-species-using-environmental-dna/"/>
    <title>Researchers improve method to identify aquatic species using environmental DNA</title>
    <summary type="text">
      <![CDATA[According to a new study, researchers have improved their method of tracking species by using the biological material those organisms leave behind known as environmental DNA (eDNA).]]>
    </summary>
    <content type="html">
      <![CDATA[<p>Determining which fish are living in various bodies of water can be a daunting task for scientists studying those populations. Identifying invasive or endangered species, for example, has often relied on the ability to catch them.</p>
<p>Now, according to a new study published in <a href="http://onlinelibrary.wiley.com/doi/10.1111/2041-210X.12836/full">Methods in Ecology and Evolution</a>, researchers have improved their method of tracking species by using the biological material those organisms leave behind known as environmental <span class="caps">DNA</span> (eDNA).</p>
<p>Traces of eDNA carry the same vital information as a direct <span class="caps">DNA</span> sample, such as a blood or tissue sample. Think of the work done by forensic scientists, who can identify individuals from a strand of hair.</p>
<p>Until now, researchers believed that <span class="caps">DNA</span> shed by organisms in their watery environments was significantly degraded and low quality, making it difficult to take those fragments and match them to a specific species.</p>
<p>It turns out that the cells fish shed into the water protect tightly coiled <span class="caps">DNA</span>.</p>
<p>“We were successful in detecting and working with long, intact pieces of <span class="caps">DNA</span>,” said <a href="http://biology.nd.edu/people/michael-pfrender/">Michael E. Pfrender</a>, director of the <a href="http://genomics.nd.edu/">Genomics &amp; Bioinformatics Core Facility</a> and associate professor in the <a href="http://biology.nd.edu/">Department of Biological Sciences</a> and the <a href="https://environmentalchange.nd.edu/">Environmental Change Initiative</a> at the University of Notre Dame. “This completely changes the prevailing view that we can only work with short fragments of highly degraded eDNA. Now, we can start using the information pulled from these long chains of <span class="caps">DNA</span> to develop more accurate species identifications and to detect genetic variation within species.”</p>
<p>Researchers collected water samples from area lakes, ponds and streams and used polymerase chain reaction (<span class="caps">PCR</span>) technology to amplify — or copy — the entire mitochondrial genomes from the eDNA found in those environments.</p>
<p>Through this improved method, scientists can get a more detailed picture of the biodiversity in various aquatic habitats.</p>
<p>“There is an ongoing effort to populate databases like the National Center for Biotechnology Information’s (<span class="caps">NCBI</span>) Genbank,” said Pfrender. “We do not have genetic signatures for all the biodiversity we’d like to monitor. These databases are critical to helping us identify the various species living within these communities.”</p>
<p>The method used in the study is not only more accurate, it is more efficient when it comes to looking for and managing invasive species.</p>
<p>Co-authors of the study include Yiyuan Li at Notre Dame, Kristy Deiner and David M. Lodge at Cornell University and Mark A. Renshaw and Brett P. Olds at the Oceanic Institute, Hawaii Pacific University. Research was funded by the U.S. Department of Defense’s Strategic Environmental Research and Development Program and was supported by the Notre Dame Environmental Change Initiative.</p>
<p><em><strong>Contact</strong>: Michael Pfrender, 574-631-0591, <a href="mailto:michael.pfrender.1@nd.edu">michael.pfrender.1@nd.edu</a></em></p>
<p class="attribution">Originally published by <span class="rel-author">Jessica Sieff</span> at <span class="rel-source"><a href="https://news.nd.edu/news/researchers-improve-method-to-identify-aquatic-species-using-environmental-dna/">news.nd.edu</a></span> on <span class="rel-pubdate">July 17, 2017</span>.</p>]]>
    </content>
    <link rel="enclosure" type="image/jpeg" href="https://pfrenderlab.nd.edu/assets/658102/sampling_water_800x440.jpg" title="Red-haired woman in blue shirt, tan pants, and blue glove leans over a rocky bank, sampling water from a stream."/>
    <author>
      <name>Jessica Sieff</name>
    </author>
  </entry>
  <entry>
    <id>tag:pfrenderlab.nd.edu,2005:News/181270</id>
    <published>2017-05-05T15:57:00-04:00</published>
    <updated>2026-07-22T13:08:11-04:00</updated>
    <link rel="alternate" type="text/html" href="https://pfrenderlab.nd.edu/news/scientists-reveal-new-and-improved-genome-sequence-of-daphnia-pulex/"/>
    <title>Scientists reveal new and improved genome sequence of  Daphnia pulex</title>
    <summary type="text">
      <![CDATA[p(image-right). !https://news.nd.edu/assets/236084/200x/daphnia2_300x350.jpg(Daphnia pulex)! By understanding how they respond to toxic elements, scientists can look at how environmental changes caused by agriculture and road runoff or warming temperatures and climate change could impact populations in lakes, rivers and standing bodies of water.]]>
    </summary>
    <content type="html">
      <![CDATA[<p class="image-right"><img title="Daphnia pulex" src="https://news.nd.edu/assets/236084/daphnia2_300x350.jpg" alt="Daphnia pulex"></p>
<p>For many, experience with Daphnia, commonly known as water fleas, ends in high school. The organism is often used for science experiments exploring water toxicity, because of its sensitivity to environmental factors. But the tiny, transparent microcrustaceans have been studied intensively for more than 150 years, and <a href="http://www.g3journal.org/content/7/5/1405">new research published and featured on the cover of the journal G3</a> reveals scientists can now take a closer look at its genome.</p>
<p>Researchers have completed a new and improved genome sequence of Daphnia pulex (D. pulex), providing a clearer roadmap of the organism’s genome so they can identify the genes and pathways that make this organism so successful in freshwater ecosystems.</p>
<p>Populations of Daphnia, barely visible to the naked eye, can be found in virtually every standing body of water on the planet, including Antarctica. They evolve quickly and are masters of responding to the conditions in their environment. Sensing the chemical cues of nearby predators, some species of Daphnia develop elaborate defensive structures such as spines and helmets that make them harder to eat. While scientists have gained a thorough understanding of what these tiny water fleas do to adapt to varying conditions, they don’t yet know how they do it.</p>
<p class="image-left"><img title="Michael E. Pfrender" src="https://news.nd.edu/assets/235995/250x/daphnia3_300x200.jpg" alt="Michael E. Pfrender"></p>
<p>“That’s why a system like this is so powerful,” said <a href="http://biology.nd.edu/people/michael-pfrender/">Michael E. Pfrender</a>, director of the <a href="http://genomics.nd.edu/">Genomics &amp; Bioinformatics Core Facility</a> and associate professor in the <a href="http://biology.nd.edu/">Department of Biological Sciences</a> and the <a href="https://environmentalchange.nd.edu/">Environmental Change Initiative</a> at the University of Notre Dame. “We need this genomic infrastructure to add to the ecological context we already have to gain a better understanding of how Daphnia adapt. Because we have an improved genome sequence, we can get a more accurate catalog of genes and when thinking about response to the environment and chemical cues, it’s the turning on and off of genes and pathways that’s important. The picture is much more complete than it was before.”</p>
<p>Calling it the “Portland Arch” genome after the Indiana Nature Preserve where the Daphnia was collected, the new assembly comes six years after the first sequence of D. pulex in 2011. The current study describes how scientists used the latest technology as part of a thorough and methodical process the result of which led to the identification of 18,440 genes.</p>
<p>D. pulex plays a vital role in Earth’s ecology. Feeding off of algae and phytoplankton in standing freshwaters, they are the primary grazer in those environments, the “cows of lakes,” said Pfrender. They’re also primary forage, transferring all of that energy to the fish that eat them. By understanding how species of Daphnia respond to toxic elements like industrial contaminants, toxic algae blooms or thermal stress, scientists can look at how environmental changes caused by agriculture and road runoff or warming temperatures and climate change could impact populations in lakes, rivers and standing bodies of water.</p>
<p>“What happens to this vital part of the ecosystem when conditions change very rapidly? What genes allow some populations to cope with these changes while others fail?” Pfrender said. “That’s what we want to find out. This genome sequence provides the toolkit.”</p>
<p>Co-authors of the study include Pfrender, Jacqueline Lopez and Brent Harker of the Notre Dame Genomics and Bioinformatics Core Facility; Zhiqiang Ye, Ken Spitze, Xiaoqian Jiang, Matthew S. Ackerman and Michael Lynch at the Department of Biology at Indiana University; Sen Xu at the Department of Biology at Indiana University and the University of Texas at Arlington; Jana Asselman, Laboratory for Environmental Toxicology at Ghent University; R. Taylor Raborn at the Department of Biology and School of Informatics and Computing at Indiana University; and W. Kelley Thomas and Jordan Ramsdell at the Hubbard Center for Genome Studies at the University of New Hampshire.</p>
<p>The study was funded through a grant from the National Institutes of Health to Michael Lynch at Indiana University, Bloomington and Notre Dame Research.</p>
<p><em><strong>Contact</strong>: Michael Pfrender, 574-631-0591, <a href="mailto:michael.pfrender.1@nd.edu">michael.pfrender.1@nd.edu</a></em></p>
<p class="attribution">Originally published by <span class="rel-author">Jessica Sieff</span> at <span class="rel-source"><a href="https://news.nd.edu/news/scientists-reveal-new-and-improved-genome-sequence-of-daphnia-pulex/">news.nd.edu</a></span> on <span class="rel-pubdate">May 05, 2017</span>.</p>]]>
    </content>
    <link rel="enclosure" type="image/png" href="https://pfrenderlab.nd.edu/assets/548768/a_hand_in_a_blue_glove_holds_a_microscope_slide_of_daphnia_bugs_also_known_as_a_water_fleas.png" title="A hand in a blue glove holds a microscope slide of Daphnia bugs, also known as water fleas"/>
    <author>
      <name>Jessica Sieff</name>
    </author>
  </entry>
  <entry>
    <id>tag:pfrenderlab.nd.edu,2005:News/181213</id>
    <published>2012-03-15T16:29:00-04:00</published>
    <updated>2026-08-05T15:18:50-04:00</updated>
    <link rel="alternate" type="text/html" href="https://pfrenderlab.nd.edu/news/new-paper-examines-poison-resistance-in-snakes-around-the-world/"/>
    <title>New paper examines poison resistance in snakes around the world</title>
    <summary type="text">
      <![CDATA[p(image-right). !https://news.nd.edu/assets/63884/t_sirtalis_staton_300.jpg(T. Sirtalis)! A new study by University of Notre Dame biologist "Michael Pfrender":http://biology.nd.edu/people/faculty/pfrender/ and a team of researchers from the University of Nevada, Reno; Utah State University; and the University of Virginia suggests that snakes from different regions of the world have evolved a similar, remarkable resistance to a deadly neurotoxin. The finding, which appeared in the "Proceedings of the National Academy of Sciences":http://www.pnas.org/content/early/2012/02/29/1113468109.abstract?sid=8caae941-d7f1-45b9-bb17-2079c87d7db7, greatly increases scientists’ understanding of the genetic basis of adaptation and is a model for understanding the limits to adaptation and the degree to which evolutionary responses are predictable.]]>
    </summary>
    <content type="html">
      <![CDATA[<p class="image-right"><img title="T. Sirtalis" src="https://news.nd.edu/assets/63884/t_sirtalis_staton_300.jpg" alt="T. Sirtalis"></p>
<p>A new study by University of Notre Dame biologist <a href="http://biology.nd.edu/people/faculty/pfrender/">Michael Pfrender</a> and a team of researchers from the University of Nevada, Reno; Utah State University; and the University of Virginia suggests that snakes from different regions of the world have evolved a similar, remarkable resistance to a deadly neurotoxin.</p>
<p>The finding, which appeared in the <a href="http://www.pnas.org/content/early/2012/02/29/1113468109.abstract?sid=8caae941-d7f1-45b9-bb17-2079c87d7db7">Proceedings of the National Academy of Sciences</a>, greatly increases scientists’ understanding of the genetic basis of adaptation and is a model for understanding the limits to adaptation and the degree to which evolutionary responses are predictable.</p>
<p>Pfrender and colleagues found species of snakes in North, Central and South Americas and Asia that are able to feed on amphibians that secrete a deadly neurotoxic poison, tetrodotoxin or <span class="caps">TTX</span>. These snakes have similar mutations in a key sodium-channel gene that makes them highly resistant to <span class="caps">TTX</span>. These mutations prevent <span class="caps">TTX</span> from blocking the sodium channels in muscle, which would otherwise immobilize the snakes by paralyzing nervous and muscle tissue.</p>
<p>“The key finding is that adaptive evolution is constrained by the functional properties of the genes involved in these evolutionary responses,” Pfrender said. “While there are many possible mutations that can improve fitness, in this case resistance to the neurotoxin <span class="caps">TTX</span>, many of these mutations have a cost because they change the normal function of the genes. So, when we look at multiple species that have independently adapted to <span class="caps">TTX</span>, we see a very similar, and limited, set of mutations involved. The story is one of repeated evolutionary change that occurs through a limited set of changes at the molecular level.”</p>
<p class="image-left"><img title="Michael Pfrender" src="https://news.nd.edu/assets/63883/pfrender_lab_250.jpg" alt="Michael Pfrender"></p>
<p>The study stems from Pfrender’s interest in understanding how organisms deal with environmental change through adaptive evolution.</p>
<p>“We would like to know what the underlying genetic mechanisms are, and what the limits are to these adaptive responses,” he said. “Ultimately, we would like to develop a predictive framework to gauge when natural populations will be able to evolve rapidly enough to persist in a changing environment and when the environmental change is too fast or too strong, leading to local extinction.”</p>
<p>An understanding of how organisms deal with environmental change is relevant to the major themes of Notre Dame’s <a href="http://environmentalchange.nd.edu/">Environmental Change Initiative</a> and to the <a href="http://globalhealth.nd.edu/">Eck Institute for Global Health</a>, which examines disease resistance coupled with human health.</p>
<p>“Many organisms are exposed to toxic chemicals in their environment, and this system is a model for understanding how they cope with this challenge through evolutionary change,” Pfrender said. “A good example of the application of this knowledge is when we are trying to understand how parasites acquire drug resistance. How do they do it and what are the limits to this response? Can we create more effective drug strategies that capitalize on these functional constraints, making it more difficult for parasites to evolve resistance?”</p>
<p>Pfrender and the Utah State researchers plan to study more snake species and to expand their research to a number of other species, including insects that prey on the toxic eggs of salamanders. They also are examining other genes closely related to the sodium channel genes that are the focus of the <span class="caps">PNAS</span> study to expand their understanding of how adaptation occurs.</p>
<p><em><strong>Contact</strong>: Michael Pfrender, 574-631-0591, <a href="mailto:Michael.Pfrender.1@nd.edu">Michael.Pfrender.1@nd.edu</a></em></p>
<p class="attribution">Originally published by <span class="rel-author">William G. Gilroy</span> at <span class="rel-source"><a href="https://news.nd.edu/news/new-paper-examines-poison-resistance-in-snakes-around-the-world/">news.nd.edu</a></span> on <span class="rel-pubdate">March 15, 2012</span>.</p>]]>
    </content>
    <link rel="enclosure" type="image/jpeg" href="https://pfrenderlab.nd.edu/assets/667359/mlc_43026_dome_01.jpg" title="Notre Dame's Golden Dome and Mary statue, framed by vibrant pink blossoms under a clear blue sky."/>
    <author>
      <name>William G. Gilroy</name>
    </author>
  </entry>
  <entry>
    <id>tag:pfrenderlab.nd.edu,2005:News/180275</id>
    <published>2011-02-04T09:01:00-05:00</published>
    <updated>2026-08-10T09:29:09-04:00</updated>
    <link rel="alternate" type="text/html" href="https://pfrenderlab.nd.edu/news/notre-dame-biologist-pfrender-plays-key-role-in-_daphnia_-sequencing/"/>
    <title>Notre Dame biologist Pfrender plays key role in Daphnia sequencing</title>
    <summary type="text">
      <![CDATA[University of Notre Dame biologist Michael Pfrender is the coauthor of a paper appearing today in the prestigious journal Science describing the sequencing of the species Daphnia pulex, often referred to as the water flea. Daphnia, a small freshwater crustacean, is the first crustacean to have its genome sequenced. It contains more than 31,000 genes, as compared to 23,000 genes of humans.]]>
    </summary>
    <content type="html">
      <![CDATA[<p>University of Notre Dame biologist <a href="http://biology.nd.edu/people/faculty/pfrender/">Michael Pfrender</a> is the coauthor of a paper appearing today in the prestigious journal <a href="http://www.sciencemag.org/content/331/6017/539.short">Science</a> describing the sequencing of the species <em>Daphnia pulex</em>, often referred to as the water flea. <em>Daphnia</em>, a small freshwater crustacean, is the first crustacean to have its genome sequenced. It contains more than 31,000 genes, as compared to 23,000 genes of humans.</p>
<figure class="image image-right"><img src="https://pfrenderlab.nd.edu/assets/653722/image1.jpg" alt="A translucent water flea (Daphnia) with visible internal organs and yellowish eggs, against a dark background." width="200" height="289"></figure>
<p>“<em>Daphnia</em> has long been a model for ecology and early in the last century significant biological findings had their origin in <em>Daphnia</em> ,” Pfrender said. “For example, the concept of phenotypic plasticity, the dose-response curve central to toxicology and the effects of inbreeding to name a few.”</p>
<p>Pfrender was one of a small group of scientists who first approached the U.S. Department of Energy’s Joint Genome Institute in 2002 with a suggestion to sequence the <em>Daphnia </em>genome. That suggestion evolved into the "Daphnia Genomics Consortium," an international group of some 450 scientists from dozens of institutions world-wide. The consortium scientists were interested in the species because of its importance in aquatic food webs and for its transformational responses to environmental stress. Some species of <em>Daphnia</em> produce exaggerated spines, neck-teeth or helmets as a means of self-defense from predators. <em>Daphnia</em> also thrives in the absence of males, using clonal reproduction, until harsh environmental conditions favor the benefits of sex.</p>
<figure class="image image-left"><img src="https://pfrenderlab.nd.edu/assets/653724/image2.jpg" alt="Bearded man in glasses inspects a beaker of clear liquid amidst rows of lab jars on metal shelving." width="225" height="207"></figure>
<p>Although Pfrender and the founding members of the consortium conceived of the project with the expectation that new gene functions would be uncovered when studied in light of the animal’s natural environment, they did not expect to discover so many more genes. The researchers reveal in their Science paper that the high number stems from the fact that <em>Daphnia</em> is creating copies of genes at an extremely high rate: more than three times that of other invertebrates and 30 percent greater than that of humans. “These duplicate genes rapidly acquire new functions in response to environmental conditions,” Pfrender said. “This evolutionary flexibility may, in part, explain why <em>Daphnia</em> is able to respond to the environment in such a flexible manner.”</p>
<figure class="image image-right"><img src="https://pfrenderlab.nd.edu/assets/653723/image3.jpg" alt="Green translucent daphnia with red compound eye and visible internal organs against a black background." width="250" height="250"></figure>
<p>The genome sequencing information described in Science can help lead to a better understanding of what genes matter for organisms to cope with environmental stress that includes pollutants and global warming. This project used modern functional genomic technologies to understand how these genes function within an animal that is easily studied in fresh water ecosystems around the globe. Pfrender notes that the collaborative sequencing effort has positioned <em>Daphnia</em> as a model organism for an emerging scientific field of environmental genomics, aimed at better understanding how the environment and the genes in natural populations interact.</p>
<p>“As a genetic model, <em>Daphnia</em> was for some time supplanted by organisms like <em>Drosophila</em>,” Pfrender said. “<em>Daphnia</em> is now poised to become the premier model for ecological and environmental genomics. This paper establishes the foundation for the next wave of research in these fields.” The <em>Daphnia</em> sequencing research received financial and material support from the Office of Science of the U.S. Department of Energy, the National Science Foundation, the Lilly Endowment Inc., Roche NimbleGen Inc., the National Institutes of Health, the U.S. Department of Health and Human Services and Indiana University.</p>
<p class="attribution">Originally published by <span class="rel-author">William G. Gilroy</span> at <span class="rel-source"><a href="https://news.nd.edu/news/notre-dame-biologist-pfrender-plays-key-role-in-_daphnia_-sequencing/">news.nd.edu</a></span> on <span class="rel-pubdate">February 04, 2011</span>.</p>]]>
    </content>
    <link rel="enclosure" type="image/jpeg" href="https://pfrenderlab.nd.edu/assets/653725/pfrender.jpg" title="Man in orange jacket holds a clear water sampler by a rocky alpine lake and snowy peaks against a blue cloudy sky."/>
    <author>
      <name>William G. Gilroy</name>
    </author>
  </entry>
</feed>
