Unprecedented Views of HIV

Visualizations can give scientists unprecedented views of complex biological processes. Here’s a look at two new ones that shed light on how HIV enters host cells.

Animation of HIV’s Entry Into Host Cells

Screen shot of the video
This video animation of HIV’s entry into a human immune cell is the first one released in Janet Iwasa’s current project to visualize the virus’ life cycle. As they’re completed, the animations will be posted at http://scienceofhiv.org Exit icon.

We previously introduced you to Janet Iwasa, a molecular animator who’s visualized complex biological processes such as cells ingesting materials and proteins being transported across a cell membrane. She has now released several animations from her current project of visualizing HIV’s life cycle Exit icon. The one featured here shows the virus’ entry into a human immune cell.

“Janet’s animations add great value by helping us consider how complex interactions between viruses and their host cells actually occur in time and space,” says Wes Sundquist, who directs the Center for the Structural Biology of Cellular Host Elements in Egress, Trafficking, and Assembly of HIV Exit icon at the University of Utah. “By showing us how different steps in viral replication must be linked together, the animations suggest hypotheses that hadn’t yet occurred to us.”

To help other researchers explore complex biological processes, Iwasa and her colleagues recently launched Molecular Flipbook Exit icon, an open-source software toolkit for making molecular animations.

Model of HIV’s Surface Proteins

Model of HIV
This model of HIV was generated by a new software program called cellPACK. Credit: Graham Johnson and Ludovic Autin, The Scripps Research Institute.

Graham Johnson Exit icon, a medical illustrator for more than 15 years, created this model of an HIV particle using an open-source software program called cellPACK Exit icon that he developed as a graduate student at The Scripps Research Institute (TSRI).

The cellPACK visualizations reconcile experimental results about the distribution of “spike” proteins on the surface of the immature HIV viral particle. These proteins help the virus enter host cells. The cellPACK models reveal that the arrangement of the proteins is not random, as had been previously suggested. This conclusion, according to the research paper, shows the power of the software to simulate and interpret results from other studies. Plus, the improved understanding of the spike proteins will further elucidate the HIV life cycle and ways to disrupt it.

Getting a closer look at HIV is just one application of the software. In a news release about the software Exit icon, Art Olson, director of the HIV Interaction and Viral Evolution Center Exit icon at TSRI and Johnson’s graduate school advisor, says, “We hope to ultimately increase scientists’ ability to target any disease.”

Illuminating Biology

This time of year, lights brighten our homes and add sparkle to our holidays. Year-round, scientists funded by the National Institutes of Health use light to illuminate important biological processes, from the inner workings of cells to the complex activity of the brain. Here’s a look at just a few of the ways new light-based tools have deepened our understanding of living systems and set the stage for future medical advances.

RSV infected cell
A new fluorescent probe shows viral RNA (red) in an RSV-infected cell. Credit: Eric Alonas and Philip Santangelo, Georgia Institute of Technology and Emory University.

Visualizing Viral Activity

What looks like a colorful pattern produced as light enters a kaleidoscope is an image of a cell infected with respiratory syncytial virus (RSV) lit up by a new fluorescent probe called MTRIPS (multiply labeled tetravalent RNA imaging probes).

Although relatively harmless in most children, RSV can lead to bronchitis and pneumonia in others. Philip Santangelo of the Georgia Institute of Technology and Emory University, along with colleagues nationwide, used MTRIPS to gain a closer look at the life cycle of this virus.

Once introduced into RSV-infected cells, MTRIPS latched onto the genetic material of individual viral particles (in the image, red), making them glow. This enabled the researchers to follow the entry, assembly and replication of RSV inside the living cells. 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

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.

Cool Image: Of Surfaces and Stem Cells

Stem cells transform into neurons.
Stem cells grown on a soft surface begin to transform into neurons. Credit: Kiessling Lab, University of Wisconsin-Madison.

If you think this image looks like the fluorescent outline of a brain, you’re on the right track. The green threads show neurons that have just formed from unspecialized cells called stem cells.

Researchers led by Laura Kiessling Exit icon of the University of Wisconsin-Madison directed the stem cells to become neurons by changing the quality of the surface on which they grew. In experiments testing different gels used to grow stem cells in the lab, the scientists found that the stiffness of those gels influenced cell fate decisions.

When grown on a soft gel with a brain tissue-like surface, the stem cells began to transform into neurons. This happened without the addition of any of the proteins normally used to coax stem cells to specialize into different types of cells.

A better understanding of how stem cell fate is influenced by the mechanical properties of a surface could help researchers who are trying to harness the blank slate cells for tissue regeneration or other therapeutic uses.

This work also was funded by NIH’s National Institute of Biomedical Imaging and Bioengineering; National Heart, Lung, and Blood Institute; and National Institute of Neurological Disorders and Stroke.

Learn more:
University of Wisconsin-Madison News Release Exit icon

Cool Image: Training Cells to Devour Dying Neighbors

A healthy cell that has ingested dying cells.
A healthy cell (green) that has ingested dying cells (purple). Credit: Toru Komatsu, University of Tokyo.

In this image, a healthy cell (green) has engulfed a number of dying cells (purple) just as a predator might ingest wounded or dying prey. A team of researchers is hoping to use this same strategy at the cellular level to help treat infection, neurodegenerative diseases or cancer.

Our bodies routinely use a process called phagocytosis to rid themselves of unhealthy cells. Takanari Inoue Exit icon at Johns Hopkins University and collaborators at the University of Tokyo set out to investigate the molecular underpinnings of phagocytosis. Their goal was to endow laboratory-grown human cells with phagocytotic skills, namely the ability to recognize, swallow and digest dying cells. The scientists tried to do this by inserting into the cells two molecules known to play a role in phagocytosis.

The engineered cells accomplished the first two tasks—they recognized and surrounded dying cells. But they didn’t digest what they’d engulfed. Now the researchers are looking for a molecular trigger to get the engineered cells to complete this last task.

Eventually, the scientific team aims to build artificial cells that are programmed to target and destroy abnormal cells, such as those ravaged by bacteria, cancer or other diseases.

Learn more:
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How Cells Take Out the Trash Article from Inside Life Science
Cellular Suicide: An Essential Part of Life Article from Inside Life Science

Cool Image: Outsourcing Cellular Housekeeping

Mouse optic nerve and retina. Credit: Keunyoung Kim, Thomas Deerinck and Mark Ellisman, National Center for Microscopy and Imaging Research, UC San Diego.
This image shows the mouse optic nerve and retina. Credit: Keunyoung Kim, Thomas Deerinck and Mark Ellisman, National Center for Microscopy and Imaging Research Exit icon, UC San Diego.

In this image, the optic nerve (left) leaves the back of the retina (right). Where the retina meets the optic nerve, visual information begins its journey from the eye to the brain. Taking a closer look, axons (purple), which carry electrical and chemical messages, meet astrocytes (yellow), a type of brain cell. Recent research has found a new and surprising role for these astrocytes.

Biologists have long thought that all cells, including neurons, degrade and reuse pieces of their own mitochondria, the little powerhouses that provide energy to cells. Using cutting-edge imaging technology, researchers led by Mark Ellisman Exit icon of the University of California, San Diego, and Nicholas Marsh-Armstrong Exit icon of Johns Hopkins University have caught neurons in the mouse optic nerve in the act of passing some of their worn out mitochondria to neighboring astrocytes, which then did the dirty work of recycling.

The researchers also showed that neurons in other regions of the brain appear to outsource mitochondrial breakdown to astrocytes as well. They suggest that it will be important to confirm that this process occurs in other parts of the brain and to determine how possible defects in the outsourcing may contribute to or underlie neuronal dysfunction or neurodegenerative diseases.

This work also was funded by NIH’s National Eye Institute and National Institute on Drug Abuse.

Learn more:
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How Cells Take Out the Trash Article from Inside Life Science

Cool Video: How a Microtubule Builds and Deconstructs

A microtubule, part of the cell’s skeleton, builds and deconstructs. Credit: Eva Nogales lab, University of California, Berkeley.

In this animation, tubulin proteins snap into place like Lego blocks to build a microtubule, part of the cell’s skeleton. When construction ends, this long hollow cylinder falls to pieces from its top end. The breakdown is critical for many basic biological processes, including cell division, when rapidly shortening microtubules pull chromosomes into each daughter cell.

Until recently, scientists didn’t know exactly what drove microtubules to fall apart. A research team led by Eva Nogales of the Lawrence Berkeley National Laboratory and the University of California, Berkeley, now has an explanation.

Using high-powered microscopy, the scientists peered into the structure of a microtubule and found how a chemical reaction puts the stacking tubulin proteins under intense strain. The only thing keeping the proteins from springing apart is the pressure from the addition of more tubulin. So when assembly stops, the microtubule deconstructs.

The team also learned that Taxol, a common cancer drug, relieves this tension and allows microtubules to remain intact indefinitely. With microtubules frozen in place, a cancer cell cannot divide and eventually dies.

Because of this research, scientists now better understand both the success behind a common cancer drug and the molecular basis underlying the workings of microtubules.

Learn more:
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An Insider’s Look at Life: Magnified, an Airport Exhibit of Stunning Microscopy Images

Bubonic plague bacteria on part of the digestive system in a rat flea
What looks like pollen on petals is actually bubonic plague bacteria on the digestive spines of a flea, viewed through a powerful microscope. Credit: B. Joseph Hinnebusch, Elizabeth Fischer and Austin Athman, NIH’s National Institute of Allergy and Infectious Diseases.

Science. Art. Airports. I’ve never used those three words together before. But I’ve been doing it a lot lately while working on Life: Magnified, an exhibit of 46 striking scientific images created by scientists around the country using state-of-the-art microscopes.

The show is at Washington Dulles International Airport, where more than a million travelers will see it over its 6-month run. As our director said in a recent post on another NIGMS blog, “What a great way to share the complexity and beauty of biomedical science with such a large public audience!”

We’ve also set up an online gallery, where the colorful images can be viewed and freely downloaded for research, educational and news media purposes.

The project itself was quite an adventure. When we asked scientists to send us images, our fears of not getting enough attractive, high-resolution options were drowned by a deluge of more than 600 submissions. Then we worried how to sort through them all and make final selections. Doing so required several rounds of online viewing, various ranking systems and a panel of experts. Then the images were printed as large, digital negatives on transparency film.

Artist's rendition of a network diagram. Credit: Allison Kudla, Institute for Systems Biology.
The midnight installation of Life: Magnified involved five people (that’s me in pink), a ladder and lots of rags and glass cleaner. Credit: Woody Machalek.

Dulles is a pretty busy place, so we set up the exhibit when it was quietest—the middle of the night (10 p.m. to 1:30 a.m., to be exact). We swapped out images from the previous photography exhibit and installed the Life: Magnified ones in LED lightboxes mounted in the airport’s Gateway Gallery. It was an eerie and exhilarating feeling to be in a noiseless, nearly empty airport without heavy bags and a long walk to a departure gate.

Less than 12 hours later, I was surprised to receive an e-mail from someone who had passed through the exhibit and sent a few photos. He called the images “stunning.” Similar sentiments were expressed by Science Exit icon, NBC News online Exit icon, The Atlantic Exit icon, The Washington Post Exit icon, National Geographic Exit icon and other publications.

Now I’m being asked about next steps, including whether the exhibit will travel. We’re investigating a variety of options. For now, I hope you’re able to see the exhibit in person. If not, take a look at the images online and see which ones you enjoy most.

Cool Image: Researching Regeneration in a Model Organism

The isolated feeding tube of a flatworm.

The feeding tube, or pharynx, of a planarian worm with cilia shown in red and muscle fibers shown in green. Credit: Carrie Adler/Stowers Institute for Medical Research.

This rainbow-hued image shows the isolated feeding tube, or pharynx, of a tiny freshwater flatworm called a planarian, with the hairlike cilia in red and muscle fibers in green. Scientists use these wondrous worms, which have an almost infinite capacity to regrow all organs, as a simple model system for studying regeneration. A research team led by Alejandro Sánchez Alvarado of the Stowers Institute for Medical Research exploited a method known as selective chemical amputation to remove the pharynx easily and reliably. This allowed the team to conduct a large-scale genetic analysis of how stem cells in a planaria fragment realize what’s missing and then restore it. The researchers initially identified about 350 genes that were activated as a result of amputation. They then suppressed those genes one by one and observed the worms until they pinpointed one gene in particular—a master regulator called FoxA—whose absence completely blocked pharynx regeneration. Scientists believe that researching regeneration in flatworms first is a good way to gain knowledge that could one day be applied to promoting regeneration in mammals.

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