From Antarctica to Mars: Growing Food in Extreme Conditions

Even those of us with the greenest thumbs are baffled by the idea of growing food in Antarctica. From my tiny desk plant to my neighbor’s cabbage patch, plants generally have the same requirements: soil, sun and water. At the southern end of the planet, however, those are all scarce commodities. Nonetheless, on April 5, 2018, the team managing the EDEN-ISS greenhouse at Neumayer III announced that they had harvested 8 pounds of salad greens, 18 cucumbers and 70 radishes. This project has implications beyond just Antarctica, from moderate climates on Earth to future Mars missions. Continue reading

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 (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 ES 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?

Kinase Inhibitors as Therapeutics: A Review

The review “Kinase Inhibitors: the road ahead” was recently published in Nature Reviews Drug Discovery. In it, authors Fleur Ferguson and Nathanael Gray provide an up-to-date look at the “biological processes and disease areas that kinase-targeting small molecules are being developed against”. 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.

The road ahead for kinase inhibitor studies.

Why Kinases? Continue reading

The Age of the Genome: Commercial DNA Sequencing, Familial Searching and What We Are Learning

Crowd of people at the street, city center

All of these people are 99% the same at the genomic level. The individuals of the human species are far more alike than different.

There are 3 billion (3,000,000,000) bases in my genome—in each of the cells of my body. Likewise, Johanna, the writer who sits next to me at work also has 3 billion bases in her genome. Furthermore, our genomes are 99% the same. Still, that’s a lot of places where my genome can differ from hers, certainly enough to distinguish her DNA from mine if we were both suspected of stealing cookies from the cookie jar. The power of discrimination is what makes genetic identity using DNA markers such a powerful crime solving tool.

The completion of the human genome project in 2003 ushered in a tremendously fast-paced era of genomics research and technology. Just like computers shrank from expensive, building-filling mainframes to powerful hand-held devices we now call mobile phones, genome sequencing has progressed from floor-to-ceiling capillary electrophoresis units filling an entire building to bench top sequencers sitting in a corner of a lab. The $99 genome is a reality, and it’s in the hands of every consumer willing to spit into a tube.

Commercial DNA sequencing services are promising everything from revealing your true ancestry to determining your likelihood to develop dementia or various cancers. Is this progress and promise or is it something more sinister?

As it turns out, that isn’t an easy question to answer. What is probably true is that whole genome sequencing technologies are being put into the hands of the consumer faster than society understands the ethical implications of making all of this genomic information so readily available. Continue reading

Beer Is Complicated: Proteome Analysis via Mass Spectrometry

still life with a keg of beer and draft beer by the glass.The art of brewing alcoholic beverages has existed for thousands of years. The process of beer brewing begins with barley grains, which are malted to allow partial germination, triggering expression of key enzymes. The germinated grains are then dried and milled. Next, starch, proteins, and other molecules are solubilized during mashing. During mashing, solubilized enzymes degrade starch to fermentable sugars, and digest proteins to produce peptides and free amino acids. Fermentable sugars and free amino acids are required for efficient yeast growth during fermentation.

After the mash, the wort is removed, and hops are added for bitterness and aroma, and the wort is boiled. After boiling, the wort is inoculated with yeast, and fermentation proceeds to produce bright beer. Typically this bright beer is then filtered, carbonated, packaged, and sold. Many proteins originating from the barley grain and the yeast are present in beer, and these have been reported to affect the quality of the final product. However, some of the biochemical details of this process remain unclear. To better understand what happens during the various steps of the brewing process,  Schultz et al. used mass spectrometry proteomics to perform a global untargeted analysis of the proteins present across time during beer production and described this work in a recent paper (1). Samples analyzed included sweet wort produced by a high temperature infusion mash, hopped wort, and bright beer. Continue reading

Genomic Breakthroughs One Letter at a Time

In honor of Human Genome Month, I delved into our Cartoon Lab archives to retrieve this example of the excitement that occurred while sequencing the Human Genome Project.

For more entertaining science cartoons, visit our Cartoon Lab.

The Pan-Cancer Atlas: “The End of the Beginning”

Yesterday, a series of 27 papers representing the most comprehensive genomic analysis of human cancers to date was published in Cell Press journals.

The collection constitutes the final outputs from the Cancer Genome Atlas (TCGA) project, a collaboration between the National Cancer Institute (NCI) and the National Human Genome Research Institute (NHGRI) involving analysis of over 11,000 tumors representing 33 different cancers. The many research teams involved analyzed tumor DNA, mRNA, miRNA and chromatin, comparing them to matched normal cellular genomes to perform a complete molecular characterization of cancer-specific changes. The results have been presented with much hope that open access to this type of comprehensive analysis will build on recent advances in understanding tumor biology and spur further progress in developing new approaches to treatment. (See this news item for more detail).

The Pan-Cancer Atlas results are collected on a cell.com portal, where they are presented in three collections grouped by topic: Cell of Origin, Oncogenic Processes and Signaling Pathways. Each collection is accompanied by a “Flagship” paper introducing the topic and summarizing the findings. It seems fitting that these findings have been published in #HumanGenomeMonth. This comprehensive analysis of the genomic and metagenomic profiles of tumors illustrates one powerful application of the type of genomic analysis pioneered by the original Human Genome Project, and shows just how much has been made possible since the initial publication of the human genome fifteen years ago. Continue reading

Back for More: Thoughts from 3 Regular Attendees on the International Forum on Consciousness

The International Forum on Consciousness offers a lively two days of information sharing and discussion regarding important—and often challenging—topics. Over the years, we have been guided through a range of topics, including creativity, near death, entheogens, intelligence in nature, business evolution and the effects of sensory inputs.  This year, we’re tackling Means and Metrics for Detecting and Measuring Consciousness.  You can find out more here: https://www.btci.org/events-symposia-2018/international-forum-on-consciousness/ .

As we work on the final details for this year and registrations flow in, I took a moment to pause and reflect on the fact that several of the registrants have joined us for many, if not all, of our past events. It’s gratifying to see that they are taking time out of their normal routines to make their way to the Promega campus again this spring.  So, I asked a few of them to share their thoughts for this post and this is what they had to say: Continue reading

Letter from Uganda: A Promega International Internship Scholarship Recipient Shares her Experiences

Sydney Roberts, left, at work at a rural community outreach health clinic outside of Kabale, Uganda where she helped conduct basic health screenings. Here she is measuring a woman’s MUAC (midupper arm circumference).

Sydney Roberts, left, at work at a rural community outreach health clinic outside of Kabale, Uganda where she helped conduct basic health screenings. Here she is measuring a woman’s MUAC (midupper arm circumference).

We were inspired by a letter we recently received from one of the recipients of the Promega International Scientific Internship Scholarship. The scholarship supports undergraduate students at the University of Wisconsin – Madison. who are undertaking an international internship aimed at using science to improve the quality of life in the world. Students from all scientific fields are eligible but preference is given to those whose internships use molecular biology techniques. Students must be based in a country other than their own for at least six weeks and cannot be in a country where the recipient has already spent significant time.

Sydney Roberts, a junior at UW Madison majoring in Community and Nonprofit Leadership with a certificate in Global Health, was awarded the Spring 2018 Promega scholarship. As a result, she’s spending her spring a long way from her hometown of Cedarburg, WI. Sydney is currently working in Kabale, Uganda, a town in the southwestern part of the country near the border of Rwanda, as an intern with the Kigezi Healthcare Foundation (KIHEFO).

KIHEFO operates a primary care clinic, HIV/AIDS clinic, Nutrition and Rehabilitation center, and works with rural community groups. Sydney is supporting local staff members as they treat clients, provide counseling sessions for families affected by disease, and work on global health initiatives that support prevention of these diseases and health complications. She has only been in Uganda for a few weeks, but she says her experiences have already been life-changing. Continue reading

How to Reduce Cell Culture Variability

Scenario 1: Jake needs a flask of MCF-7 cells for an assay, so he sends an email to the graduate student listserv asking for cells. Melissa replies that she has an extra flask of cells that she could share. Jake happily accepts the cells and begins his experiment.

Scenario 2: Michael passaged his cells yesterday and, according to the protocol, was supposed to plate cells today for treatment. However, his previous experiments were delayed, so he decides to plate them tomorrow instead. The cells look healthy, so it should be ok.

What is wrong with the above scenarios? These actions may seem harmless, but they could be the cause of variability, leading to irreproducible results. Continue reading