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The Skull’s Petrous Bone and the Rise of Ancient Human DNA: Q & A with Genetic Archaeologist David Reich

Wed, 2018-04-11 09:17
The human petrous bone in the skull protects the inner ear structures. Though it is one of the hardest, densest bones in the body, some portions (such as the area in orange, protecting the cochlea) are denser than others. Possibly because the petrous bone is so dense, DNA within the petrous bone is better preserved than in other bones. In some cases, scientists have extracted more than 100 times more DNA from the petrous bone than other bones, including teeth. Credit: Pinhasi et al., 2015, PLOS ONE.

For the past few decades, new evidence about ancient humans—in the form of skeletal remains, tools, and other artifacts—has trickled in, inching us closer to an understanding of how our species evolved and spread out across the planet. In just the past few years, however, knowledge of our deep past expanded significantly thanks to a series of technological breakthroughs in sequencing of ancient human genomes. This technology can be used to find genetic links among populations of human ancestors dating back hundreds of thousands of years.

In addition to advances in genomic technology, another factor is driving the explosion of new discoveries—an inch-long section of the human skull. Found near our ears, this pyramid-shaped portion of the temporal bone is nicknamed the petrous bone. The bone is very hard, possibly because it needs to protect fragile structures such as the cochlea, which translates sound into brain signals, and the semicircular canals, which help us maintain our balance. Perhaps because the petrous bone is so dense, it also is the bone in the body that best preserves DNA after a person dies. As a result, archaeologists are scrambling to study samples taken from this pyramid-shaped structure to unlock the mysteries of our species’ formative years.

Here’s a sampling of headlines declaring new findings about ancient peoples from around the globe that were based on genetic information obtained from the petrous bone (NIGMS-funded research indicated in black):

“How the introduction of farming changed the human genome” November 2015

“Fourth strand’ of European ancestry originated with hunter-gatherers isolated by Ice Age” November 2015

“Scientists sequence first ancient Irish human genomes” December 2015

“Genetic studies provide insight into ancient Britain’s diversity” January 2016

“The world’s first farmers were surprisingly diverse” June 2016

“Study reveals Asian ancestry of Pacific islanders” October 2016

“Ancient DNA solves mystery of the Canaanites, reveals the biblical people’s fate” July 2017

“Ancient DNA data fills in thousands of years of human prehistory in Africa” September 2017

“European Hunter-Gatherers Interbred With Farmers From the Near East” November 2017

“Surprise as DNA reveals new group of Native Americans: the ancient Beringians” January 2018

“Ancient DNA reveals genetic replacement despite language continuity in the South Pacific” February 2018

“Stone Age Moroccan Genomes Reveal Sub-Saharan African, Near Eastern Ancestry” March 2018

“Some early modern populations in Britain may have had dark skin” March 2018

To learn more about the petrous bone and its use in archaeology, as well as other advances in the field, I spoke with NIGMS grantee David Reich , a genetic archaeologist from Harvard Medical School and the Howard Hughes Medical Institute, and one of the world’s leading experts in ancient human DNA.

Credit: Howard Hughes Medical Institute.

Chris Palmer:
How would you characterize the current state of research about ancient humans?

David Reich:
We’re going through a gold-rush phase in ancient DNA. It’s a technology-driven boom like those in the past, such as the development of the microscope and telescope in the 17th century, and radiocarbon dating in the 1950s.

The first ancient human genomes were published in 2010. Just a couple of months ago, the 1,000th was published. The number has been multiplying by about 10 every two years and that trend seems to be continuing. What this means is that it’s possible to ask and answer questions about how our ancestors all around the world are related to each other. Some of these questions were just not answerable even a few years ago.

The first studies of ancient DNA were published in 2010. Since then, the number of ancient DNA samples that have been sequenced has grown exponentially. Credit: David Reich.

Chris Palmer:
Which technologies are fueling this “technology-driven boom”?

David Reich:
The first technology is next-generation sequencing, which became available at the end of the 2000’s and made sequencing literally 10- to 100- thousand times cheaper.

Another innovation was an extraordinary increase in the efficiency of methods for extracting DNA from biological samples and the ability to turn that DNA into a sequenceable form. Most of these improvements were developed by Matthias Meyer and Svante Pääbo at the Max Planck Institute for Evolutionary Anthropology in Leipzig, Germany.

Yet another important innovation has been improvements in methods for separating out human DNA from microbial DNA, which tends to dominate the DNA extracted from most ancient biological samples.

Chris Palmer:
What is so special about the petrous bone, and what role has it played in advancing research in this field?

David Reich:
Bone powder taken from the petrous bone yields on average up to 100 times more DNA than powder from other, softer bones. Also, because it’s so dense, when the rest of a skeleton has crumbled into dust, the petrous bone often still remains. So, it’s been a real game changer for the field of ancient DNA.

Using the petrous bone as the source for ancient DNA has made it possible, for the first time, to begin to regularly extract DNA from older biological material, and from biological material that does not preserve very well, such as samples found in hot tropical environments.

Chris Palmer:
Can you pinpoint when scientists realized the value of the petrous bone?

David Reich:
In 2014 to 2015, a group in Ireland led by Ron Pinhasi published a paper that clearly documents how much better this type of bone was than other types of bone as a source for ancient DNA.

Chris Palmer:
What role has petrous bone had in advancing the work of your own research team?

David Reich:
Our first big finding based on petrous bone work was a paper in late 2015 where we reported the first ancient DNA from that population of farmers in Anatolia (present-day Turkey) who went on to populate Europe.

Then, in 2016 we published a paper that reported DNA from four individuals from islands in remote Oceania. We were able to show that those people, who lived between about 2,500 and 3,000 years ago, contributed very little to many of the people who live in those places today, suggesting that there must have been at least one later wave of migration into the region. That was really a big surprise.

A third finding was published a few months ago. We obtained DNA from an approximately 3,000-year-old herder from Tanzania and a little girl. The girl turns out to be from a keystone population that left East Africa and moved in all directions around that time.

[Each of these papers was done in collaboration with the Pinhasi group.]

Chris Palmer:
In response to repeated requests, you recently published a book [“Who We Are and How We Got Here” ] that aims to make ancient DNA research accessible to anyone. Tell me about the book.

David Reich:
It’s a manifesto of the ancient DNA revolution and what its significance is, what it does and doesn’t show, and how it can be used and integrated with our current understanding of ancient humans.

While ancient DNA has already changed our views of the past, it hasn’t yet taught us much about human biology, such as how adaptations and traits spread through populations. We just haven’t yet had enough high-quality data. But the recent innovations, including the use of the petrous bone, are bringing us closer to being able to learn about the biology of ancient humans.

One of the big new findings that has emerged from the ancient DNA revolution—and that I emphasize in my book—is that human populations today are, almost without exception, highly mixed. Populations today almost never descend directly from the populations that existed in the same place even 10,000 years ago. I think that’s a very profound insight, and it should change the way we see our world.

David Reich’s research is funded in part by NIGMS under grant 5R01GM100233.

To learn more about what ancient DNA is telling us about our origins, read NIGMS program director Dan Janes’ Biomedical Beat story “Field Focus: High-Quality Genome Sequences Inform the Study of Human Evolution.”

Cellular Footprints: Tracing How Cells Move

Wed, 2018-04-04 08:38
An engineered cell (green) in a fruit fly follicle (red), or egg case, leaves a trail of fluorescent material as it moves across a fruit fly egg chamber, allowing scientists to trace its path and measure how long it took to complete its journey. Credit: David Bilder, University of California, Berkeley.

Cells are the basis of the living world. Our cells make up the tissues and organs of our bodies. Bacteria are also cells, living sometimes alone and sometimes in groups called biofilms. We think of cells mostly as staying in one spot, quietly doing their work. But in many situations, cells move, often very quickly. For example, when you get a cut, infection-fighting cells rally to the site, ready to gobble up bacterial intruders. Then, platelet cells along with proteins from blood gather and form a clot to stop any bleeding. And finally, skin cells surrounding the wound lay down scaffolding before gliding across the cut to close the wound.

This remarkable organization and timing is evident right from the start. Cells migrate within the embryo as it develops so that body tissues and organs end up in the right places. Harmful cells use movement as well, as when cells move and spread (metastasize) from an original cancer tumor to other parts of the body. Learning how and why cells move could give scientists new ways to guide those cells or turn off or slow down the movement when needed.

Glowing Breadcrumbs

Scientists studying how humans and animals form, from a single cell at conception to a complex body at birth, are particularly interested in how and when cells move. They use research organisms like the fruit fly, Drosophila, to watch movements by small populations of cells. Still, watching cells migrate inside a living fly is challenging because the tissue is too dense to see individual cell movement. But moving those cells to a dish in the lab might cause them to behave differently than they do inside the fly. To solve this problem, NIGMS-funded researcher David Bilder and colleagues at the University of California, Berkeley, came up with a way to alter fly cells so they could track how the cells behave without removing them from the fly. They engineered the cells to lay down a glowing track of proteins behind them as they moved, leaving a traceable path through the fly’s tissue. The technique, called M-TRAIL (matrix-labeling technique for real-time and inferred location), allows the researchers to see where a cell travels and how long it takes to get there.

Bilder and his team first used M-TRAIL in flies to confirm the results of past studies of Drosophila ovaries in the lab using other imaging techniques. In addition, they found that M-TRAIL could be used to study a variety of cell types. The new technique also could allow a cell’s movement to be tracked over a longer period than other imaging techniques, which become toxic to cells in just a few hours. This is important, because cells often migrate for days to reach their final destinations.

Eventually, Bilder believes M-TRAIL could be used to trace the first movements of metastatic cancer cells in humans from a primary tumor out to a blood vessel and surrounding tissues. Learning how cancer cells take these first steps could uncover new ways to stop their migration.

Feet, Fans or Waves? Changing Cellular Modes of Motion In this photo, cells move by creating a fan shape at their front edges and pulling forward. Each color represents a different photo taken one minute after the last. Credit: Peter Devreotes lab, John Hopkins University School of Medicine.

Besides tracking where cells go when they migrate, scientists need to know what cues set them in motion and what controls their movement. NIGMS grantee Peter Devreotes and colleagues at the Johns Hopkins University School of Medicine, Baltimore, MD, are studying a network of connected signaling proteins inside cells. Their findings show that this network is key to controlling cell movement.

Once it’s turned on, this protein network starts up the cell’s movement machinery, including its cellular skeleton, called the cytoskeleton. In response to signals from the network, the cell begins to change shape, an early step in cell migration.

The movement network can start up at random, but it also responds to cues from outside the cell. Devreotes and his team tested this by putting the amoeba cells in a dish of swirling water. Amoeba cells need to be able to respond to liquid moving around them as well as to other signals coming from the surrounding environment. The researchers found that the network proteins within the cells responded to the swirling water in the same way that they respond to other environmental cues. Devreotes thinks the network gives the cell a sophisticated way of interpreting and adjusting to real-world situations.

Once on the move, different cells use different techniques to propel themselves forward. Some, like amoeba or our own white blood cells, reach out with bumps called pseudopods, cellular “feet” that pull the cell forward. Others create a large fan-shaped bulge all along the leading edge of the cell that drives it along, and still others make waves from their centers that ripple through the cell, pulling them forward.

Scientists had thought that each kind of cell used only one of these modes to move. Instead, when Devreotes and his team changed the proteins in the movement network inside cells they found that amoebas altered their movement behavior, switching from pseudopods to fans to rippling waves and back again. So, the network Devreotes studies might be both powerful and universal. It may be similar across many kinds of cells from different species, coordinating signals from outside and determining what mechanism the cells will use to move. Further defining this network could help reveal ways to tweak cell movement when it goes awry.

Saving Resources: Every Cell for Itself Bacteria in a biofilm move together in ordered columns across a surface. Credit: Scott Chimileski, Nick Lyons and Roberto Kolter of Harvard University Medical School.

Understanding how individual cells move tells only part of the story. Cells often move as a group, and when they do, they can do complex jobs that you might not expect. For example, instead of using an every-cell-for-itself approach, bacteria can coordinate their behavior to move the entire colony in an orderly way. Scott Chimileski, an NIGMS-funded research fellow and imaging specialist in the laboratory of Roberto Kolter at Harvard University School of Medicine, uses time-lapse photography to observe how bacteria do this.

Moving as a group has benefits for bacteria, but it is also expensive. For example, making and secreting surfactant, a substance that reduces the tension of the surface and makes it easier to slide across, takes a lot of energy for each cell. So, bacteria want to make sure that none of their competitors can use the surfactant they make for a free ride. Bacteria have evolved many methods for telling their close relatives from their enemies. They even release antibiotics that they are immune to but that will kill bacterial cells not related to them. Kolter and his team believe that the weapons bacteria use to compete successfully also make them into close-knit colonies and promote cooperation. Learning about the balance between cooperation and competition in bacterial colonies, Chimileski said, will help clarify what happens in places like our own gut microbiomes, which, we are learning, are highly complex microbial environments very important to our health.

Dr. Bilder’s research is supported by NIH Grants 5R01GM068675-13 and 5R01GM111111-04. Dr. Devreotes’s research is supported by NIH Grant 5R35GM118177-02, and Dr. Kolter’s research is supported by NIH Grant R01GM058213-20.

Genomic Gymnastics of a Single-Celled Ciliate and How It Relates to Humans

Wed, 2018-03-28 08:37

Credit: Denise Applewhite. Laura Landweber
Grew up in: Princeton, New Jersey
Job site: Columbia University, New York City
Favorite food: Dark chocolate and dark leafy greens
Favorite music: 1940’s style big band jazz
Favorite hobby: Swing dancing
If I weren’t a scientist I would be a: Chocolatier (see “Experiments in Chocolate” sidebar at bottom of story)

One day last fall, molecular biologist Laura Landweber surveyed the Princeton University lab where she’d worked for 22 years. She and her team members had spent many hours that day laboriously affixing yellow Post-it notes to the laboratory equipment—microscopes, centrifuges, computers—they would bring with them to Columbia University, where Landweber had just been appointed full professor. Each Post-it specified the machinery’s location in the new lab. Items that would be left behind—glassware, chemical solutions, furniture, office supplies—were left unlabeled.

As Landweber viewed the lab, decorated with a field of sunny squares, her thoughts turned to another sorting process—the one used by her primary research subject, a microscopic organism, to sift through excess DNA following mating. Rather than using Post-it notes, the creature, a type of single-celled organism called a ciliate, uses small pieces of RNA to tag which bits of genetic material to keep and which to toss.

Landweber is particularly fond of Oxytricha trifallax, a ciliate with relatives that live in soil, ponds and oceans all over the world. The kidney-shaped cell is covered with hair-like projections called cilia that help it move around and devour bacteria and algae. Oxytricha is not only bizarre in appearance, it’s also genetically creative.

Unlike humans, whose cells are programmed to die rather than pass on genomic errors, Oxytricha cells appear to delight in genomic chaos. During sexual reproduction, the ciliate shatters the DNA in one of its two nuclei into hundreds of thousands of pieces, descrambles the DNA letters, throws most away, then recombines the rest to create a new genome.

Landweber has set out to understand how—and possibly why—Oxytricha performs these unusual genomic acrobatics. Ultimately, she hopes that learning how Oxytricha rearranges its genome can illuminate some of the events that go awry during cancer, a disease in which the genome often suffers significant reorganization and damage.

Oxytricha’s Unique Features

Oxytricha carries two separate nuclei—a macronucleus and a micronucleus. The macronucleus, by far the larger of the two, functions like a typical genome, the source of gene transcription for proteins. The tiny micronucleus only sees action occasionally, when Oxytricha reproduces sexually.

Two Oxytricha trifallax cells in the process of mating. Credit, Robert Hammersmith.

What really makes Oxytricha stand out is what it does with its DNA during the rare occasions that it has sex. When food is readily available, Oxytricha procreates without a partner, like a plant grown from a cutting. But when food is scarce, or the cell is stressed, it seeks a mate. When two Oxytricha cells mate, the micronuclear genomes in each cell swap DNA, then replicate. One copy of the new hybrid micronucleus remains intact, while the other breaks its DNA into hundreds of thousands of pieces, some of which are tagged, recombined, then copied another thousand-fold to form a new macronucleus.

Following up on the work of earlier researchers who provided the first glimpse into the unique nature of sexual development in Oxytricha, Landweber’s lab sequenced the complete genomes of Oxytricha’s two separate nuclei, figured out how the organism tags its tiny pieces of DNA, and deciphered how this marked DNA is guided to the right spot in the new macronucleus.

Oxytricha is not the only unusual research organism Landweber has worked with over the years. Below is a sampling of some of the exotic, and more mainstream, organisms to have spent time under her microscope.

Click on an image below to launch slideshow.

Biology, but also math

Growing up in Princeton, New Jersey, as the daughter of academics, Landweber says her career trajectory almost felt like a foregone conclusion. Early on, her parents fostered a fondness for science, subscribing her to mail order science kits and giving her a microscope for her birthday. In particular, she recalls getting excited about biology around age 10 thanks to a human anatomy coloring book.

Landweber says that, while her “gut instinct” drew her to biology, she also “always loved the mathematical side of things.” She has explored many different ways to combine the two disciplines and often uses math and computer analogies to explain complex biological concepts.

Landweber stayed close to home for college, receiving a degree in molecular biology from Princeton. She then went to graduate school at Harvard University, where her research centered on how errors in RNA are corrected before the molecule is translated into proteins. She likens this process, called RNA editing, to correcting text using a word processor. “Imagine you’re editing a text document and you find a typo,” says Landweber. “You can just go in and fix it before printing.”

The first course Landweber taught at Princeton was “Jurassic Park: Myth or Reality?”—just one year after the dinosaurs-run-amok blockbuster had dominated movie screens. The controversial topic was a wonderful way to get students excited about reading scientific journal articles—plus they could watch a movie then talk about the real science behind it, Landweber says. Credit: Flickr, Ian Welch.

After her time at Harvard ended, Landweber returned to her roots, landing a faculty position at Princeton at the remarkably young age of 26. Initially, one research project focused on building computers based on RNA and DNA. For a few years, her lab even held the record for the most powerful molecular computer. But she abandoned the field before too long, convinced that it had no future as a serious competitor to silicon-based computers.

Ciliate Sex

The next field Landweber latched onto, and the one which dominates her current research, was ciliate genomics. She first learned about Oxytricha’s genomic anomalies from a talk she attended by biologist David Prescott, who initially discovered the ciliate’s tiny chromosomes. Right away, Landweber was hooked. “It seemed to fit right into my interest in biological computation, because, when you think about it, ciliates—which scramble, shuffle and reassemble their genes—really are cellular computers,” she says.

Like any typical nucleus, Oxytricha’s macronucleus contains all the DNA it uses to make the RNA and proteins required for everyday life. But the way the DNA in the macronucleus is organized is anything but typical. Humans have 23 pairs of chromosomes. In 2013, Landweber’s team discovered that Oxytricha’s macronucleus contains roughly 16,000 unique chromosomes—nearly 700 times more than we have!

Oxytricha’s micronucleus supplies the pool, or reservoir, of genetic material that it can exchange with another Oxytricha cell. During mating, the micronuclei provide all the drama—they divide by meiosis, discard unneeded material, exchange DNA with the partner cell, shatter into thousands of pieces, shuffle and scramble their DNA. Meanwhile, the macronuclei completely degrade.

Oxytricha reproduction, Credit: NIGMS.

The entire process is quite complicated, but here’s the basic idea (see illustration for a simplified version). Two Oxytricha cells fuse, creating a connecting structure that bridges the insides of both cells. About one half of the DNA in each cell’s micronucleus travels across this bridge into the partner cell. In each cell, the fresh DNA combines with existing DNA to create a hybrid micronucleus.

The two cells split apart, and the hybrid micronucleus in each makes a copy of itself. In each cell, one of the two new micronuclei remains intact, while the DNA in the other one breaks apart into nearly 250,000 disordered pieces.

Then, Oxytricha spends two days discarding about 95 percent of the DNA from shattered micronucleus. The remaining 5 percent of its DNA rearranges (sometimes scrambled or turned upside down), and reassembles to construct the creature’s new macronucleus.

At this point, the macronucleus contains about 16,000 different nanochromosomes—some of which are just a single gene in length, or about 3,000 letters. These nanochromosomes are then amplified another thousand-fold, yielding about 16 million nanochromosomes in the completed macronucleus, which explains its larger size.

At the end of the process, which can take three or four days, the micronucleus and macronucleus of both Oxytricha cells are genetically rejuvenated, incorporating DNA from each cell’s original cache as well as new bits from its partner.

Landweber digs deeper into Oxytricha genomics

While Landweber and her team initially thought the discarded, or leftover, DNA of the shattered micronucleus was “junk,” they later discovered that a substantial chunk of this DNA encodes enzymes called transposases, which are partly responsible for shuffling and reordering the genes of the micronucleus and stitching them together into the new macronucleus.

Landweber and her colleagues subsequently learned a few additional details about the process that harken back to her early interest in RNA. They discovered that small, non-coding RNAs called piRNAs play the role of Post-it notes, flagging the 5 percent of micronucleus DNA to keep for Oxytricha’s macronucleus. In addition, Landweber’s team discovered that long, non-coding RNAs help steer the tagged DNA to the right location in the remodeled macronucleus.

Given the rather convoluted nature of Oxytricha sex, one question Landweber is often asked is “Why does such a complicated system exist?” Landweber offers a few possibilities. First, encrypting its DNA may protect Oxytricha against viruses that attempt to take up residence in its genome. Second, the ability to come up with new combinations of DNA can be used to create new genes, but this happens rarely enough that she thinks it’s something of a side benefit. Instead, Landweber leans more toward the idea that the system evolved as an error-correction mechanism that relies on RNA to ensure the precise transfer of genetic information across generations.

No matter what the ultimate reason turns out to be, Landweber continues to be enthralled with Oxytricha. “It is just truly marvelous that nature has invented such a clever mechanism,” she says.

Bringing Oxytricha to the clinic

While Oxytricha can provide insights to the burgeoning field of genome editing, particularly relevant to human health is the observation that so many human cancers are defined by fairly drastic chromosome reorganization. One extreme example is chromothripsis—a rare occurrence linked to a variety of cancers, in which a single catastrophic event triggers thousands of chromosomal rearrangements.

Oxytricha can teach us a lot about the possibilities of maintaining genome integrity in the face of destructive forces that can corrupt it, including cancer,” says Landweber.

Landweber hopes that her lab’s discoveries in Oxytricha will help improve our understanding of events that can lead to cancer. “It’s as though Oxytricha’s process of rebuilding its chromosomes runs the clock in reverse, starting from a shattered genome and restoring integrity,” she says. “We need to tap into that.”

Within a short walk of her new lab overlooking the Hudson River at Columbia University Medical Center, Landweber has found many potential clinical collaborators. “I’m now actually surrounded by a lot of people studying problems of cancer biology,” she says.

As Landweber prepares to apply her knowledge of ciliate biology to combating cancer, she plans to continue seeking to understand exactly how Oxytricha can manage the chromosomal chaos that would be catastrophic to human cells.

Experiments in Chocolate

Like Landweber herself, Landweber’s three daughters with husband Steven Gubser, a theoretical physicist at Princeton, are growing up in a household steeped in academia. However, while conversations around the dinner table might revolve around science, Landweber says her and Steven’s best collaborations occur in the kitchen.

“That’s where he can be an experimentalist,” Landweber adds, “And we absolutely do like to experiment with making things like what we claim to be healthy chocolate cakes.”

While the healthiness of her cakes may be in question, Landweber’s bona fides as a chocolate lover are not. Just after graduate school, she served as Chocolate Steward of the Harvard Society of Fellows.

“Among other things, being steward meant that I had a little bit of clout when I’d walk into a chocolate shop,” says Landweber. “I would get a few more tastings and a few more tips, and I learned a lot about chocolate.”

She poured most of what she learned into one of the first online guides to chocolate in Boston, which, to her surprise, was for years the number one page resulting from a Google search of “chocolate” and “Boston.”

Landweber’s research is funded in part by NIGMS grant R01GM059708.

Have Nucleus, Will Travel (in Three Dimensions)

Tue, 2018-03-20 12:41
These two human cells are nearly identical, except that the cell on the left had its nucleus (dyed red) removed. The structures dyed green are protein strands that give cells their shape and coherence. Credit: David Graham, UNC-Chapel Hill.

Both of the cells above can scoot across a microscope slide equally well. But when it comes to moving in 3D, the one without the red blob in the center (the nucleus) stalls out. That’s sort of like an Olympic speed skater who wouldn’t be able to perform even a single leap in a figure skating competition.

Scientists have known for some time that the nucleus is involved in moving cells across a flat surface—it slides to one side of the cell and “pushes” from behind. However, scientists have also shown that cells with their nuclei removed can migrate along a flat surface just as well as their brethren with intact nuclei. But they had no idea that, without a nucleus, a cell could no longer move in three dimensions.

This discovery was made by UNC-Chapel Hill biologists Keith Burridge and James Bear and their colleagues. These NIGMS-funded researchers also observed that cells whose nuclei had been disconnected from the cytoskeleton could not move through 3D matrices. The cytoskeleton is the microscopic network of actin protein filaments and tubules in the cytoplasm of many cells that provides the cell’s shape and coherence. It has also has been thought to play a major role in cell movement.

The gray, stringy background of these videos is a 3D jello-like matrix. The cell in the top half of this video has a nucleus and can migrate through the matrix. Both cells in the bottom half have been enucleated (a fancy term for having its nucleus removed) and cannot travel through the matrix. Credit: Graham et al., Journal of Cell Biology, 2018.

The researchers speculate that the reason cells without nuclei (or those whose nuclei have been disconnected from the cytoskeleton) don’t navigate in 3D has to do with complex mechanical interactions between the cytoskeleton and the nucleoskeleton. The nucleoskeleton is a molecular scaffold within the nucleus supporting many functions such as DNA replication and transcription, chromatin remodeling, and mRNA synthesis. The interface between the cytoskeleton and nucleoskeleton consists of interlocking proteins that together provide the physical traction that cells need to push their way through 3D environments. Disrupting this interface is the equivalent of breaking the clutch in a car: the motor revs, but the wheels don’t spin, and the car goes nowhere.

A better understanding of the physical connections between the nucleus and the cytoskeleton and how they influence cell migration may provide additional insight into the role of the nucleus in diseases, such as cancer, in which the DNA-containing organelle is damaged or corrupted.

This research was funded in part by NIGMS grants 5R01GM029860-35, 5P01GM103723-05, and 5R01GM111557-04.

Carole LaBonne: Neural Crest Cells and the Rise of the Vertebrates

Thu, 2018-03-08 09:30

The stunning pigmentation of tigers, the massive jaws of sharks, and the hyper-acute vision of eagles. These and other remarkable features of higher organisms (vertebrates) derive from a small group of powerful cells, called neural crest cells, that arose more than 500 million years ago. Molecular biologist Carole LaBonne of Northwestern University in Illinois studies how neural crest cells help give rise to these important vertebrate structures throughout development.

Very early during embryonic development, stem cells differentiate into different layers: mesoderm, endoderm, and ectoderm. Each of these layers then gives rise to different cell and tissue types. For example, the ectoderm becomes skin and nerve cells. Mesoderm turns into muscle, bone, fat, blood and the circulatory system. Endoderm forms internal structures such as lungs and digestive organs.

These three layers are present in vertebrates—animals with a backbone and well-defined heads, such as fish, birds, reptiles, and mammals—as well as animals without backbones, such as the marine-dwelling Lancelets and Tunicates (referred to as non-vertebrate chordates). Unlike cells in these layers, neural crest cells, which are found only in vertebrates, don’t specialize until much later in development. The delay gives neural crests cells the extra time and flexibility to sculpt the complex anatomical structures found only in vertebrate animals.

Scientists have long debated how neural crest cells manage to finalize their destiny so much later than all other cell types.

Using the frog Xenopus as a model system, LaBonne and her colleagues performed a series of experiments that revealed the process and identified key genes that control it.

In this video, LaBonne describes the power of neural crest cells and how they can be useful for studies of human health, including how cancer cells can metastasize, or migrate, throughout the body.

Dr. LaBonne’s research is funded in part by NIGMS grant 5R01GM116538.

Computational Geneticist Discusses Genetics of Storytelling at Sundance Film Festival

Thu, 2018-03-01 11:03

About 10 years ago, University of Utah geneticist Mark Yandell developed a software platform called VAAST (Variant Annotation, Analysis & Search Tool) to identify rare genes. VAAST, which was funded by NHGRI, was instrumental in pinpointing the genetic cause of a mystery disease that killed four boys across two generations in an Ogden, UT family.

NIGMS has been supporting Yandell’s creation of the next generation of his software, called VAAST 2, for the past few years. The new version incorporates models of how genetic sequences are conserved among different species to improve accuracy with which benign genetic sequences can be differentiated from disease-causing variations. These improvements can help identify novel disease-causing genes responsible for both rare and common diseases.

Yandell and his colleagues in the Utah Genome Project recently took part in a panel at the Sundance Film Festival called the “Genetics of Storytelling” to discuss film’s ability to convey the power of science and medicine. Yandell told the audience his story about his efforts to use VAAST to trace the Ogden boys’ genetic variation back to their great-great-great-great-great grandmother.

Below is a blog post published on January 30 by University of Utah science writer Julie Kiefer about the event.

Finding the Story Within: Utah Genome Project at the 2018 Sundance Film Festival

When Helen’s two sons died before they were a year old, she thought she had terrible luck. But when her grandsons died as babies, she knew that something was horribly wrong. In 2011, University of Utah geneticists uncovered the reason for the boys’ deaths. They all had a genetic mutation that caused a serious condition, now known as Ogden syndrome , named after the Utah town where they lived.

Knowledge is nothing if not power. Armed with this information, Helen’s extended family and others like them can make informed decisions about whether or not to have children, and what to expect if they do.

Mark Yandell, Ph.D., a computational geneticist and Utah Genome Project (UGP) investigator, relayed the tale as part of the “Genetics of Storytelling” panel last Friday at the Sundance Film festival in Park City, Utah. A collection of artists and scientists, the panel discussed film as a dynamic medium for conveying the power of science and medicine.

“We hope to discover new narratives in our heart, our history, and our genes which is where the story lives,” said moderator Geralyn Dreyfous.

Within the UGP, those stories abound. Already, The Atlantic has explained how the 14-generation story of a pilgrim family led to discoveries that are preventing modern descendants from dying young of inherited colon cancer. These “previvors” are outliving their ancestors.

“The research has progressed to the point that people with this disease no longer need to fear cancer,” said UGP and Huntsman Cancer Instituteinvestigator Deborah Neklason, Ph.D.

UGP investigator and cardiologist Martin Tristani-Firouzi, M.D., described his team’s work searching for families who have no idea that their heart could seize unexpectedly. Giving them a simple treatment of beta-blockers could prevent them from becoming the casualty of a misspelled gene.

There is no need to invent stories when telling a true tale can fill a valuable role, said film director Christian Frie. That job could be to raise awareness, bolster support, or stir conversation.

His movie “Genesis 2.0 ” fills the latter category by depicting legendary geneticist George Church’s ethically dicey efforts to resurrect the wooly mammoth that has been extinct for over three millennia. “Our job as artists is to turn science into a language people can understand,” he says.

The Ogden syndrome story is one that’s ripe for the telling, but it’s far from over.

With sophisticated algorithms, Yandell is tracing the boys’ genetic variation back in time. Born in 1807, their great-great-great-great-great grandmother also carried the mutation.

Consider what it could mean to go back even further, he mused. We rarely think about the effects that genetic disease had on our caveman ancestors. “When we can extrapolate data, it has a huge impact on understanding human health and death.”

Group picture: Martin Tristani-Firouzi, Mark Yandell, Vineet Mehra (Ancestry DNA), Deborah Neklason, Christian Frei, Geralyn Dreyfous. Credit: Charlie Ehlert

These aren’t just stories of despair. There are many stories of hope. “It’s natural to think about the bad side of knowing your genetics, particularly when you have family dying around you,” said Yandell. “Genetics can also bear good news. It might say that no, you don’t have the mutation, and you never have to worry about it again.”

Utah Genome Project is all about understanding the narrative that lives within us. Along with drama, intrigue, and glory, there is a story that continues to unfold.

Sounds like the making of a good movie.


What Zombie Ants Are Teaching Us About Fungal Infections: Q & A with Entomologists David Hughes and Maridel Fredericksen

Wed, 2018-02-21 10:32


I can still remember that giddy feeling I had seven years ago, when I first read about the “zombie ant.” The story was gruesome and fascinating, and it was everywhere. Even friends and family who aren’t so interested in science knew the basics: in a tropical forest somewhere there’s a fungus that infects an ant and somehow takes control of the ant’s brain, forcing it to leave its colony, crawl up a big leaf, bite down and wait for the sweet relief of death. A grotesque stalk then sprouts from the poor creature’s head, from which fungal spores rain down to infect a new batch of ants.

A fungal fruiting body erupts through the head of a carpenter ant infected by a parasitic fungus in Thailand. Credit: David Hughes, Penn State University.

The problem is, it doesn’t happen quite like that. David Hughes , the Penn State University entomologist who reported his extensive field observations of the fungus/ant interactions in BMC Ecology , which caused much excitement back in 2011, has continued to study the fungus, Ophiocordyceps unliateralis, and its carpenter ant host, Camponotus leonardi.

In late 2017, Hughes and his colleagues published an article in PNAS in which they used sophisticated microscopy and image-processing techniques to describe in great detail how the fungus invades various parts of the ant’s body including muscles in its legs and head.

Although Hughes’s earlier BMC Ecology paper showed fungus in the head of an ant, the new study reveals that the fungus never actually enters the brain.

To me, the new finding somehow made the fungus’ control over the ant even more baffling. What exactly was going on?

To find out, I spoke with Hughes and his graduate student Maridel Fredericksen.

David Hughes (left) and Maridel Fredericksen. Credit, Penn State University and Maridel Fredericksen.

Chris Palmer:
How did you first encounter the fungus O. unilateralis?

David Hughes:
I was doing my PhD on a group of parasites called Strepsiptera that control ant and wasp behavior. They’re very interesting, and they do cool things just like this fungus. But they’re not amenable to experimentation: they don’t infect their hosts in the lab, and you can’t look at their genes or the chemicals they produce.

Then I read about Ophiocordyceps unliateralis in a dusty old publication. So, I made a trek to a rainforest in southern Thailand to observe them, probably 12 years ago now, and it’s been fun ever since.

Chris Palmer:
What does the fungus do to the carpenter ant?

David Hughes:
This is a highly specialized fungal parasite that enters the body of a foraging ant. Over the course of a couple weeks the fungus grows within the ant’s body from a small clump of cells to a large interconnected group of cells that cooperate and communicate with each other.

It’s at this stage that the fungus manipulates the ant’s behavior to leave the colony. Ants are extremely good at keeping the interior of their colony clean. If the fungus were to kill its ant inside the colony and try to grow from its dead body, which is a necessary part of the lifecycle, it would not be successful because fellow ants would dispose of the body before the fungus could sprout. Instead, the fungus manipulates the ant to go die outside of the colony.

Chris Palmer:
What else have you learned about this fungus in the years since your initial observations?

David Hughes:
We knew nothing about this system, even though it had been first recorded in 1859 by Alfred Russel Wallace, the co-discoverer of natural selection along with Charles Darwin. So, our early work was descriptive natural history. A few years later, we studied the ant’s genes and the chemicals the fungus produced. We also conducted field geographic studies aimed at understanding where and when the fungus evolved. We learned that a wide range of insects—from caterpillars to moths to beetles—are infected by this group of fungi. But it’s when the fungus infects ants and wasps that it manipulates behavior so gloriously.

Chris Palmer:
What motivated the new study?

Maridel Fredericksen:
As David mentioned, we knew a lot about the behavior of the ants. We also had the fungus genome and knew the chemicals the fungus secretes to manipulate the ant. But we didn’t really have anything in between, at the cellular level, which is the level at which the fungus itself behaves. Specifically, we wanted to look more closely at how the fungal cells were interacting with the ant’s muscle cells and, potentially, its brain.

Chris Palmer:
What did you find?

David Hughes:
We saw something rather special—a three-dimensional network of interconnected fungal cells surrounding muscle fibers in both the leg and the jaw. Some of those fungal cells had hyphae, which is the exploratory part of a fungus, entering into the muscles. From this, we concluded that the networks of fungal cells are used for communicating and coordinating a collective action. In this case, we suspect the hyphae feed from the energy-rich muscle and pass food down through the network.

Chris Palmer:
Were you surprised to learn that the fungus wasn’t in fact invading the brain?

David Hughes:
We had always suspected this. Earlier studies showed it was in the head, but the anatomical images didn’t have the spatial resolution to conclude that it was definitely in the brain. In retrospect, as is often the case in scientific discoveries, you would say, “Of course, it doesn’t need to go to the brain because it’s focused on controlling the muscle.” It’s one of those things that becomes very clear in hindsight.

Chris Palmer:
Do you know how the fungus is controlling the muscles?

David Hughes:
Two things are required for muscle movement: a signal from the nervous system and muscle fibers that contract. In the infected ant the fungus is forming this sprawling three-dimensional collective unit around the muscle. We suspect that the fungus produces chemicals that affect muscle contraction.

This is extremely interesting when one thinks of the wide variety of human diseases, including spinal cord injuries and carpal tunnel syndrome, where muscles break down following a disruption to nervous-system input.

In infected ants, the muscles don’t die off. Instead, they begin to be controlled by the fungus, rather than the nervous system. We suspect that the fungus starts producing chemicals that cause muscle contractions, and they do this at a set rate. This enables the fungus to make the ant move from point A to point B—in this case from the center of the colony to outside the colony and up on a twig to drop down spores on a new batch of ants.

Chris Palmer:
In your latest paper, you use a technique called serial block-face scanning electron microscopy combined with an automated image-processing algorithm. Can you describe that technique and how you used it to arrive at your conclusions?

Maridel Fredericksen:
We first collected the ants and the fungus in South Carolina. So, yeah, this odd behavior occurs in the U.S., too. It’s not just an exotic, tropical thing. We then took a few small tissue samples from the leg muscles and jaw muscles of infected ants. A technician places the tissue inside the microscope, which automatically cuts each tissue into nanometer-thick slices using a diamond knife. The result is thousands of slices per micrometer (one thousandth of a millimeter). Our co-author and microscopy expert, Missy Hazen, then took high-resolution photographs of each slice using an electron microscope. The whole process took about 24 hours per sample.

The parasitic fungus controls ant behavior not by infecting ant brains, but by chemically controlling their muscles. This 3-D reconstruction shows an ant jaw muscle (red) surrounded by a network of fungal cells (yellow). Credit: Hughes Laboratory, Penn State.

Chris Palmer:
How did you combine all those images into something useful?

Maridel Fredericksen:
We’d get stacks of images and I would align them to reconstruct 3-D images. At first, I worked on one muscle fiber with the fungus wrapped around it. It took a long time—about a month—to reconstruct, even though it was a really, really small part of one stack of images. For each image, I used a computer program to draw around a muscle fiber and the surrounding fungal cells. Then I did that for each of the one thousand images that were in the stack. It was a pretty tedious process.

But then we collaborated with Danny Chen and Yizhe Zhang  from Notre Dame, and thankfully they were able to automate the process with their image-processing algorithms. To create this movie, the scientists sliced a 50-micron-thick sample of an ant’s head near the jaw (and away from the brain) into 1,000 incredibly thin sections. Using an electron microscope, they took a black-and-white photo of each slice. Then they assembled the 2-D photos with an automated, image-processing algorithm. The resulting 3-D, colorized image shown at the end of this video is a single jaw muscle fiber (red) surrounded by 25 interconnecting strands of fungus (yellow). Credit: Fredericksen et al., PNAS, 2017.

Chris Palmer:
How does the algorithm work?

Maridel Fredericksen:
We would all look at images and say, “Okay, this is muscle, this is fungus.” We did that for just two images. They used those marked-up images to train their algorithm, which then differentiated fungus from muscle for the thousands of remaining images.

Chris Palmer:
And did you use the same procedure to look at the brain?

Maridel Fredericksen:
No. We used a different microscopy technique to examine the brain. That technique revealed that the fungal hyphae bodies did not penetrate the brain. 

Chris Palmer:
How much time do you think the algorithm saved compared to doing it by hand?

Maridel Fredericksen:
Literally years. It took them a while to develop their model, but afterwards everything went super fast.

Chris Palmer:
So, the fungus is controlling the leg muscles directly. But is it also controlling the jaw muscles to produce the biting down behavior that anchors the ant to the leaf?

Fungus-infected carpenter ant biting down on a leaf. Credit: David Hughes, Penn State University.

David Hughes:
Yes, right, except for that last bit about the biting. We have no idea how that happens, but we think the brain is involved. It’s the magical element of the whole thing, which will take quite a number of years to figure out, I suppose.

Chris Palmer:
What’s your plan for learning how the biting works?

David Hughes:
We’re working on a rather nice technique that can scan across the brain on a micron-by-micron scale to measure the chemical composition of tissue inside the brain. Because, while we didn’t find the fungus inside the brain, we strongly suspect based upon some initial images that there are far more protein receptors for the neurotransmitter serotonin in the brains of infected ants. Perhaps the increase in serotonin receptors, which can result in significant changes to behavior, is driven by chemicals released by the fungus.

Chris Palmer:
What ultimately do you hope a full understanding of this fungus can bring to science and human health?

David Hughes:
The micron-level understanding of a parasitic microbe in a body is really advanced in this system compared to other systems. So, it’s easier and faster to study fungal infections in ants than in humans.

Also, there is a lot of research on human diseases caused by bacteria and viruses. We’ve largely ignored fungal diseases, which, as a group, kill more humans every year—more than 1.3 million—than malaria. But we don’t really have anything in our arsenal to kill them.

Chris Palmer:
Why are fungal diseases so hard to treat?

David Hughes:
A lot of people will be surprised to hear this, but fungi are more related to animals than they are to plants. Because of this relationship, virtually everything that we throw at a fungus to kill it is going to kill human cells just as quickly.

Our work provides a unique insight into how fungi communicate and coordinate inside an animal’s body, which could help in designing drugs to target fungi. For example, if it turns out that it’s critical that they form these interconnected tubes from one cell to another, then perhaps we can derive something that stops tube formation and ultimately thwarts infection.

Interview With a Scientist: Joel Kralj, Electromicist

Tue, 2018-02-13 10:51

Every one of our thoughts, emotions, sensations, and movements arise from changes in the flow of electricity in the brain. Disruptions to the normal flow of electricity within and between cells is a hallmark of many diseases, especially neurological and cardiac diseases.

The source of electricity within nerve cells (i.e., neurons) is the separation of charge, referred to as voltage, across neuronal membranes. In the past, scientists weren’t able to identify all the molecules that control neuronal voltage. They simply lacked the tools. Now, University of Colorado biologist Joel Kralj has developed a way to overcome this hurdle. His new technique—combining automated imaging tools and genetic manipulation of cells—is designed to measure the electrical contribution of every protein coded by every gene in the human genome. Kralj believes this technology will usher in a new field of “electromics” that will be of enormous benefit to both scientists studying biological processes and clinicians attempting to treat disease.

In 2017, Kralj won a New Innovator Award from the National Institutes of Health for his work on studying voltage in neurons. He is using the grant money to develop a new type of microscope that will be capable of measuring neuronal voltage from hundreds of cells simultaneously. He and his research team will then attempt to identify the genes that encode any of the 20,000 proteins in the human body that are involved in electrical signaling. This laborious process will involve collecting hundreds of nerve cells, genetically removing a single protein from each cell, and using the new microscope to see what happens. If the voltage within a cell is changed in any way when a specific protein is removed, the researchers can conclude that the protein is essential to electrical signaling.

In this video, Kralj discusses how he plans to use his electromics platform to study electricity-generating cells throughout the body, as well as in bacterial cells (see our companion blog post “Feeling Out Bacteria’s Sense of Touch” featuring Kralj’s research for more details).

Dr. Kralj’s work is funded in part by the NIH under grant 1DP2GM123458-01.

Feeling Out Bacteria’s Sense of Touch

Mon, 2018-02-05 10:46

Our sense of touch provides us with bits of information about our surroundings that inform the decisions we make. When we touch something, our nervous system transmits signals through nerve endings that feed information to our brain. This enables us to sense the stimulus and take the appropriate action, like drawing back quickly when we touch a hot stovetop.

Bacteria are single cells and lack a nervous system. But like us, they rely on their “sense” of touch to make decisions—or at least change their behavior. For example, bacteria’s sense of touch is believed to trigger the cells to form colonies, called biofilms, on surfaces they make contact with. Bacteria may form biofilms as a way to defend themselves, share limited nutrients, or simply to prevent being washed away in a flowing liquid.

Humans can be harmed by biofilms because these colonies serve as a reservoir of disease-causing cells that are responsible for high rates of human infection. Biofilms can protect at least some cells from being affected by antibiotics. The surviving reservoir of bacteria then have more time to evolve resistance to antibiotics.

At the same time, some biofilms can be valuable; for example, they help to break down waste in water treatment plants and to drive electrical current as part of microbial fuel cells.

Until recently, scientists thought that bacteria formed biofilms and caused infections in response to chemical signals they received from their environments. But research in 2014 showed that the bacterium Pseudomonas aeruginosa could infect a variety of living tissues—from plants to many kinds of animals—simply by making contact with them. In the past year, multiple groups of investigators have learned more about how bacteria sense that they have touched a surface and how that sense translates to changes in their behavior. This understanding could lead to new ways of preventing infections or harmful biofilm formation.

Making Contact

Pili (green) on cells from the bacterium Caulobacter crescentus (orange). Scientists used a fluorescent dye to stain pili so they could watch the structures extend and retract. Credit: Courtney Ellison, Indiana University.

When they first make contact with a surface, bacteria change from free-ranging, swimming cells to stationary ones that secrete a sticky substance, tethering them in one place. To form a biofilm, they begin replicating, creating an organized mass stable enough to resist shaking and to repel potential invaders (see

How do swimming bacteria sense that they have found a potential surface to colonize? Working with the bacterium Caulobacter crescentus, Indiana University Ph.D. student Courtney Ellison and her colleagues, under the direction of professor of biology and NIGMS grantee Yves Brun , recently showed that hair-like structures on the cell’s surface, called pili, play a role here. The researchers found that as a bacterial cell swims in a fluid, its pili are constantly stretching out and retracting. When the cell makes contact with a surface, the pili stop moving, start producing a sticky substance and use it to hold onto the surface.

To watch what the pili were doing, the Brun team tagged the tiny structures with fluorescent dye so that they would light up when imaged. The researchers also attached a large molecule to some pili to prevent them from retracting. Most of the cells with these large-molecule bound pili were fooled into secreting their adhesive substance, even though they were not in contact with a surface. The scientists believe that when the bacterium tries and fails to retract its pili, the tugging or tension triggers the signal that causes the cell to start attaching to the surface. This finding may eventually lead to new drugs that can trick bacteria into not initiating infection or aggregating into biofilms.

Swimming bacteria have another outer structure that also could be involved in sensing a surface. Urs Jenal and colleagues at the University of Basel, Switzerland, also studied Caulobacter crescentus and the action of its flagellum, a rotating tail that powers the bacterium around like a propeller. The flagellum extends from one end of the swimming cell and works in tandem with the pili. In a result mirroring that of Brun’s team, Jenal and his team concluded that when a cell’s flagellum touches a surface and can no longer rotate, the motor inside the cell that powers the flagellum stops, providing the signal to start attaching.

Whether the pili or the flagellum motor lies behind the cell’s ability to sense a surface may depend on surrounding conditions. According to Brun, “The more we know about the mechanism of surface adhesion, the more we will be able to design strategies to inhibit adhesion.”

Interfering with bacteria’s sense of touch and preventing their colonization instead of killing them with antibiotics could help prevent antibiotic resistance. The strategy could ward off infection before it even starts.

A Shocking Development

Culture sample of electrically excited bacteria as seen under a microscope. Credit: Giancarlo Bruni.

Besides reacting to signals from their flagella or pili, bacteria have another means for reacting to surface touch, one that closely mimics our own. It is based on electrical signals inside the cell.

NIGMS grantee Joel Kralj and colleagues from the University of Colorado, Boulder, are finding that bacteria sense touch using electrical signals. Studying E. coli, Kralj and his team found that these electrical signals arise from the flux of calcium ions into and out of the cell. Such signals are used to convey information in nerve cells.

According to Kralj, this kind of signaling in response to touch could trigger more than just biofilm formation. Bacteria may use this sense to identify a food source or another cell, such as an enemy. They also might use electrical signaling to recognize how many of their own kind are in the surrounding area.

When an E. coli bacterium was touched, the cell sent out an electrical pulse, opening channels in its membrane and allowing calcium ions to flow into it. Higher calcium concentrations can set off several cellular changes, including speeding the movement of the flagella and ramping up the production of proteins that bacteria use in the infection process. Indeed, Kralj and his team saw that E. coli’s response to being touched triggered changes in levels of a pathogenic protein inside the bacterial cells.

Kralj’s team believes the electrical-signal response to touching a surface could tell the bacterium to get ready for a change in its activity. Although bacteria are known to respond this way to chemical signals, scientists had not previously seen them respond to an electrical one.

For Kralj, the most exciting aspect of his team’s work is the fact that E. coli can use electrical signaling the way higher organisms do. “This finding places electrically excitable behaviors WAY back in the evolutionary tree and suggests that every organism has the potential to use voltage to sense and react to its environment,” he said. The sense of touch has certainly kept its value over all that time.

The research in Dr. Brun’s lab was funded in part by NIGMS under grants 1R35GM122556, 5R01GM104540, 2R01GM051986, and 5R01GM102841. The research in Dr. Kralj’s lab was funded in part by NIGMS under grants 1DP2GM123458 and 2T32GM065103.


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Two NIGMS MARC Scholars Receive Prestigious Rhodes Scholarship

Fri, 2018-01-12 11:53
Oxford University. Credit: Andrew Shiva, Wikimedia Commons CC BY-SA.

MARC U-STAR Scholars Jasmine Brown and Naomi Mburu were among 32 Americans to recently receive the prestigious Rhodes Scholarship at Oxford University in England. Rhodes Scholars are chosen for their academic and research achievements, as well as their commitment to others and leadership potential.

As current MARC U-STAR Scholars, Brown and Mburu are part of an NIGMS research training program for undergraduate junior and senior honor students. MARC is designed to increase the number of people from groups underrepresented in biomedical sciences by preparing students for high-caliber, doctorate-level training.

Here’s more about these two distinguished women:

Credit: The Source, Washington University in St. Louis.

Jasmine Brown, 21

Brown, of Hillsborough, New Jersey, is a senior at Washington University in St. Louis and works as a research assistant at the Washington University School of Medicine. There, she studies genes that are protective against mental defects that result from West Nile-induced brain inflammation. After she receives her bachelor’s degree in biology, she plans to earn a doctorate degree in neuroscience as a Rhodes Scholar at Oxford University.

In addition to her current training as a MARC Scholar, Brown has spent her summers as an undergraduate research assistant, engaging in the study of these other notable subjects:

  • Lung cancer, at the Broad Institute of MIT and Harvard (2017)
  • Specific drugs’ cough-suppressing effects, at Johns Hopkins University School of Medicine (2015)
  • Long-term neurological effects of cocaine and other stimulants on the teen brain, at the University of Miami Miller School of Medicine (2014)

“What I love about science is that it gives me tools to generate answers and to improve human health. It’s a fun process for me, but also a satisfying one because I can make an impact,” Brown said in a statement.

Equally important to her studies, Brown is a champion for other underrepresented students in the sciences. After her own experience as the target of prejudice, Brown started the Minority Association of Rising Scientists (MARS) to support underrepresented students participating in research and inform faculty members about implicit bias. With the help of the National Science Foundation, Brown is working to expand MARS nationwide.

Brown has given back to the community in other ways. She was a member of The Synapse Project , which prepares high school students for a neuroscience competition called Brain Bee . She was also a 2014-2015 candidate for Mx. WashU , an organization that raises money for a children’s program called City Faces .

Naomi Mburu, 21

Credit: Marlayna Desmond for UMBC.

Naomi Mburu, of Ellicott City, Maryland, is the daughter of Kenyan immigrants and the first student in the history of the University of Maryland Baltimore County (UMBC) to receive the Rhodes Scholarship. The senior in chemical engineering plans to complete a doctorate in engineering science and to research heat transfer applications for nuclear fusion reactors.

“I believe the Rhodes Scholarship will allow me to foster a stronger community amongst my fellow scholars because we will all be attending the same institution,” Mburu said in a statement.
Mburu is currently working with Gymama Slaughter , UMBC associate professor of computer science and electrical engineering, to develop a machine that ensures human organs remain healthy as they await transplant.
During her recent summer internship with Intel, Mburu developed an interactive model to estimate the cost of coatings applied to equipment. Her work helped improve pricing negotiations and established additional cost estimates for other chemical processes.

Her other areas of research have included:

  • Assessing phosphate’s effects on the ribosomal protein L4 as a student at Mount Hebron High School
  • Measuring the impurities found in the Large Hadron Collider particle accelerator, at the European Organization for Nuclear Research, Geneva, Switzerland

Mburu’s aspirations involve not just science but education advocacy. Her passion for STEM education and increasing diversity in STEM fields led to her current involvement as a MARC trainee, where she’s learned to communicate her desire to make a global impact through her science research and her efforts to remove barriers to education equality.

In her free time, Mburu has helped K-12 students with their homework during her time at UMBC. She continues to mentor youth and helps high school girls on STEM-related research projects.

The changing needs of a cell: No Membrane? No Problem!

Wed, 2018-01-03 10:21

Russian nesting dolls. Credit: iStock.

How “membrane-less” organelles help with key cellular functions

Scientists have long known that animal and plant cells have specialized subdivisions called organelles.  These organelles are surrounded by a semi-permeable barrier, called a membrane, that both organizes the organelles and insulates them from the rest of the cell’s mix of proteins, salt, and water.  This set-up helps to make cells efficient and productive, aiding in energy production and other specialized functions. But, because of their semi-permeable membranes, organelles can’t regroup and reform in response to stress or other outside changes. Cells need a rapid response team working alongside the membrane-bound organelles to meet these fluctuating needs. Until recently, who those rapid responders were and how they worked has been a mystery.

Recent research has led biologists to learn that the inside of a cell or an organelle is not just a lot of different molecules dissolved in water. Instead, we now know that cells contain many pockets of liquid droplets (one type of liquid surrounded by a liquid of different density) with specialized composition and function that are not surrounded by membranes. Because these “membrane-less organelles” are not confined, they can rapidly come together in response to chemical signals, such as those that indicate stress, and equally rapidly fall apart when they are no longer needed, or when the cell is about to divide. This enables membrane-less organelles to be “rapid responders” They can have complex, multilayered structures that help them to perform many critical cell functions with multiple steps, just like membrane-bound organelles. Scientists even suspect that the way these organelles form as droplets may shed light on how life on Earth first took shape (see sidebar below).

The Many Membrane-less Organelles

Scientists have identified more than a dozen membrane-less organelles at work in mammalian cells. Several kinds found inside the nucleus—including nuclear speckles, paraspeckles, and Cajal bodies—help with cell growth, stress response, the metabolizing (breaking down) of RNA, and the control of gene expression—the process by which information in a gene is used in the synthesis of a protein. Out in the cytoplasm, P-bodies, germ granules, and stress granules are membrane-less organelles that are involved in metabolizing or protecting messenger RNA (mRNA), controlling which mRNAs are made into proteins, and in maintaining balance, or homeostasis, of the cell’s overall health.
The nucleolus, located inside the nucleus, is probably the largest of the membrane-less organelles. It acts as a factory to assemble ribosomes, the giant molecular machines that “translate” messenger RNAs to make all cellular proteins.

The nucleolus is a large organelle without a membrane that forms in the cell nucleus. Scientists have learned that the nucleolus (pictured here) actually contains three layers, separated not by membranes but by differences in surface tension, much like a mixture of oil, water and certain types of alcohol will naturally settle into three layers. The rRNA starts in the central layer and works its way outward, receiving modifications along the way. The completed subunits travel out of the nucleus to the cytoplasm to assemble into ribosomes. Credit: NIGMS.

The rate that ribosomes are assembled allows cells to regulate their growth and activity. Behind this growth is the nucleolus. It can increase ribosome production to allow for more growth, such as when the cell is preparing to divide in two or halt ribosome production to respond to changes in the cell’s environment, such as those brought on by stress. Recently, scientists found that, at least in some animals, the nucleolus itself grows in parallel with the growth of both the cell and the organism. Its growth levels out as the organism reaches maturity, when the cell no longer needs an increasing number of ribosomes to produce proteins. As a membrane-less organelle, the nucleolus has the flexibility to respond quickly to changes in the cell’s environment. And with its prominent role in cell growth it’s believed to be at the center of many human diseases. For example, it may be a good target for cancer treatments, because out-of-control cell growth and enlarged nucleoli are hallmarks of cancer.

Free-Flowing Proteins
Imagine a lava lamp with its slowly flowing colored globules. Those drops of color can maintain clear separation from the surrounding liquid because they contain molecules that are electrostatically attracted to each other, like the static electricity that causes two socks just taken out of a dryer to weakly cling to each other. They condense to form a separate droplet, or phase. This is known as phase separation, and membrane-less organelles follow the same principle.

Lava lamp. Credit: Wikimedia Commons, Risa1029.

Membrane-less organelles only exist temporarily and there needs to be a mechanism to both bring them together (condense them) and separate them when they’re no longer needed. Richard Kriwacki and his colleagues at St. Jude Children’s Research Hospital in Memphis, Tennessee, have discovered that a protein called nucleophosmin (NPM1) helps the chemical building blocks of the nucleolus phase separate to form a droplet. NPM1 acts as a glue, forming loose networks with many different proteins and RNAs. The researchers believe such networks are necessary for the proteins and RNAs in the nucleolus to condense and separate in response to stress. These findings provide the first insights into the role of NPM1 in the molecular organization of the nucleolus. The next challenge is to understand how this organization promotes the production of ribosomes and helps the cell to respond to stressful situations.

Kriwacki and his colleagues also found recently that NPM1 is among the targets of toxic “repeat” polypeptides that are produced in amyotrophic lateral sclerosis (ALS, also known as Lou Gehrig’s disease) and other neurodegenerative diseases. The repeat polypeptides’ structure changes NPM1’s glue-like activity and interferes with the function of the nucleolus. These changes could lead to the rapid deterioration of nerve cells seen in such diseases.

Cell as cruise-director: keeping membrane-less organelles in line and under control

Although they appear to take shape spontaneously, membrane-less organelles are very much under the cell’s control. Cells can raise and lower the concentrations of key structural molecules to affect whether a droplet forms. Ashok Deniz and his colleagues at the Scripps Research Institute in La Jolla, California, recently studied the effects of different amounts of RNA on the formation of membrane-less ribonucleoprotein (RNP) granules, which are involved in regulating gene expression. The scientists found that while initial increases in RNA concentrations play a role in inducing granule formation, further increases in RNA can make the RNP granules dissolve. The phenomenon resembles using Elmer’s glue for an elementary school project: you need to add enough to get one piece of construction paper to stick to another piece, but if you add too much glue, both pieces turn into mush and the project is ruined. This RNA mechanism provides the cell with a simple way to control RNP granule activity. The study helps scientists learn more about how membrane-less organelles form in real cells as well as in artificial (man-made) cells. This could be important because there may be diseases where the treatment could be to ramp production of membrane-less organelles up or down.

Adding single-stranded RNA to synthetic peptides—or chains of amino acids—leads to the formation of RNP granules inside of cells. When RNA levels get too high, the granules are disrupted. Credit: The Scripps Research Institute.

From the Inside Out

Proteins and RNA pooling together, or “condensing,” in response to changing environmental conditions explains how a droplet can form through phase separation, but it doesn’t explain how these membrane-less organelles are able to do complex jobs. Organelle functions, such as ribosome assembly (see figure above), often involve several steps, and they benefit from a complex structure that can separate and organize these steps. Clifford Brangwynne, a biophysicist at Princeton University, and his colleagues found that the surface tension of droplets made of different mixtures of proteins may explain how membrane-less organelles self-organize to do even the most complicated jobs.
Studying the nucleolus, Brangwynne and his team discovered that each layer of proteins and rRNA formed its own droplet, with one nested inside another like a set of Russian matryoshka dolls. One layer did not mix with the others, even when the researchers removed the proteins from cells and tested them on microscope slide cover slips. The different droplets acted like oil and water, co-existing but not actually mixing.
The researchers then learned that the interactions between protein molecules in each layer helped determine each droplet’s surface tension. When a nucleolus forms, the center layer has the greatest surface tension, and each surrounding layer has progressively lower surface tension relative to its surroundings. Using a device that shuttles liquids through millimeter-sized channels and a new technology they developed called optoDroplet that uses light to induce phase transitions inside living cells, Brangwynne and his group will continue to uncover details about how the proteins in membrane-less organelles undergo phase separation so effectively and how precise protein interactions can be derailed in some diseases.

A new tool, the optoDroplet, lets scientists control the formation of membrane-less granules in living cells using light. As shown here, granules are slow to appear. Then as the light is increased, the number of granules grows dramatically, as if a switch has been turned on. The scientists are using this technique to study what happens when healthy granules appear and dissolve as well as how the process may change when the proteins gather into gels or solids, as they do in diseases such as ALS. Credit: Clifford Brangwynne lab.

 Disease Implications

As scientists learn how sensitive membrane-less organelles are to the changing conditions in a cell, they have become interested in these structures’ potential roles in disease. For example, if some proteins found in membrane-less organelles are altered, they can form a more gel-like droplet with less fluid structures. This may affect how well the organelles function, and how easily they can be disassembled, potentially contributing to heart and neurological conditions. Also, cancerous cells often contain bloated and oddly shaped nucleoli that overproduce ribosomes and contribute to cell growth and division that races out of control. Learning more about membrane-less organelles may lead to new ways to influence their function to treat such health conditions.
This research was funded in part by NIH under grants: R01GM115634, R01GM083159, R01GM066833, DP2GM105437, F32GM113290, T32GM007276, 7DP2GM119137-02, R01CA082491, DP2EB024247, U01DA040601, S10RR027425, P30CA021765, R35NS097974, R01AG047928, and R01NS056114.

Could This Be How Life First Took Shape?

Droplets of chemicals within a primordial soup can stretch and split (top row). The process can repeat (bottom row) to create new generations of droplets, in a process that mimics reproduction and reveals a possible way by which life on Earth first took shape. Credit: David Zwicker et al., Nature Physics, 2016.

In the early 2000s, scientists began to identify membrane-less organelles and describe how they form droplet structures. These discoveries reinvigorated a hypothesis put forth by Russian biochemist Alexander Oparin in 1924 that the first protocells—the forerunner of the first modern cell-like structures on Earth—were naturally forming liquid droplets rather than membrane-bound compartments. Oparin’s hypothesis received another boost in 2016 when German scientists reported “chemically active” liquid droplets, which cycle molecules in and out of the surrounding fluid and also grow to near cell size and divide, just like cells.

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