Bioimaging /biofrontiers/ en For BioFrontiers and Syncroness collaboration, imaging is everything /biofrontiers/2018/03/19/biofrontiers-and-syncroness-collaboration-imaging-everything <span>For BioFrontiers and Syncroness collaboration, imaging is everything</span> <span><span>Anonymous (not verified)</span></span> <span><time datetime="2018-03-19T00:00:00-06:00" title="Monday, March 19, 2018 - 00:00">Mon, 03/19/2018 - 00:00</time> </span> <div> <div class="imageMediaStyle focal_image_wide"> <img loading="lazy" src="/biofrontiers/sites/default/files/styles/focal_image_wide/public/article-thumbnail/syncroness_0.jpg?h=7563d999&amp;itok=NLosRcuK" width="1200" height="600" alt="L-R: Josh Peifer, Joanne Vozoff, Joe Dragavon"> </div> </div> <div role="contentinfo" class="container ucb-article-categories" itemprop="about"> <span class="visually-hidden">Categories:</span> <div class="ucb-article-category-icon" aria-hidden="true"> <i class="fa-solid fa-folder-open"></i> </div> <a href="/biofrontiers/taxonomy/term/20"> News </a> </div> <div role="contentinfo" class="container ucb-article-tags" itemprop="keywords"> <span class="visually-hidden">Tags:</span> <div class="ucb-article-tag-icon" aria-hidden="true"> <i class="fa-solid fa-tags"></i> </div> <a href="/biofrontiers/taxonomy/term/144" hreflang="en">Bioimaging</a> <a href="/biofrontiers/taxonomy/term/461" hreflang="en">Jian Tay</a> <a href="/biofrontiers/taxonomy/term/328" hreflang="en">Joe Dragavon</a> <a href="/biofrontiers/taxonomy/term/134" hreflang="en">Microscopy</a> </div> <span>Chris Yankee</span> <a href="/biofrontiers/lindsay-diamond">Lindsay Diamond</a> <div class="ucb-article-content ucb-striped-content"> <div class="container"> <div class="paragraph paragraph--type--article-content paragraph--view-mode--default"> <div class="ucb-article-content-media ucb-article-content-media-above"> <div> <div class="paragraph paragraph--type--media paragraph--view-mode--default"> <div> <div class="imageMediaStyle large_image_style"> <img loading="lazy" src="/biofrontiers/sites/default/files/styles/large_image_style/public/article-image/syncroness_0_0.jpg?itok=IBUobYiq" width="1500" height="707" alt="L-R: Josh Peifer, Joanne Vozoff, Joe Dragavon"> </div> </div> </div> </div> </div> <div class="ucb-article-text d-flex align-items-center" itemprop="articleBody"> <div><div class="image-caption image-caption-none"> <p></p> <p>L-R: Josh Peifer, Joanne Vozoff, Joe Dragavon</p> </div> <p>When Syncroness, a Westminster-based technical product development and engineering firm, needed a highly technical solution to satisfy a client need, it turned to 精品SM在线影片 and the&nbsp;<a href="/biofrontiers/" target="_blank" rel="nofollow">BioFrontiers Institute</a>&nbsp;for assistance.</p> <p>The decision paid off, providing access to the BioFrontiers Advanced Light Microscopy Core facility, allowing Syncroness to deliver a solution to its customer and demonstrating how academic research communities can facilitate innovative solutions to commercial challenges.</p> <p>鈥淭his is the kind of mutually-beneficial relationship with high-tech business partners we would like to build on,鈥 said Mike Traxler, industry program manager for 精品SM在线影片鈥檚&nbsp;<a href="/industry/" rel="nofollow">Office of Industry Collaboration</a>, which serves as a kind of matchmaker between non-university partners and 精品SM在线影片 faculty and facilities.&nbsp;鈥淲e have an incredible range of specialized equipment, facilities and research expertise across campus, and much of it can be leveraged by industry to gain a competitive edge. That has certainly been the case with Syncroness. This is also a scenario that allows our faculty and students to collaborate with a company to design world-class products.鈥</p> <p>Recently, a Syncroness client commissioned the company to design a diagnostic tool to help prevent fouling in industrial equipment. The tool would need to measure the size and density of microscopic particles in a substrate, and Syncroness needed a baseline to measure performance of the system. The project demanded advanced imaging acquisition and analysis 鈥 not the kind of thing you just pick up at the local office supply store.</p> <p>It is not feasible for Syncroness to invest in specialized equipment for each individual project, let alone the time to cultivate deep expertise, given the rapid commercial schedules it executes. To maintain a sustainable business model, Syncroness seeks cutting-edge partnerships and collaborations that 鈥渆xtend expertise beyond what we have at Syncroness,鈥 said Todd Mosher, Syncroness鈥 VP of Engineering. 鈥淲e appreciate 精品SM在线影片 as a partner because we can leverage the university鈥檚 extensive investments in research equipment and expert staff.鈥</p> <h2>A match made in ... Boulder</h2> <p>Syncroness determined that the best solution would be to partner with experts in imaging analysis. Joanne Vozoff, PhD, the systems engineer on the project, reached out to a connection at 精品SM在线影片 who helped her identify the Advanced Light Microscopy Core facility at BioFrontiers Institute as a potential partner.</p> <p>Syncroness staff and representatives from Syncroness鈥 client visited BioFrontiers and worked with facility director Joe Dragavon on image acquisition. Next, Image Analysis Specialist Jian Wei Tay&nbsp;constructed unique algorithms for the image analysis to create known references to test the system鈥檚 performance. Syncroness used these known references to update the particle detection algorithms used by the equipment in the field.</p> <p>The BioFrontiers Advanced Light Microscopy Core facility primarily serves academic collaborations across 精品SM在线影片 and the Front Range, although five to 10 percent of the facility鈥檚 revenue comes from industry and third-party partners. While its academic customers are the top priority, providing access to industrial partners expands collaborative opportunities for the university and adds a modest but important revenue stream.</p> <p>Mosher anticipates that there will be more collaboration between Syncroness and the BioFrontiers Advanced Light Microscopy Core facility, but the opportunities don鈥檛 end there. In addition to its work with the microscopy facility, Syncroness frequently partners with engineering faculty at 精品SM在线影片 on projects in both research and product design, and has hired numerous graduates of the College of Engineering and Applied Science and the Leeds School of Business. 鈥淎s a CU alumni myself, I think it is important for CU Buffs to hire Buffs to build their businesses,鈥 Mosher said.</p> <p>Faculty, students and interested potential partners can visit the&nbsp;<a href="/industry/" rel="nofollow">Office of Industry Collaboration</a>&nbsp;website to learn more about university-industry opportunities.&nbsp;</p></div> </div> </div> </div> </div> <div>Traditional</div> <div>0</div> <div>On</div> <div>White</div> Mon, 19 Mar 2018 06:00:00 +0000 Anonymous 726 at /biofrontiers Bacteria have feelings, too /biofrontiers/2017/08/15/bacteria-have-feelings-too <span>Bacteria have feelings, too</span> <span><span>Anonymous (not verified)</span></span> <span><time datetime="2017-08-15T15:31:19-06:00" title="Tuesday, August 15, 2017 - 15:31">Tue, 08/15/2017 - 15:31</time> </span> <div> <div class="imageMediaStyle focal_image_wide"> <img loading="lazy" src="/biofrontiers/sites/default/files/styles/focal_image_wide/public/article-thumbnail/bacteriacanf.png?h=ae21ae52&amp;itok=KLm5OZ-k" width="1200" height="600" alt="Bacteria microscope image"> </div> </div> <div role="contentinfo" class="container ucb-article-tags" itemprop="keywords"> <span class="visually-hidden">Tags:</span> <div class="ucb-article-tag-icon" aria-hidden="true"> <i class="fa-solid fa-tags"></i> </div> <a href="/biofrontiers/taxonomy/term/150" hreflang="en">Bacteria</a> <a href="/biofrontiers/taxonomy/term/144" hreflang="en">Bioimaging</a> <a href="/biofrontiers/taxonomy/term/132" hreflang="en">Joel Kralj</a> </div> <span>Ula Chrobak</span> <div class="ucb-article-content ucb-striped-content"> <div class="container"> <div class="paragraph paragraph--type--article-content paragraph--view-mode--default"> <div class="ucb-article-content-media ucb-article-content-media-above"> <div> <div class="paragraph paragraph--type--media paragraph--view-mode--default"> <div> <div class="imageMediaStyle large_image_style"> <img loading="lazy" src="/biofrontiers/sites/default/files/styles/large_image_style/public/article-image/bacteriacanf.png?itok=DkgPC-WB" width="1500" height="1767" alt="Bacteria microscope image "> </div> </div> </div> </div> </div> <div class="ucb-article-text d-flex align-items-center" itemprop="articleBody"> <div><p>For humans, our sense of touch is relayed to the brain via small electrical pulses. Now, 精品SM在线影片 scientists have found that individual bacteria, too, can feel their external environment in a similar way.</p><p>In a new study, 精品SM在线影片 researchers have demonstrated that&nbsp;<em>E. coli</em>&nbsp;bacteria cells get excited when poked, sending out voltage induced calcium ion signals鈥攖he same way a vertebrate鈥檚 sensory nervous system works. The results are believed to be the first documented observation of electrical excitability in individual bacteria cells.</p><p>The findings, which could advance fundamental bacteria research and may eventually aid drug development for infectious diseases, were&nbsp;<a href="http://www.pnas.org/cgi/doi/10.1073/pnas.1703084114" rel="nofollow">published today</a>&nbsp;in the journal&nbsp;<em>Proceedings of the National Academy of Sciences</em>.</p><p>鈥淧eople typically think that [bacteria] are these little things, that all they are doing is trying to divide and create more energy,鈥 said Giancarlo Bruni, a doctoral candidate in 精品SM在线影片鈥檚&nbsp;<a href="https://mcdb.colorado.edu/" rel="nofollow">Department of Molecular, Cellular, and Developmental Biology</a>&nbsp;and the lead author of the new research. 鈥淸But] we鈥檙e not all that different.鈥</p><p>Scientists have long known that bacteria respond to certain chemical cues. Feed them sugar, and their populations explode. Douse them in antibiotics and their cell walls rip apart. More recently, though, scientists have noticed that physical signals, too, seem to activate these microbes. For example,&nbsp;<em>Salmonella</em>&nbsp;become more efficient at infecting human cells when placed on a stiff surface as opposed to a soft one.</p><p>鈥淲hat we think could be happening is that they鈥檙e using these electrical signals to modify their lifestyle,鈥 said Joel Kralj, the senior author of the study and an assistant professor in MCDB and the&nbsp;<a href="http://www.colorado.edu/biofrontiers/about" rel="nofollow">BioFrontiers Institute</a>.</p><p>To study how bacteria feel their surroundings, the team inserted special genes into&nbsp;<em>E. coli</em>&nbsp;bacteria that glow when calcium ions or electricity pulse through them. The cells were placed in a sticky substrate under a microscope. Left alone, the cells remained dim. But when the scientists pushed a pad against them, the bacteria lit up. The sparks of light indicated that proteins, ions and electricity were moving around in the bacteria.</p><p>The results indicate that bacteria and other creatures share a common tool for sensing their environment鈥攁n electrical pathway with the same functionality as human sensory neurons. From an evolutionary perspective, this signaling trait could be billions of years old and used by some of the oldest organisms on Earth.</p><p>The study also sheds new light on bacterial activity with regard to infection. For example, when exposed to antibiotics, a few bacteria cells with unique electric signals usually survive. These survivors then go on to reproduce and share their drug-resistant capabilities with other bacteria, eventually rendering the antibiotic useless.</p><p>The 精品SM在线影片 researchers now plan to study how bacteria鈥檚 electric pulses are used to sense when to infect human cells. In the future, they hope to test for small, masking molecules that can dull these signals when introduced. Such molecules could eventually translate into drugs that help treat bacterial infections and overcome antibiotic resistance.</p><p>鈥淚f we can block bacterial electrical activity, they may be less likely to infect, because now they don't know that they have landed on your soft delicious gut cell,鈥 said Kralj. 鈥淲e could cut their hands off so they can no longer feel.鈥</p><p>Additional co-authors of the new study include Andrew Weekley and Benjamin Dodd of MCDB and BioFrontiers. The National Institutes of Health and the Searle Scholars Program provided funding for the research.</p></div> </div> </div> </div> </div> <div>Traditional</div> <div>0</div> <div>On</div> <div>White</div> Tue, 15 Aug 2017 21:31:19 +0000 Anonymous 616 at /biofrontiers Kralj NIH Innovation Award /biofrontiers/2016/10/04/kralj-nih-innovation-award <span> Kralj NIH Innovation Award</span> <span><span>Anonymous (not verified)</span></span> <span><time datetime="2016-10-04T00:00:00-06:00" title="Tuesday, October 4, 2016 - 00:00">Tue, 10/04/2016 - 00:00</time> </span> <div> <div class="imageMediaStyle focal_image_wide"> <img loading="lazy" src="/biofrontiers/sites/default/files/styles/focal_image_wide/public/article-thumbnail/kralj.jpg?h=37a4e2d8&amp;itok=wsjYzfRx" width="1200" height="600" alt="Assistant Professor in Molecular, Cellular and Developmental Biology, Joel Kralj, a BioFrontiers Institute faculty member, became interested in measuring cellular voltage as a postdoctoral researcher."> </div> </div> <div role="contentinfo" class="container ucb-article-tags" itemprop="keywords"> <span class="visually-hidden">Tags:</span> <div class="ucb-article-tag-icon" aria-hidden="true"> <i class="fa-solid fa-tags"></i> </div> <a href="/biofrontiers/taxonomy/term/26" hreflang="en">Awards</a> <a href="/biofrontiers/taxonomy/term/144" hreflang="en">Bioimaging</a> <a href="/biofrontiers/taxonomy/term/132" hreflang="en">Joel Kralj</a> </div> <span>BioFrontiers</span> <div class="ucb-article-content ucb-striped-content"> <div class="container"> <div class="paragraph paragraph--type--article-content paragraph--view-mode--default"> <div class="ucb-article-content-media ucb-article-content-media-above"> <div> <div class="paragraph paragraph--type--media paragraph--view-mode--default"> <div> <div class="imageMediaStyle large_image_style"> <img loading="lazy" src="/biofrontiers/sites/default/files/styles/large_image_style/public/article-image/kralj.jpg?itok=PC6SPVOi" width="1500" height="1001" alt="Assistant Professor in Molecular, Cellular and Developmental Biology, Joel Kralj, a BioFrontiers Institute faculty member, became interested in measuring cellular voltage as a postdoctoral researcher."> </div> </div> </div> </div> </div> <div class="ucb-article-text d-flex align-items-center" itemprop="articleBody"> <div><h2><strong>Innovator Award winner brings to light the electrical changes in cells</strong></h2><p>Electric voltage powers life: Our brains use electrical transients to process every thought and every heartbeat arises from voltage changes in heart cells.&nbsp; Traditional measurements of voltage inside cells involve scientists making tiny wires and impaling cells, exactly the same way you could measure voltage flowing through a copper wire.&nbsp; However, due to the small size and fragile nature of cells, it has been technically impossible to measure voltage in neurons in a high throughput manner.</p><p>Assistant Professor in Molecular, Cellular and Developmental Biology, Joel Kralj, a BioFrontiers Institute faculty member, became interested in measuring cellular voltage as a postdoctoral researcher and developed a protein based sensor that converts changes in voltage to changes in fluorescence, finally bringing to light the electrical changes in cells.</p><p>鈥淭he fact that we can convert changes in voltage to something visible allows us to make movies showing these biological processes,鈥 says Kralj, 鈥淎nd because it鈥檚 really easy to take a movie, we now have a way of collecting vast amounts of voltage data without a physical connection to the cell, which is faster and easier.鈥</p><p>Kralj recently won a New Innovator Award from the National Institutes of Health for his work on voltage in neurons. According to the NIH, the New Innovator Award supports 鈥渦nusually innovative research鈥 from young investigators like Kralj. The NIH does not award these grants easily, giving out only about 50 per year. The program is meant to support creative researchers doing high risk, high-impact science鈥攁 description that Kralj easily matches</p><p>As part of this award, Kralj will receive $1.5 million to support his research, and the Innovator Awards allow more flexibility in spending than most grants. He plans to spend the grant money to develop automated microscopy hardware that will be capable of measuring neuronal voltage from hundreds to thousands of conditions. Kralj is joining Andrew Goodwin, assistant professor of Chemical and Biological Engineering, as 精品SM在线影片鈥檚 only Innovator awardees.</p><p>In order to study neurons Kralj plans to focus on the approximately 20 thousand proteins that transmit genetic information to find out how each protein affects voltage in neurons. This intensive process will involve removing a single protein in each measurement to see how its removal impacts the cell. Kralj will then create a database that includes the effects each of the 20 thousand proteins on the electrical changes in neurons鈥攃hanges that lead to neurological diseases like epilepsy and Amyotrophic Lateral Sclerosis, or ALS.</p><p>鈥淚 am hoping that our sensors, and the database we鈥檙e creating, will help us identify the full complement of proteins essential for normal function, and also how their absence might give rise to disease. The New Innovator Award is going to give me the flexibility to follow a lead in this research,鈥 says Kralj.</p></div> </div> </div> </div> </div> <div>Traditional</div> <div>0</div> <div>On</div> <div>White</div> Tue, 04 Oct 2016 06:00:00 +0000 Anonymous 154 at /biofrontiers Cracking the code on bacterial voltage /biofrontiers/2015/04/13/cracking-code-bacterial-voltage <span>Cracking the code on bacterial voltage</span> <span><span>Anonymous (not verified)</span></span> <span><time datetime="2015-04-13T00:00:00-06:00" title="Monday, April 13, 2015 - 00:00">Mon, 04/13/2015 - 00:00</time> </span> <div> <div class="imageMediaStyle focal_image_wide"> <img loading="lazy" src="/biofrontiers/sites/default/files/styles/focal_image_wide/public/article-thumbnail/kralj_0.jpg?h=3f2d4968&amp;itok=lIKldlFk" width="1200" height="600" alt="Joel Kralj is using fluorescent proteins to reveal how bacterial use electricity to stay alive."> </div> </div> <div role="contentinfo" class="container ucb-article-tags" itemprop="keywords"> <span class="visually-hidden">Tags:</span> <div class="ucb-article-tag-icon" aria-hidden="true"> <i class="fa-solid fa-tags"></i> </div> <a href="/biofrontiers/taxonomy/term/26" hreflang="en">Awards</a> <a href="/biofrontiers/taxonomy/term/150" hreflang="en">Bacteria</a> <a href="/biofrontiers/taxonomy/term/144" hreflang="en">Bioimaging</a> <a href="/biofrontiers/taxonomy/term/132" hreflang="en">Joel Kralj</a> </div> <span>BioFrontiers</span> <div class="ucb-article-content ucb-striped-content"> <div class="container"> <div class="paragraph paragraph--type--article-content paragraph--view-mode--default"> <div class="ucb-article-content-media ucb-article-content-media-above"> <div> <div class="paragraph paragraph--type--media paragraph--view-mode--default"> <div> <div class="imageMediaStyle large_image_style"> <img loading="lazy" src="/biofrontiers/sites/default/files/styles/large_image_style/public/article-image/kralj_0.jpg?itok=GVpz7LZw" width="1500" height="1001" alt="Joel Kralj is using fluorescent proteins to reveal how bacterial use electricity to stay alive."> </div> </div> </div> </div> </div> <div class="ucb-article-text d-flex align-items-center" itemprop="articleBody"> <div><h2><strong>Searle Scholars Award winner is cracking the code on bacterial voltage</strong></h2><p>Electric voltage powers life 鈥 Our brains use electrical transients to process every thought; every heartbeat arises from voltage changes in heart cells. Despite its importance, voltage changes in bacteria were never really studied because the cells were just too small to measure. In fact, biologists historically assumed that these voltage changes were only present in plants and animals. BioFrontiers Institute faculty member, Joel Kralj, an Assistant Professor in Molecular, Cellular and Developmental Biology, developed a method to encode a fluorescent protein into bacterial cells that allow it to become visible, revealing how bacteria use electricity to stay alive.</p><p>鈥淰oltage really is everywhere, and life has harnessed it for billions of years in order to evolve. That鈥檚 what is amazing,鈥 says Kralj. 鈥淔inding these electrical transients in bacteria gives us an entirely new perspective on their evolution.鈥</p><p>Kralj recently became a Searle Scholar for his work on voltage in bacteria. The Searle Scholars Program supports the research of scientists who recently started their appointments at the assistant professor level, and who are in their first tenure-track position at one of 153 participating academic or research institutions. Kralj was one of 15 researchers who were named Searle Scholars this year. As part of this award, he will receive $100,000 per year for three years to support his research.</p><p>The evolutionary story of bacteria is interesting enough but Kralj is looking at how bacteria use voltage changes to access hosts or signal other bacteria to colonize a host. The equipment he uses is highly specialized with fluorescent monitors developed specifically for use in bacteria, and a laser microscope to measure the tiny changes in voltage. Kralj鈥檚 lab is relatively new. He joined BioFrontiers last year and is in the process of staffing for his research. He is looking forward to using the funds from the Searle Scholars program to build more equipment to do bacterial research, including automatic scanning microscopes.</p><p>Although his research subjects are small, Kralj鈥檚 research has the potential to make a big impact. He is unlocking the secrets around how bacteria are using voltage to survive antibiotic exposure. He鈥檚 hoping to discover whether many of the antibiotic resistant 鈥渟uperbugs鈥 are staying alive because they are modulating their voltage to attack hosts, colonize and evade the drugs developed to kill them. If Kralj finds this to be the case, he hopes to understand how voltage could be inhibited in bacterial cells so that antibiotic drugs could be more effective.</p><p>鈥淭he Searle Scholar grants are going to give me the flexibility to follow a lead in this research,鈥 says Kralj. 鈥淩esearchers looked for twenty years to find a way to measure this voltage, and now that we can measure it, there is so much to study.鈥</p><p>The University of Colorado in Boulder currently has six other Searle Scholars, including Natalie Ahn, Min Han, Arthur Pardi, Roy Parker, Gia Voeltz and Ding Xue.</p></div> </div> </div> </div> </div> <div>Traditional</div> <div>0</div> <div>On</div> <div>White</div> Mon, 13 Apr 2015 06:00:00 +0000 Anonymous 180 at /biofrontiers CU-Boulder lab awarded $14.6 million DARPA contract /biofrontiers/2014/02/03/cu-boulder-lab-awarded-146-million-darpa-contract <span>CU-Boulder lab awarded $14.6 million DARPA contract</span> <span><span>Anonymous (not verified)</span></span> <span><time datetime="2014-02-03T00:00:00-07:00" title="Monday, February 3, 2014 - 00:00">Mon, 02/03/2014 - 00:00</time> </span> <div> <div class="imageMediaStyle focal_image_wide"> <img loading="lazy" src="/biofrontiers/sites/default/files/styles/focal_image_wide/public/article-thumbnail/will_old.jpg?h=cd3e571c&amp;itok=uUvZ5PdQ" width="1200" height="600" alt="BioFrontiers' Will Old is leading the SPARTA team."> </div> </div> <div role="contentinfo" class="container ucb-article-tags" itemprop="keywords"> <span class="visually-hidden">Tags:</span> <div class="ucb-article-tag-icon" aria-hidden="true"> <i class="fa-solid fa-tags"></i> </div> <a href="/biofrontiers/taxonomy/term/26" hreflang="en">Awards</a> <a href="/biofrontiers/taxonomy/term/144" hreflang="en">Bioimaging</a> <a href="/biofrontiers/taxonomy/term/166" hreflang="en">William Old</a> </div> <span>BioFrontiers</span> <div class="ucb-article-content ucb-striped-content"> <div class="container"> <div class="paragraph paragraph--type--article-content paragraph--view-mode--default"> <div class="ucb-article-content-media ucb-article-content-media-above"> <div> <div class="paragraph paragraph--type--media paragraph--view-mode--default"> <div> <div class="imageMediaStyle large_image_style"> <img loading="lazy" src="/biofrontiers/sites/default/files/styles/large_image_style/public/article-image/will_old.jpg?itok=8rWcFqeY" width="1500" height="995" alt="BioFrontiers' Will Old is leading the SPARTA team."> </div> </div> </div> </div> </div> <div class="ucb-article-text d-flex align-items-center" itemprop="articleBody"> <div><p>The University of Colorado was recently awarded a cooperative agreement worth up to $14.6 million from the Defense Advanced Research Projects Agency (DARPA) to develop a new technological system to rapidly determine how drugs and biological or chemical agents affect human cells.</p><p>The project, called the Subcellular Pan-Omics for the Advanced Rapid Threat Assessment (SPARTA) will be conducted by an interdisciplinary CU-Boulder team led by Research Assistant Professor William Old of the chemistry and biochemistry department.</p><p>DARPA, an arm of the U.S. Department of Defense, wants to better understand the biochemical mechanisms at work during cellular exposures to biological or chemical agents to help prevent mortality during potential conflicts. The research also is expected to lead to new broad-scale techniques to analyze cellular processes to wide societal benefit.</p><p>"We believe the technology developed under this program will go far beyond military and commercial applications," said SPARTA Program Manager Emina Begovic. "We envision powerful applications of these new tools in a biomedical setting. Understanding how cells are affected by bacterial infection, for example, could lead to the development of new treatments."</p><p>"Traditionally it takes decades to figure out how drugs affect an organism's biology," says Old. "Our goal is to rapidly speed up the process, identifying how these compounds work, in weeks. This could lower the barriers to developing effective drugs that have minimal side effects."</p><p>Old's team will comprehensively measure all major classes of biomolecules that respond to any cellular treatment or biological signal within milliseconds to days. This will help to determine the key molecular events that mediate cellular responses. The team is developing new microfluidic devices to control and manipulate individual cell components to obtain subcellular resolution that will provide new insights into the functions of individual organelles and proteins within cells.</p><p>One example that illustrates the complexities of the project is the nerve gas, sarin, which causes a malfunction in a key cellular enzyme used to control muscles, resulting in their overstimulation.</p><p>"We know this drug causes negative effects in multiple signaling pathways," said Tristan McClure-Begley, a pharmacologist and analytical chemist working on the SPARTA team. "But what we lack a comprehensive understanding of the mechanisms that lead to long-term systemic damage in individuals the survive exposure."</p><p>The Jennie Smoly Caruthers Biotechnology Building already houses seven mass spectrometers in the Proteomics and Mass Spectrometry Core Facility directed by Old. These powerful instruments can identify the molecular components of a cell by measuring the mass of different molecules. The mass spectrometers are used for a range of projects, from identifying biomarkers for Alzheimer's disease to finding the mechanisms of drug resistance in metastatic melanoma.&nbsp;Under the DARPA contract, Old's facility will install to additional next-generation mass spectrometers at a cost of $2.2 million, which will also be used by scientists, students and local biotechnology companies who use the spectrometry facility.</p><p>SPARTA team members include Professor of Chemistry and Biochemistry and BioFrontiers Associate Director, Natalie Ahn; Associate Professor Michael Stowell of the molecular, cellular and developmental biology department; Professor Y.C. Lee of the mechanical engineering department; and Associate Professor Xuedong Liu of the chemistry and biochemistry department. The team also includes Associate Professor Nichole Reisdorph of the University of Colorado School of Medicine and National Jewish Health in Denver.</p></div> </div> </div> </div> </div> <div>Traditional</div> <div>0</div> <div>On</div> <div>White</div> Mon, 03 Feb 2014 07:00:00 +0000 Anonymous 218 at /biofrontiers BioFrontiers partners with Avery Brewing /biofrontiers/2014/01/31/biofrontiers-partners-avery-brewing <span>BioFrontiers partners with Avery Brewing</span> <span><span>Anonymous (not verified)</span></span> <span><time datetime="2014-01-31T00:00:00-07:00" title="Friday, January 31, 2014 - 00:00">Fri, 01/31/2014 - 00:00</time> </span> <div> <div class="imageMediaStyle focal_image_wide"> <img loading="lazy" src="/biofrontiers/sites/default/files/styles/focal_image_wide/public/article-thumbnail/brewry_0.jpg?h=240faa5d&amp;itok=BS7abIGc" width="1200" height="600" alt="Huntley, Dowell and Driscoll work in the Sequencing Facility (Photo: Casey Cass)"> </div> </div> <div role="contentinfo" class="container ucb-article-tags" itemprop="keywords"> <span class="visually-hidden">Tags:</span> <div class="ucb-article-tag-icon" aria-hidden="true"> <i class="fa-solid fa-tags"></i> </div> <a href="/biofrontiers/taxonomy/term/144" hreflang="en">Bioimaging</a> <a href="/biofrontiers/taxonomy/term/126" hreflang="en">Biomaterials</a> <a href="/biofrontiers/taxonomy/term/142" hreflang="en">Computational Biology</a> </div> <span>BioFrontiers</span> <div class="ucb-article-content ucb-striped-content"> <div class="container"> <div class="paragraph paragraph--type--article-content paragraph--view-mode--default"> <div class="ucb-article-content-media ucb-article-content-media-above"> <div> <div class="paragraph paragraph--type--media paragraph--view-mode--default"> <div> <div class="imageMediaStyle large_image_style"> <img loading="lazy" src="/biofrontiers/sites/default/files/styles/large_image_style/public/article-image/brewry.jpg?itok=H0kOB-CR" width="1500" height="939" alt="Huntley, Dowell and Driscoll work in the Sequencing Facility (Photo: Casey Cass)"> </div> </div> </div> </div> </div> <div class="ucb-article-text d-flex align-items-center" itemprop="articleBody"> <div><h2><strong>BioFrontiers partners with world鈥檚 oldest biotech industry: Breweries</strong></h2><p>In the basement of the Jennie Smoly Caruthers Biotechnology Building on CU-Boulder鈥檚 East Campus sits a machine that can sequence roughly 6 billion DNA segments in about a week.</p><p>By comparison, human DNA consists of roughly 3 billion bases, and it took more than a decade for the first human genome to be sequenced by an international team of scientists.</p><p>The machine, an Illumnia HiSeq2000, is the centerpiece of the BioFrontiers Institute鈥檚 Next-Gen Sequencing Facility, and it has become a critical piece of equipment for researchers across campus. But it鈥檚 also an important resource for the Front Range鈥檚 thriving biotech industry, which routinely relies on the facility for sequencing work.</p><p>The facility has partnered with all kinds of local biotech big hitters, including a company that makes biofuels and another that makes tests for genetic mutations. But in 2013, the Next-Gen Sequencing Facility forged a new relationship with a well-loved but less-obvious local biotech company: Boulder-based Avery Brewing.</p><p>鈥淚 would argue that brewing and brewing chemistry is one of the oldest biotechnologies in the world,鈥 said Jim Huntley, director of CU-Boulder鈥檚 sequencing facility. 鈥淭hey do a lot of analysis on the quality of their product. Any biotech company does that. I don鈥檛 care if you鈥檙e making beer or you鈥檙e making an enzyme that鈥檚 used to catalyze some reaction; there鈥檚 always a degree of quality control.鈥</p><p>Huntley and Robin Dowell, an assistant professor at BioFrontiers, are helping Avery find a way to maintain its much-lauded beer quality less expensively by sequencing the genomes of six of the yeast strains used at Avery during the fermentation process.</p><h3><strong>An IPA that tastes like an IPA</strong></h3><p>The problem Avery wants to fix is the possible cross-contamination of yeast strains. Unlike large brewing operations, microbreweries use the same equipment to brew multiple types of beer using more than one yeast strain, which can occasionally lead to the yeast strains growing where they don鈥檛 belong.</p><p>The yeast used in the brewing process feeds on sugar to produce alcohol and carbon dioxide. But along the way, the yeast produces other products that affect the flavor of the beer, including fruity esters, buttery ketones and spicy phenolics. Different strains of yeast produce different flavors, and so using the correct yeast is key to brewing the desired beer.</p><p>鈥淔or example, our IPA is fermented with a different strain of yeast than our Belgian wit,鈥 said Dan Driscoll, Avery鈥檚 staff microbiologist. 鈥淲e occasionally see our Belgian wit yeast is growing in an IPA tank and that鈥檚 a problem because that yeast is incredibly phenolic so the resulting beer smells clovy and spicy.&nbsp; In the interest of consistency, we can鈥檛 call our IPA our IPA if it tastes and smells different than the last batch.鈥</p><p>[video:https://www.youtube.com/watch?time_continue=4&amp;v=4yehwrdKRGM]</p><p>Though it鈥檚 rare, when cross-contamination occurs, the entire tank of beer, typically about 240 barrels, has to be flushed.</p><p>In the past, Avery has uncovered cases of cross-contamination by sampling the beer while it鈥檚 in the fermentation tanks, streaking the sample on an agar plate, putting the plate in an incubator and waiting 48 hours for the yeast to grow.</p><p>鈥淲hat I said, being a microbiologist, when I first got here was, 鈥業t would be great if we could find a way to both identify this cross-contamination sooner and determine how severe it needs to be in order for us to start picking up on those off flavors,鈥 鈥 Driscoll said.</p><p>Driscoll, a veteran of the more traditional biotech industry, knew that Avery could purchase a machine that would allow it to quickly differentiate the yeasts based on their genetic codes. But there was a catch: the genetic codes were not known.</p><p>Through a connection in the biotech industry, Driscoll got in contact with Huntley, who said he might be able to help Avery with its problem.</p><blockquote>鈥淪ince we get funding from the state to maintain and operate the facility and purchase equipment, we really want to engage with the local biotech communities and other regional research organizations to provide them access to cutting-edge instrumentation,鈥 Huntley said.</blockquote><p>Because Avery uses commercially available yeast strains, and because the microbrew industry has a culture of openly sharing techniques and tools, working with Avery could benefit Colorado鈥檚 entire brewing industry, which has a total annual economic benefit to the state of more than $400 million.</p><h3><strong>鈥楾hink globally, sequence locally鈥</strong></h3><p>Avery provided Huntley with six of its yeast strains, including its house ale yeast, which is used in a half dozen of the brewery鈥檚 beers. At the Next-Gen Sequencing Facility, Huntley loaded the samples into the HiSeq 2000, which works by shredding multiple copies of the yeast鈥檚 DNA into tiny little pieces and then sequencing all those overlapping pieces at the same time to produce a coherent picture of its entire genetic code.</p><p>But just knowing the genetic code isn鈥檛 enough to solve Avery鈥檚 problem. Driscoll also needs to know exactly how the yeasts鈥 genetic codes differ from each other to be able to tell the yeast strains apart鈥攚hich is where BioFrontiers researcher Robin Dowell comes in.</p><p>Dowell鈥檚 lab specializes in differences between yeasts, though she doesn鈥檛 typically study the strains that are used to brew beer.</p><p>鈥淲e focus on two strains that, from a genetic perspective, are about as different as any two random people,鈥 Dowell said. 鈥淲e look at inter-strain differences all the time, and what Avery really cares about is identifying strain differences they can actually leverage to say, 鈥楾his strain is this one and that strain is that one.鈥 鈥</p><p>Once the differences in the strains have been identified, Avery Brewing Company will be able to determine if a tank is contaminated with the wrong kind of yeast in a matter of hours rather than days. The contaminated beer will still have to be flushed, but the test will make it possible for Avery to free up the tank sooner, allowing them to start brewing another beer that they can actually sell.</p><p>For the Next-Gen Sequencing Facility, the continued partnership with Avery is just part of what they are charged to do鈥攈elp strengthen the local biotech community.</p><p>鈥淲hen the local biotech community is stronger, it allows for more startups and more product development, which brings more jobs to the area,鈥 Huntley said. 鈥淎s I always quip, 鈥楾hink globally, but sequence locally.鈥 鈥</p></div> </div> </div> </div> </div> <div>Traditional</div> <div>0</div> <div>On</div> <div>White</div> Fri, 31 Jan 2014 07:00:00 +0000 Anonymous 216 at /biofrontiers Lights, Cells, Action! /biofrontiers/2011/10/19/lights-cells-action <span>Lights, Cells, Action!</span> <span><span>Anonymous (not verified)</span></span> <span><time datetime="2011-10-19T00:00:00-06:00" title="Wednesday, October 19, 2011 - 00:00">Wed, 10/19/2011 - 00:00</time> </span> <div role="contentinfo" class="container ucb-article-tags" itemprop="keywords"> <span class="visually-hidden">Tags:</span> <div class="ucb-article-tag-icon" aria-hidden="true"> <i class="fa-solid fa-tags"></i> </div> <a href="/biofrontiers/taxonomy/term/158" hreflang="en">Amy Palmer</a> <a href="/biofrontiers/taxonomy/term/150" hreflang="en">Bacteria</a> <a href="/biofrontiers/taxonomy/term/144" hreflang="en">Bioimaging</a> </div> <span>BioFrontiers</span> <div class="ucb-article-content ucb-striped-content"> <div class="container"> <div class="paragraph paragraph--type--article-content paragraph--view-mode--default"> <div class="ucb-article-content-media ucb-article-content-media-above"> <div> <div class="paragraph paragraph--type--media paragraph--view-mode--default"> </div> </div> </div> <div class="ucb-article-text d-flex align-items-center" itemprop="articleBody"> <div><h3>Lights, Cells, Action!</h3><p>&nbsp;</p><p>One of the best ways to really see something is to turn on the lights. Amy Palmer, assistant professor in the Department of Chemistry and Biochemistry and Biofrontiers Institute faculty member, is the kind of professor that can shine a light on subjects for her students, and shine a light on the cellular subjects in her lab.</p><p>Shining a light was the kernel of the idea behind fluorescent proteins:&nbsp; proteins that absorb energy at a specific wavelength and re-emit the energy at a different wavelength. Osamu Shimomura discovered the first fluorophore, called the green fluorescent protein (GFP), in jellyfish. GFP was then popularized and turned into a useful tool for cell biology by Martin Chalfie and Roger Tsien.&nbsp; Together, the three scientists shared the Nobel Prize in chemistry in 2008 for their contributions.&nbsp; GFP gave scientists the ability to put these glow-in-the-dark molecules in cells and living organisms and watch action within cells that had never been seen.</p><p>鈥淪napshots of a football game won鈥檛 tell you how to play the game,鈥 says Palmer, 鈥淔luorescent proteins allow us to watch the game while it is in motion.鈥</p><p>Palmer鈥檚 group is developing tools and technologies around these pretty proteins, which now come in a rainbow of colors in addition to the original jellyfish green. She recently attached fluorescent proteins to the Salmonella bacteria to follow it as it invaded a host organism with the hopes of learning how to prevent the bacteria from taking over and wreaking havoc.</p><p>Palmer鈥檚 next target is not animal, not vegetable鈥t鈥檚 a mineral. Zinc is an essential trace mineral found in all humans, totaling almost two grams in the average adult. Next to iron, zinc is the most common mineral in the body and is found in every cell, and in large concentrations in the brain, retinas, pancreas and prostate.</p><p>Imbalances in zinc levels can cause a myriad of troubles, from Alzheimer鈥檚 to diabetes to prostate cancer. In addition, zinc plays important roles in growth and reproduction; taste, vision and smell; and even proper insulin and thyroid function. Zinc deficiency is a worldwide challenge causing problems ranging from stunted growth to fatal diseases.</p><p>Palmer is developing fluorescent probes that can attach to zinc. Defining the location of zinc and how it fluctuates in an organism is the first step in knowing how cells regulate it, and how we can regulate it in patients that have imbalances. For example, prostate cancer is difficult to diagnose and predict how it will respond to treatment. By measuring zinc levels, scientists may be able to predict the aggressiveness of the tumors and give a more accurate prognosis of the disease.</p><p>鈥淲e know very little about what zinc is doing at the cellular level,鈥 says Palmer. 鈥淔luorophores allow us to see how this metal is playing a role in some diseases like prostate cancer and diabetes.鈥 She is aiming for a zinc-tracking technique to catch diseases early in their processes, but don鈥檛 expect to be injected with glow-in-the-dark proteins at your next doctor鈥檚 visit.</p><p>鈥淭here isn鈥檛 a clinical use for fluorescent proteins right now,鈥 says Palmer. 鈥淭here isn鈥檛 a machine for them that a doctor would use to look inside your body. What makes these proteins special is looking at what happens at the cellular level of an organism. We can see into cells and witness what an X-ray or MRI machine cannot. That fundamental level of understanding is going to lead us to bigger solutions.鈥</p><p>Related content</p><p><a href="https://biofrontiers.colorado.edu/about/directory/apalmer" rel="nofollow">Amy Palmer</a></p></div> </div> </div> </div> </div> <div>Traditional</div> <div>0</div> <div>On</div> <div>White</div> Wed, 19 Oct 2011 06:00:00 +0000 Anonymous 282 at /biofrontiers Biomarkers light the way to cancer diagnosis /biofrontiers/2011/09/13/biomarkers-light-way-cancer-diagnosis <span>Biomarkers light the way to cancer diagnosis</span> <span><span>Anonymous (not verified)</span></span> <span><time datetime="2011-09-13T00:00:00-06:00" title="Tuesday, September 13, 2011 - 00:00">Tue, 09/13/2011 - 00:00</time> </span> <div> <div class="imageMediaStyle focal_image_wide"> <img loading="lazy" src="/biofrontiers/sites/default/files/styles/focal_image_wide/public/article-thumbnail/yin_lab.jpg?h=e41ff0ee&amp;itok=Qz-CeNzE" width="1200" height="600" alt="Biofrontiers scientist, Hubert Yin, is using fluorescent biomarkers to develop a better screening method for cancer."> </div> </div> <div role="contentinfo" class="container ucb-article-tags" itemprop="keywords"> <span class="visually-hidden">Tags:</span> <div class="ucb-article-tag-icon" aria-hidden="true"> <i class="fa-solid fa-tags"></i> </div> <a href="/biofrontiers/taxonomy/term/144" hreflang="en">Bioimaging</a> <a href="/biofrontiers/taxonomy/term/140" hreflang="en">Cancer</a> <a href="/biofrontiers/taxonomy/term/148" hreflang="en">Hubert Yin</a> </div> <span>BioFrontiers</span> <div class="ucb-article-content ucb-striped-content"> <div class="container"> <div class="paragraph paragraph--type--article-content paragraph--view-mode--default"> <div class="ucb-article-content-media ucb-article-content-media-above"> <div> <div class="paragraph paragraph--type--media paragraph--view-mode--default"> <div> <div class="imageMediaStyle large_image_style"> <img loading="lazy" src="/biofrontiers/sites/default/files/styles/large_image_style/public/article-image/yin_lab.jpg?itok=TVjoJOh0" width="1500" height="2258" alt="Biofrontiers scientist, Hubert Yin, is using fluorescent biomarkers to develop a better screening method for cancer."> </div> </div> </div> </div> </div> <div class="ucb-article-text d-flex align-items-center" itemprop="articleBody"> <div><h3>Biomarkers light the way to cancer diagnosis<a href="/p1e18ae28049/sites/default/files/styles/large/public/article-image/yin_lab.jpg?itok=RNVFe8w2" rel="nofollow"> </a></h3><p>&nbsp;</p><p>In an 18-year study released this summer by the National Cancer Institute, widespread screening for ovarian cancer was found to be ineffective in catching the disease. In fact, the screening often did more harm than good, leading women to unnecessary surgery and the complications that often come with it.</p><p>Similar issues have been raised about annual mammography screenings increasing breast cancer risk in women with a predisposition to the disease. The low-dose radiation used in the screening ratcheted up the susceptibility to cancer for women who were already at a higher risk鈥攖he women who need the screenings the most. Biofrontiers scientist, Hubert Yin, is on the hunt for a better way to find cancer early, without harming patients in the process.</p><p>Hubert, an assistant professor in chemistry and biochemistry, is studying biomarkers, which are traceable substances that allow scientists to track a process within the body. Using a biomarker is like tying a balloon to a friend moving through a crowd. Because you can see the balloon above the crowd, you are easily able to locate your friend. In Hubert鈥檚 experiments, the balloons are fluorescent molecules called a fluorophores, which chemically attach themselves to cells that indicate cancer is present, glowing so they can be seen and tracked.</p><p>Microvesicles are the objects of the fluorophores鈥 chemical spotlight. They are shed from the surface of cells and can actually help the spread and release of metastatic cancer cells. The presence of microvesicles is a key indicator that cancer is at work, and fortunately, they are easy to find in a simple blood or urine sample. Once Hubert chemically attaches fluorophores to these microvesicles, screening someone for cancer becomes as easy as looking for the glow. A lack of microvesicles means there is nothing for the fluorophores to attach to, which means they don鈥檛 glow. And no glow means no cancer.</p><p>鈥淭his is a great diagnostic concept,鈥 he says. 鈥淏iomarkers like fluorophores give us efficient, non-invasive ways to detect cancer before it is diagnosed and after it is treated. Being a smaller, research focused organization gives us an advantage over big pharmaceutical companies when it comes to designing biomedical solutions. It is easier for us to collaborate across labs, and to innovative methods that lead us in the direction of new ways of treating cancer.鈥</p><p>Related content</p><p><a href="https://biofrontiers.colorado.edu/about/directory/yinh" rel="nofollow">Hang Hubert Yin</a></p></div> </div> </div> </div> </div> <div>Traditional</div> <div>0</div> <div>On</div> <div>White</div> Tue, 13 Sep 2011 06:00:00 +0000 Anonymous 348 at /biofrontiers