Category Archives: Science No Chaser

Caltech grows miniature “river deltas” in a lab

About half a billion people live on fan-shaped floodplains that form where rivers meet the sea.

Those plains, called river deltas, share the same fan-like shape the world over. Even after controlling for factors like the size of the river, the slope of the land its channel traverses, and the makeup of the local soil, river deltas have a remarkably consistent shape.

Seriously. Here’s The Nile: [satelite image via NASA Godard Space Flight Center’s Flickr]

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Here’s the Yukon River in Alaska [satelite image via NASA Godard Space Flight Center’s Flickr

Image acquired September 22, 2002 Countless lakes, sloughs, and ponds are scattered throughout this scene of the Yukon Delta in southwest Alaska. One of the largest river deltas in the world, and protected as part of the Yukon Delta National Wildlife Refuge, the river's sinuous waterways seem like blood vessels branching out to enclose an organ. Credit: NASA/USGS/Landsat NASA image use policy. NASA Goddard Space Flight Center enables NASA’s mission through four scientific endeavors: Earth Science, Heliophysics, Solar System Exploration, and Astrophysics. Goddard plays a leading role in NASA’s accomplishments by contributing compelling scientific knowledge to advance the Agency’s mission. Follow us on Twitter Like us on Facebook Find us on Instagram
Image acquired September 22, 2002
Countless lakes, sloughs, and ponds are scattered throughout this scene of the Yukon Delta in southwest Alaska. One of the largest river deltas in the world, and protected as part of the Yukon Delta National Wildlife Refuge, the river’s sinuous waterways seem like blood vessels branching out to enclose an organ.
Credit: NASA/USGS/Landsat
NASA image use policy.
NASA Goddard Space Flight Center enables NASA’s mission through four scientific endeavors: Earth Science, Heliophysics, Solar System Exploration, and Astrophysics. Goddard plays a leading role in NASA’s accomplishments by contributing compelling scientific knowledge to advance the Agency’s mission.
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Continue reading “Caltech grows miniature “river deltas” in a lab” »

Inside the Pancreas: How Beta Cells Change as We Age

[A diabetic supply kit, complete with a knitted pouch that’s shaped like a pancreas. Photo by Erin Stevenson O’Connor via Flickr and Creative Commons.] 

The box arrived around 5:00 pm. Many of Efsun Arda’s colleagues were already heading home for Thanksgiving, but Arda had work to do. As a post-doc in Seung Kim’s lab at Stanford, Arda studies one of the body’s most unknowable vital organs– the pancreas.

Although the pancreas plays a crucial role in diabetes–which impacts almost 1 in 10 Americans, according to the CDC–and although pancreatic cancer is extremely lethal, the pancreas remains largely a mystery, Kim and Arda say.

(A quick Google Scholar search turned up 20,500 papers mentioning the pancreas in 2016 so far, but that’s a stark contrast to the 124,000 papers for “liver” and 113,000 for “kidney”.) 

Much of what doctors do know about the pancreas comes from inference based on physiological and blood chemistry studies.

Collecting pancreas samples from living people is extremely risky and highly impractical. The pancreas itself is a large gland, full of active enzymes, nestled in a tough-to-reach spot behind the stomach. The enzymes inside the pancreas itself are “like a pack of wolves” Kim says; the slightest damage will cause the organ to start digesting itself, which would likely kill the patient.

Consequently, most studies that peek under the pancreas’ hood rely on cadavers.  Continue reading “Inside the Pancreas: How Beta Cells Change as We Age” »

5 Amazing Feats Performed by “Meta-Genes”

[Image via the NIH Image Gallery. Photo by Alex Ritter, Jennifer Lippincott Schwartz, and Gillian Griffiths. Full video, complete with narration here.] 

Under the Radar: A series of listicles about biology concepts you definitely won’t find in newspaper headlines.

#1: Be a Navigation App for Immune Cells

Natural killer cells, or “NK cells” are the human body’s best defense against cancer.  While other types of immune cells often ignore tumor cells, natural killer cells specialize in finding and destroying human cells that look either infected or like cancer mutants. In leukemia patients,  a higher number of active natural killer cells ups the patient’s chances for survival, so much so that  researchers are experimenting with transfusing NK cells into patients.

Just one problem there: Active natural killer cells die without a strong support network.

Dormant NK cells can survive in the bloodstream for a long time, but once activated, natural killers have to make a b-line for cells carrying a marker called IL-15 or die,  but until a study in Monday’s edtion of PNAS , no one knew how natural killers knew to look for IL-15. The study, led by Vanderbilt immunologist Eric Sebzda and grad student Whitney Rabacal, traced NK cells’ IL-15 homing ability back to a biochemical with the horrendous name “Kruppel-like Factor 2” (KLF2).

KLF2, oddly enough, also exerts a strong navigational influence on the immune system’s T-cells and B-cells.  Even though all three types of cells fall under the “white blood cell” umbrella, the notion that one protein could control navigation in all three is pretty weird.  Crawling and navigating are complex tasks, requiring coordination between dozens of genes. “[NK cell migration] is totally different from how t-cells and b-cells circulate,” Sebzda said.

Additionally, taking away KLF2 has distinctive effects on each type of cell: KLF2-less t-cells vacate the central body and crawl out to lab mice’s fingers and toes, KLF2-less b-cells all congregate at the spleen (which creates some serious problems for those lab mice), and KLF2-less natural killers end up dying alone.

So KLF2 could be super-useful for improving cancer immunotherapy. But why is KLF2 so versatile in the first place?

The answer lies in KLF2’s ability to bind to a certain recurring DNA base pair sequence, one that presumably earmarks the genes needed in each immune system navigation system, and it’s far from the only protein with such abilities…

Continue reading “5 Amazing Feats Performed by “Meta-Genes”” »

Some people learn from pain, others learn by avoiding it

[Photo by Tomas Fano via Flickr/Creative Commons]

Last August, a paper in Nature debuted with evidence supporting an idea that many suspected but few wanted to hear: If two teams of scientists run the same psychological experiment, the two sets of results end up mismatched.  (In fact,  when a network of 270 researchers retried 100 psych experiments, they found that only about 1 in 3 yielded results matching the original paper.)

Since consistent results are the hallmark of scientific truth,  this is a pretty big problem for the field. But, interestingly, many psychologists and neuroscientists have embraced the “Replication Crisis” as an opportunity to change their science for the better.

Others have doubled down on the methods that have always gotten them out of scientific credibility jams in the past— re-crunching numbers, critiquing the initial paper’s findings in dense journal articles, and reminding everyone just how hard scientists work.

I couldn’t help but think of the two drastically different responses to the “Replication Crisis” when I read a paper about learning and pain in last week’s Early Online edition of PNAS.  Researchers at University College London found that some people learned best by experiencing pain and remembering what-NOT-to-do in the future.

Others learned best when they managed to avoid pain in the first place; they simply kept repeating previously successful pain-preventing strategies.

The fMRIs of the study’s  19 “no-pain-no-gain” learners and 22 “playin-it-safe” learners detected slight differences in the shape of a brain structure called the striatum.

Continue reading “Some people learn from pain, others learn by avoiding it” »

HIV Vaccine Origins: New Insight Into League of Extraordinary Immune Cells

[Portrait of an HIV virus by Dominic Alves via Creative Commons & Flickr]

Y’know that feeling when you stumble across a study that makes you think, “Holy s***! Scientists actually did this!!!!”? And then like two weeks later, another team of scientists manages to kind of upstage the first team’s finding?

It’s been that sort of month for HIV vaccine research. A few weeks back, I wrote  about a team of researchers who managed to decrypt the origin story of an extremely effective strain of HIV-fighting antibodies for The Atlantic

I highly recommend reading The Atlantic piece for a full explanation (and also reading The Atlantic’s science and health coverage more generally, because the whole crew over there is pretty awesome)  but here’s the context you need to know:

“Immune cells called B cells build antibodies, tiny protein warheads that seek out and destroy viruses. But because HIV mutates so rapidly, these antibodies are generally ineffective—by the time B cells learn to build antibodies against one version of HIV, a new viral mutant has already taken over.” -me in The Atlantic

B-cells change their antibody designs by mutating at the DNA level. You literally have a team of microscopic mutants protecting your bloodstreams. 

The vast majority of antibodies that those mutant b-cells build suck. But in a few HIV-infected people, the b-cells manage to start building “broadly-neutralizing” antibodies that can disable all sorts of HIV mutants. Researchers love those broadly-neutralizing antibodies (which they’ve nicknamed “Bnabs”) because if researchers could find a way to get HIV-binding bnabs into uninfected people’s blood streams, those people would probably be immune to HIV. 

The Cell paper I wrote up for The Atlantic was a big deal because it marked the first time researchers were able to observe all of the changes that went into transforming an ineffective antibody into an HIV-killing bnab. Then, two weeks later, Science drops this bomb:

Another team of researchers found a way to measure whether individual b-cells have the potential to make a versatile HIV-killing antibody.

Turns out: about 1 in every 700,000 b-cells has the talent.

Continue reading “HIV Vaccine Origins: New Insight Into League of Extraordinary Immune Cells” »

Splice of Life: 3 Examples of How Nature Edits Its Own Genes

About the “Under the Radar” series: Some scientific concepts come up again and again in interviews with scientists but never find their way into newspaper headlines. Each post in this series follows one of those biology “bogeys” that fly under journalism’s radar through 3 different mini-stories.

Story #1: Scientists splice up a CRISPR chicken…and find an evolutionary shortcut

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Birds’ brains have all of the tools to make mammal-like neurons, according to a study in Science from August And, incredibly, the researchers behind the study only had to tinker with one gene  that changes how chicken cells edit their RNA to unlock several seemingly unrelated mammal neuron traits in chicken neural precursor cells.

It was as if the chicken cells instantly acquired a whole bunch of mutations at once, instead of just one. 

Researchers think that this gene editing process– aka “alternative splicing”–may explain why some traits seem to have evolved at such high speeds.

“This is a process that has diverged very rapidly during evolution to produce different versions of proteins,” University of Toronto geneticist Ben Blencowe explained in a phone interview.

500 million years is a long time to evolve, but it’s still hard to account for all of the diversity in vertebrates based on variation in DNA base pairs alone.

The key to animal diversity lies in an aspect of biology that your high school biology class kinda sorta covered, but lots of people forget all the steps after they’re done cramming for the test.

Continue reading “Splice of Life: 3 Examples of How Nature Edits Its Own Genes” »