DNA – Agilent Technologies Blog

Agilent and the Zombie Fungus

Russell Lee — Tue, 30 Oct 2018 14:30:06 +0000

It’s the plot of every zombie horror story. Humans are infected by parasites that take over their brains. In one tale, M.R. Carey’s “The Girl with All the Gifts,” the victims also end up as hosts for the parasites’ plant spores.

Here’s the scariest part: there is an actual parasite that does this.

The pathogen is Ophiocordyceps unilateralis, also known as “zombie fungus.” The good news is that the parasite only targets ants. The bad news is that it is terrifying.

The fungus attacks the victim’s brain and nervous system to take over its behavior. The zombified ant is mind-controlled into leaving its colony for an environment where the fungus can reproduce. The fungus consumes the ant’s internal organs before erupting a plant-like stalk out of the ant’s head. Then, this stalk releases spores in a 10-foot “kill zone” to attack other ants.

(You can google photos of this – I won’t share any here. But I warn you: they will give you nightmares.)

In three separate studies, researchers used an Agilent Bioanalyzer System, RNA Nano Kit and High Sensitivity DNA Analysis Kit to learn more about how this parasite operates.

In the first study, researchers looked into how zombie fungus is able to control the behavior of its victims. They discovered that O. unilateralis expresses a set of unique genes into the brains of infected ants. These genes inhibit the ants’ immune and stress responses, as well as its chemosensory communications processes.

In the second study, researchers examined five different Ophiocordyceps species across three continents. They discovered that candidate manipulation genes are not shared between species, suggesting that different methods of behavior modification have evolved.

In the third study, researchers noted that behavioral manipulation occurs at certain times of day. Using bioinformatics and transcriptional profiling, they discovered that zombie fungus secretes a significant number of enzymes, toxins and bioactive compounds during the nighttime.

Nighttime? Sounds like a classic zombie horror story!

For more information go to:

Agilent and the Armed Spider

Russell Lee — Thu, 06 Sep 2018 14:30:09 +0000

Who doesn’t love a good, icky spider story?

Phoneutria nigriventer is one of the world’s largest spiders, with a leg span of 6 inches. It is more affectionately known as the “Brazilian Wandering Spider,” the “Armed Spider” or the “Banana Spider.”

(Regarding the “Banana” nickname — phoneutria doesn’t actually eat bananas. In fact, you could argue with the “Brazilian” nickname as well – one of these was once found in the produce section of an Oklahoma Whole Foods Market.)

What happens if you get bitten by the wandering spider? It depends on whom you ask.

“Within minutes you will have breathing problems,” says biologist Terry Childs. “You’ll start to lose control of your muscles, you’ll start to drool and within 20 to 25 minutes you’ll probably collapse on the floor and die of asphyxiation.” For years, the Guinness Book of World Records called phoneutria “the world’s most deadly spider.”

On the other hand, arachnologist Jo-Anne Nina Sewlal says that humans shouldn’t panic. While “venom from these spiders caused death in mice,” she says, “we are many times larger than a mouse.”

Brazilian researchers studied how phoneutria venom disrupts the blood-brain barrier (BBB) in bite victims. They also found that the body activates a protective mechanism by upregulating and downregulating several BBB-associated proteins. The researchers used an Agilent qPCR system and AffinityScript cDNA Synthesis Kit in their work.

One last note: phoneutria venom boosts nitric oxide, a chemical that increases blood flow. So one unfortunate effect of the spider’s bite is priapsism (um… look it up). As a result, researchers have investigated the venom as a treatment for erectile dysfunction. (Personally, I wouldn’t recommend it.)

Want more? You can view a one-minute video about phoneutria here.

For more information go to:

How Long Can You Hold Your Breath?

Russell Lee — Tue, 04 Sep 2018 14:30:40 +0000

The average person can hold his or her breath for 20 to 60 seconds. With training, you might get close to 2 minutes.

A group of people in the South Pacific can hold their breath underwater for much longer. Researchers have now determined that they are genetically different.

The Bajau Laut are an ethnic people near Malaysia, Indonesia and the Philippines. For centuries, these “sea nomads” have lived almost entirely at sea. Their homes are small houseboats. They are expert free divers, spending 60 percent of their day swimming to depths of more than 230 feet with no flippers or tanks. They can literally walk on the ocean floor.

You can view a video of a Bajau (“Badjao”) diver from BBC’s Human Planet here.

International researchers studied the Bajau using comparative genomics. They discovered that the Bajau have spleens that are 50 percent larger than average, providing them with more oxygenated blood. This is true even for Bajau who are not divers. In other words, the Bajau have evolved to be genetically different from other ethnicities.

The researchers found 25 single nucleotide polymorphisms (DNA variations) that were unique to the Bajau genome. They used an Agilent Bioanalyzer System and High Sensitivity DNA Kit in their DNA analysis.

For more information go to:

Agilent and the Alien Autopsy

Russell Lee — Tue, 27 Mar 2018 14:30:45 +0000

Fifteen years ago, a skeleton was discovered in a deserted town of Chile’s Atacama Desert. The fully-formed skeleton was only 6 inches tall. The skull was long and angular. The eye sockets were slanted. And there were only 10 pairs of ribs. (Normal humans have 12 pairs.)

For years, UFO aficionados have pointed to the Atacama skeleton (nicknamed “Sirius”) as evidence of extraterrestrials on Earth.

(I can’t include any photos here for copyright reasons. But you can view photos and videos of the Atacama skeleton here.)

The skeleton was originally thought to be ancient, but genetic tests indicated it was about 40 years old. And now, after five years of DNA testing, researchers have announced their conclusion.

The skeleton is human, probably a South American female. While originally thought to be about six years old, she was more likely a pre-term fetus. And she suffered from several mutations, including bone disorders.

From a scientific viewpoint, the case is fascinating. “Ata” (as the scientists call her) had 64 unusual skeletal mutations. Two of the variants were new to science. An Agilent Bioanlayzer High Sensitivity Chip was used to assess DNA quality.

“Although the extraordinary phenotype of the specimen drove broad discussion as to its origin (Sirius), and no hypothesis was left off the table during analysis,” the researchers write, “the specimen is shown here to have a purely earthly origin.”

What caused Ata’s high number of genetic abnormalities?

“Although we can only speculate as to the cause for multiple mutations in Ata’s genome,” the researchers write, “the specimen was found in La Noria, one of the Atacama Desert’s many abandoned nitrate mining towns, which suggests a possible role for prenatal nitrate exposure leading to DNA damage.”

And among UFO hunters, the search for evidence continues…

For more information go to:

Exit Smallpox. Enter Monkeypox.

Russell Lee — Tue, 12 Dec 2017 15:30:42 +0000

Smallpox is the only infectious disease ever to have been completely eradicated around the world. With a 35-percent fatality rate, smallpox killed millions of people before it was stopped by a meticulous global vaccination program.

Now, a relative of smallpox is increasingly threatening humans.

Monkeypox is less severe than smallpox, with a 10 percent fatality rate. But unlike smallpox, there is no cure or vaccine for monkeypox. The first human cases were identified in 1970 in West Africa.

Monkeypox can spread from animals to humans, as well as between humans. In 2003, 47 people in the Midwestern United States were infected. The outbreak was traced to an exotic pet dealer, whose imported African animals infected prairie dogs that were later sold as pets.

And now, human cases of monkeypox are spiking. Earlier this month, Nigeria confirmed its 38th case, up from nine only a week earlier. More than a hundred people in total may be infected.

Type I interferons (a type of anti-viral protein) play an important role your cells’ defense against viral infections. Spanish and German scientists studied how monkeypox and other viruses are able to block IFNs and prevent them from doing their protective work. The researchers used an Agilent Bioanalyzer System to analyze the quality of RNA samples.

The U.S. Centers for Disease Control use prairie dogs as a model in monkeypox virus research. CDC scientists studied the use of analgesic therapy in prairie dogs for pain management. They used an Agilent HPLC, autosampler, UV detector, column and OpenLab software to analyze plasma samples.

U.S. and Swiss researchers studied “signatures” in the human microbiome that are unique to ovarian cancer. In the process, they discovered a unique signature that may indicate a heretofore uncharacterized human variant of monkeypox virus. (NOTE: There have been no reports of pox virus association with ovarian cancer.)

They used Agilent SurePrint microarrays, a SureTag DNA labeling kit and a SureScan array scanner in their work.

For more information go to:

Do You Think You Have a Concussion? Try Spitting…

Russell Lee — Thu, 07 Dec 2017 15:30:17 +0000

U.S. researchers say it may be possible to diagnose and predict the duration of a concussion… by examining your spit. The new approach has potential for children, teens and young adults.

According to the study, a third of children who experience a traumatic brain injury also develop prolonged concussion symptoms (PCS). These symptoms can include nausea, fatigue, dizziness, confusion and headache, as well as memory, learning and attention problems. “To our knowledge,” the researchers say, “there are currently no objective or easily administered tests for predicting prolonged concussion symptoms.”

The researchers studied 52 patients aged 7 to 21 years old who had received a clinical diagnosis of concussion. When examining the patients’ saliva, they found five microRNAs that could identify prolonged concussion symptoms with 85 percent accuracy.

“Salivary miRNA measurement may provide an accurate, noninvasive technique for identifying children with PCS,” the study concludes. “Such information could reduce parental anxiety and improve care for patients by providing a simple tool for concussion management.” The study also stresses that further validation of this approach is needed.

The researchers used an Agilent Bioanalyzer System to assess RNA yield and quality.

For Research Use Only. Not for use in diagnostic procedures.

For more information go to:

A “Silent Disease” is Striking Vietnam Veterans

Russell Lee — Tue, 28 Nov 2017 15:30:35 +0000

The Vietnam War ended more than 40 years ago. But for those who once served overseas, there is a newly emerging health problem.

Between 1964-1973, more than 2.7 million young Americans served in Vietnam. This represents almost 10 percent of their generation. (US War Dogs)

While overseas, many soldiers ate raw or undercooked fish. As a result, they may have ingested small parasitic worms called liver flukes (fasciola). The bad news is that liver flukes can live for decades in your intestines and liver with absolutely no symptoms.

The worse news is that the parasites are linked with bile duct cancer (cholangiocarcinoma). This cancer is called a “silent disease” because the signs and symptoms can go unnoticed until the cancer is in an advanced stage. (Cholangiocarcinoma Foundation)

Last year, the Associated Press reported that 700 veterans with bile duct cancer have been seen by the U.S. Department of Veterans Affairs over the past 15 years. This spring, the VA commissioned a pilot study. Out of 50 blood samples submitted, more than 20 percent came back positive or bordering positive for liver fluke antibodies.

Research is being done to find ways to detect this cancer sooner.

An international team of scientists performed the first comprehensive study that used microarrays and microRNA expression to detect intrahepatic cholangiocarcinoma (ICC). They found that each different grade and subtype of ICC displayed a distinct miRNA profile. Furthermore, when tumor samples were compared to adjacent non-tumor tissue, similar miRNA dysregulation profiles were observed.

“These profiles could be used to enhance the early detection and improve the personalized treatment for ICC,” the study concludes.

The researchers used several Agilent genomics solutions in their work. An Agilent Bioanalyzer System, Nano Kit and Small RNA kit determined RNA concentration, purity and integrity. An Agilent human miRNA microarray profiled microRNA expression. Agilent MiRNA labeling and hybridization kits hybridized the samples. Agilent GeneSpring and Feature Extraction software digitized the data.

For Research Use Only. Not for use in diagnostic procedures.

For more information go to:

Return of the Plague

Russell Lee — Mon, 20 Nov 2017 15:30:54 +0000

There is a new outbreak of the plague. Yes, I’m talking about *that* plague.

Over the past three months, Madagascar has confirmed more than 2,000 cases of bubonic plague and pneumonic plague. The outbreak has resulted in 171 deaths, a fatality rate of 8 percent. It is the country’s worst outbreak in half a century, for the first time striking densely populated cities. (WSJ)

While the plague appears to be peaking in Madagascar, it is now in danger of spreading to nine neighboring countries and territories. Comoros, Ethiopia, Kenya, Mauritius, Mozambique, La Réunion (France), Seychelles, South Africa and Tanzania are currently on alert for possible outbreaks.

Fortunately, at this point “the overall global risk is considered to be low.” (WHO)

Bubonic plague is caused by the bacterium Yersinia pestis. It can spread to humans from the bite of infected fleas. The fleas in turn are carried by rats. Pneumonic plague is a more virulent form of the disease, and can be transmitted through the air from simply coughing and sneezing.

One of the most infamous plague outbreaks was “The Black Death,” which originated in Asia and spread throughout Europe from 1346-1353. It is estimated to have killed up to 50 million people, a whopping 60 percent of Europe’s entire population. (History Today)

U.S. researchers studied the cellular and molecular mechanisms underlying Y. pestis’ effect on the lungs, and discovered two distinct phases. In the first 24-36 hours, the infection begins in an anti-inflammatory state. By 48 hours it progresses to a highly pro-inflammatory state, resulting in death after three days. The researchers used an Agilent Bioanalyzer System and GeneSpring software in their analysis.

Chinese researchers studied the body’s transcriptomic (cellular RNA) responses to pneumonic plague. They found that within 12 hours of infection, 600 genes in the lungs are differentially expressed. Within 48 hours, this number grows to 2,000 genes. Overall, the results suggest that fully virulent Y. pestis inhibits both innate and adaptive immune responses. The researchers used an Agilent Bioanalyzer System and RNA 6000 Nano kit in their analysis.

For more information go to:

How the Nobel Prize Celebrated Halloween

Russell Lee — Mon, 30 Oct 2017 14:30:37 +0000

In many countries, October 31 is “All Hallows Evening,” a time for remembering the dead. Halloween is celebrated with ghosts and other scary things.

Speaking of scary things, some German geneticists were studying the fruit fly Drosophila melanogaster. They discovered a few key genes that control embryonic development. When these genes were mutated, they would drastically affect the fly’s exoskeleton. For their work, the geneticists received the 1995 Nobel Prize for Physiology or Medicine.

These geneticists apparently had a sense of humor, because they named the genes according to the physical defects they cause:

Disembodied (“no differentiation of cuticle and head skeleton”)
Haunted (“only head skeleton visible”)
Mummy (“mouth parts and denticles poorly differentiated”)

As other genes were discovered, they were named spook, spookier, phantom, ghost, shroud, shadow and shade.

Years later, an American geneticist dubbed the collective group the “Halloween Genes.” The name has stuck ever since.

Agilent technologies, which are just about everywhere, are used in Halloween Gene research.

Australian researchers are using an Agilent Bioanalyzer System to study some currently unnamed Drosophila melanogaster genes, to determine if they should be given the status of “Halloween Genes.”

Chinese researchers used an Agilent liquid chromatograph, QQQ mass spectrometer and Agilent Jet Stream to study the role that phantom plays in the white-backed planthopper insect Sogatella furcifera.

And another group of Australian researchers are studying the Halloween Genes in crustaceans. They are using an Agilent UHPLC, mass spectrometer, multimode source and MassHunter software in their work.

For more information go to:

For the Love of Olive Oil

Russell Lee — Tue, 03 Oct 2017 14:30:26 +0000

The Mediterranean Diet is considered one of the healthiest in the world. And a main staple of this diet is olive oil.

Olive oil has been shown to reduce bad cholesterol, cardiovascular disease, stroke and depression.

Italian scientists demonstrated the anti-aging benefits of olive oil. One group of middle-aged mice was fed extra-virgin olive oil rich in phenols. A second group was fed the same olive oil without phenols. The phenol-rich group showed cognitive and motor improvement. In fact, gene expression was similar to that of young mice.

The researchers concluded that even a dietary change beginning in middle age can improve “cognitive, motor and emotional behavior.”

Agilent genomics technologies used in the study included an Agilent Bioanalyzer system, RNA Nano LabChip kit, microarrays, DNA microarray scanner and software.

Agilent also helps ensure the quality and integrity of olive oil.

European scientists have developed a method for detecting different varieties of extra-virgin olive oils. They used an Agilent High-Performance Liquid Chromatograph to measure the chromatic fingerprints of 140 samples processed from fruits of seven olive varieties. The researchers believe theirs is the most accurate classification method for monovarietal extra-VOO.

Agilent has application notes available for analyzing stigmastadienes, polymerized triglycerides, chlorophyll, tocopherols, squalene, phenolic compounds and triacylglycerols in olive oils.

For more information go to: