Cellular stress is associated with global misfolding and aggregation of the endogenous proteome. Monitoring stress-induced abnormalities remains one of the major technical challenges facing established sensors. Misfolded monomers induced by mild stresses, however, remain largely invisible with current sensors.
In a recent publication (1) Fares and colleagues describe a new sensor based upon a fluorescent molecular rotor that is conjugated to a Halo mutant (AgHalo). In non-stressed cells, the AgHalo sensor remains largely folded, and is fluorescent when misfolded. The fluorescent molecular rotor, when conjugated to purified AgHalo to form the proteome stress sensor, is able to report on urea-induced partially unfolded (misfolded) conformations with a higher fluorescent increase than the previously reported fluorophore-based sensors. Heat-induced misfolding is also effectively monitored by the fluorescence change of the sensor that is based on fluorescent molecular rotor, but not the solvatochromic fluorophore. The unique feature of the fluorescent molecular rotor makes the new generation of the AgHalo proteome sensor more sensitive to misfolded conformations that are primarily induced by mild proteome stress. Further, the new sensor exhibits a higher fluorescence signal when detecting soluble and insoluble protein aggregates that are induced by more severe proteome stress. These data collectively suggest that thermo-labile Halo conjugated with a fluorescent molecular rotor serves as a suitable sensor to detect a wide range of proteome stress conditions.
During the week of March 26, 2018, while many students were having fun and relaxing during Spring Break, others were busy doing extra lab work at the BTC Institute. This four-day workshop was designed to provide an introduction to the molecular biology laboratory for students affiliated with the Center for Educational Opportunity (CeO) on the UW-Madison campus. As noted on its website: โCeO promotes access to resources, academic achievement and personal growth for students whose parents have not received a four-year degree, students who meet specific federal family income guidelines, and students with documented disabilities.โ
It is well known that first-generation college students, women and students of color persist in STEM fields at lower rates than the general population. This interferes with the creation of a diverse STEM talent pool, in turn needed to ensure diverse problem-solving perspectives.
Further, STEM fields are often seen as being stressful, given their competitive learning environments. This may be especially discouraging for students from racial/ethnic minorities who may not have as many mentors and role models to turn to.
Introduction to the Laboratory attendees
This workshop aimed to give students an experience that would strengthen their skills and confidence as they continue to pursue scientific paths. In addition to laboratory work, students discussed the importance of clear communication in written and oral presentations, were required to work as partners to experience teamwork, and were encouraged to use reflection and lab reporting as ways to internalize what they learned throughout the week.
Dr. David Russell presenting at the 13th Wisconsin Stem Cell Symposium. The session was moderated by Dr. James Thomson.
โ20 years ago, when I first heard about the creation of human embryonic stem cells, I knew that this was the future. I immediately requested the cells from Dr. Thomson and dropped almost everything else we were doing in our lab. It has been my focus to this day.โ The person presenting is Dr. David Russell, a professor at the University of Washington. He is just one of the hundreds of researchers gathered at the BioPharmaceutical Technology Center Institute (a nonprofit supported by Promega) in Madison, Wisconsin for the 13th Annual Wisconsin Stem Cell Symposium that happened this week. This year, itโs not just a symposium, but also a celebrationโitโs the 20-year anniversary of the first-ever isolation and culture of human embryonic stem cells (ES cells).
In 1998, Dr. James Thomson, at the University of Wisconsin-Madison, created the first ES-cell line using donated (unused) embryos from a fertility clinic. The study sent a shockwave through the scientific community and general public. We now had the technology to grow human pluripotent ES cellsโwith the potential to develop into every cell type in the human bodyโin a dish! Thomson quickly became a celebrity scientist. (Thomsonโs headshot was on the cover of the August 20, 2001 issue of Time Magazine, next to big text that read: โThe Man Who Brought You Stem Cellsโ.)
However, not all were excited about the news. Backlash from conservative communities, who opposed the use of human embryos, resulted in a temporary ban on developing new ES cell lines with government funding. Nonetheless, the ban did not deter researchers from studying ES cells using private or state funding. By 2001, human ES cells have been successfully derived into neural, cardiac, hematopoietic, endothelial, and insulin-producing cells. In 2010, the first in-human clinical trial was initiated; which used human ES cell-derived materials to treat spinal cord injury.
2006 marked another milestone in stem cell research: the discovery of induced pluripotent stem (iPS) cells. Dr. Shinya Yamanaka at Kyoto University successfully reprogrammed adult fibroblasts (common cells in connective tissue that form the extracellular matrix and collagen) to revert back into an embryonic-like pluripotent stateโsimply by expressing four specific genes. He named these reprogrammed cells โinduced pluripotent stem cellsโ or iPS cells. A year later, human iPS cells were made in a similar fashion by both Thomson and Yamanaka. Yamanaka later received the 2012 Nobel Prize (some argue that Thomson deserved to share the prize).
Photo credit: 123rf stock photos.
The ability to reprogram adult cells back into a pluripotent state suggested we could create an unlimited supply of pluripotent cells that genetically matched a specific individualโwithout the ethical baggage of using human embryos. This meant, in theory, you could take fibroblasts from a patient with a neurological disorder, such as Parkinsonโs disease, revert the fibroblasts into iPS cells, edit the โfaulty genesโ in those cells, then redifferentiate the healthy iPS cells into neural stem cells that can be introduced back into the same patient to produce healthy neurons. Of course, this is easier said than done. The technical difficulties and high cost of generating and editing iPS cells from individual patients have complicated the development of iPS-based treatments. Currently, there is only one human clinical trial using cells derived from iPS cells, which treats macular degeneration (an incurable eye disease that leads to blindness).
Despite the emergence of iPS cells, ES cells have continued to dominate in the clinical realm. To this date, there are 18 clinical trials using ES cells to treat various disorders, including macular degeneration, Parkinsonโs disease, spinal cord injury, heart disease and diabetes. The future is bright, but there is still one major problem in ES cell-based therapies. Because ES cell treatments use donor cells from other healthy individualsโnot the patientsโ own cellsโthere is a high risk of immune rejection. But no fear, scientists have a plan.
In 2017, Dr. David Russell (mentioned in the beginning of this blog) re-engineered human embryonic stem cells to remove specific proteinsโhuman leukocyte antigens (HLA)โfrom the cell surface. HLA proteins allow the immune system to determine whether the presenting cell is โselfโ or โforeignโ. Removing HLA proteins is like wrapping the foreign cell with an invisible cloak, rendering it unnoticeable by the immune system. In his talk at the Stem Cell Symposium, Russell discussed the many advantages of using these โuniversal donor cells (UDCs)โ to treat diseases. Only one cell line is needed, which reduces the cost, complexity and time required for clinical trials. Also, it does not require immunosuppression, which weakens the patientโs immune system. Russell and many others believe that UDCs are the future of regenerative medicine. In fact, UDC-based therapies to treat cancer, macular degeneration, skin wounds and type 1 diabetes are already being developed.
It is amazing to see how far we have come over the last 20 years. Thanks toย visionary scientists like James Thomson, Shinya Yamanaka, David Russellโand countless other principal investigators, post-docs and grad students who work tirelessly in the lab every dayโtreatments for many life-threatening diseases may be available in the near future. Nonetheless, there is still much more to learn and many more challenges to overcome. Who knows where the next 20 years will take us?
The review โKinase Inhibitors: the road aheadโ was recently published in Nature Reviews Drug Discovery. In it, authors Fleur Ferguson and Nathanael Gray provide an up-to-date look at the โbiological processes and disease areas that kinase-targeting small molecules are being developed againstโ. They note the related challenges and the strategies and technologies being used to efficiently generate highly-optimized kinase inhibitors.
This review describes the state of the art for kinase inhibitor therapeutics. To understand why kinase inhibitors are so important in the development of cancer (and other) therapeutics research, let’s start with the role of kinases in cellular physiology.
Forty-some years ago fat was just fat. And it was regarded with disdain, to say the least.
An entire industry existed to help get rid of fat, using what was then the latest mass media technology, television. If you wanted to get rid of fat you could exercise with Jack LaLanne as he worked out on television. We exercised in elementary school PE class to a vinyl recording of โChicken Fatโ. You could strap into a device that employed shaking to get rid of the fat from your โhipsโ, or eat a piece of chocolate fudge with a hot beverage before meals to curb your appetite.
Fat was not our friend. We knew long before the current diabetes epidemic that being overweight was not good for our health.
Fast forward to the 21st century, where weโve learned that some forms of fat are actually good for you–important in metabolism, growth and immunity. The variety of types of mammalian fat include brown adipose tissue, beige adipose tissue and white adipose tissue, and itโs possible to convert one to the other under certain conditions. For details on these types of adipose tissue, read this article โafter you finish this blog.
Everyone has their favorite microscopic creatureโyou all do have a favorite, right? Mine is unquestionably the tardigrade. Tardigrades, also called water bears or moss piglets, are microscopic invertebrates that are composed of five segments: one head segment and four body segments, each with a pair of legs. They are 0.1โ1.2mm in length, making them easy to see under low magnification, and have a brain and well-developed nervous system. Tardigrades are found in just about every environment on earth. Termed โextremophilesโ, they have adapted to survive in even extremely harsh environments. Your neighborhood pond? The Himalayas? Antarctica? Deep sea? Tardigrades live in all those places.
Although many of us fell in love with these microscopic animals the first time we saw themโbecause there is no denying that they are darn cuteโ there are other good reasons why scientists are so fascinated by these creatures. Tardigrades are incredibly resilient. And by resilient, I mean almost indestructible. Continue reading “The Amazing, Indestructibleโand CuddlyโTardigrade”
By US Environmental Protection Agency [Public domain], via Wikimedia Commons
February 11 is the International Day of Women and Girls in Science, a reminder that there is still a gender gap in science. Despite the obstacles that women need to overcome, their contributions to field of science have benefited not only their fellow researchers but also their fellow humans. From treatments for diseases to new discoveries that opened up entire fields, women have advanced knowledge across the spectrum of science. Below is a sampling of the achievements of just a few women in science. What other living female scientist or inventor might you add?
Hate malaria? You can thank Tu Youyou for discovering artemisinin and dihydroartemisinin, compounds that are used to treat the tropical disease and save numerous lives. Her discovery was so significant, she received the 2015 Nobel Prize in Physiology or Medicine.
Recently, I had the opportunity to attend a fascinating symposium held at Promega featuring conservationist Steward Brand, where he described some of the projects developed by his foundation, Revive & Restore.
The organizationโs mission is to apply emerging biotechnology techniques to endangered and extinct species with the intent to increase genetic diversity, provide disease resistance and facilitate adaptation to changing climates. Although the overall message of enhancing biodiversity through the application of new genetic technology was inspiring, the project that resonated most for me was related to the plight of horseshoe crabs.
Horseshoe crabs, often referred to as living fossils, include four extant species with origins dating back about 450 million years. Although they look like crabs, they belong to their own subphylum and are more closely related to spiders. When horseshoe crabs spawn, they leave their usual habitat on the ocean floor and migrate to shore in large numbers. As a result, they have been exploited for bait and fertilizer for decades.
Enter endotoxins, an indicator for bacterial contamination in biologicals, drugs and medical devices. U.S. Food & Drug Administration regulations dictate that finished products be tested for the presence of endotoxins. These pyrogenic compounds, found in the cell wall of Gram-negative bacteria, can cause fever and affect a wide range of biological activity, possibly leading to aseptic shock and death. The most common method for testing is the gel clot and Limulus Amebocyte Lysate (LAL) Test.
I first learned about the LAL test during graduate school, where it was presented as a ubiquitous and standard requirement for testing bacterial contamination in injectable drugs. I remember being fascinated that horseshoe crabs (Limulus sp.), contain a substance that could be used to detect endotoxins. Although the instructors mentioned the need to collect blood from horseshoe crabs in order to produce the test, the method or scale of this harvest wasnโt discussed, nor were the true costs of using this method of endotoxin testing.
The LAL test has served as a faster, more inexpensive endotoxin testing replacement for the rabbit pyrogens test for the past 35 years. Every year during mating season horseshoe crabs move to shallow water, where they are removed in huge numbers. (To get an idea of scale for the harvest and read a much more comprehensive investigation of the issue, check out this article in The Atlantic, which features an archive photo of Delaware Bay horseshoe crab harvest from 1928โfor fertilizer, not pharmaceutical testing.)
After collection, the crabs end up in a lab where up to 30% of their blood is drained from a needle stuck in tissue around their heart. The LAL is extracted from the blood and can yield a product worth up to $15,000/quart. In order to avoid recollection, the crabs are returned to the ocean far from the shore where they were collected a few days before. Although itโs estimated that only 10-30% of these crabs die as a result of the process, there are indications that the horseshoe crab population and their ecosystems are impacted in other ways.
Researchers at the University of New Hampshire and Plymouth State University used accelerometers attached to recently bled female horseshoe crabs to test the hypothesis that harvesting for LAL was affecting their ability to spawn. While the research supported previous estimates with a death rate of 18%, females were found to be less likely to mate after being bled.
During his talk, Brand shared results from a study still in review that confirm the effect of over-harvesting Limulus on the survival of long distance migratory shorebirds. These birds synchronize their migration with horseshoe crab spawning, which provides a needed feast of eggs before the homestretch of their journey. Along with other ecosystem threats from climate change, the accelerated decline in the horseshoe crab population and dependency of migratory birds will likely to lead to a devastating ecological domino effect.
Fortunately, a synthetic alternative to LAL, recombinant factor C (rFC), has been available for nearly 20 years. Alas, there has been no significant shift by pharmaceutical companies away from the test based on horseshoe crab blood. rFC was patented and licensed to one company, Lonza, which Brand posited as one reason for the reluctance of drug companies to adopt its use.
Obviously, relying on one source for an essential testing reagent with no competition to temper cost is quite unattractive. But that argument has less bearing now that the patent is scheduled to expire in a few months, opening the door for additional manufacturers and creating an economic incentive for switching to the synthetic test.
Another reason may be that implementing a new test would require additional resources to validate the synthetic test for products that are already being tested with the LAL. Since the LAL has been specified in FDA guidance documents on endotoxin testing for decades, quality standards for existing products are based on the LAL, limiting momentum to change.
If both tests offered the same benefits, these arguments would make sense; however, research by one of the discoverers of rFC, Jeak Ling Ding of the National University of Singapore, shows that in many respects rFC is more efficacious than LAL. Since the raw material for the LAL test depends on an organism, there is seasonal variation in the components of the processed blood that must be taken into account. The reaction of the LAL also depends on a cascade of multiple compounds that can be affected by temperature, pH and proteinsโleaving the test vulnerable to false positive results.
Although Eli Lilly is the only pharmaceutical company to date to use rFC in place of LAL, It seems the tide may be turning. According to Brand, others are interested in making the transition. It seems foolish not to, given the source for LAL shows signs of dwindling due to overexploitation. Perhaps pharmaceutical companies are beginning to see the value of a โslower/betterโ philosophy (the cornerstone of the Long Now Foundation, another brainchild of Brandโs), rather than โfaster/cheaper.โ I have certainly gained a new perspective on endotoxin testing and a deep appreciation for the work of Brand and his foundation.
Does your organization use the LAL test? What is preventing you from switching to the synthetic alternative? Let us know!
Say the words โclimate changeโ in a room full of people and you are bound to inspire some passion in the responseโand very likely start an argument. There is no question that emotions and opinions run high whenever this topic is introduced. Most often the debate centers around who or what might be causing changes in the earthโs climate and what should be done about it. So for the sake of everyoneโs blood pressure, I want to set some expectations around this blog.
This is not a blog about the causes of climate change. I am not going to talk about who or what might be causing it, nor am I going to discuss ways the changes could be stopped, slowed down or altered.
The earthโs climate has warmed and cooled before. Looking at ice-core and geological records, we know that the earth has been much warmer than it is now, and we know that it has been much colder. Climate is dynamic, there are always fluctuations in temperature and moisture from year to year and decade to decade. Some of these fluctuations become trends where the changes consistently track in one direction, and some are anomalies, with more extreme climate conditions and less predictable patterns. Plant and animal populations are unquestionably affected by both the year-to-year fluctuations and the long-term trends. In this blog I am going to talk about two rather dramatic examples of the effects climate change. One example looks at the impact of warming global temperatures over time on the breeding populations of green sea turtles. The other is an example of the devastating results of one warm, remarkably humid, spring on the calving aggregations of the saiga antelope.
Salmonella. Streptococcus. Shigella. The most well-known bacteria are those that cause disease. Our relationship with them is one of combat. With good reason, we look for ways to avoid encountering them and to eliminate them when we do meet.
But not all bacteria are bad for us. Of course we have known for years that we are colonized by harmless bacteria, but recently, studies on the human microbiome have revealed many surprising things about these bacterial tenants. Studies are showing that the teeming multitudes of organisms living in and on the human body are not just harmless bystanders, but complex, interrelated communities that can have profound effects on our health.
Three studies published in Scienceย in 2018 add more to the growing body of microbiome surprises, showing that certain gut bacteria are not only good for us, but may even be required for the effectiveness of some anti-cancer immunotherapies.
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