Searching for Secrets in Single Cells

There has been a lot of effort recently to perform whole genome sequencing, for humans and other species. The results yield new frontiers of data analysis that offer a lot of promise for groundbreaking scientific discoveries.

One objective of human genome sequencing has been to identify sources of disease and new therapeutic targets. This movement has opened the door to create personalized medicine for cancer, whereby the genetic makeup of an individual’s tumors can be used to determine the most effective drug intervention to administer.

Interest in studying the characteristics unique to individual cells seems obvious when considering the function of healthy cells versus tumor cells, or brain cells compared to heart cells. What has surprised scientists is the realization that two cells in the same tissue can be more different from each other, genetically, than from a cell in another organ.

For example, a small number of brain cells with a specific mutation can lead to some forms of epilepsy while healthy people may also carry cells with these mutations, but too few to cause disease. The lineage of a cell, where it came from and what events shaped its development, ultimately determines what diseases can exist.

Continue reading

Creating ART from 3D Printed Ovaries

It is remarkable to me how quickly in vitro fertilization has gone from an experimental, controversial and prohibitively expensive procedure to becoming a mainstream option for those struggling with fertility issues. What was unheard of in my parents’ generation is nothing extraordinary among my friends who are having children.

My personal observations are supported by the CDC, which reported that 1.6% of all infants born in the U.S. in 2015 were the result of assisted reproductive technology (ART). This is a 33% increase since 2006, which can be attributed to rapid advances and refinements of the various technologies available to those seeking reproductive assistance.

It challenges the mind to imagine what reproductive technologies might be widespread when my children and their friends are adults. When experts speculate about the future of human reproduction, there always seems to be a lot of focus on provocative scenarios that portend a dystopian future, such as designer babies. What gets lost are some of the more general scientific advances that are being applied to ART in fascinating ways.

While improvements in reproductive technologies serve many, one group that remains underserved are pediatric cancer patients. As a result of treatment, these patients are often faced with impaired ovarian function that can prevent puberty and result in infertility. In vitro fertilization and ovarian transplants are currently used, but do not provide lasting solutions for all individuals.

In response to this need, researchers are working to develop an organ replacement that can provide long-term hormone function and fertility for all patients.  A recent study in Nature Communications presented encouraging results in mice using bioprosthetic ovaries that may further revolutionize the field of ART. Continue reading

Knots: Friend or Foe?

Knots affect our lives in perplexing ways. They can perform life-saving assistance, such as during rock climbing, or provide Sisyphean puzzles of entanglement. Often, knots seem to have the contrarian personality of an adolescent. They loosen and unwind when you want them to stay fastened, and inevitably form tangles of confounding complexity when you seek to avoid them. These puzzling characteristics of knots were brought to mind when I read two recent articles about the scientific investigation of knots.37190697-May-5-Darcia---Option-2

Why Knots Fail

The explanation of how shoelaces come untied, published in Proceedings of the Royal Society A, was quite prevalent in the news cycle recently. After observing slow-motion video footage of the shoelaces of a runner on a treadmill, researchers were able to explain how motion affects knots and results in untied shoelaces.

First, they observed that the failure of a knot is not a gradual process, but happens abruptly over the course of only one or two strides. This is possible due to the surprising amount of force generated by the impact of one step, which this study calculated to be an average of 7 g—more than twice the g-force experienced by the Space Shuttle upon reentry into the Earth’s atmosphere. Continue reading

Making a Case for Basic Research Funding

The value of public funding for “basic” versus “applied” research has long been questioned. To address this debate, the authors of a recent report in Science performed a large-scale evaluation of the value of public investment in biomedical research. After analyzing the relationship between the U.S. National Institutes of Health (NIH) grants and private patents, they found that distinguishing research as basic or applied is not useful in determining the productivity of grant funding.

Genetic research at the laboratoryThe $30 billion annual budget of the NIH makes it the largest source of life science funding in the world and provides a third of all US biomedical research and development. Although there has long been a strong argument for public investment in scientific research, attacks on the tangible benefits of this research persist. In particular, some opponents argue that “basic” research is too far removed from practical applications to be worthy of investment.

To quantify the effects of NIH funding for basic versus applied research, the authors looked at data from 365,380 grants awarded between 1980–2007 and compared their direct and indirect influence on patent filed. In particular, they decided to use patent-article citations as a measure of the influence of publicly funded science on commercial developments.

The researchers determined two ways in which research funded by the NIH could impact patenting; patents could be filed by the NIH-funded scientists or by private entities that cited research funded by NIH grants. This study found that roughly 10% of NIH grants were directly responsible for a patent while nearly a third of NIH grants had an indirect influence on patents. This indirect influence was attributed to articles associated with grant research that were later cited by a patent.

Delving deeper into the data, the authors found a similar pattern when looking at drugs brought to market that were associated with NIH grants; less than 1% of grants were directly linked to a patent associated with a drug, while 5% resulted in a publication cited by a patent for a drug. Despite public policies like the Bayh-Dole Act, that encourage academic researchers to file their own patents, the traditional route of applying public research to private patents continues to predominate.

For those that question the value of basic research and aim to steer public policy toward supporting applied research, this report makes a strong case against this way of thinking. The findings also suggest that using direct generation of patents as a metric for the return on investment of publicly funded biomedical research is not very useful since most of the effects of NIH research appear to be indirect.

In fact, the authors posit that basic research is just as productive as applied research in terms of patenting since the amount of grant research cited by private patents is much greater than the number of grants directly associated with patents. Perhaps it is time policy makers consider studies like this and forgo disseminating grant funds based on whether research is basic or applied.

So NASA Found Some New Exoplanets…Now What?

34412848-March-8-Planets-600x600-WEBYou have probably heard a lot of excitement over NASA’s recent announcement about the discovery of seven earth-size planets found orbiting around the star TRAPPIST-1, which is part of the constellation Aquarius.

These exoplanets are notable because they exist within the habitable zone of the star (nicknamed Goldilocks planets because this area is not too hot and not too cold) and are probably rocky with the potential to contain water on their surface.

A lot of the enthusiasm revolves around the hope that one of these planets might harbor extraterrestrial life or could be suitable for human inhabitants. Of course, many further observations must be made to determine if these scenarios are plausible, not to mention the huge advances in technology that would need to occur so we could actually verify the planetary conditions or send humans 40 light-years away. Continue reading

Familial Searching Solves Cold Cases—At What Cost?

A cold case that had stumped investigators for nearly 41 years was solved last month. The 1976 sexual assault and murder of Karen Klass, ex-wife of Righteous Brother’s singer Bill Medley, shocked her Hermosa Beach, CA community and captured the public interest. Failing to make any arrests for decades, detectives were able to use DNA evidence to eliminate suspects in 1999 but were unable to find a database match. In 2011, investigators decided to try a new technique called a familial search and, after a few attempts, successfully identified the perpetrator.

Familial searching (FS) involves taking a DNA profile obtained from a crime scene and comparing it to profiles in CODIS and other databases to identify male relatives. The DNA profile of an immediate family member, such as a sibling, parent or child, can provide a match that generates new leads for law enforcement. Detectives can then collect additional evidence to narrow down that new pool of individuals to a single suspect.DNA-Handcuffs-double-exposure-R2

Last May I wrote a blog featuring a Q & A about FS provided by Mr. Rockne Harmon, a respected member of the forensic community and passionate advocate for FS. Supporters, like Harmon, and opponents agree that this method of obtaining matches to DNA evidence has demonstrated scientific precision and successful outcomes, as in the Klass case. However, it is still considered controversial and most states have not implemented specific policies regarding the application of FS to criminal investigations. So why isn’t the use of FS more widespread?

Continue reading

Did Dinosaurs Take Too Long to Hatch?

A new approach to dinosaur embryology has revealed another layer to our understanding of the demise of dinosaurs and rise of mammals as a result of the end-Cretaceous mass extinction event. In a recent Proceedings of the National Academy of Sciences paper, a group of researchers led by Gregory Erickson hypothesized that dinosaur eggs may have growth lines present on embryonic teeth that could be used to determine incubation times.

dinosaur-embryoNot much is understood about dinosaur embryology, aside from what is known about birds. This is in part because fossils of dinosaur eggs, especially those containing embryonic skeletons, are among the rarest in the world. Despite this difficulty, using these fossils to refine estimated incubation times of dinosaur embryos can shed light on their development, life history and evolution.

Historically, paleontologists have assumed that dinosaur incubation periods were rapid based on their extant counterparts, birds. Considered living dinosaurs, birds are a logical surrogate from which to extrapolate dinosaur incubation times. It is important to note that embryonic incubation in birds is different from other living relatives of dinosaurs, modern reptiles. While reptile embryos develop slowly, birds differ by laying fewer, larger eggs with rapid incubation. Continue reading

What’s Art Got to Do with It?

While some may see the Art Showcase that Promega has sponsored for the past 20 years as tangential to the mission of the biotechnology company, these quarterly exhibits of local and global artists contribute to Promega’s commitment to creativity and innovation in the arts, culture and sciences. The exhibits also foster connections between members of the community that probably would not otherwise exist.

Promega President and CEO Bill Linton with Daniel Swadener, curator of the Promega Art Showcase, at the 2016 Fall Art Showcase Opening and Symposium.

Promega President and CEO Bill Linton with Daniel Swadener, curator of the Promega Art Showcase, at the 2016 Fall Art Showcase Opening and Symposium.

It is obvious how the show serves to advance the arts and culture, but its relationship to science is less clear. Based on my experience attending the symposium and viewing the artwork, the science at Promega benefits from this endeavor as well.

Let me begin by describing the work included in this fall’s Art Showcase, “Wis-Con-Sin.” This exhibit features three centuries of Wisconsin photographers that each created life-long photographic projects based in Wisconsin:

  • Charles Van Schaick (1852-1946) was a studio photographer in Black River Falls, WI who left behind nearly 6,000 glass plate negatives of mostly studio portraits (which have been featured in two books, Wisconsin Death Trip and People of the Big Voice), as well as street scenes, major events in the region, outdoor family and group photos, buildings, picnics, people and livestock.
  • Eugene Von Bruenchenhein (1910 – 1983) was a self-taught artist who created several thousand works including apocalyptic oil paintings, ceramic crowns and vessels, and photographs that he and his wife Marie collaborated on, staging her in provocative poses and costumes.
  • J. Shimon & J. Lindemann collaborated as artists since 1983, focusing on rural Wisconsin towns where they both grew up and using antiquarian cameras and printing techniques to record post-industrial settings, rural landscapes, small towns, and shifting modes of life.

Continue reading

iGEM: Building Living Machines

Life forms are often compared to machines, whether you are referring to a single cell or a complex organism. This concept is the basis for the International Genetically Engineered Machine (iGEM) Competition. Each year, high school and university students around the world assemble teams that create genetically engineered systems. In addition to the building work, teams document their process and progress through wikis that are assessed by judges at the end of the competition.

teamfoto-900x250

Some members of iGEM 2016 Team Duesseldorf.

In order to synthesize these living machines, iGEM teams use standard biological parts called biobricks—each biobrick is a sequence of DNA encoding a particular biological function. Teams receive a kit of standard biobricks and work over the summer to build and test biological systems in living cells. These basic units are put together to make more complex parts which can then be grouped together to make “devices” that can function within living cells. Continue reading

Seeing Science: Discovering What is Hidden in Plain Sight

Recently, I stumbled upon a few new discoveries that I would have guessed had already been figured out. These discoveries were surprising to me because they fell into the category of “obviously someone else knows this,” even though I didn’t—you know, the stuff you would just do a quick Google search to find out about.

29980708-August-10-blog-Darcia-FINAL-WEBAnyway, it made me reflect on the world we live in, filled with endless information. At times, it seems as if we know it all (at least all the obvious stuff), which can stifle discovery by limiting the sources from which we seek new information. It can appear futile to embark upon research in established fields. But sometimes discoveries occur when you look in familiar places from a new vantage point.

Today’s blog illustrates how seeing science in new ways can lead to this type of unexpected discovery.

Sometimes  seeing science is about how you are looking. 

The first discovery that got my attention was in an article that described the use of drones and Google Earth by archaeologists to discover a monument made of stone hidden below the sand at a World Heritage Site in Petra, Jordan. This is one of the most visited and well-studied archaeological sites in the world. Yet, a huge structure had remained undiscovered despite continual investigation of the site.

I imagine it would be like finding a new room in the house you’ve lived in your entire life. Applying new technology to see science in different ways expands the reach of archaeological discovery. This approach could open the door for remarkable discoveries in other scientific fields. Continue reading