Remotely and Noninvasively Controlling Genes and Cells in Living Animals

Remote control car key.
Researchers are developing a system to remotely control genes or cells in living animals with radio wave technology similar to that used to operate remote control car keys. Credit: Stock image.

One of the items on biomedical researchers’ “to-do” list is devising noninvasive ways to control the activity of specific genes or cells in order to study what those genes or cells do and, ultimately, to treat a range of human diseases and disorders.

A team of scientists recently reported progress on a new, noninvasive system that could remotely and rapidly control biological targets in living animals Exit icon. The system can be activated remotely using either low-frequency radio waves or a magnetic field. Similar radio wave technology operates automatic garage-door openers and remote control car keys and is used in medicine to control electronic pacemakers noninvasively. Magnetic fields are used to activate sensors in burglar alarm systems and to turn your laptop to hibernate mode when the cover is closed.

One of the two components of the new system is a natural iron storage particle called ferritin. This particle is tethered to a temperature-sensitive channel protein that controls the flow of calcium into a cell. Together, the two molecules work as a nano-machine that can be used to trigger gene activity, or expression, in cells. When the ferritin particle is exposed to radio waves or a magnetic field, it opens the channel, activating a gene engineered to respond to calcium.

The researchers found that radio waves and magnets may have different ways of causing the calcium channel to open. Low-frequency radio waves cause mild heating of the ferritin’s iron core, tripping a switch that opens the channel, while the tug of a magnetic field most likely causes the ferritin particles to move slightly and nudge the channel open. Calcium then flows into the cell and turns on the calcium-responsive gene.

As proof of principle, the team, led by Jeffrey Friedman Exit icon at Rockefeller University and Jonathan Dordick Exit icon at Rensselaer Polytechnic Institute, showed that they could use their system to turn on insulin production and thereby lower blood sugar in diabetic mice. The researchers used genetic techniques to introduce the ferritin-tethered channels into mice along with a calcium-responsive version of the insulin gene.

In a news release, Friedman says that the system could potentially be used to control the production of a missing protein in conditions like hemophilia or to control neural activity in the brain. Indeed, another member of the research team, Sarah Stanley of Rockefeller University, is leading a follow-up study to adapt the system to switch neurons on and off so she can study their roles within the brain.

While other techniques exist for remotely controlling gene expression or cell activity in living animals, those methods have limitations. Systems that use light as an on/off signal require permanent implants or are only effective close to the skin, and those that rely on drugs can be slow to switch on and off.

In a commentary on the new study, Ingo Leibiger and Per-Olof Berggren of Sweden’s Karolinska Institute write: “A genetically encoded switch to control biological systems in the living organism by either low-frequency radio waves or by a magnetic field is an exciting noninvasive approach with many potential applications.”

This research was funded in part by NIH under grants R01GM095654 and T32GM067545.

Delivering Gene-Editing Proteins to Living Cells

Illustration of a DNA strand being cut by a pair of scissors.
Researchers are testing new ways to get gene editing proteins into living cells to potentially modify human genes associated with disease. Credit: Stock image.

Over the last two decades, exciting tools have emerged that allow researchers to cut and paste specific sequences of DNA within living cells, a process called gene editing. These tools, including one adapted from a bacterial defense system called CRISPR, have energized the research community with the possibility of using them to modify human genes associated with disease.

A major barrier to testing medical applications of gene editing has been getting the proteins that do the cutting into the cells of living animals. The main methods used in the laboratory take a roundabout route: Researchers push the DNA templates for making the proteins into cells, and then the cells’ own protein factories produce the editing proteins.

Researchers led by David Liu Exit icon from Harvard University are trying to cut out the middleman, so to speak, by ferrying the editing proteins, not the DNA instructions, directly into cells. In a proof-of-concept study, their system successfully delivered three different types of editing proteins into cells in the inner ears of live mice. Continue reading

E. Coli Bacteria as Medical Sensors and Hard Drives?

E.Coli
Modified E. coli bacteria can serve as sensors and data storage devices for environmental and medical monitoring. Credit: Centers for Disease Control and Prevention. View larger image

E. coli bacteria help us digest our food, produce vitamin K and have served as a model organism in research for decades. Now, they might one day be harnessed as environmental or medical sensors and long-term data storage devices Exit icon.

MIT researchers Timothy Lu Exit icon and Fahim Farzadfard modified the DNA of E. coli cells so that the cells could be deployed to detect a signal (for example, a small molecule, a drug or the presence of light) in their surroundings. To create the modified E. coli, the scientists inserted into the bacteria a custom-designed genetic tool.

When exposed to the specified signal, the tool triggers a series of biochemical processes that work together to introduce a single mutation at a specific site in the E. coli’s DNA. This genetic change serves to record exposure to the signal, and it’s passed on to subsequent generations of bacteria, providing a continued record of exposure to the signal. In essence, the modified bacteria act like a hard drive, storing biochemical memory for long periods of time. The memory can be retrieved by sequencing the bacteria or through a number of other laboratory techniques. Continue reading

Correcting a Cellular Routing Error Could Treat Rare Kidney Disease

AGT protein and peroxisomes in untreated and treated cells.
The altered AGT protein (red) and peroxisomes (green) appear in different places in untreated cells (top), but they appear together (shown in yellow) in cells treated with DECA (bottom). Credit: Carla Koehler/Reproduced with permission from Proceedings of the National Academy of Sciences USA. View larger image.

Our cells have organized systems to route newly created proteins to the places where they’re needed to do their jobs. For some people born with a rare and potentially fatal genetic kidney disorder called PH1, a genetically altered form of a particular protein mistakenly ends up in mitochondria instead of in another organelle, the peroxisome. This cellular routing error of the AGT protein results in the harmful buildup of oxalate, which leads to kidney failure and other problems at an early age.

In new work led by UCLA biochemist Carla Koehler Exit icon, researchers used a robotic screening system to identify a compound that interferes with the delivery of proteins to mitochondria. Koehler’s team Exit icon showed that adding a small amount of the compound, known as DECA, to cells grown in the laboratory prevented the altered form of the AGT protein from going to the mitochondria and sent it to the peroxisome. The compound also reduced oxalate levels in a cell model of PH1.

The team’s findings suggest that DECA, which is already approved by the Food and Drug Administration for treating certain bacterial infections, could be a promising candidate for treating children affected by PH1. And, Koehler notes, the screening strategy that she and her team used to identify DECA as a potential therapy may help researchers identify other new therapies for the disorder.

This work was funded in part by NIH under grant R01GM061721.

How Instructions for Gene Activity Are Passed Across Generations

C. elegans embryos
Images of C. elegans embryos show transmission of an epigenetic mark (green) during cell division from a one-cell embryo (left) to a two-cell embryo (right). Credit: Laura J. Gaydos.

Chemical tags that cells attach to DNA or to DNA-packaging proteins across the genome—called epigenetic marks—can alter gene activity, or expression, without changing the underlying DNA code. As a result, these epigenetic changes can influence health and disease. But it’s a matter of debate as to whether and how certain epigenetic changes on DNA-packaging proteins can be passed from parents to their offspring.

In studies with a model organism, the worm C. elegans, researchers led by Susan Strome Exit icon of the University of California, Santa Cruz, have offered new details that help resolve the debate.

Strome’s team created worms with a genetic change that knocks out the enzyme responsible for making a particular methylation mark, a type of epigenetic mark that can turn off gene expression at certain points of an embryo’s development. Then the scientists bred the knockout worms with normal ones. Looking at the chromosomes from the resulting eggs, sperm and dividing cells of embryos after fertilization, the researchers found that the methylation marks are passed from both parents to offspring. The enzyme, however, is passed to the offspring just by the egg cell. For embryos with the enzyme, the epigenetic marks are passed faithfully through many cell divisions. For those without it, the epigenetic mark can be passed through a few cell divisions.

Because all animals use the same enzyme to create this particular methylation mark, the results have implications for parent-to-child epigenetic inheritance as well as cell-to-cell inheritance in other organisms.

This work was funded in part by NIH under grants R01GM034059, T32GM008646 and P40OD010440.

Learn more:

University of California, Santa Cruz News Release Exit icon
Dynamic DNA Section from The New Genetics Booklet

Stem Cells Do Geometry

Human embryonic cells
As seen under a microscope, human embryonic cells (colored dots) confined to circles measuring 1 millimeter across start to specialize and form distinct layers similar to those seen in early development. Credit: Aryeh Warmflash, Rockefeller University. View larger image

Each fluorescent point of light making up the multicolored rings in this image is an individual human embryonic cell in the early stages of development. Scientists seeking to understand the molecular cues responsible for early embryonic patterning found that human embryonic cells confined to areas of precisely controlled size and shape begin to specialize, migrate and organize into distinct layers just as they would under natural conditions.

Read the Inside Life Science article to learn more about this research, which has opened a new window for studying early development and could advance efforts aimed at using human stem cells to replace diseased cells and regenerate lost or injured body parts.

 

4 Timely Facts About Our Biological Clocks

Illustration of circadian rhythm.
Genes and proteins run biological clocks that help keep daily rhythms in synch. Credit: Wikimedia Commons. View larger image

After you roll your clocks back by an hour this Sunday, you may feel tired. That’s because our bodies—more specifically, our circadian rhythms—need a little time to adjust. These daily cycles are run by a network of tiny, coordinated biological clocks.

NIGMS’ Mike Sesma tracks circadian rhythm research being conducted in labs across the country, and he shares a few timely details about our internal clocks:

1. They’re incredibly intricate.

Biological clocks are composed of genes and proteins that operate in a feedback loop. Clock genes contain instructions for making clock proteins, whose levels rise and fall in a regular cyclic pattern. This pattern in turn regulates the activity of the genes. Many of the results from circadian rhythm research this year have uncovered more parts of the molecular machinery that fine-tune the clock. Earlier in the month, we blogged about an RNA molecule that cues the internal clock.

2. Every organism has them—from algae to zebras.

Many of the clock genes and proteins are similar across species, allowing researchers to make important findings about human circadian processes by studying the clock components of organisms like fruit flies, bread mold and plants.

3. Whether we’re awake or asleep, our clocks keep ticking.

While they might get temporarily thrown off by changes in light or temperature, our clocks usually can reset themselves.

4. Nearly everything about how our body works is tied to biological clocks.

Our clocks influence alertness, hunger, metabolism, fertility, mood and other physiological conditions. For this reason, clock dysfunction is associated with various disorders, including insomnia, diabetes and depression. Even drug efficacy has been linked to our clocks: Studies have shown that some drugs might be more effective if given earlier in the day.

Learn more:
Circadian Rhythms Fact Sheet
Resetting Our Clocks: New Details About How the Body Tells Time Article from Inside Life Science

Outwitting Antibiotic Resistance

Marine scene with fish and corals
The ocean is a rich source of microbes that could yield infection-fighting natural molecules. Credit: National Oceanic and Atmospheric Administration Exit icon.

Antibiotics save countless lives and are among the most commonly prescribed drugs. But the bacteria and other microbes they’re designed to eradicate can evolve ways to evade the drugs. This antibiotic resistance, which is on the rise due to an array of factors, can make certain infections difficult—and sometimes impossible—to treat.

Read the Inside Life Science article to learn how scientists are working to combat antibiotic resistance, from efforts to discover potential new antibiotics to studies seeking more effective ways of using existing ones.

 
 

An RNA Molecule That Cues the Internal Clock

Clock
Dysfunction in our internal clocks may lead to insufficient sleep, which has been linked to an increased risk for chronic diseases. Credit: Stock image.

Our internal clocks tell us when to sleep and when to eat. Because they are sensitive to changes in daytime and nighttime cues, they can get thrown off by activities like traveling across time zones or working the late shift. Dysfunction in our internal clocks may lead to insufficient sleep, which has been linked to an increased risk for chronic diseases like high blood pressure, diabetes, depression and cancer.

Researchers led by Yi Liu Exit icon of the University of Texas Southwestern Medical Center have uncovered a previously unknown mechanism by which internal clocks run and are tuned to light cues. Using the model organism Neurospora crassa (a.k.a., bread mold), the scientists identified a type of RNA molecule called long non-coding RNA (lncRNA) that helps wind the internal clock by regulating how genes are expressed. When it’s produced, the lncRNA identified by Liu and his colleagues blocks a gene that makes a specific clock protein.

This inhibition works the other way, too: The production of the clock protein blocks the production of the lncRNA. This rhythmic gene expression helps the body stay tuned to whether it’s day or night.

The researchers suggest that a similar mechanism likely exists in the internal clocks of other organisms, including mammals. They also think that lncRNA-protein pairs may contribute to the regulation of other biologic processes.

Learn more:
University of Texas Southwestern Medical Center News Release Exit icon
Circadian Rhythms Fact Sheet
Resetting Our Clocks: New Details About How the Body Tells Time Article from Inside Life Science
Remarkable RNAs Article from Inside Life Science

Meet Scott Poethig

Scott Poethig
Fields: Plant biology, cell and developmental biology, genetics
Works at: University of Pennsylvania
Studied at: College of Wooster, Yale University
Favorite musicians: Nick Drake and Bruce Springsteen
High school job: Radio D.J.
Favorite book: “The Little Prince,” by Antoine de Saint-Exupéry

When Scott Poethig signed up for a developmental biology course in his senior year of college, he expected to learn how organisms transition from single cells to juveniles to adults. He did not expect to learn just how much scientists still didn’t know about this process.

“It was the first course I had taken as an undergraduate where I felt that I could ask a question that there wasn’t an answer to already,” he recalls. “I thought, ‘Wow! This is amazing.’”

Poethig already had an interest in plant biology and an independent research project studying corn viruses. He immediately saw the potential in combining his knowledge of plants with his questions about how organisms grow. “There seemed to be a lot of low hanging fruit in plant development,” he says.

Today, Poethig is the head of a plant development lab at the University of Pennsylvania. His work probes the complex molecular mechanisms that drive the transition from a young seedling to an adult plant that hasn’t yet produced seeds.

“The analogous period in human development is the interval between birth and puberty,” he explains. “People think of puberty as the major developmental transition in postnatal human development, but a lot of change happens before that point.”

His Findings

Poethig discovered that for the mustard plant Arabidopsis, a model organism frequently studied by geneticists, change begins early. Before these plants begin to flower—a sign of reproductive maturity—they undergo a process of vegetative maturation. In Arabidopsis, Poethig found that juvenile plants can be distinguished from adult plants by where hairs are produced on a leaf. Juvenile plants only produce hairs on the upper surface of the leaf, whereas adult plants produce leaves with hairs on both the upper and lower surfaces.

By studying mutant Arabidopsis plants where the adult pattern of hair development is either delayed or advanced, Poethig identified microRNAs as key players in this developmental transition.

MicroRNA molecules commonly block the expression of specific genes. Poethig found that in Arabidopsis, a type of microRNA prevents development. Young plants have high levels of this microRNA and cannot fully mature. When those levels drop, plants progress to adulthood.

MicroRNAs similarly control development in the nematode C. elegans. Scientists study the genetics of this tiny worm to better understand related developmental processes in more complex organisms. Because plants also use microRNAs to regulate development, Poethig’s discoveries may contribute to our understanding of how these molecules govern development in animals, including humans.

Poethig now wants to learn what determines the timing of developmental changes. He asks: “Why do microRNA levels drop? What’s the signal that causes that? What is the plant measuring?” His current hypothesis: sugar.

In a recent study, he found that giving plants additional sugar reduced microRNA levels and sped up development. Meanwhile, mutant plants that couldn’t produce enough sugar on their own through photosynthesis had increased microRNA levels and delayed development compared to normal plants.

This research may one day advance our understanding of how nutrition and genetics interact to affect human development. “In essentially all organisms, aging and the timing of developmental processes are strongly affected by nutrition,” Poethig explains. “In humans, childhood obesity is sometimes associated with early puberty, and it is important to understand the molecular basis for this effect.”

Poethig believes that studying microRNAs in plants may also lead to discoveries in human genetics outside of developmental biology. “MicroRNAs control a wide range of gene activity in plants and animals,” Poethig explains. “In humans, these molecules control the activity of as many as 30 percent of our genes. So understanding how microRNAs work in plants could help us understand their function in humans.”

Besides studying the Arabidopsis plants in his lab, Poethig also studies the plants in his kitchen, and uses his fascination with the history, culture and politics of food to excite others about science. Watch video.