DECODED GENOME REVEALS SECRETS OF PIGEON TRAITS AND ORIGINS

University of Utah researchers decoded the genetic blueprint of the rock pigeon, unlocking secrets about pigeons’ Middle East origins, feral pigeons’ kinship with escaped racing birds, and how mutations give pigeons traits like a fancy feather hairdo known as a head crest.

“Birds are a huge part of life on Earth, and we know surprisingly little about their genetics,” especially compared with mammals and fish, says Michael D. Shapiro, one of the study’s two principal authors and an assistant professor of biology at the University of Utah. “There are more than 10,000 species of birds, yet we know very little about what makes them so diverse genetically and developmentally.”

He adds that in the new study, “we’ve shown a way forward to find the genetic basis of traits – the molecular mechanisms controlling animal diversity in pigeons. Using this approach, we expect to be able to do this for other traits in pigeons, and it can be applied to other birds and many other animals as well.”

The study appears Jan. 31 on Science Express, the website of the journal Science. Shapiro led the research with Jun Wang of China’s BGI-Shenzhen (formerly Beijing Genomics Institute) and other scientists from BGI, the University of Utah, Denmark’s University of Copenhagen and the University of Texas M.D. Anderson Cancer Center in Houston.

Key findings of the study of pigeons, which first were domesticated some 5,000 years ago in the Mediterranean region:

– The researchers sequenced the genome, or genetic blueprint, of the rock pigeon, Columba livia, among the most common and varied bird species on Earth. There are some 350 breeds with different sizes, shapes, colors, color patterns, beaks, bone structure, vocalizations and arrangements of feathers on the feet and head – including head crests that come in shapes known as hoods, manes, shells and peaks.

The pigeon is among the few bird genomes sequenced so far, along with those of the chicken, turkey, zebra finch and a common parakeet known as a budgerigar or budgie, so “this will give us new insights into bird evolution,” Shapiro says.

– Using innovative software developed by study co-author Mark Yandell, a University of Utah professor of human genetics, the scientists revealed that a single mutation in a gene named EphB2 causes head and neck feathers to grow upward instead of downward, creating head crests.

“This same gene in humans has been implicated as a contributor to Alzheimer’s disease as well as prostate cancer and possibly other cancers,” Shapiro says, noting that more than 80 of the 350 pigeon breeds have head crests, which play a role in attracting mates in many bird species.

– The researchers compared the pigeon genome to those of chickens, turkeys and zebra finches. “Despite 100 million years of evolution since these bird species diverged, their genomes are very similar,” Shapiro says.

– The study turned up more conclusive evidence that major pigeon breed groups originated in the Middle East, and that North American feral pigeons – which are free-living but not wild – are close relatives of racing pigeons, named racing homers.

A Genome for the Birds, a Gene for Head Crests

The study assembled 1.1 billion base pairs of DNA in the rock pigeon genome, and the researchers believe there are about 1.3 billion total, compared with 3 billion base pairs in the human genome. The rock pigeon’s 17,300 genes compare with about 21,000 genes in people.

The researchers first constructed a “reference genome” – a full genetic blueprint – from a male of the pigeon breed named the Danish tumbler. They did less complete sequencing of two feral pigeons and 38 other pigeons from 36 breeds.

Shapiro says his team’s study is the first to pinpoint a gene mutation responsible for a pigeon trait, in this case, head crests.

“A head crest is a series of feathers on the back of the head and neck that point up instead of down,” Shapiro says. “Some are small and pointed. Others look like a shell behind the head; some people think they look like mullets. They can be as extreme as an Elizabethan collar.”

The study found strong evidence that the EphB2 (Ephrin receptor B2) gene acts like an on-off switch to create a head crest when mutant, and no head crest when normal. It also showed the mutation and related changes in nearby DNA are shared by all crested pigeons, so the trait evolved just once and was spread to numerous pigeon breeds by breeders. They ruled out the alternate possibility the mutation arose several times independently in different breeds.

The researchers analyzed full or partial genetic sequences for 69 crested birds from 22 breeds, and 95 uncrested birds from 57 breeds. They found a perfect association between the mutant gene and the presence of head crests.

“The way we tracked this trait was innovative,” Shapiro says. “We used gene-finding software from Mark Yandell’s group that was developed to find mutations that control human diseases. We adapted this software to find mutations that control interesting traits in pigeons. This should be extendable to other animals as well.”

The scientists also showed that while the head crest trait becomes apparent in juvenile pigeons, the mutant gene affects pigeon embryos by reversing the direction of feather buds – from which feathers later grow – at a molecular level.

Other genetic factors – not identified in the new study – determine what kind of head crest east pigeon develops: shell, peak, mane or hood, according to Shapiro.

Tracking the Origins of Pigeons

A 2012 by Shapiro study provided limited evidence of pigeons’ origins in the Middle East and some breeds’ origins in India, and indicated kinship between common feral or free-living city pigeons and escaped racing pigeons.

In the new study, “we included some different breeds that we didn’t include in the last analysis,” Shapiro says. “Some of those breeds only left the Middle East in the last few decades. They’ve probably been there for hundreds if not thousands of years. If we find that other breeds are closely related to them, then we can infer those other breeds probably also came from the Middle East. That’s what we did.”

“We found that the owl breeds – which are pigeon breeds with very short beaks and that are very popular with breeders – likely came from the Middle East,” he says. “They are very closely related to breeds we know came from Syria, Lebanon and Egypt.”

Shapiro says the study also “found a lot of shared genetic heritage between breeds from Iran and breeds we suspect are from India, consistent with historical records of trade routes between those regions. People were not only trading goods along those routes, but probably also interbreeding their pigeons.”

As for the idea that free-living pigeons descended from escaped racing pigeons, Shapiro says his 2012 study was based on “relatively few genetic markers scattered throughout the genome. We now have stronger evidence based on 1.5 million markers, confirming the previous result with much better data.”

The scientists analyzed partial genomes of two feral pigeons: one from a U.S. Interstate-15 overpass in the Salt Lake Valley, and the other from Lake Anna in Virginia.

“Despite being separated by 1,000 miles, they are genetically very similar to each other and to the racing homer breed,” Shapiro says.

He notes that pigeons were one of evolutionist Charles Darwin’s “favorite examples of how selection works. He used this striking example of artificial selection [by breeding] to communicate how natural selection works. Now we can get to the DNA-level changes that are responsible for some of the diversity that intrigued Darwin 150 years ago.”

The study’s University of Utah co-authors were Yandell; Eric Domyan, biology postdoctoral fellow; Zev Kronenberg and Michael Campbell, Ph.D. students in human genetics; Anna Vickery, biology undergraduate student; Sydney Stringham, Ph.D. student in biology; and Chad Huff, a former postdoctoral fellow in human genetics now at the University of Texas.

The study was funded by the Burroughs Wellcome Fund, the National Science Foundation, the University of Utah Research Foundation, the National Institutes of Health and the Danish National Research Foundation.

Researchers have for the first time produced human embryonic stem cells (hESCs) using somatic nuclear transfer (SCNT), a method in which the nucleus of a donor cell—in this case a skin cell or fibroblast—is transferred to an egg cell whose own nucleus has been removed.

The work, published in Cell, opens up the possibility of an alternative source of patient-specific stem cells to help scientists understand disease and develop personalized cell-based therapies. What’s more, hESCs produced via nuclear transfer (NT-hESCs) may not have the genetic and epigenetic abnormalities found in induced pluripotent stem cells (iPSCs), made by adding key genes to reprogram adult cells.

“I think it is a beautiful piece of work,” said George Daley of Boston Children’s Hospital and the Harvard Stem Cell Institute, who was not involved in the research, in an email to The Scientist. “This group has become remarkably proficient at a very technically demanding procedure and has shown that SCNT-ESCs may in fact be a practical source of cells for regenerative medicine.”

SCNT has previously been used to clone animals and to successfully reprogram somatic cells into ESCs is mice and primates, but little is known about how it works and which factors in the egg cell are responsible stimulating the reversion of the implanted mature nucleus to a pluripotent state.

Moreover, all previous attempts to produce NT-ESCs have failed. Researchers have been unable to get human SCNT embryos to progress past the 8-cell stage, never mind to the 150-cell blastocyte stage from which hESCs can be plucked. The causes of the roadblock are not clear, but likely involve certain key embryonic genes from the donor cell nucleus that could not be activated.

To overcome these obstacles, Shoukhrat Mitalipov of Oregon Health and Science University and colleagues first examined failed attempts with human cells and successful work in rhesus macaques to identify factors that could be responsible.

The researchers evaluated various activation and culture protocols that led to successful SCNT reprogramming in monkeys, and set about testing various combinations on human oocytes. They found that the optimized protocols that worked in monkeys also worked in humans. In particular, the incorporation of caffeine into the cocktails of chemicals used during host nucleus removal and donor transplantation and the use of electrical pulses to activate embryonic development in the recipient egg improved cellular reprograming and blastocyte development, allowing human SCNT embryos to reach a stage that yielded hESCs.

“[The researchers] worked diligently to overcome the early embryo blockade that we and others have confronted as a barrier to human SCNT,” said Daley. “Their distinct culture media, which was supplemented with caffeine, and their optimized activation protocol appears to have been the needed breakthrough.”

“It was a huge battery of changes to the protocols over a number of different steps,” said Mitalipov. “I was worried that we might need a couple of thousand eggs to make all these optimizations, to find that winning combination. But it actually took just 128 [eggs], which is a surprisingly low number to make 6 [hESC] lines.”

The researchers then analyzed four of these cell lines and found that their NT-hESCs could successfully differentiate into beating heart cells in vitro and into a variety of cell types in teratoma tumors on live mice. The cells also closely resembled those derived from fetal fibroblasts, had no chromosomal abnormalities, and displayed fewer problematic epigenetic leftovers from parental somatic cells than are typically seen in iPSCs. Mitalipov said more comparisons are required, however.

“We are now left to analyze the detailed molecular nature of SCNT-ES cells to determine how closely they resemble embryo-derived ES cells and whether they have any advantages over iPS cells,” added Daley. “iPS cells are easier to produce and have wide applications in research and regenerative medicine, and it remains to be shown whether SCNT-ES cells have any advantages.”

But Milatipov pointed out one fundamental difference: while their nuclear genome comes from the donor cell, NT-hESCs contain mitochondrial DNA (mtDNA) from the egg cell. So unlike in iPSCs, nuclear transfer not only reprograms the cell but also corrects any mtDNA mutations that the donor may carry, meaning that patient-specific NT-hESCs could be used to treat people with diseases caused by mitochondrial mutations. “That’s one of the clear advantages with SCNT,” Milatipov said.

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It is possible soon to be established treatment for cocaine dependence. Researchers at Cornell University, have developed a vaccine which prevents cocaine enters the brain and cause euphoria, thus helps the treatment of addiction. The vaccine provides effective treatment, even if the intake of cocaine to be repeated occasionally.

Cornell researchers have successfully implemented vaccine in animal models and are very close to clinical trials in humans. According to Dr. Ronald Crystal, research should begin by the end of the year.

Cocaine blocks the reverse capture of dopamine in the synaptic cleft, which connect the nerve cells to each other. Dopamine is a neurotransmitter that creates a feeling of pleasure and enjoyment. Increasing levels of dopamine in the synaptic cleft is responsible for the euphoria that occurs after taking cocaine.

It prevents the excessive accumulation of domapin in synapses. It contains inactivated viruses on which is "attached" substance chemically resembling cocaine. This allows the immune system to recognize cocaine and his relatives compounds that neutralize it.

For the occurrence of cocaine euphoria necessary cocaine molecules to occupy at least 47% of the dopamine in nerve cells. Of the vaccine in human primates show that cocaine molecules able to occupy less than 20% of dopamine transporters.

Researchers expect the vaccine to be effective in humans, but still can not say how often you should be administered to maintain its effect. For now, just be sure that it will be necessary to apply booster doses.
 
According to official data, in the U.S. there are 1.9 million people using cocaine, 1.4 million of whom are dependent on it. Every year there are over 2 million visits to emergency departments due to drug abuse. Almost 500,000 of them are making the cocaine. Anti-cocaine vaccine has the potential to drastically reduce this number.