March 9, 2025 Uncategorized Post a Comment

Stand Up for Science

At a recent Stand Up for Science rally at the federal plaza in Chicago, one of the speakers mentioned that the most important six words are “let me tell you a story” when it comes to trying to explain why science funding is important. The idea is to explain to everyday people how the work we (scientists) do makes life better for everyone.

Group of people at a rally with signs. One sign says "freedom of science" and another says" science is a candle in the dark. Don't let fascism snuff it out."

I’ve been thinking about how to explain how vital the National Institutes of Health (NIH) is to biomedical research and advances in medicine. I was already thinking about explaining how the peer-review process works and give a few examples of research that I have worked on. I’m still working on that but I think it’s important to keep the momentum going from the rally.

So let me tell you a story. A lot of traditional (older) chemotherapies have a lot of side effects. Essentially the doctors are trying to find the dose that kills more tumor cells and spares good, normal tissue. One size does not fit all. The dose of a chemotherapeutic drug needs to be titrated. That means you start at the recommended dose for someone’s size, sex, tumor type, etc. Then you adjust the dose on the subsequent visits.

Rather than rely on the patient reporting how they feel after each dose, what if you could see “off target” side effects? What if you could take an image of the patient and see which organs are getting damaged from the chemotherapy and also see how much the tumor is responding to chemotherapy. With that information you could personalize medicine for that particular patient. That’s one of the projects that I’m working on. Let me continue the story.

Every cell has a membrane where the machinery of the cell is behind a membrane, like the skin of a balloon. The surface of the cell membrane might have receptors, that you probably have heard of. Double negative breast cancer refers to two types of receptors that breast tumors typically have.

When a cell is damaged or dying, it often exposes the inner portion of the cell membrane. One of my colleagues has developed an imaging probe that identifies damaged and dying cells by latching onto the exposed inner cell membrane with a radioisotope. We use an imaging technique called Single Photon Emission Computed Tomography (SPECT) to make an image of the whole body, where we can visualize the damaged tissue. I wrote about SPECT a long time ago when I was doing #SciCom on #GooglePlus, which I converted to a blog.

You can read our paper here:

Johnson SE, Ugolkov A, Haney CR, Bondarenko G, Li L, Waters EA, Bergan R, Tran A, O’Halloran TV, Mazar A, Zhao M. Whole-body Imaging of Cell Death Provides a Systemic, Minimally Invasive, Dynamic, and Near-real Time Indicator for Chemotherapeutic Drug Toxicity. Clin Cancer Res. 2019 Feb 15;25(4):1331-1342. doi: 10.1158/1078-0432.CCR-18-1846. Epub 2018 Nov 12.

https://pubmed.ncbi.nlm.nih.gov/30420445

In another application, this technology can be used to see how damaged heart tissue is after a heart attack. This is useful in deciding if a patient is a good candidate for bypass surgery. If there is too much damaged tissue, bypass surgery would be a useless risk. On the other hand, if there is damaged heart tissue but not a lot of dead tissue, that patient would be a better candidate for bypass surgery.

None of this happens without funding from the NIH. You might have also heard that NIH funding was frozen or that indirect costs for research covered by the NIH is being reduced. Indirect costs pay for things like veterinary staff, facilities maintenance, electricity, etc. Charging this overhead, item by item, would be inefficient.

I will be working on a more in depth writeup on Small Business Innovative Research (SBIR)/Small Business Technology Transfer (STTR) funding from the NIH, that’s related to this project. However, I wanted to say that the Stand Up for Science rally helped focus my energy.

protest signs: Science is for Everyone. Make figures not signs. Got plague? Me neither. Thanks Science.
June 30, 2019 ScienceEveryday (medical imaging is separate) Post a Comment

Dilated cardiomyopathy (DCM) and taurine

Ana always ready for more food.

Heart disease affects about 10-15% of all cats and dogs. Dilated cardiomyopathy (DCM) is a genetic heart condition in dogs, typically larger breeds like Doberman Pinscher, Great Dane, or the Irish Wolfhound. It is also seen in Cocker Spaniels associated with taurine deficiency but I’ll get to taurine in a bit. Interestingly, the FDA has seen a bias in reporting of DCM in Golden Retrievers and they believe it’s due to breed specific social media groups that have raised awareness of DCM. DCM presents slowly and its presentation is similar to congestive heart failure (CHF). DCM can actually become CHF.

Is grain-free diet the cause of DCM in atypical breeds? It’s not clear. The FDA is studying the situation. You can read more from their latest announcement. In some cases, blood tests have shown low levels of taurine and a change of diet combine with taurine supplements have reversed DCM in atypical breeds. Again, it’s not clear if the grain-free diets are causing DCM simply because there is low levels of taurine or if it has something to do with specific ingredients found in grain-free dog food, e.g., peas and legumes. Tufts University wrote a good introduction/summary of DCM and grain-free food.

So what is taurine and what’s the big deal? Taurine is an amino acid. Amino acids are the building blocks for proteins. Both humans and dogs can make taurine from methionine (an essential amino acid) and cysteine (a nonessential amino acid). As a refresher, essential amino acids are required in our diets. We cannot produced them. Conversely, nonessential amino acids are produced in our bodies. There are 20 amino acids (9 are essential) that are common in proteins. Taurine isn’t one of them. So what’s the fuss? Again, it isn’t clear what is going on with DCM, grain-free diets, and taurine. The FDA is still investigating.

What should you do? As always, try to educate yourself as much as possible. Chicken and turkey are high in taurine, especially dark meat. Perhaps rotating your pet’s diet will help while the research continues. Another thing you can do is learn to read dog food labels. You should be familiar with the AAFCO nutrient profile. Don’t worry about which ingredient is first, second, etc. Base your pet’s diet on facts and science. Talking to your vet, especially a veterinary nutritionist, is a lot more sensible than misguided advice on the Internet or word-of-mouth.

When we first got our dog (she’s a rescue), she had diarrhea. The vet said she had worms so we de-wormed her. Anytime a dog has digestive problems, we always switch to a bland diet: rice, pumpkin, and a little chicken meat. Every time we put Ana back on her puppy food, she got diarrhea again. We knew she was worm free, so we figured it might be the food. It was a reputable brand. We stumbled on the Dog Food Advisor website and figured out that Ana is allergic to corn meal. So we learned to read labels for exotic and/or questionable ingredients. Dog Food Advisor listed corn meal as a questionable ingredient. Check out their advice on grain-free diet and DCM.

Here’s another good resource to get up to speed with taurine and DCM.

November 18, 2018 ScienceEveryday (medical imaging is separate) Post a Comment

New kg definition: Kibble Balance

New kg definition: Kibble Balance

By now, many of you should have heard that the kg is being redefined.

You can read more about it here:

https://www.sciencemag.org/news/2018/11/metric-system-overhaul-will-dethrone-one-true-kilogram

For 130 years, the kilogram (kg) was defined by a cylinder of platinum-iridium alloy in Sèvres, France. You should also know that scientists and standards agencies have been trying to define SI units with measurable techniques based on physical constants. Here’s an example and an explanation of the new kilogram definition from the article above:

The new SI generalizes the trade-off already exploited to define the meter more precisely in terms of the speed of light. Until 1983, light’s speed was something to be measured in terms of independently defined meters and seconds. However, that year, the 17th CGPM defined the speed of light as exactly 299,792,458 meters per second. The meter then became the measurable thing: the distance light travels in 1/299,792,458 seconds. (The second was pegged to the oscillations of microwave radiation from cesium atoms in 1967.)

The new SI plays the same game with the other units. For example, it defines the kilogram in terms of the Planck constant, which pops up all over quantum mechanics. The constant is now fixed as exactly 6.62607015×10-34 kilogram meters squared per second. Because the kilogram appears in that definition, any experiment that previously measured the constant becomes a way to measure out a kilogram instead.

Such experiments are much harder than clocking light speed, a staple of undergraduate physics. One technique employs a device called a Kibble balance, which is a bit like the mythical scales of justice. A mass on one side is counterbalanced by the electric force produced by an electrical coil on the other side, hanging in a magnetic field. To balance the weight, a current must run through the coil. Researchers can equate the mass to that current times an independent voltage generated when they remove the mass and move the coil up and down in the magnetic field.

That’s were the Kibble balance comes in and the linked article below does a better job of explaining it than I could.

https://www.nist.gov/si-redefinition/kilogram-kibble-balance

November 2, 2018 ScienceEveryday (medical imaging is separate) Post a Comment

Basic Science for the sake of curiosity

Basic Science for the sake of curiosity

We can’t always put a dollar amount on basic science research, especially when politicians want to talk about return-on-investment when discussing funding basic science research. There are so many examples of breakthroughs that build on a wealth of knowledge that started out as a curiosity in basic science research. Good examples of seeing the value of basic science research (and then losing sight of it) are Bell Labs and Xerox PARC. Look at all of their contributions to everyday technology and science, yet they were eventually closed down.

Although it’s preaching to the choir, please read this excellent post from Buddhini Samarasinghe.

Originally shared by Buddhini Samarasinghe

Nanopore sequencing: a story about discovery science

Ever since I began a career as a scientist (and even more so as a science communicator now), I’ve been a passionate advocate for discovery science. ‘Discovery science’ is a term used interchangeably with ‘basic science’, or ‘blue skies research’, but essentially it means curiosity-driven research rather than a specific goal-oriented research programme. Discovery science asks open ended questions, like “what does this protein do?” as opposed to “how do you block this protein so we can make a new drug?”.

Many of the serendipitous discoveries in science, especially the ones that improved our lives, happened the way they did because there already existed a strong scientific base upon which to develop those initial ideas. Put another way, no matter how healthy a seedling is, it won’t grow and flourish unless the soil it’s growing on is fertile.

But tracking these stories is not easy – how do you look at a technology that exists now, a technology that we take for granted, and then attribute it’s existence to previous discoveries? We like to quote Newton’s “If I have seen further, it is by standing on the shoulders of giants” but can we actually find out exactly who those giants were?

Several months ago, I started asking this question in the very specific context of genome sequencing. We are now at a place where genome sequencing is unimaginably easy and cheap compared to how it used to be several decades ago. For about $1000, you can buy a portable USB powered DNA sequencer that is the size and weight of a chocolate bar, and hook it up to a laptop. This technology, known as ‘nanopore sequencing’, would not have been possible were it not for decades of discovery science preceding it. Even more interesting is the fact that the pioneer of nanopore sequencing didn’t even set out with the intention of developing a brand new, disruptive sequencing technology; he started out studying a tiny protein found in a humble bacterial species!

I hope that this story highlights the importance of curiosity-driven research, and the unexpected benefits we can glean from them. It took me a while to pull these disparate threads together to weave this story, and yes a lot of it does have a focus on the UK’s Medical Research Council’s work (because I did this as part of my day job, yay!). But I hope you enjoy it, and more importantly, are inspired to advocate for discovery science like I am, because we probably need it now more than ever.

https://mrc.ukri.org/news/browse/decades-of-discovery-set-to-revolutionise-healthcare/

https://mrc.ukri.org/news/browse/decades-of-discovery-set-to-revolutionise-healthcare/

October 14, 2018 ScienceEveryday (medical imaging is separate) Post a Comment

Nikon Small World challenge 2018

Nikon Small World challenge 2018

I wished The Atlantic would have reminded people that these are often colorized. When you use fluorescent microscopy the images are greyscale and people often colorize them later. Note, a lot of the images are NOT fluorescent.

https://www.theatlantic.com/photo/2018/10/photographing-the-microscopic-winners-nikon-small-world-2018/572737/?utm_medium=social&utm_term=2018-10-12T01:37:23&utm_source=twitter&utm_campaign=the-atlantic&utm_content=edit-promo

September 19, 2018 ScienceEveryday (medical imaging is separate) Post a Comment

4 Personality types, only 4?

4 Personality types, only 4?

By now, I’m sure many of you have read about the 4 personality types that have come out of the research from Profs. Amaral and Revelle at Northwestern University. I think it’s interesting to see engineering and psychology come together for a study like this.

https://news.northwestern.edu/stories/2018/september/are-you-average-reserved-self-centered-or-a-role-model/

August 14, 2018 ScienceEveryday (medical imaging is separate) Post a Comment

Primal Posture

Primal Posture

I plan to investigate a bit more on the work by Esther Gokhale on “primal posture”. Here’s her TED talk.

https://www.youtube.com/watch?v=k1luKAS_Xcg

It kind of makes sense but I’d like to learn more. I heard this on the radio on the way to work then saw it posted by Jennifer Freeman

https://www.npr.org/sections/goatsandsoda/2018/08/13/636025077/to-fix-that-pain-in-your-back-you-might-have-to-change-the-way-you-sit