Tag Archives: genetic research

DNA survey of New York subway finds traces of Anthrax, the plague and Mozzarella Cheese

The most extensive DNA survey of the NYC subway has revealed that New Yorkers really like pizza and mozzarella, but also that drug-resistant microbes are widespread. They also found traces of the plague, anthrax, and learned that a tasmanian devil never took the subway in the city.

Subway stations are teeming with life – microbial life – of which we know very little.

In a way, the human body is very similar to the subway – both harbor a rich biodiversity when it comes to microbes and other microscopic living creatures. The average human, for example, contains about 100 trillion microbial cells – 10 times more than it contains human cells. Even in the bloodstream, about a third of all cells are microbial. We may think ourselves as being human, but in a way, we are like a petri dish, tightly connected to the microbes that live, breathe, feed and reproduce on and inside our bodies; we couldn’t live without them.

“A city is like an organism,” said IBM Corp. computational biologist Robert Prill, who is among those at the company investigating ways to better collect and analyze these immense new public-health genome databases. “It has a circulating system consisting of the movement of people.”

Also, as we move, we leave behind a trace – we basically shed our skin, dropping about 1.5 million skin cells every hour. If you look really carefully, you could find plenty of human skin cells, as well as the microbial cells that come along with them. This is what this survey aimed to do: see what microbial populations inhabit the subway, in order to better understand how they behave and develop in urban environments. These areas are very understanding, despite playing a key role in events such as disease outbreaks.

“We know next to nothing about the ecology of urban environments,” evolutionary biologist Jonathan Eisen at the University of California at Davis told the WSJ. “How will we know if there is something abnormal if we don’t know what normal is?”

This is where the PathoMap project steps in. PathoMap is a research project by Weill Cornell Medical College to study the microbiome and metagenome of the built environment of NYC. This huge project involved tests at 466 open stations in New York City, including on the kiosks, benches, turnstiles, garbage cans, and railings, over an 18-month period. Researchers dug their way through rats, vomit, and condoms to gather the DNA they needed for the survey.

By its end, researchers had over 10 billion fragments of biochemical code, which they then fed into a supercomputer armed with the extensive genetic databases of all known plants, animals, viral and bacterial life. With it, they were able to create an amazing map with 15,152 different types of life-forms this DNA belonged to were spread throughout the city. Here are just some of the results:

  • 46.9 DNA came from bacteria, mostly harmless
  • 48 percent did not match any known organism
  • harmful drug resistant bacteria were found at almost half of all the stations
  • a trace of anthrax and three traces of the bubonic plague were found, but this doesn’t mean that there’s a risk of these diseases actually developing
  • food poisoning bacteria are plentiful in the subway
  • cross the measured sites, genetic material from beetles and flies was the most prevalent – the cockroach genome hasn’t been sequenced yet so that DNA wasn’t identified
  • the cucumber DNA ranked third (of the known ones), probably due to left over foods
  • no Tasmanian devils, Himalayan yaks and Mediterranean fruit flies have ever traveled with the NY subway.

See the results in an interactive map here. Raw data is also online here.

The results, which were published in the journal Cell Systems, paints a very interesting (and expected) picture of the microbial life and DNA traces from the NY subway. I really hope this kind of survey would be conducted in other areas as well, because as Eisen said, we need to know what are the “normal” microbial levels in heavily used areas such as subways. Different subways with different environmental conditions are likely to harbor different microbial populations.

“Unintentionally, architects and engineers are creating ecosystems without much thought at all as to whether they are healthy or harmful to humans,” said biologist Jessica Green, director of the University of Oregon’s Biology and The Built Environment Center. “Different urban conditions might promote the growth of different microbial ecosystems.”

It is a monumental task, but one which might prove to be very important in the future. As Science Alert brilliantly puts it, scientists are the real heroes.

Scientific Article.

Pina colada pineapple coconut flavored

Coconut-flavored pineapple engineered by scientists

Pina colada pineapple coconut flavored

Some scientists alter genes and breed glow in the dark puppies, others breed pineapples that also taste like coconut, like Australian horticulturalists at Queensland’s department of agriculture.

The fruit of their 10 years labor of love was quickly dubbed the “piña colada pineapple” by the press, since it tastes like the two main ingredients of the famous beverage. What’s remarkable is that the scientists reached this unique flavor by mistake.

Queensland, Australia produces more than 80,000 tons of pineapples a year, still the country imports a lot more because of competing imports that are cheaper and tastier. Commissioned by the government to breed a new generation of pineapples that are sweeter and easier to grow, the horticulturalists ended up with a unique blend that far exceeded their expectations.

“When we are doing the breeding, we are not actually looking for a coconut-flavored pineapple or any other particular flavor,” said Garth Sanewski, a senior horticulturalist at Queensland’s department of agriculture. All in all, they embraced it. He adds, “It’s sweet, low acid, very juicy. It has this lovely coconut flavor which you won’t find in any other pineapple in Australia.”

The coconut flavored pineapple could first ship across the world in as early as two years, according to Australian officials. Rather disappointingly, the new fruit carries the official name of AusFestival. I have a feeling the name won’t last too much, though. For me and most other people this is clearly the piña colada pineapple.

via Gizmodo

The fly's tendency to perform left or right turns (yaw torque) is measured continuously and fed into the computer. In closed-loop, the computer controls arena rotation (single stripe or uniform texture as patterns on the arena wall). An additional white screen (not shown) covered the arena from above for all groups. (c) Maye A, Hsieh C-h, Sugihara G, Brembs B (2007)

Fruit flies, and most likely other animals, have free will as well

We could go on about what free will is until dusk and still not reach a conclusion. Indeed, philosophers have been theorizing free will for thousands of years, but haven’t we neglected an important aspect? There seems to be a general consensus that free will is entirely a human trait, but what of other animals? An older study, published in a 2007 edition of PLoS ONE, showed that free will and true spontaneity exist … in fruit flies.

The common fruit fly is easy to care for, breeds quickly, and lays many eggs, which is why it has been used for decades in biological research, especially genetics. Actually it was one of the first organisms to be used in genetic research, and a number of advances, especially basic principles of heredity, have been proven and documented with the help of this insect.

Are animals, insects as well, simple robot-like minded organisms that merely respond to external stimuli and thus lack even the smallest hints of free will? This used to be the general understanding, among scientists at least, and when animals were observed behaving differently than expected, even to the same external stimuli,  this variability was attributed to random errors in a complex brain.

An international team of scientists, however, proved that this kind of variability in behavior cannot be due to simple random events but is generated spontaneously and non-randomly by the brain.

 The fly's tendency to perform left or right turns (yaw torque) is measured continuously and fed into the computer. In closed-loop, the computer controls arena rotation (single stripe or uniform texture as patterns on the arena wall). An additional white screen (not shown) covered the arena from above for all groups. (c) Maye A, Hsieh C-h, Sugihara G, Brembs B (2007)

The fly’s tendency to perform left or right turns (yaw torque) is measured continuously and fed into the computer. In closed-loop, the computer controls arena rotation (single stripe or uniform texture as patterns on the arena wall). An additional white screen (not shown) covered the arena from above for all groups. (c) Maye A, Hsieh C-h, Sugihara G, Brembs B (2007)

The scientists placed fruit flies in an environment where its surroundings were of completely uniform white, and recorded their turning behavior. No external stimuli whatsoever was introduced in the chamber – no light, no sound, no vibrations, nothing. Lacking absolutely no input, the fruit flies movement in the chamber should have resembled a random pattern, like the noise the radio makes when its tuned between stations. Using a combination of automated behavior recording and sophisticated mathematical analyses, the scientists found that the structure of the fly’s behavior was very much different from what one would call noise. A myriad of complex random computer models were introduced, but none could adequately model the fruit flies behavior.

 “I would have never guessed that simple flies who otherwise keep bouncing off the same window have the capacity for nonrandom spontaneity if given the chance,” said Alexander Maye from the University of Hamburg, lead author of the 2007 paper.

“We found that there must be an evolved function in the fly brain which leads to spontaneous variations in fly behavior” co-author George Sugihara said. “The results of our analysis indicate a mechanism which might be common to many other animals and could form the biological foundation for what we experience as free will”.

What is free will?

Just recently, another research team, this time from Harvard University, assembled a new experiment to test the fruit fly’s free will. The scientists used isogenic fruit flies – genetically similar from inbreeding, but not identical – which they introduced in a contraption they appropriately name the “FlyVac”. You’ll see why.

Fruit fly free will testing device T maze

Fruit fly free will testing device T maze

The device which the Harvard researchers employed has a T-shaped maze, like a fork in the road, with LEDs at each of the two ends. The end of the fork to be illuminated was chosen on random, and as the fruit fly entered the maze, it had to make a phototactic choice: either it went towards the light making the decision photopositive or move away from it, in which case the decision was photonegative. No matter its predispositions towards light, photons and such, the fly was vacuumed away from the maze rather unceremoniously, and taken back to its initial position. It then started all over again, and again, and again. I didn’t understand from the paper how many times per fly they did this, by I presume a lot – for 17,600 flies!

I bet your curious to find out what they got. Well, for instance one photopositive fruit fly strain chose light about 80% of the time. However, one oddball fly in this group chose light 100% of the time. When verifying other fruit fly strains involved in the experiment, similar results were found. The variability encountered was much grater than that possibly occurring from chance alone. The results were published in the journal PNAS.

 “The question of whether or not we have free will appears to be posed the wrong way,” says Brembs. “Instead, if we ask ‘how close to free will are we”‘ one finds that this is precisely where humans and animals differ”.

MRI of one of the authors (MK) is used for illustration. A, with the landmark for left zygion (ZygL) highlighted, where a clipping plane was used to uncover the bone; B, with the landmarks for left (EyeL) and right pupils (EyeR) highlighted, where a clipping plane was used to uncover the vitreous humor; C, with the four nasal landmarks highlighted, including the left alare, nasion (Nsn), pronasale (Prn), and subnasale (Sbn).

DNA could be used to visually recreate a person’s face

 MRI of one of the authors (MK) is used for illustration. A, with the landmark for left zygion (ZygL) highlighted, where a clipping plane was used to uncover the bone; B, with the landmarks for left (EyeL) and right pupils (EyeR) highlighted, where a clipping plane was used to uncover the vitreous humor; C, with the four nasal landmarks highlighted, including the left alare, nasion (Nsn), pronasale (Prn), and subnasale (Sbn).

MRI of one of the authors (MK) is used for illustration. A, with the landmark for left zygion (ZygL) highlighted, where a clipping plane was used to uncover the bone; B, with the landmarks for left (EyeL) and right pupils (EyeR) highlighted, where a clipping plane was used to uncover the vitreous humor; C, with the four nasal landmarks highlighted, including the left alare, nasion (Nsn), pronasale (Prn), and subnasale (Sbn).

No person is the same, thanks to genetic variation. While skin color, hair, or body proportions are elements that might be exactly the same for two persons, you can be sure that one’s face is unique – even in identical twins, if you look extremely closely. While life style, body weight, diet, accidents and so on influence the shape and general appearance of one’s face, the classic elements like skin color, facial hair, the distance between eye sockets, symmetry, cheek bone and so on are entirely genetically driven. With this in mind, with a highly established genome map, scientists could be capable of recreating a person’s face based solely on his DNA sample, and this is exactly what an international team of researchers have been seeking out to do.

A wanted criminal could be identified much easier, based on the DNA ‘footprint’ he left behind at the crime scene and thus lead to a swifter apprehension. A victim of a calamity could be identified and offer peace to the family. Applications would be numerous, especially for secret services.

It’s worth noting, however, that this type of research is still in its infancy. So far, scientists have managed to pinpoint five genes (PRDM16PAX3TP63C5orf50, and COL17A1) that contribute to facial shape and features, although they caution that the genes they found only have small effects, and are only linked with a limited number of features, limiting their use until more genes of relevance are found.

Predicting eye, hair and skin color are fairly well established, however where it truly gets complicated is in facial features. For instance, the researchers found  that a certain gene called TP63 was a predictor of the gap between the centers of each eye socket being narrower by about nine millimeters. PAX3 contributes to facial shape variation at the genome-wide scale and so on. Once these parameters are well correlated and identified, facial features could be predicted just as accurate as eye or hair color can be today. If anything, something like a sort of portrait sketch could be recreated.

“It’s a start,” says Manfred Kayser from the Erasmus University Medical Center in Rotterdam, the Netherlands. “But we are far away from predicting what someone’s face looks like.”

Kayser and colleagues surveyed DNA samples from 10,000 Europeans and looked at nine specific facial “landmarks” in three-dimensional MRI scans of their heads. Another eight landmarks were subsequently analyzed, but from portrait photos.

Findings were published in the journal PLOS Genetics.

DANA SMITH

Beating cancer by making it forget what it is [TED VIDEO]

DANA SMITH

(c) DANA SMITH

Dr. Jay Bradner, a physician and chemical biologist at the Dana-Farber Cancer Institute in Boston, makes beating cancer sound easy – darn easy! Through the wonderful information that epigenetics science has delivered in the past decade, he believes cancer can be defeated simply by re-writing its genetic information such that it forgets that it’s a cancer, and starts behaving like a regular cell.

“With all the things cancer is trying to do to kill our patient, how does it remember it is cancer?” asks Bradner.

Researchers in Bradner’s lab have developed a compound that  manipulates epigenetic instructions, and he has sent it out to hundreds of collaborators worldwide. “That’s not common in practice,” says Bradner, “but from first principles, it’s the right thing to do.”

Almost exclusively, research for a prototype drug is kept top-secret by labs, keeping its structure and research findings completely oblivious to the rest of the world. Bradner took an alternate route and simply made it freely accessible from the get to, first by reporting his findings in a paper, then by sending samples to just about any lab interest (you too can ask the good doctor for a sample – you just need to e-mail). Results poured in just after a few months, as possible treatments for other afflictions, besides the rare form of cancer Bradner’s research targeted, such as leukemia, while another lab showed that the compound could be used to poise fat cells to forget they’re fat cells as well. Yes, you could basically eat all you want without gaining weight or fatty tissue.

This research is phenomenal, right on the cutting edge of science, and while Bradner and his team still have quite a while before the first clinical trial is released, their progress is worth noting and, especially, following. For more scientific info and details on results, please check this article on Nature. For an easy to digest pill of insight on the subject at hand, book 10 minutes of your day and watch this incredible TED speech at Boston by Bradner himself.