Cool Tools: Pushing the Limits of High-Resolution Microscopy

Cell biologists would love to shrink themselves down and actually see, touch and hear the inner workings of cells. Because that’s impossible, they have developed an ever-growing collection of microscopes to study cellular innards from the outside. Using these powerful tools, researchers can exhaustively inventory the molecular bits and pieces that make up cells, eavesdrop on cellular communication and spy on cells as they adapt to changing environments.

In recent years, scientists have developed new cellular imaging techniques that allow them to visualize samples in ways and at levels of detail never before possible. Many of these techniques build upon the power of electron microscopy (EM) to see ever smaller details.

Unlike traditional light microscopy, EM uses electrons, not light, to create an image. To do so, EM accelerates electrons in a vacuum, shoots them out of an electron gun and focuses them with doughnut-shaped magnets onto a sample. When electrons bombard the sample, some pass though without being absorbed while others are scattered. The transmitted electrons land on a detector and produce an image, just as light strikes a detector (or film) in a camera to create a photograph.

This image, showing a single protein molecule, is a montage. It was created to demonstrate how dramatically cryo-EM has improved in recent years. In the past, cryo-EM was only able to obtain a blobby approximation of a molecule’s shape, like that shown on the far left. Now, the technique yields exquisitely detailed images in which individual atoms are nearly visible (far right). Color is artificially applied. Credit: Veronica Falconieri, Subramaniam Lab, National Cancer Institute.

Transmission electron microscopes can magnify objects more than 10 million times, enabling scientists to see the outline and some details of cells, viruses and even some large molecules. A relatively new form of transmission electron microscopy called cryo-EM enables scientists to view specimens in their natural or near-natural state without the need for dyes or stains.

In cryo-EM—the prefix cry- means “cold” or “freezing”—scientists freeze a biological sample so rapidly that water molecules do not have time to form ice crystals, which could shove cellular materials out of their normal place. Cold samples are more stable and can be imaged many times over, allowing researchers to iteratively refine the image, remove artifacts and produce even sharper images than ever before. Continue reading

Cool Image: Adding Color to the Gray World of Electron Microscopy

Color electron micrograph of an endosome, a cell organelle. Credit: Ranjan Ramachandra, UCSD

As his Christmas gift to himself each year, the late biochemist Roger Tsien treated himself to two weeks of uninterrupted research in his lab. This image is a product of those annual sojourns. While it may look like a pine wreath dotted with crimson berries, it is in fact one of the world’s first color electron micrographs—and the method used to create it may dramatically advance cell imaging.

Electron microscopy (EM) is a time-honored technique for visualizing cell structures that uses beams of accelerated electrons to magnify objects up to 10 million times their actual size. Standard EM images are in grayscale and any color is added in with computer graphics programs after the image is made. With their new technique, Tsien, who received a Nobel Prize for his development of green fluorescent protein into a tool for visualizing details in living cells using light microscopes, and his colleagues have found a way to incorporate color labeling directly into EM. Continue reading

The Irresistible Resistome: How Infant Diapers Might Help Combat Antibiotic Resistance (sort of)

Gautam Dantas
Credit: Pablo Tsukayama, Ph.D.,
Washington University School of Medicine
Gautam Dantas
Born: Mumbai, India
Most proud of: His family, which brings him joy and pride
Favorite lab tradition: OOFF! Official Optional Formal Fridays, when members of his lab can dress up, eat bread—made in the lab’s own bread machine—and drink beer and wine together at the end of the day
When not in the lab, he: Enjoys home brewing, pickling and canning, and spending time with his wife and children. He also attends musical performances, including those of his wife, who sings in the St. Louis Symphony Chorus
Advice to aspiring scientists: Pursue hobbies, take risks, explore beyond your comfort zone. “You can do a Ph.D., but also have other experiences.” He says his own outside activities refine his focus in the lab, keep him grounded and help him be an empathetic mentor to his students. Plus, he met his wife while singing in the chorus of Macalester College in St. Paul, Minnesota

When I Grow Up…

Gautam Dantas remembers the day in 10th grade when he first wanted to be a scientist. It was the day he had a new biology teacher, a visiting researcher from the U.S. The teacher passionately described his own biochemical studies of how organisms live together in communities. By the end of the class, Dantas had resolved to earn a Ph.D. in biochemistry.

He ended up doing much more—gaining expertise in computational biology, protein design and synthetic biology. He now combines his skills and knowledge in multifaceted research that spans four departments at Washington University in St. Louis. His goal: to better understand and help combat a vital public health threat—drug-resistant bacteria.

“Our motivation is that we are living in the antibiotic era, and antibiotic resistance is getting out of control,” Dantas says. “We have very few new antibiotics we can use, so we’re kind of scrambling [to find new ways to treat bacterial diseases].”

His research focuses on one of the groups most vulnerable to bacterial infections—newborn babies.

According to his lab’s website Exit icon, the research is “at the interface of microbial genomics, ecology, synthetic biology, and systems biology,” and it aims “to understand, harness, and engineer the biochemical processing potential of microbial communities.” They do it by scrounging around in infant diapers.

Antibiotic Angst

Since their introduction in the 1940s, antibiotic drugs have saved countless lives. Simultaneously, they weeded out strains of bacteria easily killed by the drugs, allowing drug-resistant strains to thrive. Every year, at least 2 million people in the U.S. become infected and at least 23,000 die from drug-resistant bacteria, according to the Center for Disease Control and Prevention. Continue reading

Lighting Up the Promise of Gene Therapy for Glaucoma

Retinal ganglion cells in the mouse.

Retinal ganglion cells in the mouse retina that do (yellow) and do not (blue) contain a specific gene that scientists introduced with a virus. Credit: Kenyoung (“Christine”) Kim, Wonkyu Ju and Mark Ellisman, National Center for Microscopy and Imaging Research, University of California, San Diego.

What looks like the gossamer wings of a butterfly is actually the retina of a mouse, delicately snipped to lay flat and sparkling with fluorescent molecules. Researchers captured this image while investigating the promise of gene therapy for glaucoma, a progressive eye disease. It all happened at the National Center for Microscopy and Imaging Research Exit icon (NCMIR) at the University of California, San Diego.

Glaucoma is the leading cause of irreversible blindness. It is characterized by the slow, steady death of certain nerve cells in the retina. If scientists can prevent the death of these cells, which are called retinal ganglion cells, it might be possible to slow the progression of glaucoma. Some researchers are examining the possibility of using gene therapy to do just that.

A major challenge of gene therapy is finding a way to get therapeutic genes into the right cells without damaging the cells in any way. Scientists have had success using a non-disease-causing virus (adeno-associated serotype 2) for this task. Continue reading

Newly Identified Cell Wall Construction Workers: A Novel Antibiotic Target?


A family of proteins abbreviated SEDS (bright, pink) help build bacterial cell walls, so they are a potential target for new antibiotic drugs. Credit: Rudner lab, Harvard Medical School.

Scientists have identified a new family of proteins that, like the targets of penicillin, help bacteria build their cell walls. The finding might reveal a new strategy for treating a range of bacterial diseases.

The protein family is nicknamed SEDS, because its members help control the shape, elongation, division and spore formation of bacterial cells. Now researchers have proof that SEDS proteins also play a role in constructing cell walls. This image shows the movement of a molecular machine that contains a SEDS protein as it constructs hoops of bacterial cell wall material.

Any molecule involved in building or maintaining cell walls is of immediate interest as a possible target for antibiotic drugs. That’s because animals, including humans, don’t have cell walls—we have cell membranes instead. So disabling cell walls, which bacteria need to survive, is a good way to kill bacteria without harming patients.

This strategy has worked for the first antibiotic drug, penicillin (and its many derivatives), for some 75 years. Now, many strains of bacteria have evolved to resist penicillins—and other antibiotics—making the drugs less effective.

According to the Centers for Disease Control and Prevention, drug-resistant strains of bacteria Exit icon infect at least 2 million people, killing more than 20,000 of them in the U.S. every year. Identifying potential new drug targets, like SEDS proteins, is part of a multi-faceted approach to combating drug-resistant bacteria.

The Extracellular Matrix, a Multitasking Marvel

In part II of this series, we reveal how the ECM helps body cells move around, a process vital for wounds to heal and a fetus to grow. Here we introduce the extracellular matrix (ECM) and discuss how it makes our tissues stiff or squishy, solid or see-through.

When we think about how our bodies are made and what they do, we usually focus on organs, tissues and cells. These structures have well-known roles. But around, within and between them is a less understood material that also plays an essential part in making us what we are.

This gelatinous filler material is known as the extracellular matrix (ECM). Once thought to be the biological equivalent of bubble wrap, we now know that the ECM is a dynamic, physiologically active component of all our tissues. It guides cell shape, orientation and function.

The ECM is found in all of our body parts. In some tissues, it’s a thin layer separating cells, like mortar between bricks. In other tissues, it’s the major constituent.

The ECM is most prevalent in connective tissue, the material that forms our skeletons, cushions our internal organs and winds between blood vessels and around nerves. In connective tissue, the ECM is more abundant than the cells suspended within it.

The extracellular matrix meets the needs of each body part. In teeth and bones, it’s rock-hard. In corneas, it’s a transparent gel that acts like a camera lens. In tendons, it forms strong fibers that bind muscle to bone. Credit: Stock image.

What makes the ECM truly unique is its variability: Its texture, composition and functions vary by body part. That’s because the ECM’s deceptively simple recipe of water, fibrous proteins and carbohydrates has virtually endless variations.

In general, the fibrous proteins give the ECM its texture and help cells adhere properly. Carbohydrates in the ECM absorb water and swell to form a gel that acts as an excellent shock absorber. Continue reading

Pigment Cells: Not Just Pretty Colors

If you’ve ever visited an aquarium or snorkeled along a coral reef, you’ve witnessed the dazzling colors and patterns on tropical fish. The iridescent stripes and dots come from pigment cells, which also tint skin, hair and eyes in all kinds of animals, including humans. Typically, bright colors help attract mates, while dull ones provide camouflage. In humans, pigment helps protect skin from DNA-damaging UV light.

Researchers study cellular hues not only to decipher how they color our world, but also to understand skin cancers that originate from pigment cells. Some of these researchers work their way back, developmentally speaking, to focus on the type of cell, known as a neural crest cell, that is the precursor of pigment cells.

Present at the earliest stages of development, neural crest cells migrate throughout an embryo and transform into many different types of cells and tissues, including nerve cells, cartilage, bone and skin. The images here, from research on neural crest cells in fish and salamanders, showcase the beauty and versatility of pigment cells in nature’s palette.

Pigment cells called xanthophores, shown here in the skin of the popular laboratory animal zebrafish, glow brightly under light. Credit: David Parichy, University of Washington.
Dark pigment cells, called melanocytes, like these in pearl danio, a tropical minnow and relative of zebrafish, assemble in skin patterns that allow the animals to blend into their surroundings or attract mates. Credit: David Parichy, University of Washington.
Fin of pearl danio
Pigment cells can form all sorts of patterns, like these stripes on the fin of pearl danio. Credit: David Parichy, University of Washington.
Salamander skin
Pigment cells arise from neural crest cells. Here, pigment cells can be seen migrating in the skin of a salamander where they will form distinct color patterns. Credit: David Parichy, University of Washington.


A Labor Day-Themed Collection: Hard-Working Cell Structures

Hard labor might be the very thing we try to avoid on Labor Day. But our cells and their components don’t have the luxury of taking a day off. Their non-stop work is what keeps us going and healthy.

Scientists often compare cells with small factories. Just like a factory, a cell contains specialized compartments and machines—including organelles and other structures—that each play their own roles in getting the job done. In the vignettes below, we give a shout out to some of these tireless cellular workers.

Energy Generators
Credit: Thomas Deerinck, National Center for Microscopy and Imaging Research
Mitochondria are the cell’s power plants. They convert energy from food into a molecule called ATP that fuels virtually every process in the cell. As shown here, mitochondria (brown) often have distinct, oblong shapes. Like most other organelles, mitochondria are encased in an outer membrane. But they also have an inner membrane that folds many times, increasing the area available for energy production. In addition, mitochondria store calcium ions, help make hemoglobin—the vital iron-containing protein that allows red blood cells to carry oxygen—and even take part in producing some hormones. Defects in mitochondria can lead to a host of rare but often incurable diseases that range from mild to devastating. Researchers are studying mitochondria to better understand their manifold jobs in the cell and to find treatments for mitochondrial diseases.

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New Views on What the Cell’s Parts Can Do

Studying some of the most well-tread territory in science can turn up surprising new findings. Take, for example, the cell. You may have read in textbooks how the cell’s parts look and function during important biological processes like cellular movement and division. You may have even built models of the cell out of gelatin or clay. But scientists continue to learn new facts that require those textbooks to be updated, and those models to be reshaped. Here are a few examples.

Nuclear Envelope: More Than a Protective Barrier

Damaged heterochromatin represented by nucleotides GCAT
Damaged heterochromatin, a tightly packed form of DNA, travels to the inner wall of the nuclear envelope for repair. Credit: Irene Chiolo and Taehyun Ryu, University of Southern California.

Like a security guard checking IDs at the door, the nuclear envelope forms a protective barrier around the cell’s nucleus, only letting specific proteins and chemical signals pass through. Scientists recently found that this envelope may also act as a repair center for broken strands of heterochromatin, a tightly packed form of DNA.

Irene Chiolo of the University of Southern California and Gary Karpen of the University of California, Berkeley, and the Lawrence Berkeley National Laboratory were part of a team that learned that healthy fruit fly cells mend breaks in heterochromatin by moving the damaged DNA strands to the inner wall of the nuclear envelope. There, proteins embedded in the envelope make the necessary repairs in a safe place where the broken DNA can’t accidentally get fused to the wrong chromosome. Continue reading

Cool Images: A Holiday-Themed Collection

Here are some images from our gallery that remind us of the winter holidays—and showcase important findings and innovations in biomedical research.

Ribbons and Wreaths
This wreath represents the molecular structure of a protein, Cas4, which is part of a system, known as CRISPR, that bacteria use to protect themselves against viral invaders. The green ribbons show the protein’s structure, and the red balls show the location of iron and sulfur molecules important for the protein’s function. Scientists have harnessed Cas9, a different protein in the bacterial CRISPR system, to create a gene-editing tool known as CRISPR-Cas9. Using this tool, researchers can study a range of cellular processes and human diseases more easily, cheaply and precisely. Last week, Science magazine recognized the CRISPR-Cas9 gene-editing tool as the “breakthrough of the year.”

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