Beneath the Writing: Non-Invasive DNA Sampling from Modern and Historic Writing Surfaces

We can learn a lot about the past and its people from the written records of the time. What people write and how they write it can gives us glimpses into historical events, interpersonal relationships, social standing and even social and cultural norms. From paper to papyrus to clay tablets, the surface that holds the writing can tell us things that the words cannot.

For plant-based writing surfaces, the quality of the surface or even the technique used to make it can give historians and archeologists insight into the people who used them. What more could we learn if we knew what plant, or plants, were used in the production of ancient writing material? Continue reading “Beneath the Writing: Non-Invasive DNA Sampling from Modern and Historic Writing Surfaces”

Factors Influencing Compound Potency in Biochemical and Cellular Assays

Late in 2017, a group here at Promega launched an exciting new assay, the NanoBRET™ Target Engagement (TE) Intracellular Kinase Assay.

It’s easy for me to call this assay exciting; I was an editor on the project team. But judging by the reviews on the SelectScience® web site, others are excited about NanoBRET™ Target Engagement Intracellular Kinase Assay too.

A review of the NanoBRET TE Kinase assay from SelectScience® .
A review of the NanoBRET TE Kinase assay from SelectScience® .
Continue reading “Factors Influencing Compound Potency in Biochemical and Cellular Assays”

Millions of Pickles, Pickles in the Sea

For a few years beginning late in 2013, warmer ocean conditions in the eastern Pacific prompted the appearance of unexpected species and toxic algal blooms that devastated others. When temperatures cooled in 2017, the marine ecosystems seemed to be returning to normal. Except for the pyrosomes. Although these previously rare organisms did start to wash up on beaches during the periods of warming, they began to appear by the millions from Oregon to Alaska that spring.

Pyrosomes
Photo by Steven Grace.

Some combination of ideal conditions led pyrosomes to multiply, dominate the ocean surface and wash up on beaches along the US and Canadian Pacific Coasts. Pyrosomes typically exist offshore, far below the surface in warm, tropical waters all over the world. Their sudden proliferation in other areas is likely due to the warm, Pacific ocean “blob,” although atypical sea currents and changes in pyrosome diet have been offered as other possible explanations.

While the appearance of pyrosomes impeded the efforts of fisherman by clogging nets and filling hooks, greater ecological effects have yet to be observed. As we celebrate World Oceans Month, pyrosomes offer a mesmerizing example of the astounding biological diversity our oceans have to offer and, perhaps, a cautionary tale of the impact climate change can have on those marine lifeforms.

The pyrosome species common in the NE Pacific, Pyrosoma atlanticum, goes by a few other colorful names. Each name reveals something captivating about these creatures. Commonly called “sea pickles” due their size, shape and bumpy texture (like a transparent cucumber), these are not single organisms, but colonies formed by hundreds or thousands of individual multicellular animals call zooids.

Continue reading “Millions of Pickles, Pickles in the Sea”

High-Throughput Purification with Experts Included

Implementing automated nucleic acid purification or making changes to your high-throughput (HT) workflow can be complicated and time-consuming. There are also many barriers to success such as challenging samples types and maintaining desirable downstream results that can add to the stress, not to mention actually getting the robotic instrumentation to do what you want it to. All of this makes it easy to understand why many labs avoid automating or own expensive instrumentation that goes unused. Continue reading “High-Throughput Purification with Experts Included”

Wonders of the Conscious and Unconscious Mind—What I Learned from the International Forum on Consciousness

When Heather Berlin was 5 years old, she realized that, at some point in the future, she was going to die. This disturbed her so much that she couldn’t sleep all night. The next morning, she asked her father where she could store all her thoughts so they could live on after she died. There’s no way to do that, said her physician father. “What can I do to make this happen?” she asked. “Maybe become a psychiatrist?” said her dad. Decades later, she became an Assistant Professor of Psychiatry at Icahn School of Medicine at Mount Sinai. Her research focuses on interactions of the brain and mind, with the goal of treating and preventing psychiatric and neurological disorders.

Dr. Heather Berlin told this story at the International Forum on Consciousness held at the BioPharmaceutical Technology Center Institute in Madison, Wisconsin last week. This annual forum gathers scientists from around the world, all interested in understanding how our conscious and unconscious minds work. This year, the forum focused on the newest research and technology for detecting and measuring consciousness. As someone with limited knowledge in this field, my mind was blown by how much researchers have learned so far about consciousness. (No, we can’t store our thoughts in a box…yet.) Here are a few takeaways:

Continue reading “Wonders of the Conscious and Unconscious Mind—What I Learned from the International Forum on Consciousness”

From Dating Apps to In Vitro Fertilization, the Challenges to Saving the Endangered Northern White Rhino

In April of 2017 a profile appeared on the dating app Tinder. Describing himself as “One of a kind”, the poster was 43 years old, not in great physical shape, and yet so sought after he required around the clock body guards. His name was Sudan, and he was the last living male northern white rhino. His keepers at the Ol Pejeta Conservancy in Kenya weren’t expecting Sudan to find love. They were hoping to raise awareness of the species’ dire situation and money for the research and development of an in vitro fertilization (IVF) method for rhinos.

Northern white rhino
With only two remaining, can we save the northern white rhino? © Matt Caldwell / 123RF Stock Photo.

Northern white rhinos used to range over all or parts of Uganda, Sudan, Chad, the Democratic Republic of the Congo and the Central African Republic. In the 1960s there were an estimated 2,360 northern white rhinos left in the wild (1). Civil unrest in the region made conservation difficult, and by 2003 poaching and other pressures had reduced the number of northern white rhinos living in the wild to four individuals living in the Garamba National Park in the Democratic Republic of the Congo. There has been no sign of that wild population since 2007 (2), and they are considered extinct in the wild as of 2008. Continue reading “From Dating Apps to In Vitro Fertilization, the Challenges to Saving the Endangered Northern White Rhino”

Kinase Drug R & D: Helping Your Inhibitor Make the Cut

Finding the best inhibitor for your kinase doesn’t have to be a long trip.

A recent paper in Journal of Medicinal Chemistry, “Discovery of GDC-0853: A Potent, Selective and Noncovalent Bruton’s Tyrosine Kinase Inhibitor in Early Clinical Development” (1) details some elegant work in chemical modification and extensive testing during exploration of inhibitors for BTK. As a warmup to the article, here is a brief BTK backstory.

BTK (Bruton Tyrosine Kinase): Importance in Health and Disease 

Bruton’s tyrosine kinase (BTK) was initially identified as a mediator of B-cell receptor signaling in the development and functioning of adaptive immunity. More recent and growing evidence supports an additional role for BTK in mononuclear cells of the innate immune system, especially dendritic cells and macrophages. For example, BTK functions in receptor-mediated recognition of infectious agents, cellular maturation and recruitment processes, and Fc receptor signaling. BTK has recently been identified as a direct regulator of a key innate inflammatory machinery, the NLRP3 inflammasome (2). Continue reading “Kinase Drug R & D: Helping Your Inhibitor Make the Cut”

HaloTag Application: Fluorescence Under Stress

diagram illustrating the mechanism of the stress reporter

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.

Literature Cited

Fares, M. et al. (2018) A Molecular Rotor-Based Halo-Tag Ligand Enables a Fluorogenic Proteome Stress Sensor to Detect Protein Misfolding in Mildly Stressed Proteome. Bioconjugate Chem 29, 215–24.

Learn more about protein analysis using HaloTag here.

Introduction to the Laboratory: A New Workshop in Partnership with the UW-Madison Center for Educational Opportunity

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: “CeO 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.”

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.

Group photo of attendees
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.

Continue reading “Introduction to the Laboratory: A New Workshop in Partnership with the UW-Madison Center for Educational Opportunity”

20 Years of Human Embryonic Stem Cells

Dr. David Russell presenting at the 13th Wisconsin Stem Cell Symposium. The session was moderated by Dr. James Thomson.

“20 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.” 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, it’s not just a symposium, but also a celebration—it’s 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 cells—with the potential to develop into every cell type in the human body—in a dish! Thomson quickly became a celebrity scientist. (Thomson’s headshot was on the cover of the August 20, 2001 issue of Time Magazine, next to big text that read: “The Man Who Brought You Stem Cells”.)

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 state—simply by expressing four specific genes. He named these reprogrammed cells “induced pluripotent stem cells” 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 individual—without the ethical baggage of using human embryos. This meant, in theory, you could take fibroblasts from a patient with a neurological disorder, such as Parkinson’s disease, revert the fibroblasts into iPS cells, edit the “faulty genes” 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, Parkinson’s 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 individuals—not the patients’ own cells—there 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 proteins—human leukocyte antigens (HLA)—from the cell surface. HLA proteins allow the immune system to determine whether the presenting cell is “self” or “foreign”. 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 “universal donor cells (UDCs)” 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 patient’s 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 to visionary scientists like James Thomson, Shinya Yamanaka, David Russell—and countless other principal investigators, post-docs and grad students who work tirelessly in the lab every day—treatments 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?