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.

The researchers call the new technology SCRIBE, for Synthetic Cellular Recorders Integrating Biological Events. It’s not only able to detect the presence of a chosen signal, but also the magnitude and duration of exposure.

SCRIBE could be used to indicate chemical contaminants, pollutants or other substances in the environment. Conceivably, it could also serve as a sensor for virtually any molecule in the body—blood proteins, dietary products, immune factors, hormones, disease markers, pharmaceuticals, toxins—to monitor health, detect disease and track the progress of countless medical conditions.

If you’re interested in SCRIBE’s technical details, which include harnessing an enzyme from another type of bacteria, producing a specific RNA-DNA hybrid and generating single-stranded DNA containing the desired mutation, you can read a perspective Exit icon on the paper or watch an animation Exit icon of the process.

This work was funded in part by NIH under grants P50GM098792 and DP2OD008435.

Forecasting Infectious Disease Spread with Web Data

Just as you might turn to Twitter or Facebook for a pulse on what’s happening around you, researchers involved in an infectious disease computational modeling project are turning to anonymized social media and other publicly available Web data to improve their ability to forecast emerging outbreaks and develop tools that can help health officials as they respond.

Mining Wikipedia Data

Screen shot of the Wikipedia site
Incorporating real-time, anonymized data from Wikipedia and other novel sources of information is aiding efforts to forecast and respond to emerging outbreaks. Credit: Stock image.

“When it comes to infectious disease forecasting, getting ahead of the curve is problematic because data from official public health sources is retrospective,” says Irene Eckstrand of the National Institutes of Health, which funds the project, called Models of Infectious Disease Agent Study (MIDAS). “Incorporating real-time, anonymized data from social media and other Web sources into disease modeling tools may be helpful, but it also presents challenges.”

To help evaluate the Web’s potential for improving infectious disease forecasting efforts, MIDAS researcher Sara Del Valle of Los Alamos National Laboratory conducted proof-of-concept experiments involving data that Wikipedia releases hourly to any interested party. Del Valle’s research group built models based on the page view histories of disease-related Wikipedia pages in seven languages. The scientists tested the new models against their other models, which rely on official health data reported from countries using those languages. By comparing the outcomes of the different modeling approaches, the Los Alamos team concluded that the Wikipedia-based modeling results for flu and dengue fever performed better than those for other diseases. Continue reading

Field Focus: Bringing Biology Into Sharper View with New Microscopy Techniques

Composite image of mitochondria in a cell
In this composite image of mitochondria in a cell, the left panel shows a conventional optical microscopy image, the middle panel shows a three-dimensional (3-D) STORM image with color indicating depth, and the right panel shows a cross-section of the 3-D STORM image. Credit: Xiaowei Zhuang laboratory, Howard Hughes Medical Institute, Harvard University. View larger image.

Much as a photographer brings distant objects into focus with a telephoto lens, scientists can now see previously indistinct cellular components as small as a few billionths of a meter (nanometers). By overcoming some of the limitations of conventional optical microscopy, a set of techniques known as super-resolution fluorescence microscopy has changed once-blurry images of the nanoworld into well-resolved portraits of cellular architecture, with details never seen before in biology. Reflecting its importance, super-resolution microscopy was recognized with the 2014 Nobel Prize in chemistry.

Using the new techniques, scientists can observe processes in living cells across space and time and study the movements, interactions and roles of individual molecules. For instance, they can identify and track the proteins that allow a virus to invade a cell or those that enable tumor cells to migrate to distant parts of the body in metastatic cancer. The ability to analyze individual molecules, rather than collections of molecules, allows scientists to answer longstanding questions about cellular mechanisms and behavior, such as how cells move along a surface or how certain proteins interact with DNA to regulate gene activity. Continue reading

Meet Alfred Atanda Jr.

Alfred Atanda Jr.
Credit: Cynthia Brodoway, Nemours/Alfred I. duPont
Hospital for Children
Alfred Atanda Jr.
Fields: Pediatric orthopedic surgery, sports medicine
Works at: Nemours/Alfred I. duPont Hospital for Children
Blogs: as Philly.com’s Sports Doc at http://bit.ly/sportsdoc Exit icon
Family fact: Youngest of seven children
Musical skills: Piano and trumpet
Kitchen talent: Baking chocolate desserts for his pediatrician wife and their two young children

As a kid, Alfred Atanda loved science, sports and tinkering. He dreamed of being a construction worker or an engineer. Today, he works on one of the most complex construction projects of all: the human body.

As a pediatric orthopedic surgeon, Atanda focuses on sports medicine and injuries to children. He has a special passion for young baseball pitchers who have torn the ulnar collateral ligament (UCL) in the elbow of their throwing arm.

This sort of injury is most often caused by overuse. Many small tears accumulate over a long period, resulting in pain and slower, less accurate pitches. Decades ago, this sort of damage occurred almost exclusively in elite athletes. Now, Atanda sees it in children as young as 12 years old. He aims not only to study and treat these injuries, but also to find ways to prevent them.

His Findings

Atanda was first introduced to research on UCL injuries while working alongside team physicians for the Phillies, the professional baseball team in Philadelphia. The physicians wanted to determine whether ultrasound imaging could detect early warning signs—slight anatomical changes in the ligament—before the damage became severe enough to warrant an operation known as Tommy John surgery.

The research focused on Phillies pitchers who had no pain or other symptoms of injury. The multi-year project showed that the UCL in the throwing elbows of these players got progressively thicker and weaker compared to the same ligament in the players’ nonthrowing elbows. The scientists concluded that these physical changes are caused by prolonged exposure to professional-level pitching.

Alfred Atanda Jr. with Joe Piergrossi
Atanda examines the elbow of a young patient. Courtesy: Cynthia Brodoway, Nemours/Alfred I. duPont Hospital for Children

Atanda wondered whether ultrasound imaging could also detect early signs of UCL damage in young pitchers—those in Little League through high school. There has been a dramatic rise in the number of young pitchers who are experiencing the same injuries and undergoing the same surgery as the pros.

Atanda secured funding for this project from an Institutional Development Award (IDeA). The IDeA program builds research capacities in states like Delaware, where Atanda works, that historically have received low levels of funding from the National Institutes of Health.

Atanda’s project began about a year ago, and has examined 55 young athletes so far.

“We found similar results to what we found with the Phillies,” Atanda says, indicating that the UCL in the throwing elbows of young athletes was noticeably thicker than the UCL in the nonthrowing elbows. And the damage seems progressive, he says: “We saw that these ligaments got thicker as the pitchers got older and had more pitching experience.”

The immediate goal of this project, which he hopes to continue for another 3 years, is prophylaxis. “We’re trying to prevent any kind of overuse elbow injuries and the need for Tommy John surgeries later on,” Atanda says. He also hopes to establish quantitative correlations between pitching behavior and anatomical changes.

Atanda also has longer-term aspirations. “My goal is to change the culture in sports for young athletes in general,” he says. “I want to show there are downsides to pitching so much.”

In addition to championing pitch count limits Exit icon recommended by the American Sports Medicine Institute, Atanda advises a focus away from excess competition and toward getting exercise, enjoying social inter­action, building self-confidence and having fun.

Atanda’s research is funded by the National Institutes of Health through grant P20GM103464

Content adapted from the NIGMS Findings magazine article Game Changer

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.

Molecules Known to Damage Cells May Also Have Healing Power

Free radicals in an ying-yang symbol
Biology in balance: Molecules called free radicals—like the peroxide molecules illustrated here—have a reputation for being dangerous. Now, they’ve revealed healing powers. In worms, at least. Credit: Stock image

When our health is concerned, some molecules are widely labeled “good,” while others are considered “bad.” Often, the truth is more complicated.

Consider free radical molecules. These highly reactive, oxygen-containing molecules are well known for damaging DNA, proteins and other molecules in our bodies. They are suspected of contributing to premature aging and cancer. But now, new research shows they might also have healing powers Exit icon.

Using the oft-studied laboratory roundworm known as C. elegans, a research group led by Andrew Chisholm Exit icon at the University of California, San Diego, made a surprising discovery. Free radicals, specifically those made in cell structures called mitochondria, appear necessary for skin wounds to heal. In fact, higher (but not dangerously high) levels of the molecules can actually speed wound closure.

If further research shows the same holds true in humans, the work could point to new ways to treat hard-to-heal wounds, like diabetic foot ulcers.

This work was funded in part by NIH under grants R01GM054657 and P40OD010440.

Cells by the Numbers

Cells are the basic unit of life—and the focus of much scientific study and classroom learning. Here are just a few of their fascinating facets.

3.8 billion

Nerve Cells
Developing nerve cells, with the nuclei shown in yellow. Credit: Torsten Wittmann, University of California, San Francisco.

That’s how many years ago scientists believe the first known cells originated on Earth. These were prokaryotes, single-celled organisms that do not have a nucleus or other internal structures called organelles. Bacteria are prokaryotes, while human cells are eukaryotes.

0.001 to 0.003

This is the diameter in centimeters of most animal cells, making them invisible to the naked eye. There are some exceptions, such as nerve cells that can stretch from our hips to our toes, sending electrical signals throughout the body.

1665

Red blood Cells
Oxygen-transporting red blood cells. Credit: Dennis Kunkel, Dennis Kunkel Microscopy, Inc.

In that year, British scientist Robert Hooke coined the term cell to describe the porous, grid-like structure he saw when viewing a thin slice of cork under a microscope. Today, scientists study cells using a variety of high-tech imaging equipment as well as rainbow-colored dyes and a green fluorescent protein derived from jellyfish.

200

That’s how many different types of cells are in the human body, including those in our skin, muscles, nerves, intestines, blood and bones.

3 to 5

Believe it or not, that’s the approximate number of pounds of bacteria you’re carrying around, depending on your size. Even though bacterial cells greatly outnumber ours, they’re much smaller than our cells and therefore account for less than 3 percent of our body mass. Scientists are learning more about how our body bacteria contribute to our health.

24

Snapshot of a phase of the cell cycle.
A snapshot of a phase of the cell cycle. Credit: Jean Cook and Ted Salmon, UNC School of Medicine.

This is the typical length in hours of the animal cell cycle, the time from a cell’s formation to when it splits in two to make more cells.

120

That’s the approximate lifespan in days of a human red blood cell. Other cell types have different lifespans, from a few weeks for some skin cells to as long as the life of the organism for healthy neurons.

50 to 70 billion

Each day, approximately this many cells die in the human body as part of a normal process that serves a healthy and protective role. Those that die in the largest numbers are skin cells, blood cells and some cells that line structures like organs and glands.

Get stats on what scientists have learned so far about genetics.

Learn more:

Inside the Cell Booklet
Studying Cells Fact Sheet

Asking Our Expert About Modeling Ebola

Irene Eckstrand
NIGMS’ Irene Eckstrand answers questions about modeling Ebola. Credit: National Institute of General Medical Sciences.

Ebola is the focus of many NIH-supported research efforts, from analyzing the genetics of virus samples to evaluating the safety and effectiveness of treatments and vaccines. Researchers involved in our Models of Infectious Disease Agent Study, or MIDAS, have been using computational methods to forecast the potential course of the outbreak and the impact of various intervention strategies.

Wondering how their work is going, I recently asked our modeling expert Irene Eckstrand a few questions.

How useful are the forecasts?

Forecasts give us a range of possible outcomes. In addition to being a useful public health tool to prepare for an outbreak, they’re an important research tool to test assumptions about how a disease may spread. When we compare the predicted and actual outcomes, we can confirm assumptions, such as the groups of individuals who are more likely to spread the infection to others. Continually doing this helps refine the models and ensure that their forecasts are as accurate as possible.

What are some of the challenges the modelers face?

Ebola virus
Ebola virus particles (green) attached to and budding from a cell (blue). Credit: National Institute of Allergy and Infectious Diseases.

We need data to build and test models. The data available from this outbreak have been more limited than in most previous outbreaks of Ebola simply because the public health systems are overwhelmed with sick people, and recording information is a secondary priority.

Another issue with forecasting future trends is incorporating information about the deployment of resources and the implementation of interventions that actually slowed the outbreak. We also need to incorporate changes in people’s behavior. If people think an outbreak is leveling off, they may relax the precautions they’ve been taking—and that could lead to another spike in the disease.

What other Ebola-related projects are the MIDAS modelers working on?

The MIDAS researchers are:

  • Modeling logistical factors such as the number and placement of treatment beds and staffing needs.
  • Tracking potential transmission within and between communities and at hospitals and funerals.
  • Developing a method to estimate the amount of underreporting of case data.
  • Applying models of “tipping points” to look for evidence that the disease curve is slowing.
  • Estimating the number of people who are infected but not symptomatic.
  • Creating new resources for Ebola modelers, including standards for using infectious disease data.
  • Calculating the risk of importation of cases for a wide variety of countries based on travel networks.

How are the modelers working together?

The MIDAS modelers conference call 1-2 times a week to discuss results, modeling strategies, data sources and questions amenable to modeling. They also participate in discussions with government and other academic groups, so there’s a sizable number of modelers working on a wide variety of public health, logistical and basic research questions.

If you’re interested in learning more about Ebola, Irene recommends a video overview of the 2014 outbreak from Penn State University Exit icon and a slide presentation on the myths and realities of the disease from Nigeria’s Kaduna State University Exit icon.

Cool Image: Snap-Together Laboratory

Modular microfluidics system

Modular microfluidics system. Credit: University of Southern California Viterbi School of Engineering.

Like snapping Lego blocks together to build a fanciful space station, scientists have developed a new way to assemble a microfluidics system, a sophisticated laboratory tool for manipulating small volumes of fluids.

Microfluidics systems are used by scientists to perform tasks as diverse as DNA analysis, microbe detection and disease diagnosis. Traditionally, they have been slow and expensive to produce, as each individual “lab on a chip” had to be built from scratch in a special facility.

Now, researchers including Noah Malmstadt Exit icon of the University of Southern California have harnessed 3-D printing technology to create a faster, cheaper, easier-to-use system Exit icon. The team first identified the smallest functional pieces of a microfluidics system. Each of these pieces performs one simple task like detecting the size of fluid droplets or mixing two fluids together. After 3-D printing individual components, the team showed that they could be snapped together by hand into a working system in a matter of hours. The individual pieces can be pulled apart and re-assembled as needed before use in an actual experiment, which was impossible with the traditional microfluidics systems.

The researchers have created eight block-like components so far. They hope to start an online community where scientists will share designs for additional components in an open-source database, helping to speed further development of the technology.

This work was funded in part by NIH under grant R01GM093279.

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