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Tag: dna

Another example of how humans and dogs are becoming more alike: our poop


It’s never really looked at it in its entirety, as one phenomenon, but how alike dogs and humans are — and keep becoming — continues to astound scientists around the globe.

Compassion? Both species seem to have it. Cognition? Dogs are quite capable of that, perhaps even exceeding us in certain areas. The diseases and disorders we get? Pretty much the same.

Not too many people look at the forest — at what all this, cobbled together, might mean — but scientists from particular disciplines, locked in a lab with a narrow focus, keep discovering new similarities, such as this latest one, deep in our intestines.

The microorganisms that live in dog’s intestines are more similar to the microbes inside us than to those in other animals, says a new study published in the journal Microbiome.

The dog microbiome “has some of the same species [of bacteria] as the human’s,” said lead author Luis Pedro Coelhos, “but different strains.”

The researchers were surprised because they expected that dogs would share only a few strains of bacteria with their owners. Instead, their intestinal flora could be cousins, says a summary of the study in Popular Science.

The study was not really about those similarities; it was aimed at better understanding canine weight loss.

Researchers at the European Molecular Biology Laboratory and Nestlé Purina Research worked with a sample of 32 beagles and 32 Labrador retrievers. Half of the members of each breed were overweight, while the other half were a healthy weight. For four weeks, they fed all of the dogs the same diet of Purina.

Then, they collected poop and conducted DNA analyses as they further altered the diets of the dogs.

They found the leaner dogs’ microbiomes changed much less than that of the overweight dogs. The findings, they say, gave then a baseline for how a healthy dog microbiome should behave, and suggested dogs may be better subjects for research into human weight loss than other species that have been used for that purpose.

Jack Gilbert, a researcher at the University of Chicago’s Microbiome Center who does research for Purina but was not involved in the study, told Popular Science the study was significant for what it showed about the similarities between the guts of dogs and our own.

“You can control a dog’s diet much more than you can do a human’s,” says Gilbert. The same is true for pigs and mice, but the fact that dogs have such a similar microbiomes to humans means that studying their response to certain diets could produce the best results.

The cause of the similarities isn’t entirely understood, but the study pointed out, “Dogs were domesticated early in modern human history and frequently shared food resources with humans.”

Over time, their digestive systems might have grown even more like our’s, and their obesity rates have come to mirror that of humans.

Further proof that we don’t just like each other, we are like each other — and in ways that continue to be discovered, as we sit around learning, bonding, loving, overeating and growing fat together, becoming, more and more, reflections of each other.

(Photo: Digital Vision/Getty)

Darwin’s Dogs: Organization tests dog DNA for free as part of research project

We doubt this is going over well with those companies who want to charge you upwards of $100 to tell you what breeds are in your dog, but a research-based organization is offering to do the same thing for free.

You might have to wait, though, and there will be some paperwork.

Darwin’s Dogs is a research project affiliated with the University of Massachusetts Medical School that uses your dog’s DNA, and other information you supply, to study the connection between DNA and behavior.

Thousands of dogs are now enrolled in the project, the initial goal of which was to look at obsessive-compulsive behavior in dogs. It has since branched into exploring food allergies among pets, CBS in Pittsburgh reports.

The first step in signing a dog up, though, remains providing a dog owner with a free DNA test, and a report on the findings.

That’s followed up with online questionnaires in which dog owners provide information on their dog’s traits and behaviors.

“We can study behavior in dogs really easily by just working with the dog owners, by just asking them with a goal of trying to look at how differences in a dog’s DNA matches up with differences in their behavior,” says Darwin’s Dogs researcher Elinor Karlsson.

They hope that causes to diseases and disorders can be found in dogs’ genetics — and that those could lead to breakthroughs in treating the same conditions in people.

“We don’t understand what causes these diseases and the only way to really find new treatments and new effective ways of treating them is to know what the cause is,” Karlsson said.

“Even though there are a lot of differences between dogs and humans, you look at the really important things that are relevant to health, there’s not that many differences. Dogs get the same cancers, the same psychiatric diseases that we do,” she added.

The DNA information the organization provides on your dog is roughly similar to that offered by products such as Wisdom Panel, DNA My Dog and Embark.

Darwin’s Dogs tests a saliva sample that you mail to them. Commercially available DNA tests use either saliva or, through veterinarians, blood.

Darwin’s Dogs is free — for now.

According to the Darwin’s Dogs website, demand has been so high for the test they might have to limit participants, or start charging in the future.

“We have been brainstorming ways of allowing our participants to contribute financially. We are committed to keeping the Darwin’s Dogs project free to anyone who is willing to participate, but with the cost of the genotyping this means we currently have to pick-and-chose which dogs to genotype based on the grant funding support we can receive. We are considering options to allow participants to contribute to offset those costs.

More information about the project can also be found in this Scientific American description.

After 38 years in prison, innocent man freed — and gets to bring his dog home, too

At first glance this story made no sense — a man who spent the past 38 years in prison wins his freedom when his innocence is finally proven and is reunited with his dog.

No dog — no matter how loyal to his owner — lives that long.

Turns out though, that Malcolm Alexander came into possession of the dog while serving his sentence at the Louisiana State Penitentiary at Angola, a facility which, while it has a reputation as a tough place, offers several dog programs and even breeds its own guard dogs.

Alexander, 58, had been proclaiming his innocence since he was convicted of sexual assault and sent to prison at age 20.

On Tuesday, he was welcomed home by his 82-year-old mother, his son and his grandson – both named Malcolm, and other relatives.

Earlier in the day, A Jefferson Parish judge vacated Alexander’s 1980 aggravated rape conviction and his mandatory life sentence after finding that Alexander had not been provided with adequate legal assistance, and that DNA evidence discovered in 2013 excluded Alexander as a suspect in the sexual assault.

After the ruling, Alexander did not return to the prison, where both his belongings and his dog remained.

innocenceThe next day, he was reunited with the huge black Lab, Nola.com reported.

“You ain’t got nothing to worry about no more,” he told the 9-month-old pup upon reuniting with him. “I told you we gonna be free. I told you they was gonna get us out.”

Alexander’s case was undertaken by The Innocence Project, which helped him gain his freedom.

Alexander had raised the dog since shortly after his birth. He named the dog Innocence, and calls him Inn for short.

Inn was born at the prison to another dog at the facility, according to Vanessa Potkin, an attorney with The Innocence Project.

Potkin and other staffers traveled to Angola Wednesday to retrieve Inn and Alexander’s property and return them to Alexander.

(Photo: Michelle Hunter \ NOLA.com | The Times-Picayune)

Researchers say the hyper-friendliness of dogs results from gene mutation

Researchers say they have pinpointed a gene mutation that explains why dogs are so hyper-friendly — one they believe could have played a role in their domestication.

The scientists say they have isolated two genes, variations in which lead to the hyper-friendliness and tail-wagging sociability that most dogs exhibit.

When I read the headlines I had two reactions. First, I didn’t want to believe that the love dogs display resulted from something as stark sounding as a “mutation.” Second, I decided I wanted those genes, and those mutations, inside me — and all humans.

Imagine how much better a place the world would be if we all got so excited we nearly peed when we greeted each other, covered the faces of friends and strangers with licks, and had that unconditional love and loyalty that dogs possess.

Interestingly, though, similar variations in those same genes are already inside a small number of us. The genes at issue — GTF2I and GTF2IRD1 — are the same ones that have been associated with a human disease called Williams-Beuren Syndrome (WBS), which causes developmental disabilities and many other health issues.

The condition is characterized by mild to moderate intellectual disability, unusual facial features, cardiovascular problems and other health issues. But it also can often lead to affected individuals having highly outgoing, engaging personalities and extreme interest in other people.

Having written about people with developmental disabilities for eight years as a reporter, I met more than a few people like that — in institutions, group homes, and living with their families. They’d come up and hug a complete stranger. They’d follow me around, paying attention to everything I did and said. They seemed to indiscriminately love everybody. They were hard to say goodbye to.

I didn’t know it was a result of their Williams-Beuren syndrome, or that there even was a Williams-Beuren syndrome (this was the 1980’s), just that they possessed an innocence and trust uncommon in our species. I can’t remember if, at the time, I saw that behavior as “dog-like.”

But some researchers did.

vonholdtBridgett vonHoldt, an evolutionary geneticist at Princeton University, and Monique Udell, who studies animal behavior at Oregon State University, met three years ago and started talking about dogs.

In an earlier study, vonHoldt had identified a gene that’s mutated more often in dogs than wolves — one that possibly led to their domestication.

Together, Udell and vonHoldt decided to examine the social behavior of a group of dogs and a group of wolves and then analyze their DNA in the region that included the genes in question.

The study they co-authored, using a combination of genetic sequencing and behavioral tests, pinpointed a couple genetic differences that seem to track with friendliness.

Using 16 dogs and eight captive, socialized wolves, they were able to establish that the dogs showed a greater variation, or mutation, of those genes. Animals with these mutations appeared to pay more attention to the humans than those without, the researchers said.

“We find that hyper-sociability, a central feature of WBS, is also a core element of domestication that distinguishes dogs from wolves,” the study concluded.

brubaker

The findings, in addition to providing new insights into the human disorder, could explain a large part of what led wolves to become domesticated, and how dogs evolved to become man’s best friend.

To learn more about the study, check out these reports from the
Los Angeles Times, Science and Princeton University.

(Photos: At top, Bridgett vonHoldt, an assistant professor in ecology and evolutionary biology at Princeton and the study’s lead co-author, cuddles with her Old English Sheepdog, Marla, by Chris Fascenelli, Princeton University Office of Communications; at bottom, Lauren Brubaker, a graduate research assistant in the Department of Animal and Rangeland Sciences at Oregon State University and one of the study’s authors, interacts with a gray wolf, by Monty Sloan, via Princeton University Office of Communications)

Photo bomb: That wasn’t Amelia Earhart, after all; so, doggonit, the mystery lives on

notearhart

Two of the biggest news stories of the week — or at least the two most shouted about by the news media — were new evidence surfacing regarding Trump’s ties to Russia and new evidence surfacing in the disappearance of Amelia Earhart.

Revelations that Donald Trump Jr. had a meeting during the campaign with a Russian who promised some dirt on Hillary Clinton were called a “nothing burger” by Trump supporters. But, as the week progressed, it all started looking pretty meaty.

The other so-called investigative breakthrough — “experts” saying they found a photo that shows Earhart and her navigator in the custody of the Japanese on the Marshall Islands after their crash and disappearance in 1937 — turned out to be a totally meatless whopper.

apearhartBy which we don’t mean a lie — just a tremendously lazy mistake. The photo in question, it turns out, originally appeared in a travel book published two years before Earhart and navigator Fred Noonan even began the journey they wouldn’t return from.

The photo was the basis of an hour-long History Channel special Monday — one that was widely promoted in news programs as a possible solution to an 80-year old mystery.

Instead, the whole theory ended up holding about as much as (sorry, Geraldo) Al Capone’s vault.

It’s all just more proof that, when it comes to truth, when it comes to uncovering things, when it comes to unburying treasures, we’re better off putting our faith in dogs. Dogs aren’t concerned with making money, or getting famous, or one-upping, or getting in the last word, or getting interviewed by Matt Lauer.

We talked about the “Earhart photo” in a post earlier this week, but that post pertained more to another, less publicized effort to get to the bottom of the Earhart mystery, and how it had turned to some “bone sniffing dogs” in an attempt to find Earhart’s bones.

Operating on an alternate theory, and not buying the “photographic evidence,” a Pennsylvania-based group called The International Group for Historic Aircraft Recovery (TIGHAR) sent four border collies to a site they have been focusing on — a small coral atoll about 400 miles south of Howland Island.

Four dogs alerted to a spot in the area, and excavation ensued, but no bones were found.

They had hoped to find bones and, through DNA testing, link them to Earhart. Some small glimmers of hope remain. Dirt from the site has been sent to a lab though to see if any traces of human DNA remain in it, and there’s a possibility that human DNA could be found in crabs that scavenged on any bones.

nothing burgerThat quest could turn out to be a “nothing burger,” too, but even so it won’t be as embarrassing as the efforts of Les Kinney, the former treasury agent who came across a photo in the National Archives that he and others were highly convinced depicted Earhart and her navigator in Japanese custody.

That led to History Channel documentary, “Amelia Earhart: The Lost Evidence,” which aired Sunday and concluded that, based on the photo and other evidence, Earhart and navigator Fred Noonan ended up in Japanese custody on the Marshall Islands after they survived a crash landing.

The documentary touted the image as “the key to solving one of history’s all-time greatest mysteries.”

Many a news organization billed the photo that way, too, until Wednesday, when they all started backtracking after learning a Tokyo-based blogger unearthed the same photograph in the archives of Japan’s national library. It had appeared in a book — published in 1935.

Kota Yamano, a military history blogger, ran an online search using the keyword “Jaluit atoll” and a decade-long time frame starting in 1930.

“The photo was the 10th item that came up,” he said, along with its source — a travel book published two years before Earhart began the attempted around the world journey in 1937.

The Internet search took all of 30 minutes, he said.

“I was really happy when I saw it, Yamano said. “I find it strange that the documentary makers didn’t confirm the date of the photograph or the publication in which it originally appeared. That’s the first thing they should have done.”

Major news media didn’t do that, either, opting to put more effort into hyping the story than doing a little digging of their own.

So thanks to Koto Yamano for letting us know the “Earhart photo” was a “nothing burger.” (Maybe we should have him figure out this whole Russia and Trump thing.)

According to the website knowyourmeme.com — if we are to believe it — the earliest known usage of the term “nothing burger” was by Hollywood gossip columnist Louella Parsons. She used it in reference to actor Farley Granger, whose acting chops she apparently questioned.

When the actor was released from his contract with Samuel Goldwyn’s studio, MGM, in 1953, she wrote “After all, if it hadn’t been for Sam Goldwyn Farley might very well be a nothing burger.”

The concept — though the term wasn’t used — was pretty much the basis of Wendy’s old “Where’s the beef?” advertising campaign, and the phrase itself has enjoyed a revival this year, thanks mainly to politics, and the presidential campaign, and the Internet, where we don’t seem to agree on anything except what cool-sounding phrase we all want to use, be it “game changer” or “nothing burger.”

If the Amelia Earhart mystery ever is solved, I suspect dogs will be part of that resolution, probably DNA, too — but not emails, not quickie documentary makers trying to sell a story, and definitely not politicians.

(Photos: At top, the photo some investigators said included Earhart, after her plane crashed, as it appeared in Umi no seimeisen : Waga nannyou no sugata, a photo book in Japan’s national library published in 1935; below, the actual Earhart in an Associated Press photo; at bottom, an actual nothing burger)

Pawprint in the mud leads to discovery that New Guinea highland wild dogs still exist

hihgland2

After nearly half a century of fearing that the New Guinea highland wild dog had gone extinct in its remote and inhospitable habitat, high in the mountains of New Guinea, a pawprint in the mud has led researchers to confirm the existence of at least 15 of them.

Photographs taken with camera traps and DNA analyses of biological samples confirm the dogs — considered the most ancient breed on earth — are living along New Guinea’s remote central mountain spine.

“The discovery and confirmation of the highland wild dog for the first time in over half a century is not only exciting, but an incredible opportunity for science,” says the group behind the discovery, the New Guinea Highland Wild Dog Foundation (NGHWDF).

hihgland1An expedition by the foundation last year led to the discovery of the population — after a member of the group noticed a pawprint in the mud.

New Guinea highland wild dogs were only known from two unconfirmed photographs in recent years — one taken in 2005, and the other in 2012.

They had not been documented with certainty in their native range in over half a century, and experts feared that what was left of the ancient dogs had dwindled to extinction.

Last year, a NGHWDF expedition led by zoologist James K. McIntyre, was joined by local researchers from the University of Papua, who were also seeking the the elusive dogs.

A muddy paw print spotted in September 2016 finally gave them what they were looking for — recent signs that the wild canids still wandered the dense forests of the New Guinea highlands.

The footprint was one McIntyre had left, with his bare feet, while going up the mountain. On the group’s way down the mountain, he noticed it had been joined by a paw print.

Bait was laid. Camera traps were set. And the cameras captured more than 140 images of Highland Wild Dog.

highland3

DNA analysis of fecal fecal samples confirmed that the breed is related to Australian dingos and New Guinea singing dogs – the captive-bred variants of the New Guinea highland wild dog.

The species established itself on the island at least 6,000 years ago, either arriving with human migrants or migrating independently of humans.

The dogs most commonly have a golden coat, but can also be black, tan or cream colors. Their tails curl up over their backsides and their ears sit erect on their heads.

According to the NGHWDF, there are roughly 300 New Guinea singing dogs remaining in the world, living in zoos and private homes. They are known for their high-pitched howls, often carried out in chorus with one another.

A scientific paper on the discovery is expected to be released in the coming months.

(Photos: NGHWDF)

Could a DNA test prove dog’s innocence?

Up to now, DNA testing on dogs has been used mostly to satisfy owner curiosity over what breeds are in their mutt, or by apartment managers who want to identify dogs whose owners didn’t pick up after them.

Now comes a chance to put it to more noble use. (Cue up the “Law & Order” theme.)

jebThe owners of a Belgian Malinois accused of killing a neighbor dog say a DNA test could clear their dog of a murder rap.

A district judge in Michigan ordered Jeb, the Belgian Malinois, to be euthanized after hearing the evidence against him on Sept. 19.

But Jeb’s owners, Pam and Kenneth Job, have filed a motion for DNA testing to be conducted on the dead dog, a Pomeranian named Vlad.

Vlad died Aug. 24, and his owner, St. Clair resident Christopher Sawa, says he saw Jeb standing over his dog’s body. Both dogs were inside his backyard.

St. Clair County Animal Control took possession of Jeb after that.

Vlad was found with severe bruising over both shoulders and a puncture wound on his right front leg. There was another deep wound found on his left side that penetrated his chest and broke two ribs, the Detroit Free Press reported.

vladThe veterinarian who examined Vlad said his injuries were consistent with being picked up and shaken by a larger animal.

Ed Marshall, the lawyer for the Jobs, is asking the judge to allow them time to have an independent lab test conducted on Vlad’s body — to see if traces of Jeb’s DNA can be found in his wounds.

A hearing on his motion is set for Monday.

The Jobs say Jeb is an unofficial service dog who helps Kenneth with a condition that causes his muscles to deteriorate.

They say Jeb is a gentle soul and that Vlad’s death could have been caused by a fox or coyote, both of which can be seen from time to time in the rural area in which they live.