Category Archives: Microbiology


How a retrovirus replicates

This animation does a great job of explaining the devious infection methods of retroviruses, such as HIV. It also demonstrates how a variety of antiretroviral drugs interfere with those processes.


How a virus invades your body

Microbiology billboard

To promote its new movie, Contagion, Warner Brothers commissioned the creation of living billboards. Infected with fungi and bacteria spread on giant petri dishes, the billboards blossomed in warm Toronto windows.

The billboard after five days of growth.

The Inner Life of the Cell

Often the illustrations in textbooks depict cells as flat, like a fried egg. I am always reminding students that cells are three-dimensional. Like a balloon or a bubble, they have space inside. This is where the business of the cell happens and where the organelles live, surrounded by cytoplasm.

This incredibly beautiful animation depicts the inner workings of a eukaryotic cell. Harvard University selected the scientific animation company XVIVO to develop an animation that would take the university’s cellular biology students on a journey through the microscopic world of a cell.

This award-winning piece was the first topic in a series of animations XVIVO is creating for Harvard’s educational website BioVisions at Harvard.

New microbe defies “law” of life

California's Mono Lake

There was big news from NASA today.

A team of scientists from NASA’s Astrobiology Institute and the U.S. Geological Survey in Menlo Park, Calif., announced it has found a microbe that exists in a way that was never thought possible.

Felisa Wolfe-Simon

The group, led by Felisa Wolfe-Simon, has found a bacterium that “eats” and uses toxic arsenic,  substituting the arsenic for phosphorus in its essential functions, including building new cells.

In all lifeforms that scientists have studied so far, the “backbone” of DNA is made of sugar and phosphorus in the form of phosphate. In this microbe, arsenic bonds with the sugar to make a new type of DNA.

This is a really big deal. As most science students know, there are six elements that are thought of as the “building blocks” of life – carbon, hydrogen, oxygen, nitrogen, phosphorus, and sulfur. (Sometimes they are written like this: CHONPS.) When scientists consider whether other environments may be hospitable to life – like another planet, for example – one of the things they consider is the availability of CHONPS.

This new microbe was found in mud from the bottom of California’s Mono Lake. Mono Lake is located in the eastern part of the Sierras. The lake is volcanic in origin, and now a closed basin, meaning no rivers or streams feed it fresh water, and none carry water away from the lake. (Once upon a time, the lake had feeder streams, but they were diverted by the Los Angeles Department of Water and Power and the lake was left to dry up and die.) As a result, all of the minerals and substances naturally found in a lake are very concentrated there. Mono Lake is almost three times as salty as the ocean. It is highly alkaline and rich in carbonates, phosphorus, arsenic and sulfur. It is filled with shrimp, flies and algae that can survive the lake’s strange chemistry.

So what makes NASA so interested in stuff on the bottom of a lake? Well, think about it this way: When astrobiologists look for life on other planets, they usually look for planets with environments like Earth, that include CHONPS. Now they can now vastly expand their searches to include other places and planets.

“We’ve cracked open the door to what’s possible for life elsewhere in the universe,” said Wolfe-Simon. “What else might we find?”


Here is a bigger story about the microbe’s discovery in the New York Times.

Here is a great website for learning more about Mono Lake, including its geological and human-influenced histories.

Otters threatened by toxic algae

Kit is an otter that was stranded as a pup. She now lives at the Monterey Bay Aquarium.

For several years now, dead otters have been puzzling marine biologists. The mystery began in 2007 when nearly a dozen otters mysteriously died in Monterey Bay. Their carcasses were taken to the California Department of Fish and Game laboratory in Santa Cruz for analysis.

It turns out the otters are being poisoned by a microbe, a type of cyanobacteria that appears to be on an upsurge in warmer, polluted waters around the world. Cyanobacteria are commonly called blue-green algae, blue-green bacteria, and Cyanophyta. They are a type of algae that get their energy from photosynthesis, and their name from their vivid color – cyan.

This particular cyanobacteria is called Microcystis, and it’s not new or rare. It’s an ancient ancestor of modern-day bacteria and algae, and it dominated the planet more than 2.5 billion years ago. Scientists have found that strains of it are reappearing in stagnant water polluted with nitrogen from agriculture, and waste from human activities. It’s been found in water in every country in the world.

Microcystis is absorbed into the tissues of shellfish in contaminated water. There it remains, becoming more than 100 times more concentrated that it is in the surrounding water. Otters eat the shellfish and get sick and die.

The otter population off the California coast has dropped in recent years, which means that adult otters are dying faster than baby otters are being born.

California’s otters were hunted, almost to extinction, by fur traders in the early part of the 19th century. Otter fur had long been prized by Native Americans and other cultures for it’s incredible warmth and softness. Otter fur soon became in demand as a luxury item in many parts of the world and otters were hunted until they were almost entirely wiped out.

The rebound of the otter population on the North Coast has been an ecological success. However, they are still an endangered species and are always subject to threats such as sharks, watercraft, parasites, and food shortages.

Right now, there are about 2,700 otters living on the California coast.

The discovery that the algae is killing otters was made by Melissa Miller, a state wildlife veterinarian who has been tracking the mysterious deaths like a detective. (Visit her website here.) You can read more about how she made this important discovery in this fascinating article in the Los Angles Times.