The study, published in Cell Systems, demonstrates that it is possible and useful to develop a “pathogen map” — dubbed a “PathoMap” — of a city, with the heavily traveled subway a proxy for New York’s population. It is a baseline assessment, and repeated sampling could be used for long-term, accurate disease surveillance, bioterrorism threat mitigation, and large scale health management for New York, says the study’s senior investigator, Dr. Christopher E. Mason…
The PathoMap findings are generally reassuring, indicating no need to avoid the subway system or use protective gloves, Dr. Mason says. The majority of the 637 known bacterial, viral, fungal and animal species he and his co-authors detected were non-pathogenic and represent normal bacteria present on human skin and human body. Culture experiments revealed that all subway sites tested possess live bacteria.
Strikingly, about half of the sequences of DNA they collected could not be identified — they did not match any organism known to the National Center for Biotechnology Information or the Centers for Disease Control and Prevention. These represent organisms that New Yorkers touch every day, but were uncharacterized and undiscovered until this study. The findings underscore the vast potential for scientific exploration that is still largely untapped and yet right under scientists’ fingertips.
WTF? They’re under everyone’s fingertips.
“Our data show evidence that most bacteria in these densely populated, highly trafficked transit areas are neutral to human health, and much of it is commonly found on the skin or in the gastrointestinal tract,” Dr. Mason says. “These bacteria may even be helpful, since they can out-compete any dangerous bacteria.”
But the researchers also say that 12 percent of the bacteria species they sampled showed some association with disease. For example, live, antibiotic-resistant bacteria were present in 27 percent of the samples they collected. And they detected two samples with DNA fragments of Bacillus anthracis (anthrax), and three samples with a plasmid associated with Yersinia pestis (Bubonic plague) — both at very low levels. Notably, the presence of these DNA fragments do not indicate that they are alive, and culture experiments showed no evidence of them being alive.
RTFA to see why the researcher say we shouldn’t worry. Certainly, the diversity of microorganisms is a positive activator for our immune systems.
Interesting how they went about the research – and what this presents as a baseline for future evaluations. And an added plus is the unique – and still closed – station shuttered since Superstorm Sandy. Marine species still alive and stable in what should be an abnormal environment for them.
Fruits and vegetables have changed a lot since the onset of agriculture 10,000 years ago, as generation after generation of farmers artificially bred crops to select for more desirable traits like size and taste.
But that change can be hard to visualize. So James Kennedy, a chemistry teacher in Australia, created some terrific infographics to show just how drastic the evolution has been. This one, for instance, shows how corn has changed in the last 9,000 years — from a wild grass in the early Americas known as teosinte to the plump ears of corn we know today…
Mind you, not all attempts at selective breeding turn out so well. As Sarah Yager recently wrote at The Atlantic, apple-growers in the United States during the 20th century tried to breed Red Delicious apples to be as bright and shiny as possible and stay on shelves for as long as possible without noticeable bruising. The result? “As genes for beauty were favored over those for taste, the skins grew tough and bitter around mushy, sugar-soaked flesh.” Nowadays, as storage and transport have become more advanced, tastier apple varieties like the Honeycrisp or Gala are surpassing the Red Delicious.
The article gives watermelon and peaches the same treatment and ends with links to FDA definitions that range from selective breeding to the difference between cisgenesis and transgenesis. I’ll launch into that some other time – once again – trying to explain to the Vegan Left that science doesn’t define DNA as good or evil.
Consumption of sugary soda drinks such as cola and lemonade may be linked to accelerated DNA ageing, say researchers who have studied the impact of the drinks in more than 5,000 people.
High-sugar fizzy drinks have been under fire from campaigners for contributing to obesity and type-2 diabetes, but this is the first study to suggest a link with ageing. The researchers found that people who reported drinking a 350ml bottle of fizzy drink per day had DNA changes typical of cells 4.6 years older.
Yes, this sort of sugar consumption shortens your life much as smoking.
The study, published in the American Journal of Public Health, asked 5,309 healthy adults aged between 20 and 65 about their consumption of fizzy drinks and examined the DNA from each participant’s white blood cells.
The team found that telomeres – protective DNA caps on the end of chromosomes – were shorter in people who reported habitually drinking more fizzy drinks.
Telomeres are repetitive sections at the end of chromosomes that get shorter each time cells divide. They act as a kind of genetic ticking clock and in the past have been associated with human lifespan as well as the development of some forms of cancer, heart disease and diabetes. Other studies have suggested a link between telomere length and lifestyle factors such as smoking and psychological stress.
Prof Elissa Epel, of UCSF, stressed that the study only showed an association and did not prove that sugary drink consumption caused cell ageing. If high soda consumption was to blame, it may be due to the huge rush of sugars into the blood after a drink, leading to oxidative stress and inflammation – “the perfect storm for degrading telomeres,” said Epel.
Next in line for study – a tighter focus on sugar. Overdue as far as I’m concerned.
A Boston-area man long suspected of two 2004 rapes was formally charged after a new DNA test linked him to the crimes and excluded his twin brother.
Dwayne McNair, 33, of Dedham pleaded not guilty Monday. His bail was set at $500,000.
McNair had been charged earlier and spent almost two years in jail. A judge ordered him released, and prosecutors dropped the charges while the new test, which can distinguish between identical twins, was conducted.
Prosecutors in Suffolk County said the test, used for the first time in Massachusetts, found there was only a 1 in 2 billion chance the DNA in the samples being tested could have come from McNair’s brother, Dwight. McNair was indicted on eight counts of rape and two of armed robbery.
Another man, Anwar Thomas, 32, pleaded guilty in the case in 2011. But the prosecution of McNair was stymied by the possibility the DNA could have been his brother’s.
Silly me. I wrote the headline up top because CSI Cop Shows will lose part of a favorite plot-line. Now, they have acquired a new twist to the same old plot.
And, yes, “same old plot” isn’t especially appropriate since police-level DNA analysis has only been around 1986.
Leon Brown and Henry McCollum
Henry McCollum, North Carolina’s longest-serving death row inmate, and his half-brother Leon Brown were released after more than 30 years in prison on Tuesday after DNA tests proved their innocence of rape and murder. The exoneration followed dogged investigations by the two men’s lawyers and by the North Carolina Innocence Inquiry Commission, an independent body that operates with the full statutory powers of the state.
The exoneration and release of the two men now puts the spotlight on the police department in Red Springs, North Carolina, that carried out the initial investigation leading to the 1984 convictions of the then teenagers and their subsequent languishing behind bars.
Here are five questions the police authorities in Red Springs now have to answer:
1. Why did the Red Springs police department consistently deny that it had any evidence in its possession relevant to the murder convictions of McCollum and Brown? Only last month the commission found a box full of physical evidence being held by the police that had been in the department’s possession since the early 1990s.
2. Why did the Red Springs police department consistently fail to disclose to lawyers for the two men or to the local district attorney’s office that detectives had requested a potentially critical fingerprint test just days before the 1984 McCollum-Brown trial? The test would have compared the print found on a beer can at the crime scene with the fingerprints of Roscoe Artis, a convicted sex offender and murderer who lived just feet away from the field in which the body of the victim, Sabrina Buie, was found. Neither the request for the test, nor the fact that it was cancelled a year later before being completed, was ever disclosed.
3. Why was the crime scene investigator, who knew all the details of the crime scene as well as key findings from the autopsy of the victim, involved in the interrogation of McCollum, thus risking that his “confession” would be contaminated?
4. Why did detectives write out confessions for both Brown, then 15, and McCollum, then 19, and ask them to sign the statements? Why did they do so knowing that the confessions were incriminating, that the boys were both intellectually disabled and that they were being interrogated in the absence of any legal representation?
5. Why did the police continue to pursue McCollum and Brown knowing that key elements of their confessions were inconsistent with each other? In their “confessions” the two boys incriminated three other youths as accomplices, and yet when the police investigated those three individuals they found they had watertight alibis and were never prosecuted?
Incompetent racist creeps! And you can extend that subtle description all the way up to the Supreme Court and scumbags like Anthony Scalia.
Take a wander through this companion article at slate.com – the second half of the article focuses in on Scalia’s Old Testament ideology. He actually advocates that if someone [by his low-life standards] receives a fair trial, they should be executed even if innocent!
The cow in question
A woman in the southern Indian state of Kerala is set to win a court battle to keep a cow after DNA tests proved it belongs to her, her lawyer says…The woman, TS Sashilekha, had been accused by her neighbour Geetha of stealing the animal.
It is thought to be the first time an ownership battle over an animal has been decided by DNA tests in India, where Hindus consider cows to be holy.
The legal battle between the two women began last year when Geetha claimed that a cow in her herd was the mother of the disputed animal…But DNA tests ordered by the court did not match, meaning that Sashilekha will get to keep the cow.
…N Chandra Babu, lawyer for Sashilekha, told the BBC, “It is a rare case and possibly the first of its kind in history. Perhaps this is the first time a DNA test was held on a cow to find out its real owner.”
After the disputed cow was produced in court, Sashilekha was allowed to keep it in her possession – but only after paying 45,000 rupees in securities.
I understand why the court would ask the eventual victor to provide security presumably covering the value of the cow. Hopefully, returned without charges. Another good reason why she is suing the accuser for costs and compensation.
Modern chickens are descended primarily from the red junglefowl
The meat and eggs of domestic chickens are a source of protein for billions. Yet how and when the birds were domesticated remains a mystery. The answers to these questions could reveal a wealth of information about the genetics of domestication, as well as human behaviour, and how we can improve our husbandry of the birds.
In a bid to learn more about the chicken and its lineage, the UK government is funding a £1.94-million (US$3.3-million) effort to determine how the chicken went from being a wild fowl roaming the jungles of southeast Asia several thousand years ago to one of the world’s most abundant domesticated animals. The Cultural and Scientific Perceptions of Human–Chicken Interactions project — ‘Chicken Coop’ for short — will examine human history from the perspective of the fowl…
But no domestic animal has been moulded and remoulded by humans as extensively as chickens, says Greger Larson, an evolutionary geneticist. The animals have been bred for eating, egg-laying and fighting. And in the case of one particularly vocal breed, the creatures have even been strapped to the masts of Polynesian boats to act as foghorns. “Chickens are polymaths,” he says…
Because…mutations are so common in contemporary chickens, Larson’s team and others assumed that humans influenced these traits through selective breeding early in the course of domestication. But DNA from chickens recovered at archaeological sites across Europe, spanning the period from around 280 bc to ad 1800, has turned that idea on its head. In an analysis published last month, Larson’s team reported that none of 25 ancient chickens would have had yellow legs, and that just 8 out of 44 birds carried two copies of the TSHR variant…universal in modern breeds. So even 200 years ago, chickens may have been very different from those we know today.
With the help of other Chicken Coop members, Larson is also trying to get to grips with the wider evolutionary forces that shaped modern chickens. He hopes to determine why, for instance, chickens have not been wiped out by disease. This might have been expected because their very rapid selection — much of which has taken place since 1900 — should have led to inbreeding and, by whittling down immune genes, a reduced ability to respond to infections.
I love chicken almost as much as I love pork. I wasn’t raised with any religious or philosophical beliefs that inhibit the consumption of animal protein. So, no problem there. :)
Until modern science comes up with a sound reason to avoid healthfully-raised specimens of foods my progenitors used to catch in the wild – and eat – I will continue to do the same. Though restricting my hunt to the aisles of markets of all types, from chain stores to local farmers.
Eastern Asia, Western Asia, Japan, Beringia and even Europe have all been suggested origination points for the earliest humans to enter the Americas because of apparent differences in cranial form between today’s Native Americans and the earliest known Paleoamerican skeletons. Now an international team of researchers has identified a nearly complete Paleoamerican skeleton with Native American DNA that dates close to the time that people first entered the New World…
The skeleton of a teenage girl was found in Hoyo Negro, a deeply submerged chamber in the Sac Actun cave system in the eastern Yucatan Peninsula, Mexico. Alberto Nava Blank and a team of science divers discovered the skeleton along with many extinct animal remains deep inside this inundated cave in 2007. The divers named the girl Naia…
Kennett and Brendan J. Culleton, postdoctoral fellow in anthropology, Penn State, were originally asked to directly date the skeleton. After traditional and well accepted direct-dating methods failed because the bones were mineralized from long emersion in warm salty water within this limestone cave system, they worked closely with colleagues to build a geochronological framework for Naia using a unique combination of techniques to constrain the age of the skeleton to the end of the ice age.
To build the case for a late Pleistocene age they collaborated with Yemane Asmerom and Victor Polyak from the University of New Mexico using global sea level rise data to determine when the cave system, which at the time Naia and the extinct animals entered was dry, filled with water. The site where Naia lies is now 130 feet below sea level and sea level rise would have raised the groundwater level in the cave system and submerged everything between 9,700 and 10,200 years ago. So initial estimates of the latest that animals and humans could have walked into the cave system was 9,700 years ago.
At the same time, the researchers experimented with uranium thorium dating the skeleton directly. Asmerom and Polyak tried to directly date Naia’s teeth using this method, but that also did not work well.
The bones were found deep below today’s ground surface in a collapsed chamber connected to the surface via a web of now flooded tunnels that Naia once walked along to fall to her untimely death. Because the caves are limestone, mineral deposits continued to form while the cave was largely dry. Working with Patricia Beddows, Northwestern University, Chatters noticed accumulations of calcium carbonate — tiny rosettes of calcite deposited by water dripping off the cave roof — which could be accurately dated using the uranium thorium method. Because these drip water deposits formed on top of Naia’s bones, their date must occur after she fell in the cave. The oldest one dated so far is 12,000 years old.
Naia’s tooth enamel was also radiocarbon dated to 12,900 years ago by Kennett’s lab…
Morphologically, Naia does not look like a contemporary Native American, but mitochondrial DNA testing — maternally inherited DNA — carried out by Brian Kemp, Washington State University, and his collaborators shows that she has a D1 haplotype. This is consistent with the hypothesis that her ancestors’ origins were in Beringia, a now partially submerged landmass including parts of Siberia, Alaska and the Yukon. Early humans moved into this area from elsewhere in Asia and remained there for quite some time. During that time they developed a unique haplotype that persists today in Native Americans. Genetically, Paleoamericans have similar attributes as modern Native Americans even if their morphology appears different.
There is so much more that can be determined about paleolithic finds with the aid of modern chemistry and the tools grounded in DNA. Has to make paleontologists a heck of a lot happier about the focus and improved accuracy they can bring to their studies.
Lifetime science students like me really appreciate the difference between sound hypothesis and certified measurement. Even if the increments are centuries. :)
Leaving a hair at a crime scene could one day be as damning as leaving a photograph of your face. Researchers have developed a computer program that can create a crude three-dimensional model of a face from a DNA sample.
Using genes to predict eye and hair colour is relatively easy. But the complex structure of the face makes it more valuable as a forensic tool — and more difficult to connect to genetic variation, says anthropologist Mark Shriver of Pennsylvania State University…who led the work…
Shriver and his colleagues took high-resolution images of the faces of 592 people of mixed European and West African ancestry living in the United States, Brazil and Cape Verde. They used these images to create 3D models, laying a grid of more than 7,000 data points on the surface of the digital face and determining by how much particular points on a given face varied from the average: whether the nose was flatter, for instance, or the cheekbones wider. They had volunteers rate the faces on a scale of masculinity and femininity, as well as on perceived ethnicity.
Next, the authors compared the volunteers’ genomes to identify points at which the DNA differed by a single base, called a single nucleotide polymorphism (SNP). To narrow down the search, they focused on genes thought to be involved in facial development, such as those that shape the head in early embryonic development, and those that are mutated in disorders associated with features such as cleft palate. Then, taking into account the person’s sex and ancestry, they calculated the statistical likelihood that a given SNP was involved in determining a particular facial feature.
This pinpointed 24 SNPs across 20 genes that were significantly associated with facial shape. A computer program the team developed using the data can turn a DNA sequence from an unknown individual into a predictive 3D facial model…Shriver says that the group is now trying to integrate more people and genes, and look at additional traits, such as hair texture and sex-specific differences…
At the moment, such genetic analyses are limited, imprecise. If you think scientists will leave it alone you don’t understand curiosity. If you think someone like the FBI or any other Alphabetoid snoop will leave it alone you don’t understand paranoia.
What would you do if you discovered an odd strain of bacteria that exhibited unconventional behavior? Why, name it after Frank Zappa of course!…This is exactly what a team of Italian and Austrian researchers did when they found a bacterium that had apparently transitioned from causing acne in human skin to infecting the bark of grape vines.
“This is the first time it’s been found that a microorganism can switch from a human to a plant,” study author and self-professed Zappa fan Andrea Campisano, a microbiologist at the Edmund Mach Foundation in Italy, told the Los Angeles Times.
In addition to being a tribute to the late musician, the naming of P. acnes zappae is also a hat-tip to the Italian word for “hoe,” which is “zappa.”
Campisano is such a big fan of the experimental musician – he said he even has a quote from him prominently displayed on his lab computer screen: “If you end up with a boring miserable life because you listened to your mom, your dad, your teacher, your priest, or some guy on television … then you deserve it.”