Archive for the ‘Male Genetics’ Category

Ken Baker, Columnist Published 12:27 p.m. ET Jan. 14, 2020

Ken Baker and Cocoa(Photo: Submitted)

According to the Chinese Calendar, the 13 months from Jan.25, 2020, through Feb.21, 2021 will be the Year of the Ratthe Gold Rat.

Each of the 12 Chinese Zodiac signs (rat, ox, tiger, rabbit, dragon, snake, horse, goat, monkey, rooster, dog and pig) is associated with one of five elements: water, wood, fire, earth or metal (gold). So all told, it takes 60 years (12 x 5) to cycle through all possible combinations.

A person born under the sign of the Rat is purported to be quick-witted and resourceful, with a rich imagination though, perhaps, a bit shy in courage. Since Chinese culture attributes diligence and thriftiness to the rat, its expected those born in a Rat year will do pretty well for themselves.

Or so its said.

Setting aside such cultural personifications along with any aversion we might harbor towards the animal, what have we learned about the rats biology and the way it actually lives its life?

In our area and indeed throughout North America and Europe, the species youd be most likely to encounter today is the brown or Norway rat (Rattus norvegicus). But thats only been the case over the last several centuries.

The black rat (Rattus rattus), also known as the roof or ship rat, is thought to have invaded Europe from Southeast Asia sometime between the 4th and 2nd century BC and North America in the 16th century. The somewhat larger and more aggressive Norway rat appears to have reached Europe as stowaways on trading ships from Northern China during the 1500s and North American shores some 200 years later.

In cooler northern climates, the Norway has largely replaced the once abundant black rat, which is still the more common species in tropical areas.

The Chinese Zodiac calendar celebrates 2020 as the Year of the Rat, which gives recognition to this Norway rat.(Photo: Submitted)

It should be noted that there are many other species of larger-than-a-mouse rodents commonly referred to as rats. The genus Rattus alone has over 50 such species and there are interesting beasts called rats in several unrelated genera (Neotoma, Dipodomys and Bandicota, for example).

But the black and Norway are the two species that have played the largest role in human history. In fact to ask about the natural habitat of either mammal poses an interesting challenge. Both have been so closely associated with human habitations for so long that the best description of their normal habitat in nature might simply be wherever people live.

Which is not to say their biology is any less complex and interesting. Female Norway rats, for example, commonly live in colonies of six or so related individuals. Each female will have her own nest chamber within a shared (often underground) burrow. Intriguingly, members of the group will often nurse their young collectively.

While daughters commonly remain with the colony, males disperse soon after being weaned. If the population of rats in the area is relatively low, one adult male will typically dominate the colony, vigorously defending it against other males and mating with its females.

In dense populations, however, there will be too many intruders for him to maintain exclusive control of the colony and he will have to suffer the presence of other males seeking to mate with females when they come into breeding condition (about once every 4 -5 days if not impregnated).

In the wild (that is excluding rats kept as pets or in a scientific laboratory), the average lifespan of a Norway rat is probably less than one year. Studies of several European populations found about 95 percentannual mortality, with just a (very) few venerable old-timers making it to three years.

The rats perception of the world (its mvelt in the language of behavioral biologists) is very different from our own. Their eyesight is quite weak beyond a foot away, they can only detect large shapes and movement and, like most other mammals, they cannot detect the color red.

But this doesnt make them less effective in navigating their environment. Norway rats, which are primarily active at night, live in a world of textures, sounds and smells. When moving about, the Norways long whiskers whisk back and forth several dozen times per second, lightly touching all nearby objects.

They can hear (and communicate with) sounds much higher in pitch than we can detect, and its been estimated that over 1 percentof their genetic material is devoted to the detection of odors.

Finally a word on the connection between rats and the Bubonic Plague that swept through the Eastern Hemisphere in the mid-1300s, killing 25 to 60 percentof the human population of Europe. The so-called Black Death, caused by the bite of a flea carrying the Yersinia pestis bacterium, has long been blamed on the spread of flea-infested black rats.

However more recent studies have strongly suggested Yersinias initial invasion of Europe might be better pinned on gerbils, of all things, which unlike rats can carry the bacteria in their blood for some time without killing them.

Oh, and regardless of its name, the Norway rat has no special association with Scandinavia.

Ken Baker is a retired professor of biology and environmental studies. If you have a natural history topic you would like Dr. Baker to consider for an upcoming column, please email your idea to fre-newsdesk@gannett.com.

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Ken Baker: 2020 is the Year of the Rat, but what do we know about the rodents? - The News-Messenger

An announcement from our friends at White River Growpro.

White River Growpro, a specialty gardening store located in downtown White River Junction, is currently running a cannabis pheno hunt and is giving away free cannabis seeds to anyone who would like to participate in the contest.

This is not a traditional cannabis cup in which the biggest and best buds win, its a challenge looking for a particular phenotype amongst many.

This contest, which was announced last spring and has been extended through July 1st, 2020, has already given out over 2500 free seeds and still has several thousand seeds available for those whod like to play. They are specifically searching for an old cannabis strain: East Coast Sour Diesel.

We have always felt that the original cut of East Coast Sour Diesel (ECSD) is one of the finest cannabis cultivars.

Here at Growpro, explains Growpro co-owner and cannabis breeder Kendall Smith, we have always felt that the original cut of East Coast Sour Diesel (ECSD) is one of the finest cannabis cultivars. With wide ranging appeal, this uplifting variety has smells of sour lemon skunk and earth. The problem is that the original is clone only and its become finicky to grow. Were trying to change that.

Ive been working on a breeding project with a 30-year-old cut of ECSD that is currently in the F2 stage, says Smith, meaning there will be a wide genetic expression throughout the seeds. Somewhere in these seeds will be a pheno that is as close to the original East Coast Sour Diesel as we can expect to find.

This crowd sourced breeding project is a creative way to take advantage of current law and share cannabis genetics with the Vermont community. Co-owner Stephanie Waterman says this project was inspired by a culture of sharing genetics amongst friends.

Vermont law only allows for 2 plants in flower, which means pheno hunting can take years and years.

Under current Vermont law, says Waterman, there is not a great way to obtain seeds other than through gifting, and we are limited by our plant counts. Vermont law only allows for 2 plants in flower, which means pheno hunting can take years and years. Thats why were enlisting an army of growers to help us find the pheno, injecting thousands of free seeds into the Vermont growing community, and giving out thousands of dollars in prizes to the winners! Its all in good fun.

Anyone whod like to participate can stop into White River Growpro and request a packet. Each pack contains 13 regular cannabis seeds, meaning they will produce both males and females.

Growers have until 7/1/2020 to submit a quarter ounce of finished flower for the judges.

If your flower is selected as a finalist, you will be asked to submit a clone of that plant that the judges will grow out to confirm the genetic is on point. The winner will be announced in December of 2020.

This contest is about having fun and sharing cannabis genetics with the greater Vermont community.

Anyone who completes the contest and submits finished flower will be able to get a cutting of the winning phenotype. In the end, says Waterman, this contest is about having fun and sharing cannabis genetics with the greater Vermont community. Weve seen some amazing phenotypes coming out of this contest and I love seeing the great work the growers are doing adds Kendall.

For more information about the contest, prizes, and the breeding project, please visit the White River Growpro website and click on Events & Classes.

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White River Growpro's "Hunt for the Pheno Contest" Gives Away Free Cannabis Seeds | Cannabis Events, Culture and News - Heady Vermont

Taylor Tran (left) and her mother Mai Nguyen. Taylor underwent cancer treatment when she was 2 years old, causing her to go into early menopause when she was just 16.

You pay the price for having cancer over and over again.

Mai Nguyens words are loaded with sorrow as she speaks about her 17-year-old daughter, Taylor Tran, who is dealing with fertility concerns more than a decade after she survived late-stage cancer.

Its easy to understand the exasperation Nguyen feels: Her daughter was diagnosed with stage 3 single-cell sarcoma of the kidney when she was 2 years old and was treated with intense chemotherapy and radiation. Now, the treatments that saved her life have put her into early menopause.

Its been traumatic, Nguyen said. Weve tried so hard to allow Taylor to have a normal childhood and this feels like one more thing cancer has taken from her.

Stories like Taylors inspired Seattle Childrens urologist Dr. Margarett Shnorhavorian to tackle a challenging area of research that was largely uncharted more than a decade ago. Since then, shes helped change perspectives and protocols for fertility preservation in childhood cancer survivors.

Stories like Taylors inspired Seattle Childrens urologist Dr. Margarett Shnorhavorian to tackle a challenging area of research that was largely uncharted when she started more than a decade ago.

Shnorhavorians passion stems from the encounters shes had with the families of childhood cancer patients since starting her practice 12 years ago. She often spoke with families whod just received a devastating diagnosis about the importance of fertility preservation.

One thought was that families wouldnt want to think about fertility when they were trying to deal with the chaos of cancer, Shnorhavorian said. But when I brought it up, I saw the tone in the room lift. They were grateful we were talking about their life after cancer, because it meant we believed they would have one. It was like glimpsing at the end of a rainbow.

At the time, there was little information providers could offer about how patients fertility might be affected by various cancer treatments. Families couldnt find the answers they desperately wanted.

Initially, I thought if we brought up sperm banking and an adolescent didnt want to talk about it, we should just end the conversation there, Shnorhavorian said.

That was until a study led by Shnorhavorian changed her mind. The study surveyed over 400 adolescent and young adult cancer patients finding that a significant portion had never discussed their fertility preservation options with their care team before starting treatment.

I learned not to take no for an answer when a young patient didnt want to think about it. We have an obligation to explore the subject and remind them that, even if they are not thinking about their future fertility, we are thinking about it for them, she said.

As Shnorhavorian set out to establish her research program, she was keenly aware of the hurdles shed need to overcome to study fertility in a pediatric population.

First, recruiting enough participants to study the effects of cancer treatment on fertility would be difficult. Childhood cancer is relatively rare, so there were fewer eligible patients to draw from.

Also, many providers were uncomfortable discussing fertility issues with patients and their families who were, understandably, focused on survival. If adolescent and young adult participants did enroll, it would be difficult keep track of them because they change addresses frequently.

Shnorhavorian also had to make study participants comfortable contributing specimens such as sperm samples.

The adolescent and young adult population is unique, so we developed research methods tailored to their needs, she said.

They created a data collection system where patients could participate wherever they were located. They could have blood drawn in their dorm room or collect their sperm sample at home and send it in the mail, rather than going to a clinic.

That was a game-changer in our field, Shnorhavorian said.

Today, thanks to her innovative research methods, Shnorhavorian is leading a multi-site study to investigate the effects of chemotherapy on boys and men who have survived osteosarcoma, a common type of bone cancer.

When I started, there was limited research on male fertility, mainly because everyone had been lulled into a false sense of security thinking boys can sperm bank. But that is not an option for pre-pubertal males, she said.

According to Shnorhavorian, there are still no options for young boys to preserve their fertility.

I chose osteosarcoma because it was a population of men who would not have fertility impairments due to other therapies, like radiation, or their diagnosis. We hope the lessons we learn studying this disease can be applied to other cancers.

Patients are being recruited for the study from 178 Childrens Oncology Group institutions in the U.S., Canada and Australia.

Shnorhavorian and her teammates in Seattle Childrens Center for Clinical and Translational Research are hoping to identify biomarkers of fertility risks and genetic susceptibility to fertility impairments and better understand of sperm development and how cancer therapies modify sperm DNA.

By studying these predicting factors, Shnorhavorian hopes to shed light on why some cancer survivors become infertile after treatment, eventually, leading to preventative interventions.

When Taylor learned she was going into early menopause, she decided to freeze her eggs. My cancer treatment gave me a second chance at life, but that doesnt mean I shouldnt get to have the same experiences others have.

When Taylor learned she was going into early menopause in February 2019, she decided to freeze her eggs. She feels grateful for the opportunity even though several aspects of the fertility treatment were difficult and she often felt isolated.

My cancer treatment gave me a second chance at life, but that doesnt mean I shouldnt get to have the same experiences others have, Taylor said.

Shnorhavorian hopes her research will continue to grow so providers can, one day, offer cancer patients new opportunities to preserve their fertility before treatment or treat their cancer without harming their reproductive health.

It is our obligation to give our patients hope, Shnorhavorian said. We have a long way to go to offer fertility preservation to every child, boy or girl, but from my standpoint, its no longer a question of Should we do this? but rather How do we do it?

Nguyen finds the idea exciting.

I want to see other kids, like Taylor, have the opportunity to raise their own genetic children, she said. It would be amazing if researchers can find a way to cure them without taking away that experience.

To learn more about the clinical trial Dr. Shnorhavorian is leading for osteosarcoma survivors, please visit the study page on our website. For more information on clinical trials at Seattle Childrens, please visit our current research studies page.

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Fighting to Give Every Child With Cancer a Chance to Become a Parent - On the Pulse

LA SALLE On Tuesday morning, the barn at Coyote Ridge Ranch in Weld County served as the bovine equivalent of a hair salon.

Some of the ranchs top Hereford cattle were brought in for a bath and blow-dry. Outside, workers gave the rust and white-colored animals a final clipper trim, preparations for their impending closeups.

The National Western Stock Show is back for its 114th year in Denver and Coyote Ridge Ranch Herefords are right in the thick of it, as theyve been for three decades.

The Cornelius family, lead by Jane Evans and her son Hampton, founded the ranch in Boulder County, but for the past 25 years, its operated on a 1,000-acre spread south of La Salle. The barn/cattle hair salon there is 130 years old and may be the oldest structure in the Beebe Draw valley, according to the family.

Over the decades, the Corneliuses have established a reputation as one of the countrys if not the worlds preeminent producers of top quality Herefords and Hereford genetics. And the stock show is their biggest marketing opportunity of the year.

Denver is like a trade show for us. Were not there to win a ribbon. Its cool when you win one but were there to promote our genetics and make contacts, Jane said of the National Western show, where Coyote Ridge will be showing a pen of three heifers and a pen of three bulls this year.

Were showing our spring-born 2019 cattle, Hampton said. Everything is for sale. The idea is to drum up interest to get people to come back here and take a look at our other ones.

The business-first approach doesnt mean they arent proud of how Coyote Ridge Ranch has performed at National Western. Hampton rattles off the stack of honors the operation has come away with in years past. They include three grand champion pens, two bulls that won individual championships in competitions on the hill at National Western and countless individual class champions.

Its a validation of what youre doing, Jane said.

Coyote Ridge Ranch is what is known in the cattle business as a seedstock producer. The means its herd of 160 or so Herefords is being raised to further the genetics of the breed. It sells bulls, heifers, semen and embryos to commercial Hereford ranching operations that in turn produce steers for slaughter and sale to consumers.

The ranch dates back to when Hampton and his sisters Katie and Coleman, a former Denver Post staff writer, were kids raising cows and calves as part of 4-H and Future Farmers of America programs. The hobby blossomed into a passion and the family herd grew large enough to become a viable business.

The Corneliuses were drawn to Herefords because of the breeds disposition, its hardiness and the animals deep connection to ranching culture in the American West. Nowadays, Coyote Ridge is considered an elite Hereford seedstock producer with genetics from their animals spread across ranching operations in the U.S. and all over the world.

I would describe that family as just being committed to making really good cattle and breeding Herford cattle the way they need to be bred for the commercial industry, said Jack Ward, executive vice president of the American Hereford Association.

Ward and many other staffers from his association are in Denver this week for the stock show. Among the events Ward is organizing is the national Hereford junior heifer show on Wednesday morning and the Mile High Night Hereford Sale, which is expected to bring more than 1,000 people to the National Western Stadium Arena at 6:30 p.m. Friday, Ward said. Coyote Ridge will be represented at both events, of course, with Hampton Cornelius son, John, showing a heifer in the junior show.

Beyond their work furthering the Hereford breed, the Corneliuses have become ambassadors for the cattle industry in Colorado. With a ranch thats within an hours drive of the downtown Denver and a willingness to open their operation to visitors, theyve hosted school groups, chefs, and delegations from countries including China, Japan and South Korea.

(Hamptons wife) Kay and Jane Evans are both so very well-spoken on so many segments of their industry, Colorado Beef Council marketing director Tami Arnold said. Just the typical consumer, we know we could take them out to their place and they would be able to really represent the beef industry well.

For Jane Evans, the most exciting visit came last summer when a Taiwanese trade delegation stopped at Coyote Ridge Ranch. It wasnt just because the visitors were so impressed by seeing a cattle operation where riders on horseback drive a herd across a pasture. She was pleased because the delegates were in Colorado to sign a letter of intent with Gov. Jared Polis to expand access in Taiwan for Colorado agricultural goods including beef.

It gets its moment in the sun in Denver every January during the National Western, but Jane is quick to point out the livestock industry is a major force in Colorados economy. Cattle operations alone generated $3.4 billion in cash receipts in the state last year, according to the University of Colorados 2020 business economic outlook.

Jane Evans, 78, has established a reputation of her own over the years. Cattle ranching has been a male-dominated industry, but she hasnt shied away from being at the center of it. In the mid-1990s, she became the first woman elected to the American Hereford Association board of directors.

She paved the way for women in the beef industry, specifically for leadership and we love her for that, said Arnold, who in addition to working with the Cornelius family through the Colorado Beef Council also ranches nearby and has known them most of her life.

Janes love for agriculture goes back to her childhood in Alabama, when her grandfather would let her tag along when he would assess farms and ranches as part of his work as a banker.

I was very lucky. In those days girls did one thing and boys did another, she said. My mother used to say, When Jane Evans grows up shes going to own a large cattle ranch in the West like Dale Evans, and I do. (Dale Evans was married to singing cowboy Roy Rogers and they had a popular TV show in the 1950s.)

The next week will be a busy one for the Cornelius family. But now that theyve settled into their pen in the National Western Centers evolving stock yards, they do expect to have a little fun.

These guys work alone a lot. When they get together they definitely will kick up their heels a little bit, she said of her family and her fellow ranchers at the stock show. You see people that you have a lot in common with, that you work with, that you swap genetics with. Even though there is stiff competition, there is an awful lot of camaraderie.

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National Western Stock Show: Reputation of Weld County familys Herefords spans the globe - The Denver Post

(Photo : moviehole.net)Hybrid sharks were found in Australia and they were able to swim in cold or tropical waters. This is a fact, not fiction ane researchers are now convinced that it will impact the local environment. All bets are on if there will be more found too.

Sharks are the perfect alpha predator according to nature's design, it is also the most adapted for the aquatic environments. Next question is whether they can evolve any further than they have. Like fiction turning into reality, that might soon be the scenario in the open ocean. It seems evolution, natural selection has found a way to improve an already fearsome alpha predator.

Is this disturbing or just another movie theme, for shark-buffs? No, it has gotten real and not a hoax at all. As stated, evolution and natural selection chooses the survival of the fittest. Several Australian shark scientists did find hybrid sharks, because two different species interbred and produce offspring. It was found out by accident when a survey was underway in Aussie waters.

The sharks catalogued had genetic traits that were not bound to a specific kind of species. So, the best guess it that they have mated and produced young with hybrid traits. After more sifting through the genetic data, the analysis revealed a mix of common blacktip shark and Australian blacktip shark. They must have mated in the wild, since mating is automatic when in spawning season.

Scary as it sounds, these sharks are not producing genetically infertile offspring, but normal individuals capable of reproduction. One thing to consider is they are close sister species, still distinct between each other. Researcher conclude because of the relative closeness of these shark species made the change to a mixed breed possible too.

Another tidbit might be somewhat on the negative side, climate change caused by human activitieshave influenced natural selection very unnaturally. Places where the sharks breed are changing, indirectly and this is why hybrids of mixed species are born. If the environment is steady and no changes, then both species will not stray into each other.

Though they are cartilaginous fish, reproduction is via male and female of the same kind. One big revelation is that sharks will not reproduce with other sharks because of differences in attraction the other sex. Discovery of hybrid sharks have forced shark specialists to rethink their assumptions, in regard to this. Abnormal mating behavior and breeding hybrids is just the tip of the iceberg for researchers, studying sharks.

Will these hybrids be better than their predecessors, or be eliminated by natural selectionas nature deems fit. If these hybrids do find individuals of the same hybrid kind, it will be the birthing of whole new shark species. Most animals alive today and those extinct were part of the process of natural selection, or survival of the fittest.

For sharks that have remained the same for millions of years, introduction of a new hybrid is important. The common blacktip shark and Australian blacktip sharkwill have specific gene set which is evolved to keep the species ready for better adaptations. The hybrid can adjust to different temperatures so they can enter other zones in the ocean. Unlike their parent species, who are located in different waters. This is what makes sharks such adaptable species and ancient species.

Yes, hybrid sharks might be common with the shift in the conditions of the eco-system. all because mankind is responsible for all climatic changes happening now. Will a Great White, Bull Shark, or Tiger Shark hybridcome about? It might and the common blacktip shark, and Australian blacktip shark is proof of that. An ocean with these fish will not be so exciting to go into either.

Related Article: Hybrid Sharks Ready to Take Over the Oceans: Fact and/or Fiction

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Fact or Fiction: Hybrid Sharks To Dominate the World's Oceans Very Soon - Science Times

People from across the South East are joining calls from the NHS urging more men to donate blood.

There's a worry not enough male donors are coming forward which could create problems because their cells can be more effective in helping sick people.

Danielle Jinadu knows how important blood donations are.

The 23-year-old law student has the life-threatening genetic disorder sickle cell disease, and needs eight units of blood every six weeks.

Like all patients who receive multiple transfusions, Danielle relies on a safe and secure supply of blood, and male donors help ensure blood is always there.

Danielle, who is studying law at the University of Warwick, said:"For me, blood transfusions are literally the difference between life and death. Without blood transfusions I know I would not be here alive at 23 years old.

"The people that give blood are often the hidden heroes. I will never get to know their names but they are extraordinary."

The NHS is worried though because there's an imbalance in donations.

Last year, only 40% of new blood donors in our region were men.Until the end of November, almost 12,500 women started donating blood in the South East - compared to just over 8,500 men.

Ellie Hudson knows how important male donors are.

Her son Finley needed three specialist blood transfusion when he was born...

He is one of around 120 people in the UK with the condition Diamond-Blackfan anemia which means he cannot produce red blood cells.

The two-year old now has monthly transfusions at Maidstone hospital.

Ellie said: He would go in once a year or so but since Finley was born he goes as regularly as he can. We are so thankful to everyone who donates, they really are lifesavers.

The NHS wants 48% of its donations this year in the South East to be from men.

Mike Stredder, the head of donor recruitment for NHS Blood and Transplant, said:

"All our donors are amazing. But we need more men to start donating blood in the South East during the New Year. Men's blood can be used in extraordinary, lifesaving ways, but we don't have enough new male donors coming forward. This is not about recruiting as many donors as possible - it's about getting the right gender mix.

"If you can't find an appointment right away don't worry - your blood will do extraordinary things if you donate in a few weeks instead."

You can find more information about becoming a blood donor here.

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Urgent need for male blood donors in the South East - ITV News

Jesse Bloom, left, and Lea Starita are genetic scientists pursuing advances with the technique known as Deep Mutational Scanning, which will be the subject of a symposium and workshop at the University of Washington in Seattle on Jan. 13 and 14. (GeekWire Photo / Todd Bishop)

It has been nearly two decades since scientists accomplished the first complete sequencing of the human genome. This historic moment gave us an unprecedented view of human DNA, the genetic code that determines everything from our eye color to our chance of disease, unlocking some of the biggest mysteries of human life.

Twenty years later, despite the prevalence of genetic sequencing, considerable work remains to fulfill the promise of these advances to alleviate and cure human illness and disease.

Scientists and researchers are actually extremely good at reading genomes, but were very, very bad at understanding what were reading, said Lea Starita, co-director of Brotman Baty Institute for Precision Medicines Advanced Technology Lab, and research assistant professor in the Department of Genome Sciences at the University of Washington.

But that is changing thanks to new tools and approaches, including one called Deep Mutational Scanning. This powerful technique for determining genetic variants is generating widespread interest in the field of genetics and personalized medicine, and its the subject of a symposium and workshop on Jan. 13 and 14 at the University of Washington.

I think approaches like Deep Mutational Scanning will eventually allow us to make better countermeasures, both vaccines and drugs that will help us combat even these viruses that are changing very rapidly said Jesse Bloom, an evolutionary and computational biologist at the Fred Hutchinson Cancer Research Center, the Howard Hughes Medical Institute and the University of Washington Department of Genome Sciences.

Bloom, who researches the evolution of viruses, will deliver the keynote at the symposium, held by the Brotman Baty Institute and the Center for the Multiplex Assessment of Phenotype.

On this episode of the GeekWire Health Tech Podcast, we get a preview and a deeper understanding of Deep Mutational Scanning from Bloom and Starita.

Listen to the episode above, or subscribe in your favorite podcast app, and continue reading for an edited transcript.

Todd Bishop: Lets start with the landscape for precision medicine and personalized medicine. Can you give us a laypersons understanding of how personalized medicine differs from the medicine that most of us have encountered in our lives?

Lea Starita: One of the goals of precision medicine is to use the genomic sequence, the DNA sequence of the human in front of the doctor, to inform the best course of action that would be tailored to that person given their set of genes and the mutations within them.

TB: Some people in general might respond to certain treatments in certain ways and others might not. Today we dont know necessarily why thats the case, but personalized medicine is a quest to tailor the treatment or

Starita: To the individual. Exactly. Thats kind of personalized medicine, but you could also extend that to infectious disease to make sure that youre actually treating the pathogen that the person has, not the general pathogen, if you would. How would you say that, Jesse?

Jesse Bloom: I would elaborate on what Lea said when it comes to infectious diseases and other diseases. Not everybody gets equally sick when they are afflicted with the same underlying thing, and people tend to respond very differently to treatments. That obviously goes for genetic diseases caused by changes in our own genes like cancer, and it also happens with infectious diseases. For instance, the flu virus. Different people will get flu in the same year and some of them will get sicker than others, and thats personalized variation. Obviously wed like to be able to understand what the basis of that variation is and why some people get more sick in some years than others.

TB: Where are we today as a society, as a world, in the evolution of personalized medicine?

Starita: Pretty close to the starting line still. Theres been revolutions in DNA sequencing, for example. Weve got a thousand dollar genome, right? So were actually extremely good at reading genomes, but were very, very bad at understanding what were reading. So you could imagine youve got a human genome, its three billion base pairs times two, because youve got two copies of your genome, one from your mother, one from your father, and within that theres going to be millions of changes, little spelling mistakes all over the genome. We are right now very, very, very I cant even use enough verys bad at predicting which ones of those spelling mistakes are going to either be associated with disease or predictive of disease, even for genes where we know a lot about it. Even if that spelling mistake is in a spot in the genome we know a lot about, say breast cancer genes or something like that, we are still extraordinarily bad at understanding or predicting what effects those changes might have on health.

Bloom: In our research, were obviously also interested in how the genetics of a person influences how sick they get with an infectious disease, but we especially focus on the fact that the viruses themselves are changing a lot, as well. So theres changes in the virus as well as the fact that were all genetically different and those will interact with each other. In both cases, it really comes back to what Lea is saying is that I think weve reached the point in a lot of these fields where we can now determine the sequences of a humans genome or we can determine the sequence of a virus genome relatively easily. But its still very hard to understand what those changes mean. And so, thats really the goal of what were trying to do.

TB: What is deep mutational scanning in this context?

Lea Starita: A mutation is a change in the DNA sequence. DNA is just As, Cs, Ts and Gs. Some mutations which are called variants are harmless. You can think of a spelling mistake or a difference in spelling that wouldnt change the word, right? So the American gray, which is G-R-A-Y versus the British grey, G-R-E-Y. If you saw that in a sentence, its gray. Its the color.

But then it could be a spelling mistake that completely blows up the function of a protein, and then in that case, somebody could have a terrible genetic disease or could have an extremely high risk of cancer, or a flu virus could now be resistant to a drug or something like that, or resistant to your immune response. Or, mutations could also be beneficial, right? This is what allows evolution. This is how flu viruses of all the bacteria evolve to become drug resistant or gain some new enzymatic function that it needs to survive.

Bloom: For instance, in the case of mutations in the human genome, we know that everybody has mutations relative to the average human. Some of those mutations will have really major effects, some of them wont. The very traditional way or the way that people have first tried to understand what those mutations do is to sequence the genomes of a group of people and then compare them. Maybe here are people who got cancer and here are people who didnt get cancer and now you look to see which mutations are in the group that got cancer versus the group that didnt, and youll try to hypothesize that the mutations that are enriched in the group that did get cancer are associated with causing cancer.

This is a really powerful approach, but it comes with a shortcoming which is that theres a lot of mutations, and it gets very expensive to look across very, very large groups of people. And so the idea of a technique like deep mutational scanning is that we could simply do an experiment where we test all of the mutations on their own and we wouldnt have to do these sort of complicated population level comparisons to get at the answer. Because when youre comparing two people in the population, they tend to be different in a lot of ways, and its not a very well-controlled comparison. Whereas you can set up something in the lab where you have a gene that does have this mutation and does not have this mutation, and you can really directly see what the effect of that mutation is. Really, people have been doing that sort of experiment for many decades now. Whats new about deep mutational scanning is the idea that you can do that experiment on a lot of mutations all at once.

Starita: And its called deep because we try to make every possible spelling mistake. So every possible change in the amino acid sequence or the nucleotide sequence, which is the A, C, Ts and Gs, across the entire gene or the sequence were looking at.

Bloom: Lets say we were to compare me and Lea to figure out why one of us had some disease and other ones didnt. We could compare our genomes and theres going to be a lot of differences between them, and were not really going to know what difference is responsible. We dont even really know if it would be a change in their genomes thats responsible. It could be a change in something about our environment. So the idea behind deep mutational scanning is we would just take one gene. So in the case of Lea, she studies a particular gene thats related to breast cancer, and we would just make all of the individual changes in that gene and test what they do one by one. And then subsequently if we were to see that a mutation has some effect, if we were to then observe that mutation when we sequenced someones genome, we would have some idea of what it does.

Starita: The deep mutational scanning, the deep part is making all possible changes. We have all of that information at hand in an Excel file somewhere in the lab that says that this mutation is likely to cause damage to the function of the protein or the activity of the protein that it encodes. Making all of the possible mutations. Thats where the deep comes from.

TB: How exactly are you doing this? Is it because of advances in computer processing or is it because of a change in approach that has enabled this increase in volume of the different mutations you can look at?

Bloom: I would say that theres a number of technologies that have improved, but the really key one is the idea that the whole experiment can be done all at once. The traditional, if you were to go back a few decades way of doing an experiment like this, would be take one tube and put, lets say the normal or un-mutated gene variant in that, and then have another tube which has the mutant that you care about, and have somehow do an experiment on each of those two tubes and that works well.

But you can imagine if you had 10,000 tubes, it might start to become a little bit more difficult. And so the idea is that really the same way that people have gotten very good at sequencing all of these genomes, you can also use to make all of these measurements at once. The idea is you would now put all of different mutants together in the same tube and you would somehow set up the experiment, and this is really the crucial part of the whole thing, set up the experiment such that the cell or the virus or whatever youre looking at, how well it can grow in that tube depends on the effect of that mutation. And then you can just use the sequencing to read out how the frequencies of all of these mutations have changed. You would see that a good mutation that lets say helped the cell grow better would be more representative in the tube at the end, and a bad mutation would be less representative in the tube. And by doing this you could in principle group together tens of thousands or even hundreds of thousands or millions of mutations all at once and read it all out in one experiment.

Starita: This has been enabled by that same revolution that has given us the thousand dollar genome. These DNA sequencers that were now using, not really to sequence human genomes, but were using them as very expensive counting machines. So, were identifying the mutation and were counting it. Thats basically what were using the sequencers for. Instead of sequencing human genomes, were using them as a tool to count all of these different pieces of DNA that are in these cells.

TB: At what stage of development is deep mutational scanning?

Starita: It started about 10 years ago. The first couple of papers came out in 2009 and 2010 actually from the Genome Sciences department at University of Washington. Those started with short sequences and very simplified experiments, and we have been working over the years to build mutational scanning into better and more accurate model systems, but that are increasing the complexity of these experiments. And so weve gone from almost, Hey, thats a cute experiment you guys did, to doing impactful work that people are using in clinical genetics and things like that.

TB: When youre at a holiday party and somebody asks you what you do and then they get really into it and they ask you, Wait, what are the implications of not only personalized medicine but this deep mutational scanning? Whats this going to mean for my life?

Starita: Right now it hasnt been systematically used in the clinic, but well get phone calls from UW pathology that says, Hey, I have a patient that has this variant. We found the sequence variant and this patient has this phenotype. What does this mutation look like in your assay? And were like, Well, it looks like its damaging. And then they put all of that information together and they can actually go back to that patient and say, You are at high risk of cancer. Were going to take medical action. That has happened multiple times. Were working right now to try to figure out how to use the information that we are creating. So these maps of the effect of mutations on these very important proteins and how to systematically use them as evidence for or against their pathogenicity. Right now for a decent percentage of these people who are telling them, Well, youve got changes but we dont know what they do. We want those tests to be more informative. So you go, you get the test, they say, That is a bad one. That ones fine. That mutation is good. That ones OK. That one, though. That ones going to cause you problems. We want more people to have more informative genetic testing because right now in a decent proportion of tests come back with an I have no idea, answer.

Bloom: You can also think about mutations that affect resistance to some sort of drug. For many, many types of drugs, these include drugs against viruses, drugs against cancers and so on, the viruses and the cancers can become resistant by giving mutations that allow them to escape from that drug. In many cases there are even multiple drugs out there and you might have options of which drug to administer, but you might not really know which one. Clinicians have sort of built up lore that this drug tends to work more often or you try this one and then you try this other one, but because how well the drug works is probably in general determined by either the genetic mutations in lets say the cancer or the person or the genetic mutations in the virus or pathogen, if you knew what the effects of those mutations were ahead of time, you could make much more intelligent decisions about which drugs to administer. And there really shouldnt be a drug that works only 50 percent of the time; youre probably just not giving it in the right condition 50 perfect of the time. Wed like to be able to pick the right drug for the right condition all the time.

TB: And thats what precision medicine is about.

Starita: Yes.

TB: Deep mutational scanning as a tool.

Starita: To inform precision medicine.

Bloom: These deep mutational scanning techniques were really developed by people like Jay Shendure and Stan Fields, and Lea and Doug Fowler to look at these questions of precision medicine from the perspective of changes in our human genomes affecting our susceptibility to diseases. I actually work on mutations in a different context, which has mutations in the viruses that infect us and make us sick. These viruses evolve quite rapidly. In the case of flu virus, youre supposed to get the flu vaccine every year. The reason why you have to get it every year is the virus is always changing and we have to make the vaccine keep up with the virus. The same thing is true with drugs against viruses like flu or HIV. Sometimes the viruses will be resistant, sometimes the drugs will work. These again have to do with the very rapid genetic changes that are happening in the virus. So, were trying to use deep mutational scanning to understand how these mutations to these viruses will affect their ability to, lets say, escape someones immunity or escape a drug that might be used to treat that person.

TB: How far along are you on that path?

Bloom: Were making progress. One of the key things weve found is that the same mutation of the virus might have a different impact for different people. So we found using these approaches that the ways that you mutate a virus will allow the virus sometimes to escape from one persons immunity much better than from another persons immunity. And so were really right now trying to map out the heterogeneity across different people. And hopefully that could be used to understand what makes some people susceptible to a very specific viral strain versus other people.

TB: And so then would your research extend into the mutations in human genes in addition to the changes in the virus?

Bloom: You could imagine eventually wanting to look at all of those combinations together, and we are very interested in this, but the immediate research were focusing on right now actually probably is not so much driven by the genetics of the humans. In the case of influenza virus, like I was saying, we found that if theres a virus that has some particular mutation, it might, lets say, allow it to escape from your immunity but not allow it to escape from the immunity of me or Lea. That doesnt seem to be driven as much we think by our genetics, but rather our exposure histories. So in the case of influenza, were not born with any immunity to influenza virus. We build up that immunity over the course of our lifetime because we either get infected with flu or we get vaccinated with flu and then our body makes an immune response, which includes antibodies which block the virus. Each of us have our own personal history, not genetic history, but life history of which vaccinations and which infections weve gotten. And so, that will shape how our immune response sees the virus. As a result, we think that that doesnt really have so much of a genetic component as a historical component.

TB: Just going with the flu example, could this result in a future big picture where I go in to get my flu vaccine and its different than the one the next person might go in to get?

Bloom: What we would most like to do is use this knowledge to just design a vaccine that works for everybody. So that would just be the same vaccine that everyone could get. But its a very interesting I think at this point I would say its almost in the thought experiment stage to think about this. When you think of something like cancer, like Lea was saying, you can use these tools to understand when people have mutations that might make them at risk for a cancer, but thats actually often a very hard thing to intervene for, right? Its not so easy to prevent someone from getting cancer even if you know theyre at risk. But obviously if people are able to do that, theyre interested in spending a lot of money to do it, because cancer is a very severe thing and you often have a very long window to treat it.

Something like a flu virus is very much at the other end. If I had the omniscient capability to tell you that three days from now youre going to get infected with flu and youre going to get really sick, we could prevent that. We have the technology basically right now to prevent that, if its nothing else than just telling you to put on a bunch of Purell and dont leave your bedroom. But theres also actually some pretty good interventions including prophylactics to flu that work quite well. But the key thing is, right now we think of everyone in the world as being at risk all the time and you cant be treating everybody in the world all the time against flu. Theres just too many people and the risk that any person

Starita: Not that much Tamiflu on the market.

Bloom: Not that much, and the risk of it So I think to the extent that we could really identify whos at the most risk in any given year, that might allow us to use these interventions in a more targeted way. Thats the idea.

TB: And how does deep mutational scanning lead to that potentially?

Bloom: Yeah. So the idea, and at this point, this is really in the research phase, but the idea is if we could identify that say certain people or certain segments of the population, that because of the way their immunity, lets say, is working makes them very susceptible to the viral mutant that happens to have arisen in this particular year, we could then somehow either suggest that theyre more at risk or, as you suggested, design a vaccine thats specifically tailored to work for them. So thats the idea. I should make clear that that is not anywhere close to anybody even thinking of putting it into economic practice at this point because even the concepts behind it are really quite new. But I do think that theres a lot of potential if we think of these infectious diseases not so much as an act of God, where you just happened to someone sneezed on you as youre walking down the street, but actually a complex interaction between the mutations in the virus and your own either genetics or immune system, we can start to identify who might be more at risk for certain things in certain years, and that would at least open the door to using a lot of interventions we already have.

Starita: The first year was three years ago, and some very enthusiastic graduate students started it. Basically, it was almost like a giant lab meeting where everybody who is interested in this field came. Somebody tweeted it out and then all of a sudden people from UCSF were there and were like, What the heck? It was great and we all talked about the technology and how we were using it. The next year, the Brotman Baty Institute came in and were like, OK, well, maybe if we use some of this gift to support this, we can have a bigger meeting. And then it was 200 people in a big auditorium and that was great. And now this year, its a two-day symposium and workshop, and its also co-sponsored by a grant from the National Human Genome Research Institute. But now weve got hundreds of people, so about 200 people again, but now flying in from all over the world. Weve got invited speakers, and the workshop, which is Tuesday, is a more practical, If youre interested in this, how do you actually do these experiments?

TB: Whats driving the interest in deep mutational scanning?

Bloom: We are starting to have so much genetic information about really everything. It used to be, going back a couple of decades, a big deal to determine even the sequence of a single flu virus. It was totally unthinkable to determine the sequence of a human genome, right? If you dont know what mutations are there, you dont really care that much what they do. Now we can determine the sequence of tens of thousands of flu viruses. I mean, this is happening all the time, and we can determine the sequence of thousands, even tens of thousands of human genomes. So now it becomes, as Lea said, really important to go from just getting these sequences to understanding what the mutations that you observe in these sequences actually will mean for human health.

See this site for more on the Brotman Baty Institute for Precision Medicine and the Deep Mutational Scanning Symposium and Workshop, Jan. 13 and 14 in Seattle. The symposium is free to attend if youre in the Seattle area, and it will also be livestreamed, with archived video available afterward.

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Scientists pursue new genetic insights for health: Inside the world of deep mutational scanning - GeekWire

A B.C. transgender teens bid to obtain hormone therapy was legal, B.C.s Court of Appeal ruled unanimously Jan. 10 in supporting a lower court decision.

The child A.B. is able to assert his rights, and has done so in accordance with the law, Chief Justice Robert Bauman and Justice Barbara Fisher wrote in the decision.

The 15-year-old A.B. was born female but wanted to pursue therapy, a move approved by his mother, E.F., but not by his father, C.D. The parents are separated but share parenting duties.

Doctors found A.B. sufficiently mature to make the treatment decision on his own, and C.D. began legal action.

The appeal court had to examine three Supreme Court of BC orders before arriving at its conclusion that ABs consent to that treatment is valid, and no further consent from his parents, in particular CD, is required in that regard.

A February 2019 order declared A.B. validly able to consent to treatment, and that referring to A.B. as a girl or attempting to convince him to halt treatment would be considered family violence under the Family Law Act.

An April 2019 protection order restricted the fathers ability to speak with others, including media outlets and A.B., about his decision to receive therapy.

And, a July 2019 order dismissed C.D.s action initiated by C.D. as vexatious and an abuse of process.

The father appealed.

He claimed the orders violated his Charter-protected freedoms of belief and expression and what he terms parental rights, were procedurally unfair, and not in his childs best interests.

A.B., however, said the decisions were Charter-compliant and in his best interests as well as the statutory right of mature minors to make their own medical decisions.

His mother supported that claim.

The decision said A.B. has identified as male since he was 11 years old and began socially transitioning at 12, enrolling in school under a chosen male name and using male pronouns with his teachers and peers.

Around 13 years of age, after two years of consistently identifying as male, ABs persistent discomfort with his body led him to want to take steps to appear more masculine, the court said.

He was soon diagnosed with gender dysphoria, a recognized medical condition where a person experiences significant distress because the gender identity they experience differs from their genetic or biological gender, and how others perceive them, the court said.

A doctor said he could be a good candidate for treatment and another found such treatment was reasonable and in his best interests.

The process stopped once doctors found out about C.Ds opposition.

Doctors explained to C.D. that minors are permitted to consent to their own medical treatment under a section of the Infants Act.

One doctor asked for an opinion from the Provincial Health Services Authority Ethics Service, which agreed that A.B. demonstrated capacity to understand the treatment.

The teen was further referred to the B.C. Mental Health Centre, which found that he demonstrated detailed understanding of the risks and benefits of the treatment, and that he displayed reasonable judgment and insight.

C.D. filed suit to stop treatment in late 2018. Treatment was ordered stopped until the case could be heard.

The court said where a child has consented to health care under the Infants Act, the Family Law Act doesnt provide authority to start consideration of the childs best interests over medical treatment.

The court said the father continually disrespected his childs choices and in seemed oblivious to the effect of his behaviour on A.B. But, the court added, such effects did not rise to the level of family violence.

The court said C.D.s claims he parental rights under the Charter had been violated had no merit.

jhainsworth@glaciermedia.ca

@Jhainswo

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Trans teen can decide on hormone therapy, court rules - The Tri-City News

Ultragenyx Pharmaceutical saw its shares jump around 27% in trading Friday after announcing positive top-line data out of its gene therapy trial.

Its a small number, just three patients that form part of a third cohort for the phase 1/2 study, as well as another small test but a longer-term look from the second cohort.

In cohort three testing the biotechs drug DTX301, an adeno-associated virus gene therapy for the treatment of ornithine transcarbamylase (OTC) deficiency, there were two confirmed female responders as well a third potential male responder who requires longer-term follow-up to confirm response status.

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Meanwhile, in cohort two, one female patient saw a new response after a year. The biotech added that the two previously disclosed responders in cohort one and two also remain clinically and metabolically stable at 104 and 78 weeks, respectively. Across all nine patients dosed in the study, up to six patients have demonstrated a response, it said in a statement.

RELATED: BIO: In conversation with Emil Kakkis, Ultragenyx CEO

OTC deficiency is a rare X-linked genetic disorder characterized by complete or partial lack of the enzyme OTC. Excess ammonia, which is a neurotoxin, travels to the central nervous system through the blood,

According to the National Organization for Rare Disorders, the severity and age of onset of OTC deficiency vary from person to person, even within the same family. A severe form of the disorder affects some infants, typically males, shortly after birth (neonatal period). A milder form of the disorder affects some children later in infancy. Both males and females may develop symptoms of OTC deficiency during childhood. Most carrier females are healthy, but may be prone to severe headaches following protein intake.

Analysts at Jefferies said the data looked better than expected and could be a positive spark to help turn the stock heading into 2020 events. It certainly did in the immediate term, with the biotechs shares up by 27% in mid-morning trading Friday.

We are encouraged to see a more uniform response at the higher doses including three female responders. To date, three patients in the study have discontinued alternate pathway medication and liberalized their diets while remaining clinically and metabolically stable, said Eric Crombez, M.D., chief medical officer of the Ultragenyx Gene Therapy development unit.

We are moving to prophylactic steroid use in the next cohort as we believe this could further enhance the level and consistency of expression that we have demonstrated so far.

See more here:
Ultragenyx shares jump on 'better than expected' gene therapy data - FierceBiotech

INTRODUCTION

Congenital defects are a leading cause of morbidity worldwide, accounting for the deaths of 330,000 newborns every year. Brain malformations, including microcephaly and holoprosencephaly (HPE), are the most common congenital anomalies and place a heavy burden on the affected individuals and the health care system (13). HPE is a structural anomaly of the developing forebrain affecting 1:250 embryos and 1:16,000 live-born infants. Clinically, HPE encompasses a continuum of brain malformations and is accompanied with a spectrum of craniofacial defects in 80% of the cases; microcephaly and eye defects are among the most common features in affected individuals (4). In the majority of cases, the underlying cause remains uncertain due to the high complexity and the multigenic origin of these anomalies (5, 6). Lately, it has become clear that HPE is caused by a malfunction in key signaling pathways in the early embryo, leading to developmental defects in the organizing centers and midline structures (7). The defects involve a sequence of developmental steps that begin with Nodal signaling to establish the midline progenitors in the developing primitive streak (PS). It then continues with the proper positioning of the forming prechordal plate beneath the neuroectoderm and activation of midline Hedgehog signals to maintain the anterior identity of the forebrain. However, the restriction of HPE genetic determinants to a handful of NODAL and Sonic hedgehog (SHH) pathway regulators stems from our limited understanding of the molecular events governing specification of early and late midline structures. Expansion of this genetic repertoire has become a necessity to develop therapeutic options and improve molecular diagnosis of HPE.

Genes encoding transcription factors (TFs) and epigenetic regulators are relevant etiological candidates given their central role in integrating signaling cascades and orchestrating multiple biological processes. Deficiency in their function can disturb entire transcriptional programs, involving numerous genes and molecular pathways, leading to a complex pathological outcome. Consistent with this hypothesis, we have recently identified a loss-of-function (LOF) mutation in the transcriptional regulator PRDM15 in patients with a syndromic form of HPE. Here, we combine mouse genetics and epigenomic approaches to uncover the role of this TF in congenital brain malformations. Our findings establish PRDM15 as a key regulator of NOTCH and WNT/PCP pathways in the developing embryo, implicating them in regulation of anterior/posterior (A/P) patterning and forebrain development. In addition, we uncover new genetic variants in key components of these signaling pathways in patients with HPE. Collectively, our findings refine the molecular mechanisms governing forebrain development and set the stage for the identification of new HPE candidate genes.

Homozygosity mapping and whole-exome sequencing on patients with steroid resistant nephrotic syndrome (SRNS) identified three recessive mutations in PRDM15 (NM_001040424.2). These mutations are located in the sequences coding for the PR domain (c.461T>A; p.Met154Lys-M154K and c.568G>A; p.Glu190Lys-E190K) and the 15th zinc finger (c.2531G>A; p.Cys844Tyr-C844Y), respectively (Fig. 1A). Of particular interest, in four consanguineous families that have the variant encoding PRDM15 C844Y, the affected probands exhibited a syndromic form of SRNS consistent with the Galloway-Mowat syndrome (8). Besides renal defects, the patients displayed facial (narrow forehead, microcephaly, abnormal cerebral gyration, and ophthalmic abnormalities) and extracranial defects (heart malformations and postaxial polydactyly) (9).

(A) Schematic representation of the PRDM15 mutation positions and the affected domains. (B) Alkaline phosphatase (AP) staining of ESCs; the respective genotypes are indicated in the lower panel. Data are average of four independent cell cultures (n = 4) SD. Statistical tests were applied on differences observed in the percentage of completely undifferentiated colonies. Students t test (two sided) was used to determine significance. (C) Heat map of differentially expressed genes in ESCs upon the indicated genetic manipulations. (D) mRNA levels of Rspo1 in ESCs; the respective genotypes are indicated by color code. Expression levels were normalized to Ubiquitin (Ubb), and Prdm15fl/fl (empty vector) was used as reference. Data shown are from three independent experiments (n = 3). (E) Enrichment of PRDM15 binding on promoter regions of the target gene (Rspo1) in ESCsrespective genotypes are indicated by color codeas measured by ChIP-qPCR. Depicted is the average enrichment [data from three independent cell cultures (n = 3)] over percent of input. In (B) to (E), the endogenous mouse Prdm15 has been deleted by the addition of OHT (50 nM) after ectopic expression of WT or mutant human PRDM15 (hPR15). In (D) and (E), center values, mean; error bars, SD. Students t test (two sided) was used to determine significance.

We have recently demonstrated that PRDM15 regulates the transcription of Rpso1 and Spry1, two key components of the MAPK (mitogen-activated protein kinase)/ERK (extracellular signalregulated kinase) and WNT pathways, to maintain nave pluripotency of mouse embryonic stem cells (mESCs) (10). To evaluate the effects of these mutations on PRDM15 function, we ectopically expressed the three identified human variants in Prdm15-deficient embryonic stem cells (ESCs) (Prdm15/). Only hPR15-C844Y, which is associated with brain defects in humans, failed to restore ESC self-renewal (Fig. 1B), and most importantly, the global changes in gene expression, induced by loss of endogenous PRDM15 (Fig. 1C and table S1 (A to E)]. These data strongly suggest that hPR15-C844Y is a LOF mutation. While hPR15-M154K and hPR15-E190K rescued Rspo1 expression at levels comparable to the wild-type (WT) human PRDM15 (hPR15-WT), hPR15-C844Y failed to restore its transcript levels [quantitative polymerase chain reaction (qPCR)] and to activate its transcription in a luciferase reporter assay (Fig. 1D and fig. S1A).

To gain further insights into the impact of these mutations on PRDM15 function, we tested the stability of the encoded proteins and their cellular localization. Immunofluorescence staining, in a Prdm15/ background, showed that none of the mutations affected the nuclear localization of PRDM15 (fig. S1B). On the other hand, all three mutants encoded less stable proteins (fig. S1C). We have previously shown that the zinc finger domains are required for DNA binding and transcriptional activity of PRDM15 (10). Thus, we sought to test the ability of the various mutants to bind to chromatin. Consistent with an LOF of the zinc finger mutant, chromatin immunoprecipitation (ChIP)qPCR analysis revealed reduced enrichment of hPR15-C844Y at the promoter region of Rspo1 (Fig. 1E), a result compatible with its inability to promote its transcription (Fig. 1D and fig. S1A).

To gain molecular insights on the effects of PRDM15 LOF during mammalian development, we intercrossed Prdm15lacZ/+ heterozygous mice, which are healthy and fertile. A description of all the Prdm15 alleles and deleter strains used in this study is summarized in fig. S2A. Consistent with a fundamental role of PRDM15 during embryonic development, we obtained no homozygous mutant [Prdm15lazZ/lacZ knockout (KO)] pups (Fig. 2A), while of the hundreds Prdm15lacZ/+ embryos that were dissected at various stages of development, none showed any defects. Timed matings revealed the embryonic lethality of Prdm15lazZ/lacZ (KO) embryos occurs between embryonic days 12.5 (E12.5) and E14.5 (Fig. 2A). Notably, at E12.5, KO embryos were smaller and showed a spectrum of brain malformations affecting predominantly the anteriormost structures of the head, including the eyes (Fig. 2B), consistent with the brain and facial features observed in patients with the C844Y mutation. Coronal sections of the brain at this stage confirmed that the lateral and medial ganglionic eminences were underdeveloped. Furthermore, we noted an abnormal separation of the cerebral hemispheres, reminiscent of HPE (Fig. 2C). Classic HPE encompasses a continuum of brain anomalies caused by neural tube patterning defects that affect the anteriormost structures and is often accompanied by craniofacial defects involving the eyes (4, 11, 12).

(A) Genetic distribution of embryos from Prdm15+/LacZ intercrosses, indicating lethality between E12.5 and E14.5. (B) Phenotypic continuum of brain defects in E12.5 Prdm15lacZ/lacZ KO embryos. (C) Hematoxylin and eosin (H&E) staining of serial coronal sections of E12.5 brains from Prdm15+/+ WT (upper panel) and Prdm15lacZ/lacZ KO (lower panel) embryos. The mutants lack the complex organization of the anterior forebrain, including the lateral (LGE) and medial ganglionic eminences (MGE), the epithalamic and dorsal thalamic neuropeithelium (NE), and eyes. (D) Nestin-Cremeditated deletion of Prdm15 in neuronal precursors does not affect brain development. Representative images are shown in (B) to (D). LGE/MGE, lateral and medial ganglionic eminences; NE, neuropeithelium; NCX, neocortex; E, eye; LV, lateral ventricle; V, ventricle; TOT, total. (B and D) Photo credit: Messerschmidt and Mzoughi.

These results prompted us to delete Prdm15 specifically in the developing brain by crossing Prdm15fl/fl mice to the Nestin-Cre deleter strain. This Cre recombinase is active at ~E11 in neural stem cells/progenitors and would reveal whether PRDM15 is essential for the process of neurogenesis. The resulting Prdm15/::Nestin-CRE embryos did not show any apparent defects at E12.5 (Fig. 2D), were born at the expected Mendelian ratios, and developed into healthy adults (fig. S2B). This suggests that PRDM15 is required at earlier time points of forebrain specification.

Defects in Prdm15 KO embryos are apparent before the onset of neurulation, as mutants were markedly smaller and had an abnormal morphogenesis by E7.5 (fig. S3A). Between E6.5 and E7.5, two signaling centers act sequentially to pattern the forebrain in the mouse embryo (Fig. 3A) [reviewed in (1315)]. The first resides within the extraembryonic lineages and is called the anterior visceral endoderm (AVE). The AVE imparts anterior identity to the underlying epiblast, thereby restricting the site of gastrulationthe PSto the posterior epiblast. During gastrulation, a second specialized population of cells, known as the AME, emerges from the anterior PS (APS). These cells migrate anteriorly, giving rise to the anterior definitive endoderm and prechordal plate mesoderm. Their role is to produce secondary inductive cues that reinforce anterior identity in the overlying neural plate (Fig. 3A).

(A) Schematic of the signaling centers governing A/P patterning in the mouse embryo. (B) At E6.5, Foxa2 is expressed in the AVE (red line) and APS (red asterisk). At E7.5, Lhx1 transcripts label the visceral endoderm (VE) overlying the epiblast including the AVE as well nascent mesoderm and midline axial mesendoderm. In Prdm15 mutants (mut), Foxa2 expression is confined to the distal VE, with little enrichment in the prospective AVE. Lhx1 is detected in the VE and mesoderm of the middle Prdm15 mutant, but only in the VE of the one on the right. (C) Expression of T, Lefty2, Foxa2, Chordin, and Shh in WT and Prdm15lacZ/lacZ embryos at E7.5. In Prdm15 mutants, T is expressed normally in the PS; Lefty2 transcripts are down-regulated in nascent mesoderm; Foxa2 and Chordin expression remains high distally in the region of the APS (angled black-dashed line) but does not extend anteriorly in the midline axial mesendoderm (am); and Shh expression is similarly weak in the anterior midline (asterisk). n, node. (D) Expression of Six3/Shh or Otx2/Shh in WT (upper) and Prdm15lacZ/lacZ KO (lower) embryos at E8.5. Six3 and Otx2 expression highlights the reduction in anterior forebrain (fb) development (angled black dashed lines) in Prdm15lacZ/lacZ KO mutants. no, notochord; mb, midbrain; DVE, Distal Visceral Endoderm. Representative images are shown in (B) to (D). (C and D) Photo credit: Dun and Ong.

We reasoned that loss of PRDM15 might impair forebrain specification during the earliest events of anterior patterning and therefore examined the expression of a panel of marker genes diagnostic for defects in either the AVE or AME in Prdm15 KO embryos. Foxa2 is a marker of both, AVE and APS, in early PS stage embryos at E6.5. In Prdm15 KO embryos, in situ labeling shows expression in the distal visceral endoderm overlying the epiblast in a pattern typically observed 1 day earlier in WT embryos (Fig. 3B) (16). We conclude that Prdm15 KO embryos are developmentally delayed even before gastrulation. At E7.5, Lhx1 is expressed in the nascent mesoderm and anterior midline mesendoderm. In the smaller, delayed Prdm15 KO littermate embryos, Lhx1 is expressed normally throughout the visceral endoderm, including the AVE, as well as in the nascent mesoderm (Fig. 3B) (17, 18). Both FOXA2 and LHX1 are required for the formation and function of the AVE, and their activation provides evidence that the initial specification of the primary anterior-posterior axis by the AVE is normal in Prdm15 KO embryos.

We next examined the expression of PS (T and Lefty2) and AME (Foxa2, Chordin, and Shh) marker genes. By E7.5, Prdm15 KO embryos are easily recognizable due to a characteristic ruffling in the extraembryonic visceral endoderm, with a fully extended PS that expresses both T and Lefty2 (Fig. 3C). At this stage, Foxa2 is expressed in the node, which marks the anterior end of the PS, and the AME that extends rostrally in WT embryos. In contrast, in Prdm15 KO embryos, Foxa2 transcripts are present distally but do not extend anteriorly (Fig. 3C). A similar pattern is observed with Chordin, which also labels the node and AME in WT embryos but is confined to the APS in Prdm15 KOs (Fig. 3C). Shh expression is also diagnostic for the node and AME, but in KO embryos, only a few Shh-positive cells are observed along the anterior midline (Fig. 3C). Together, these results show that loss of PRDM15 specifically affects the production of the anterior AME. Consequently, the crucial refining signals produced by these cells that orchestrate the continued patterning and morphogenesis of the anterior neuroectoderm are lost, resulting in anterior truncations that are evident by diminished forebrain expression of Six3 and Otx2 in Prdm15 KO mutant embryos at E8.5 (Fig. 3D). To further corroborate these findings, we deleted Prdm15 specifically in the epiblast, using the Sox2-Cre transgene (fig. S3B) (19), while maintaining WT extraembryonic tissues. Consistent with an essential role for PRDM15 in the PS-derived AME and not AVE specification, Prdm15/::Sox2-CRE embryos died in utero starting at E12.5 (fig. S3C) and exhibited a spectrum of brain defects similar to those observed in Prdm15 KO embryos (fig. S3D).

To examine the impact of PRDM15 depletion on early embryonic processes, namely, A/P patterning, we sequenced the transcriptome of WT versus Prdm15 KO E6.5 embryos. We reasoned this could be the most critical stage for AME specification as AME cells emerge less than 24 hours later. Unbiased clustering of global gene expression separated WT versus Prdm15 KO embryos into distinct groups, indicating marked transcriptional differences (Fig. 4A and table S1F). Gene ontology (GO) analysis of the significantly down-regulated genes identified Pattern specification process, Head development, and Neural tube development among the enriched terms. Among these genes, several are important regulators of forebrain development and A/P patterning (Fig. 4B and fig. S4A, and table S1, G to H). We noted a striking reduction in the expression of key components of three signaling pathways: WNT, NOTCH, and SHH (Fig. 4C, fig. S4B, and table S1, I and J).

(A) Unbiased clustering heat map of the entire transcriptome in WT (n = 8) versus Prdm15lacz/lacz KO (n = 10) E6.5 embryos, analyzed by RNA sequencing. Heat maps of differentially expressed genes from the indicated GO categories (B) and KEGG pathway (C) identified as top hits in the RNA sequencing. Light and dark blue rectangles on the right side indicate genes whose promoter region is directly bound by PRDM15 in ESCs only or both in ESCs and E6.5 embryos, respectively. (D) Snapshots of representative PRDM15 ChIP tracks (UCSC genome browser). Examples of conserved target genes (binding sites) between E6.5 embryos (blue) and ESCs (orange) are shown.

We have recently shown that PRDM15 recognizes a defined DNA motif present at promoters or enhancers of target genes (10). To define the set of direct PRDM15 transcriptional targets, we performed ChIP sequencing (ChIP-seq) on mESCs and WT E6.5 embryos (table S1, K and L). Despite the limited biological material available from the pre-gastrula embryos, we identified 58 high-confidence promoter-bound targets, the majority of which (~84%) were also bound by PRDM15 in ESCs (Fig. 4D, fig. S4C, and table S1M). In addition, identification of the same PRDM15 consensus binding motif in both systems implies a conservation of its targets. We therefore chose to consider PRDM15-bound promoters identified in ESCs as relevant for our follow-up analyses. Among these, a handful of PRDM15 targets, including Rbpj, Notch3, Maml3 (NOTCH), Vangl2, Wnt5b, Gpc6, Nphp4 (noncanonical WNT), and Gas1 (SHH), were of particular interest as they are significantly down-regulated in the mutant embryos (fig. S4D). Collectively, these data indicate that lack of PRDM15 leads to transcriptional down-regulation of key regulators of developmentally important signaling pathways (NOTCH, noncanonical WNT, and SHH).

These results prompted us to perform a targeted analysis of the down-regulated PRDM15 target genes in a large cohort of patients with HPE (132 trios and 188 singletons). We found heterozygous variants in 99 genes, ~17% of them were likely to be damaging (table S2A). To gain insights on potential functional interactions between these genes, we generated functional protein association networks using STRING. Although the majority of the proteins did not seem to be functionally related, two main networks representing NOTCH and WNT/PCP signaling formed (Fig. 5A and table S2B), supporting their potential involvement in HPE pathobiology.

(A) Functional groups identified by protein association network analysis of PRDM15 target genes mutated in patients with HPE using STRING. (B) mRNA levels of the indicated genes in ESCs; the respective genotypes are indicated in the lower panel. Expression levels were normalized to Ubiquitin (Ubb), and Prdm15fl/fl (empty vector) was used as reference. Rspo1 expression levels were used as positive control in Fig. 1D. Data shown are from three independent experiments (n = 3). (C) Enrichment of PRDM15 binding on promoter regions of the indicated target genes in ESCsrespective genotypes are indicated in the lower panelas measured by ChIP-qPCR. ChIP on the Rspo1 promoter was used as a positive control for PRDM15 binding. Depicted is the average enrichment [data from three independent cell cultures (n = 3)] over percent of input. In (B) and (C), the endogenous mouse Prdm15 has been deleted by the addition of OHT (50 nM) after ectopic expression of WT or mutant human PRDM15. In (B) and (C), center values, mean; error bars, SD. Students t test (two sided) was used to determine significance.

To assess the ability of the PRDM15 mutants to regulate the expression of critical components of both pathways, we took two approaches. First, we performed rescue experiments in Prdm15/ ESCs by reintroducing WT or mutant PRDM15 expression constructs. While hPR15-M154K and hPR15-E190K restored the expression of target genes at levels comparable to the WT human PRDM15 (hPR15-WT), none were significantly rescued by hPR15-C844Y (Fig. 5B and fig. S5A). In addition, ChIP-qPCR analysis confirmed a reduced enrichment of hPR15-C844Y at the promoter regions of these target genes (Fig. 5C and fig. S5B), which is consistent with the failure to promote their transcription (Fig. 5B). Second, to confirm that the C844Y mutation in humans is indeed an LOF mutation, we introduced the corresponding homozygous mutation (C842Y) in mESCs using CRISPR-Cas9 technology (fig. S5, C to E). Although the C842Y knock-in allele did not affect Prdm15 transcript levels, the resulting protein was unstable and less abundant (fig. S6, A and B). qPCR confirmed that Prdm15C842Y cells express PRDM15 target genes (i.e., Rbpj, Notch3, Vangl2, etc.) at lower levels compared with WT (fig. S6C) and that endogenous PRDM15C842Y protein is unable to bind (ChIP-qPCR) to its target promoters (fig. S6D).

Our findings call for a future functional characterization of the NOTCH and PCP gene variants and should motivate targeted genetic mapping for new HPE candidates in regulators of both pathways.

We have identified new mutations in the PRDM15 gene in patients with SNRS. Although the mutations affecting the PR domain of the protein (M154K and E190K) are associated with isolated SRNS cases only, the zinc finger mutation (C844Y) causes a syndromic form of HPE. In our in vitro ESC system, these PR domain mutations reduced the stability of the encoded protein but rescued considerably the phenotypic and molecular changes induced by loss of the endogenous protein. This is consistent with the fact that these mutations in humans cause isolated SRNS only and could imply a context-dependent requirement for the PR domain. Alternatively, the differential impact of the PR versus ZNF mutations on protein stability may support a threshold model, where different levels of PRDM15 expression are required for the development of specific organ systems. On the other hand, the ZNF mutation (C844Y) had marked effects on PRDM15 function in both settings, which we attribute here to impaired binding of the mutant protein to regulatory regions of its transcriptional targets.

Similar to the LOF mutation in humans, genetic deletion of Prdm15 in mice leads to a broad spectrum of brain defects, affecting predominantly the anteriormost structures including the eyes. Such phenotypic continua are commonly assigned to allelism, polygenic origin, and the action of modifier genes. Yet, here we report that perturbation of a single transcriptional regulator can indeed affect an entire transcriptional network, relevant to both normal development and pathological manifestations.

Our findings show that PRDM15 promotes transcription of several regulators of the NOTCH and WNT/PCP pathways to orchestrate formation of midline structures. Perturbation of these transcriptional programs, upon PRDM15 depletion, disrupts forebrain development due to impaired AME specification and lack of SHH signaling, consistent with the sequence of developmental defects associated with HPE pathobiology (7).

Of note are the prominent phenotypic similarities between Prdm15 null embryos and genetic (or microsurgical) modulation of the Nodal signaling pathway in mouse. That is, Nodal hypomorphic alleles, assorted combinations of mutations in Smad2 and Smad3, as well as the mutations in the downstream effectors Foxh1 and Foxa2, all result in embryos with defective AME production and compromised anterior forebrain development (2023).

On the other hand, the characteristic ruffling of the visceral endoderm observed in Prdm15 KO embryos at E7.5 has been observed in other mutants where extraembryonic mesoderm (ExMeso) production during gastrulation is impaired, such as in loss of Smad1 (24), combined loss of Smad2 and Smad3 in the epiblast (21), or Otx2 (chimeric analysis) (25). It is, however, important to emphasize that epiblast-specific deletion of Prdm15 (Prdm15/::Sox2-CRE embryos) equally results in smaller embryos with defects in the formation of anterior structures (fig. S3). It is additionally possible that the developmental delay we observed in Prdm15 KO embryos disproportionally affects some parts of the gastrulating embryo, rather than an overall delay in epiblast proliferation before gastrulation.

On the basis of our molecular analysis, we conclude that like modulation of the Nodal signaling pathway, loss of Prdm15 specifically affects AME specification. Given the requirement of this critical signaling center in providing reinforcing anterior patterning signals, we favor a model in which its lack or dysfunction underlies the Prdm15 phenotype, rather than a paucity of mes(endo)derm produced during gastrulation by a mutant embryo experiencing developmental delay.

The restriction of HPE genetic determinants to a handful of NODAL and SHH pathway regulators stems from our limited understanding of the molecular events governing specification of early and late midline structures. Recent studies have implicated components of the WNT/PCP pathway in regulating polarity of the node along the A/P axis and linked their deregulation to structural anomalies of this critical organizing center (2629). Thus, it is not unexpected that perturbation of the WNT/PCP pathway affects the specification of APS derivatives, namely, the AME and node (29). In addition, while the links between mutations in PCP signaling and neural tube defects are well established (6, 3032), their involvement in HPE remains uncharted. NOTCH signaling, on the other hand, has been implicated in HPE only recently (33). Besides its established neurogenic role in the developing mouse telencephalon, growing evidence supports the involvement of key NOTCH regulators (for example Dll1 and Rbpj) in node morphogenesis and midline truncations (34, 35).

Our findings prompted us to perform a targeted search for mutations in a large cohort of patients with HPE. Our analysis of exome sequencing data from 132 trios and 188 singletons revealed multiple rare heterozygous variants in PRDM15 transcriptional targets involved in forebrain development. In silico protein association network analysis of these variants identified two major functional groups regulating the NOTCH and WNT/PCP pathways. We expect that our findings will encourage validation of the reported variants/mutations as well as further mining for additional HPE candidates in both pathways.

PRDM15 KO-first mice that harbor the Prdm15lacZ allele were obtained from the European Conditional Mouse Mutagenesis Program. Hemizygous (Prdm15lacZ/+) animal intercrossings were performed to obtain homozygous (Prdm15lacZ/lacZ) embryos. Further details on these animals and the conditional Prdm15fl/fl strain can be found in (10). To generate epiblast-specific Prdm15/ embryos, Prdm15fl/fl mice were first crossed to heterozygous Sox2-CRE transgenic animals [B6.Cg-Edil3Tg(Sox2-cre)1Amc/J; JAX Laboratory] (36). The resulting males (Prdm15/+::Sox2-CRE) were then crossed again to Prdm15fl/fl females. In this generation, a quarter of the progeny is expected to be Prdm15/::Sox2-CRE. The Sox2-CRE transgene was always propagated through male animals. A similar breeding strategy, using Nestin-CRE [B6.Cg-Tg(Nes-cre)1Kln/J; JAX Laboratory] transgenics, was followed to generate Prdm15/:: Nestin-CRE mice. All mice-related procedures were approved by the local Institutional Animal Care and Use Committee (IACUC) and performed in compliance with the respective guidelines (IACUC nos. 151042 and 18/10EGDM/90).

E12.5 embryos were fixed in 4% PFA (paraformaldehyde) for 48 hours before being mounted in OCT (Optimal Cutting Temperature) embedding compounds. Then, serial coronal sections of the brains (anterior-posterior) were made using a cryostat and immediately thaw mounted on poly-l-lysinecoated histological slides for hematoxylin and eosin staining.

Prdm15fl/fl; ROSA26-CreERT2 ESCs have been described in (10). For all experiments, ESCs were cultured in the conventional [serum + Lif (Leukemia Inhibitory Factor) (SL)] medium unless otherwise stated. OHT (4-Hydroxytamoxifen) (50 nM; SIGMA-H7904) was added to the culture medium overnight (O/N) to generate Prdm15/ cells.

Embryos were isolated between E6.5 and 8.5, genotyped, then processed for whole-mount in situ hybridization as described in (37) with the following probes: Foxa2, Lhx1, T, Lefty2, Chordin, Shh, Otx2, and Six3.

Full-length human PRDM15 cDNA (NM_001040424.2) was subcloned into the PiggyBac vector (DNA2.0, PJ549). Clones encoding the various PRDM15 mutations were generated using the QuickChange II XL Site-directed Mutagenesis Kit (Agilent Technologies). The sequence of primers used can be found in table S3.

To introduce the hC844Y/mC842Y point mutation, mESCs were transfected with PX458 [pSpCas9 (BB)-2A-GFP] vector expressing a guide RNA targeting the site to be mutated, along with a single-stranded oligonucleotide containing the target point mutation, to serve as a DNA repair template. Additional eight silent mutations have been introduced to avoid editing of the template by the CAS9 protein. Single clones were sorted and expanded in 2i medium. Genomic DNA was used for screening by digestion with XMN I restriction enzyme. DNA from potential mutants was cloned into the pCR 4-TOPO TA vector following the manufacturers instructions, and 5 to 10 colonies were sequenced. Details of the strategy and the sequence of the oligonucleotides used are described in fig. S5 and table S3.

To assess protein stability, Prdm15/ ESCs expressing either wild or mutant PRDM15 were treated with cycloheximide (CHX; 150 g/ml) (Sigma, no. C-7698), and then collected at different time points (2, 4, and 6 hours) for protein extraction and analysis by Western blotting. Samples collected immediately before treatment with CHX (t = 0) served as reference. Antibodies and dilutions used were PRDM15 (in house, 1:3500) and TUBA (Alpha-TUBULIN) (Sigma T5168, 1:10,000).

To assess ESC self-renewal/differentiation, cells were stained with alkaline phosphatase staining solution (AP detection kit, Millipore, SCR 004). In brief, 500 cells per well (12-well plates) were seeded in triplicates and cultured for 5 days with daily change of medium before being stained as per the suppliers recommendations.

ESCs were seeded on gelatin-coated eight-well glass slides (Millipore, PEZGS0816), at 3 103 per well, and cultured in 2i medium. Three days later, cells were fixed in 4% PFA at room temperature, permeabilized with 0.5% Triton X-100, and then blocked using 2% bovine serum albumin (BSA) for 1 hour at room temperature before O/N staining with anti- PRDM15 (in house, 1:100) at 4C. The next day, slides were washed with phosphate-buffered saline (PBS) (three times) and stained with Alexa Fluorconjugated secondary rabbit antibody at 37C (30 min). Last, slides were washed with PBS (three times) before they were mounted with a DAPI (4,6-diamidino-2-phenylindole)containing mounting medium (VECTASHIELD, Vector Laboratory H1200).

Total RNA from cells was isolated using PureLink RNA Mini Kit (Ambion, 1283-018A) according to the manufacturers instructions. RNA was retrotranscribed into cDNA using Maxima First Strand cDNA Synthesis Kit (Thermo Scientific, K1642) and subjected to quantitative real-time PCR (qRT-PCR) on an ABI PRISM 7500 machine. qPCRs (20 l) contained 10 l of SYBR Green PCR supermix (2), 4 l of a forward and reverse primer mix (final concentration, 200 nM), and 6 l of cDNA (20 ng). Primers sequences are listed in table S4.

The detailed procedure for ChIP experiments has been described previously (38); all steps were performed at 4C and protease inhibitor was added, unless stated otherwise. In brief, 20 to 40 million ESCs were fixed in 1% formaldehyde for 10 min at room temperature before quenching with 0.125 M glycine (5 min at room temperature). Cells were then washed in PBS and harvested in lysis buffer before freezing at 20C O/N. The following day, cells were pelleted by centrifugation, resuspended in ice-cold ChIP buffer, and sonicated for six cycles (30-s ON/30-s OFF) using a BRANSON Digital Sonifier (no. S540D). Lysates were then precleared for 2 hours in Sepharose A beads (blocked in 5 mg/ml BSA) before O/N incubation with PRDM15 antibody (4C). The next day, Protein A beads were added for 4 hours before washing then de-cross-linking in 1% SDS and 0.1 M NaHCO3 (65C, O/N). Last, DNA was eluted in T-buffer (pH 8) using QIAquick PCR Purification Kit, QIAGEN. Sequences of primers used in ChIP-qPCR are listed in table S4. For the E6.5 ChIP, approximately 40 to 50 embryos per experiment were pooled together and fixed immediately after isolation.

TruSeq ChIP Sample Prep Kit (IP-202-1012) was used for DNA library preparation. Sequencing was performed in the Illumina HiSeq 2000 and NextSeq 500 at the Genome Institute Singapore. Details of the bioinformatics analysis can be found in (10). In brief, the sequenced reads were aligned to the mm9 genome assembly using bowtie version 2. Peak calling was done using MACS 2.1.1 (https://github.com/taoliu/MACS). Peaks were then annotated using the ChIPpeakAnno package in Rpromoters were defined to be 5 kb upstream and 1 kb downstream of the transcription start site. Motif discovery was done using MEME-ChIP in the MEME Suite (http://meme-suite.org).

For E6.5 embryo transcriptome analysis, RNA was extracted from 8 WT and 10 Prdm15lacZ/lacZ littermates. RNA from ESCs was collected 3 days after ethanol/OHT treatment. Library preparation was performed following the TruSeq RNA Sample preparation v2 guide (Illumina). The sequenced reads were mapped to mm9 build of the mouse genome using STAR version 2.4.2a. Differential expression analysis was performed using the DESeq2 package in R. Only genes with an average FPKM (Fragment Per Kilobase Million) >1 are considered expressed. Enriched GO terms and KEGG pathway were identified using Metascape. Genes used for GO analysis were filtered based on statistical significance (P < 0.05) and fold change (log2 fold change of 0.322) in E6.5 embryo RNA sequencing. Heatmaps of gene expressions (FPKM) were generated with in-house scripts with R.

To identify potential new candidate genes associated with HPE, we searched for genetic variants in genes/proteins acting downstream of PRDM15. Exome sequencing data from a cohort of 320 patients with HPE (132 trios and 188 singletons) were evaluated. Filter criteria are as follows: allele frequency <0.0001 in ExAC database (39) de novo (if trio available); synonymous changes were omitted; and benign changes by ACMG 2015 (40) criteria were removed. To identify protein networks and functional groups, genes with potential HPE variants were subjected to protein association network analysis using STRING database (https://string-db.org).

All experiments were repeated at least three times with similar results. Each biological repeat was done in at least two to four technical replicates/independent cell cultures, where applicable. Normal distribution was assumed for all statistical analyses. Unpaired Students t test (two sided) was applied using GraphPad Prism (version 7.0) to determine the statistical significance of the observed differences. Changes were considered statistically significant when P < 0.05.

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PRDM15 loss of function links NOTCH and WNT/PCP signaling to patterning defects in holoprosencephaly - Science Advances

How do I get stronger on the bike? you ask. Its that time of year: your races are done and you know where you stand performance-wise. You might find yourself wondering how some girls are so strong on the bike. How some guys ride by you as if youre standing still. Theres at least one explanation: strength. They have more of it than you (at present).

By Adam Johnston

If youre wondering what you can do this winter to improve your cycling (and your running and swimming, by the way), consider adding a regular strength training program to your routine (if youre not already doing so).

The majority of adult age group athletes are not limited by their muscular endurance. Theyre fond of their long training rides. They bump up to their competitive distances (whether it be standard, half or full) as quickly as they can. The ability to perform repeated muscular contractions at low levels of force is not what limits most athletes. Rather it is their muscular strength the ability to contract their muscles forcefully and/or against heavy resistance.

When most people start they typically improve almost regardless of what training they perform. Beginner and intermediate athletes get better quite simply by accumulating miles on the bike, running and in the pool. But once the initial break-in period has come and gone the next step is to focus on muscular strength.

Reams of information are available for the endurance athlete on strength training. This article isnt intended to regurgitate the research and advice thats readily available elsewhere. Rather, its meant to get you thinking of a few strength-related concerns and to consider a few things that you might not have anticipated when it comes to strength training for the endurance athlete.

Consider the following 10 strength training tips:

Be smart, be consistent, and get stronger for 2020.

Adam Johnston is the owner of WattsUp Cycling in Toronto. WattsUp Cycling offers an endurance athlete-specific strength training program on site. Visit http://www.wattsupcycling.ca to find out more.

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10 Ways to Get Stronger on the Bike - Triathlon Magazine Canada

Its well known that most industries are still overwhelmingly dominated by men. For instance, Wall Street, tech, construction, and engineering are only a few of the industries in which women are underrepresented, holding only 9 percent and 6 percent of the senior roles in venture capital and private equity. However, no one needs those statistics to confirm what we already know: There are specific fields in which women havent yet broken the infamous glass ceiling.

The most significant mistake analysts tend to make when discussing male-dominated industries is that they focus on the inequality itself. However, it can be far more fruitful to consider the advantages women bring to the table, both for themselves and for the industries involved.

The outcome of equal female representation in the workforce was summarized quite succinctly by management consulting giant McKinsey in 2018. They found that even though women make up around half of the worlds working-age population, they tend to be underrepresented, especially in the top roles of the workforce. Yet McKinsey estimates that women working at their full potential can add up to $28 trillion in additional global GDP by 2025. On a more micro level, an MIT study on workplace diversity has shown that splitting offices along gender lines drastically boosts productivity.

That gender diversity offers a workplace many benefits has been well covered, but what about the inclusion of women in a companys ranks boosts productivity and propels the business forward?

While there is abundant evidence showing women to be excellent communicators, multitaskers, and critical thinkers, psychological evidence also shows that men and women think slightly differently. Sometimes referred to as the battle of the hormones, there exists a phenomenon in which women and men bring different perspectives to the table due to their different genetic makeup and inherently opposing strengths and weaknesses. In other words, they complement each other in the workplace, joining forces to tackle obstacles neither gender would be able to face alone.

As the CEO of a tech company in the logistics industry, one of the most masculine industries imaginable, I have personally witnessed the wonders women can offer a world traditionally shaped by the minds of men. For example, I have observed how womens creativity improves specific processes inside companies thanks to their innovation, and how women who come from very little strive to achieve greatness, not just for themselves but for their companies, taking nothing for granted. And thats precisely it -- because women are aware that, despite the tremendous progress made in the fight against inequality, they are still afforded less professional opportunities than men, they know they have to work just a little harder. Armed with the mentality of fighting for every inch of progress, its hard to fail.

I also noticed this schism during my time in the Israeli Defense Forces, where I was rewarded for my hard work by perhaps the least likely of fans. Between 1999 and 2001, I served as an instructor of an infantry artillery unit, and afterward as an officer. Yes, the Israeli army has a reputation for gender diversity (as of 2011, 88-92 percent of all roles in the IDF were open to women), but military culture has been shaped by masculinity for thousands of years before any position was open to women, in any military. Also, some units are less used to having a woman around than others.

Units that absorb religious soldiers, for example, are bastions of gender bias because both religion and army culture have historically been patriarchal. And yet, even in these environments, there isnt a gap that cant be closed with a demonstration of knowledge and leadership.

During my time as an artillery training instructor, I trained a group of Yeshiva students -- deeply religious Jewish men who study Torah part-time while serving in the army. In other words, my trainees were accustomed to strict religious rules regulating the interactions between men and women. Every time I entered the infantry fighting vehicle (IFV) to train them, the soldiers backed up out of shock. It wasnt out of malice; its just that the religious rules they live by dont allow them even to touch a woman that is not their wife. Suddenly, they were expected to be trained by a woman soldier within the confined space of an IFV (for those not as familiar, they are quite small).

However, the initial feeling of confusion quickly transformed into mutual respect between the religious soldiers and me. By the end of the month-and-a-half training program, we had grown so close that they gave me a customized helmet and dog tag, with my name engraved on each. They so appreciated my professional contribution to our training sessions together that it changed their view on serving alongside a woman. It probably opened their minds in general.

Psychology is a useful tool and one that shouldnt be limited to individuals in need of guidance. The different perspectives diversity can offer industries such as cryptocurrency, blockchain, finance, and logistics, should be embraced as tried and true tools for propelling those industries forward. Since psychology teaches us about the secrets behind the ways men and women think, one of its central themes is that positivity is more effective than negativity. If were going to break bulletproof glass ceilings in boys-club industries, were going to have to explain why they would benefit from a womans touch once the shattered glass settles on those polished corporate tiles.

Hagar Valiano Rips is the CEO of Ladingo, and an entrepreneur and dynamic professional with more than 14 years of executive experience in business and product development across various industries. She started her first company at the age of 23 and sold it at 25. Valiano Rips also served as a commanding officer of an infantry unit in the Israeli Defense Forces.

Link:
Why Male-Dominated Industries Could Use a Woman's Touch: A Perspective from a Current CEO and Former Soldier - TechDay News

Every holiday, and on Black Friday and Cyber Monday and Random Discount Wednesday and Oh God Buy Stuff The High Street Is Dying Thursday, a load of miserable Opinions-For-Hire types churn out diatribes about why you absolutely should not buy anyone, including yourself, a DNA test in the sales or otherwise. And I'm here to tell you why they're wrong.

Before we get to why DNA tests are officially a good thing, let's run through some of the downsides those op-eds always bring up.

Yes, some people have found unexpected skeletons in their cupboards and sparked giant, multigenerational family arguments. But that's very rare most of us, for better or worse, don't have family histories that'd make a good daytime soap. And even if it does happen, wouldn't you rather know the truth? Where you really come from, and why you were lied to about it? It could have enormous impacts on your life choices.

Another concern is data security. Doom-mongers envisage a future where your genetic information is sold to health insurance companies, who jack up your premium as a result but that's much more of a concern for countries like the US than the UK, which still (at the time of writing, at least!) has a National Health Service. The NHS itself is on board with genetic testing, getting ready to offer a service of its own in return for contributing your anonymised data to lifesaving research.

Image: Nosha via Flickr CC

It's worth noting, too, that not all DNA testing is created equal. Some services are more geared towards looking at your ancestry and ethnicity information, while others only give surface-level results like "may be slightly more likely to have [X]", in which X can be anything from Alzheimer's to asparagus-scented wee. So depending on which service you've gone for, the information might be all but useless unless someone's trying to prove you ticked the wrong box on the ethnicity form when you applied for your job.

OK, so maybe not insurance companies, but what about your test results getting into other bad actors' hands? Well, yes, every damn company holding sensitive data has security issues, it seems the NHS very much included. However, I'm not overly worried that someone's going to download my info, insert it into some kind of biological 3D printer and start creating counterfeit versions of me. Even if that were possible, they'd needwaymore information than they'd get from a home DNA test.

The idea that your DNA test results constitute the source code for everything you are is a misconception. For starters, the tests only look at a tiny fraction of the human genome, but even if they didn't that's not how genes work. Yes, some problems and tendencies are genetic, but many are only influenced by your genes (often more than one), and some have absolutely sod-all to do with DNA whatsoever, being entirely caused by environmental factors. When you get the flu, does your DNA suddenly say "this person has the flu"? No. Is there a gay gene? No. Nobody's going to post your base pairs on Pastebin and recompile you.

As someone who's done many of these tests, I don't feel that my DNA is some kind of proprietary code I need to defend; in fact I'd open-source it if it meant we could work together on debugging some of the shit bits. Heck, maybe we can even fork me into a better person.

DNA data getting into evildoers' hands is one of those possibilities that sounds awful in theory, and it might well be awful in a few years when the whole system is more refined, but right now it would amount to "the terrorists have found out that you... HAVE A MODERATE CHANCE OF BEING BLUE EYED!" Not such a great Bond movie, is it?

You might also have seen some outcry when a popular DNA site was acquired for the purposes of solving crime, but assuming you and yours aren't massive criminals, that's probably not a huge worry either. In fact, DNA testing of relatives and descendants of suspects has solved a surprising number of cold cases in the US alone in the last few years, as well as identifying quite a few nameless bodies. Surely we can all agree that's a good thing.

While most of the worries about DNA testing are premature or arguable at this point, there are benefits that are real and tangible.

In my case, since my father is dead and I have no contact with my mother, a lot of the information I've found through DNA testing just wasn't available to me in other ways. There are plenty of people in similar situations folks who don't know who their birth parents were, have no contact with them, or aren't able to talk to them about matters of health and ancestry for one reason or another, for instance. DNA testing gives us a way to make family connections, in both the data and the relationship sense.

Last month, someone I share DNA with added me on Facebook. For some people, that might be strange and unnerving (in which case I'd say don't make your name public on your DNA profile I did because I wanted to find relatives), but for me it was wonderful. Being estranged from part of my immediate family means these connections mean more to me, and it's fascinating to look at the surnames, traits and lives of people all over the world who share my DNA segments.

For instance, until I had my DNA tested and analysed, I had zero idea about my considerable Jewish heritage. That led to a lot of genealogical research, ultimately helping me trace my family tree back to the 1700s. Now, when a new DNA relative contacts me (and they do, often it's like having email penpals), we can frequently figure out where our family trees connect, and fill each other in on cool details about our ancestors.

The health information can be life-changing too. In my case, I carry two genetic diseases that would make having a biological child pretty unwise. I already knew this from trying to donate my eggs a few years prior to the first test, and I don't want kids anyway, so it wasn't a nasty surprise but if I'd been planning babies, it would have been invaluable information. From this viewpoint, it seems almost crazy that most people go ahead and mix their genes with no idea what they might contain.

Of course, someone else with my results might have been devastated, but I would still argue it's better to know what you're facing. The same goes for the more serious heritable conditions that DNA tests can show. Yes, it's scary to think you might have a higher chance of getting a particular type of cancer, but it's not a certainty, and it might help you make those lifestyle changes you swear to every January. Or at least start living like you're not immortal, because newsflash: you're not.

In any case, the limited information you can get from home testing services can only give you clues, not the full picture, and some services are more accurate than others. As I mentioned, there's a lot besides raw DNA that makes a difference to how you turn out (see the whole field of epigenetics, for instance). Over time, we'll likely get more sophisticated information, which might one day mean we can start patching ourselves or at least developing medicines and treatments that interact with our unique makeup. But that's a long way off yet.

For now, there's a lot of valuable and fascinating data to be gleaned from testing your DNA, and a relatively low chance you'll ruin the next family reunion. Only you can decide what makes the most sense for you, and no test or article can tell you that.

Main image: Andy Leppard via Flickr CC

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Home DNA Tests Are Not the Devil - Gizmodo UK

More uniform response in Cohort 3 with two confirmed responders and one potential responder

New female responder in Cohort 2 for a total of three confirmed female responders across all cohorts

Up to six responders across all nine patients dosed in study

Prophylactic steroid cohort to begin in first half 2020; data expected in second half 2020

Ultragenyx to host conference call today at4:30 p.m. Eastern Time

NOVATO, Calif., Jan. 09, 2020 (GLOBE NEWSWIRE) -- Ultragenyx Pharmaceutical Inc. (RARE), a biopharmaceutical company focused on the development of novel products for rare and ultra-rare diseases, today announced topline positive safety and efficacy data from Cohort 3 and longer-term data from Cohort 2 of the ongoing Phase 1/2 study of DTX301, an investigational adeno-associated virus (AAV) gene therapy for the treatment of ornithine transcarbamylase (OTC) deficiency. In Cohort 3 (n=3), there were two confirmed female responders as well a third potential male responder who requires longer-term follow-up to confirm response status. In Cohort 2, one female patient has newly demonstrated a response starting at Week 52 which was confirmed at Week 78. The two previously disclosed responders in Cohort 1 and Cohort 2 also remain clinically and metabolically stable at 104 and 78 weeks, respectively. Across all nine patients dosed in the study, up to six patients have demonstrated a response.

We are encouraged to see a more uniform response at the higher doses including three female responders. To date, three patients in the study have discontinued alternate pathway medication and liberalized their diets while remaining clinically and metabolically stable, saidEric Crombez, M.D., Chief Medical Officer of the Ultragenyx Gene Therapy development unit. We are moving to prophylactic steroid use in the next cohort as we believe this could further enhance the level and consistency of expression that we have demonstrated so far.

Cohort 3 Efficacy Summary (as of December 9, 2019 cutoff date): One complete responder, one responder, and one potential responder

Patient 7 (complete responder, female): Patient 7 demonstrated a clinically meaningful 79 percent change in rate of ureagenesis, from a low of 24 percent of normal at baseline to the 51 to 64 percent range, and staying at 44 percent of normal at Week 52. During this period, she reported feeling significantly better and discontinued her alternate pathway medications and liberalized her protein-restricted diet. She has remained clinically and metabolically stable without a rise in ammonia.

Patient 8 (responder, female): Patient 8 demonstrated a significant and consistent 90 percent reduction in ammonia levels, time-normalized over a 24 hour period, from a high of 184 umol/L at baseline to 19 umol/L at Week 24, which is within the normal range. Potentially aberrant high baseline ureagenesis values inconsistent with her known more severe clinical status make her ureagenesis results uninterpretable. This patient was on a tapering course of steroids at the time of last assessment and has not yet discontinued alternate pathway medications or liberalized her diet. The investigator reported that her family says her health is the best it has ever been.

Patient 9 (potential responder, male):Patient 9 showed a 123 percent increase in rate of ureagenesis, from 25 percent of normal at baseline to 56 percent of normal at Week 12 while still on a steroid taper. Steroids have been shown to suppress rate of ureagenesis in other study patients. This patient has not yet discontinued alternate pathway medications or liberalized his diet. His ammonia levels have remained in the normal range and response status will be confirmed after additional follow-up.

Cohort 2 Efficacy Summary: Two responders including new responder and previously-disclosed male complete responder

Patient 6 (new responder, female):Patient 6 has now shown a 218 percent improvement in rate of ureagenesis, from 20 percent of normal at baseline to 61 percent at Week 52 and maintained at 64 percent at Week 78. In addition, she has shown a significant 74 percent reduction in ammonia levels from 156 umol/L at baseline to 40 umol/L at Week 78. She has started to taper her alternate pathway medications and liberalize her diet. With this new responder, there are two confirmed responders in cohort 2 out of three total patients.

Story continues

Safety SummaryAs of the data cutoff date, there have been no infusion-related adverse events and no treatment-related serious adverse events reported in the study. All adverse events have been Grade 1 or 2. All three patients in Cohort 3 had mild, clinically asymptomatic elevations in ALT levels, similar to what has been observed in other programs using AAV-based gene therapy. All three patients have been responding to reactive tapering courses of steroids, and all patients remain clinically stable.

Initiating Prophylactic Steroid Cohort As previously disclosed, a fourth cohort will enroll three patients at the 1.0 10^13 GC/kg dose, using prophylactic steroids. Patients will receive an 8-week tapering regimen of prophylactic steroids, starting at least 5 days prior to dosing with DTX301 at a starting steroid dose of 60 mg/day. The first patient is expected to be enrolled in the first half of 2020, and data from the prophylactic steroid cohort are expected in the second half of 2020.

Potential Phase 3 Study DesignUltragenyx is continuing discussions with the U.S. Food and Drug Administration (FDA) regarding the potential Phase 3 study design. Ammonia is expected to be a primary endpoint based on direct FDA feedback to date, with ureagenesis as a measure of biologic activity that supports the decision for patients to discontinue alternate pathway medications.

Conference Call and Webcast InformationUltragenyx will host a conference call today, Thursday, January 9, 2020, at 4:30 p.m. ET/ 1:30 p.m. PT during which Emil D. Kakkis, M.D., Ph.D., the company's Chief Executive Officer and President, will discuss the new data from the ongoing DTX301 Phase 1/2 Study. The live and replayed webcast of the call and slides will be available through the companys website at http://ir.ultragenyx.com/events.cfm. To participate in the live call by phone, dial (855) 797-6910 (USA) or (262) 912-6260 (international) and enter the passcode 5583103. The replay of the call will be available for one year.

About the OTC Phase 1/2 Study (DTX301)The Phase 1/2 study evaluates the change in the rate of ureagenesis, ammonia levels, neurocognitive assessment, biomarkers, and safety of DTX301 in patients with OTC deficiency. Three patients have been dosed in each of three dose cohorts of 2.0 10^12 GC/kg (Cohort 1), 6.0 10^12 GC/kg (Cohort 2), and 1.0 10^13 GC/kg (Cohort 3). Patients in the first three cohorts received steroids to reactively manage ALT elevations. In the fourth cohort, three patients will receive a 1.0 10^13 GC/kg dose and will all receive a prophylactic tapering course of steroids.

About OTC DeficiencyOTC deficiency, the most common urea cycle disorder, is caused by a genetic defect in a liver enzyme responsible for detoxification of ammonia. Individuals with OTC deficiency can build up excessive levels of ammonia in their blood, potentially resulting in acute and chronic neurological deficits and other toxicities. It is estimated that more than 10,000 patients are affected by OTC deficiency worldwide, of which approximately 80 percent are classified as late-onset and represent a clinical spectrum of disease severity. In the late-onset form of the disease, elevated ammonia can lead to significant medical issues for patients. Neonatal onset disease occurs only in males, presents as severe disease, and can be fatal at an early age. Approved therapies, which must be taken multiple times a day for the patient's entire life, do not eliminate the risk of future metabolic crises. Currently, the only curative approach is liver transplantation.

About DTX301DTX301 is an investigational AAV type 8 gene therapy designed to deliver stable expression and activity of OTC following a single intravenous infusion. It has been shown in preclinical studies to normalize levels of urinary orotic acid, a marker of ammonia metabolism. DTX301 was granted Orphan Drug Designation in both the United States and Europe.

About Ultragenyx Pharmaceutical Inc.Ultragenyx is a biopharmaceutical company committed to bringing to patients novel products for the treatment of serious rare and ultra-rare genetic diseases. The company has built a diverse portfolio of approved therapies and product candidates aimed at addressing diseases with high unmet medical need and clear biology for treatment, for which there are typically no approved therapies treating the underlying disease.

The company is led by a management team experienced in the development and commercialization of rare disease therapeutics. Ultragenyxs strategy is predicated upon time- and cost-efficient drug development, with the goal of delivering safe and effective therapies to patients with the utmost urgency.

For more information on Ultragenyx, please visit the Company's website atwww.ultragenyx.com.

Ultragenyx Forward-Looking Statements Except for the historical information contained herein, the matters set forth in this press release, including statements related to Ultragenyx's expectations regarding the timing, progress and plans for its clinical programs and clinical studies, future regulatory interactions, and the components and timing of regulatory submissions are forward-looking statements within the meaning of the "safe harbor" provisions of the Private Securities Litigation Reform Act of 1995. Such forward-looking statements involve substantial risks and uncertainties that could cause our clinical development programs, collaboration with third parties, future results, performance or achievements to differ significantly from those expressed or implied by the forward-looking statements. Such risks and uncertainties include, among others, the uncertainties inherent in the clinical drug development process, including the potential for substantial delays and the risk that earlier study results may not be predictive of future study results, the lack of predictability in the regulatory approval process, the timing of regulatory filings and approvals (including whether such approvals can be obtained), and other matters that could affect sufficiency of existing cash, cash equivalents and short-term investments to fund operations and the availability or commercial potential of our products and drug candidates. Ultragenyx undertakes no obligation to update or revise any forward-looking statements. For a further description of the risks and uncertainties that could cause actual results to differ from those expressed in these forward-looking statements, as well as risks relating to the business of Ultragenyx in general, see Ultragenyx's Quarterly Report on Form 10-Q filed with the Securities and Exchange Commission on November 6, 2019, and its subsequent periodic reports filed with the Securities and Exchange Commission.

Contact Ultragenyx Pharmaceutical Inc.Investors & MediaDanielle Keatley415-475-6876

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Ultragenyx Announces Positive Topline Cohort 3 Results and Improved Longer-Term Cohort 2 Results from Phase 1/2 Study of DTX301 Gene Therapy in...

Cara Gormallys pregnancy was shadowed by grief. As a queer woman wanting to have a baby, the biology professor had figured finding a sperm donor would be the only obstacle she and her partner faced. But thanks to Gormallys organizational skills and love of making lists, the couple landed on a donor with relative ease.

Then, Gormally struggled to conceive. Each month brought fresh disappointment and loss.

So much of the process depended on random, heart-breaking chance, she says. The emotional and financial roller coaster was exhausting.

But it wasnt the hardest part. The couple had accepted that, as much as they wanted a baby, their child wouldnt be biologically related to Gormallys spouse.

I grieved that our child wouldnt be genetically related to both of us, Gormally says. I longed for the biologically impossible.

But now, a new set of technologies have the potential to change whats possible allowing same-sex partners to have kids who share their genetic material, just like straight couples.

In mammals, pretty much every cell in the body carries two sets of genetic material. One set comes from mom and the other from dad. Eggs and sperm are the only exceptions; they have just one set. Then, when a sperm fertilizes an egg, those two sets combine, restoring the usual number to two sets per cell.

Gormally and other same-sex partners are currently barred from their dreams by a phenomenon called genomic imprinting. It uses a distinct tag from each parent to mark the DNA that mammals pass on to their offspring. The process ensures that, for a small percentage of genes, we only express the copy of genetic material provided by our mother or our father. When this imprinting process goes awry, kids can end up with inactive gene regions that cause miscarriages, developmental defects and cancer.

(Credit: Jay Smith/Discover)

During this genomic imprinting, moms distinct collection of tags typically turns off certain genes, so that just dads copy is expressed. And dad imparts his own marks that leave only the maternal copy on. (Most imprints silence gene expression, but some activate it.) Thats a problem for same-sex couples who want to have a baby. If both sets of an offsprings genes come from maternal DNA, for example, then both copies of imprinted genes will be off. So, the embryo cant make any of the genes products.

We dont get the full set of [gene] products that we need to undergo proper development unless we have both a maternal and paternal contribution to a fertilized egg, says Marisa Bartolomei, a geneticist at the University of Pennsylvania in Philadelphia, who discovered one of the first imprinted genes in mice.

Scientists discovered genomic imprinting in mammals about 30 years ago. During experiments in the mid-1980s, researchers removed either the maternal or paternal genetic contributions from newly fertilized mouse eggs. Then, they transferred in a second set of genes from another mouse to create embryos with either two sets of female genetic material or two sets of male genetic material. A surrogate mouse was able to gestate the embryos, but none survived. The finding showed normal development requires genetic material from both a father and the mother. More than that, the outcomes revealed that maternal and paternal genetic material differ from each other in meaningful ways.

Later experiments revealed mice developed differently depending on whether they happened to receive both copies of certain regions of DNA from one parent (rather than one copy from each parent).

Mice with hairpin-shaped tails were telling examples. When researchers deleted the gene region responsible for a hairpin tail from a mothers genome, mice embryos grew large and died partway through gestation. In contrast, deleting the same region from the paternal genome had no effect on the rodents growth or development.

In the three decades since, researchers have found more imprinted genes (they suspect there are between 100 and 200 such genes) and the molecular tags that silence them. Scientists have also taken strides connecting imprinting defects to developmental disorders in humans. But all along, researchers have known that imprinting prevents same-sex parents from having children.

In October 2018, researchers overcame this impossibility in mice. By deleting imprinted regions, Wei Li and a team at the Chinese Academy of Sciences in Beijing produced healthy mice from two moms. The researchers also created mouse pups from two dads for the first time. However, the offspring died just a few days after birth.

Despite the loss, Li is optimistic. This research shows us what is possible, he says.

To overcome the imprinting barrier, Li and his fellow researchers turned to CRISPR, a gene-editing technique thats made altering genomes easier than ever. They used the tool to delete gene regions from embryonic stem cells from mice mothers. The researchers then injected these modified stem cells into the egg of a female mouse and then used a third surrogate female mouse to carry the fetus to term.

The team had already seen some success two years earlier when they created mouse pups with two genetic mothers by deleting two imprinted regions. Although these bimaternal mice also grew to adulthood and produced pups of their own, they developed growth defects. On average, the bimaternal mice were 20 percent lighter than their hetero-parental counterparts. In their latest study, Li and his team also deleted a third region from the mothers genes, which restored the animals growth to normal.

But the scientists had to clear a few more hurdles to generate mice with two genetic fathers. They found, through a process of trial and error, that they needed to remove twice as many imprinted regions in the bipaternal mice as the bimaternal mice. In total, the team deleted seven imprinted regions to successfully create mice from two dads.

Still, the numbers were not in their favor. Only two and a half percent of embryos made it to term and less than half of one percent lived for two days. None made it to adulthood.

The produced bipaternal mice are not viable, which implies more obstacles are needed to cross to support their postnatal survival, if possible, Li says. The lower birth rate, on the other hand, implies the existence of an unknown barrier hindering the development of bipaternal embryos.

In contrast, the bimaternal mice fared much better. These mice grew to adulthood and were healthy enough to have pups of their own by mating with typical male mice. They also behaved the same as the control mice. As far as the researchers could tell, the bimaternal mice appear as healthy and normal as any other laboratory mice.

It does not mean that they are normal in every aspect, Li cautions. One cannot investigate all the aspects under restricted experimental conditions with a limited number of animals.

Despite the researchers success, Li says the technique is not ready for use in humans. It is never too much to emphasize the risks and the importance of safety before any human experiment, he says, particularly in regard to the bipaternal offspring, which currently are severely abnormal and cannot survive to adulthood.

The bimaternal offspring hold more promise. The team is now working to translate their findings to monkeys. And that work could bring the impossible one step closer to feasible for humans.

Lis research is encouraging but its a long way from helping Gormally and her spouse. However, its also not the only shot for same-sex couples. Another new technology called in vitro gametogenesis, or IVG, may be an alternative potential path for same-sex couples to have their own kids.

Scientists use the technique to make eggs and sperm from other cells in the body. To do so, biologists first reprogram adult skin cells to become stem cells. Then, they stimulate the skin-derived stem cells to develop into eggs or sperm.

Researchers from Japan have now perfected the technique in mice. And in groundbreaking work, Katsuhiko Hayashi and Mitinori Saitou and their team generated functional eggs from mice tail cells.

The researchers then fertilized the eggs with sperm from male mice and implanted the embryos into surrogate mothers. The offspring grew up healthy and fertile. In principle, this approach could allow a womans skin cells to be engineered into sperm and used to fertilize her partners egg.

IVG could transform same-sex couples ability to have their own children. If it had been possible at the time, we definitely wouldve have tried to do it, says Gormally, who is now a proud parent to a toddler thanks to her and her spouses sperm donor. [Its] a total game-changer.

This story is part of "The Future of Fertility" a new series on Discover exploring the frontiers of reproduction.

Read more:

Can Humans Have Babies in Space?

George Church Wants to Make Genetic Matchmaking a Reality

Human Gene Editing is Controversial. Shoukhrat Mitalipov Isn't Deterred

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The Slow March Toward the First Same-Sex Couple to Have a Baby - Discover Magazine

Researchers say theyve discovered six genetic variants associated with the development of anxiety disorders in what they call the largest study of anxiety traits to date.

In a study published Tuesday in the American Journal of Psychiatry, researchers examined genetic and health data from 200,000 U.S. veterans. The data was compiled by a research program, the Million Veteran Program, funded by the government to determine how genes, lifestyle and military exposures affect health and illness.

While there have been many studies on the genetic basis of depression, far fewer have looked for variants linked to anxiety, disorders of which afflict as many as 1 in 10 Americans, Murray Stein, a staff psychiatrist in the VA San Diego Healthcare System, said in a statement.

In the analysis, researchers discovered six genetic variants associated with higher risks of developing anxiety disorders. The variants related to anxiety disorders were found on chromosomes 1,3,6,7 and 20. The studys authors called it an important step forward in understanding how genes contribute to mental conditions.

The variant on chromosome 7 is identified to be correlated with higher occurrences of bipolar disorder and schizophrenia.

Its also associated with the reception of estrogen, but researchers were reluctant to draw the conclusion on if this could explain perhaps why women are twice as likely than men to be affected by anxiety disorders. Thats because while women veterans were included in the study, more than 90 percent of the participants were male. The studys authors say more research is needed on the issue.

The study also found five of the genetic variants were found in white Americans, while an additional variant was found in African Americans.

Minorities are underrepresented in genetic studies, and the diversity of the Million Veteran Program was essential for this part of the project, Dan Levey, of the VA Connecticut Healthcare Center and Yale University said in a statement.

The genetic variant we identified occurs only in individuals of African ancestry, and would have been completely missed in less diverse cohorts.

According to the Anxiety and Depression Association of America, nearly 40 million people in the U.S. experience an anxiety disorder in any given year.

See more here:
Scientists discover six genetic links to anxiety - The Hill

A new collaborative research study of over 200,000 military veterans has discovered six genetic variants that are linked to anxiety.According to statistics from the Anxiety and Depression Association of America, anxiety disorders are the most common mental illnesses in the U.S., affecting a staggering 18.1% of the population each year.

Suffering from an anxiety disorder can have major adverse effects on an individual's quality of life; it may prevent them from being able to socialize, to work, or to engage in relationships, for example. Individuals with an anxiety disorder are three to five times more likely to go to the doctor, and six times more likely to be hospitalized when compared to those who do not suffer from an anxiety disorder.

Anxiety disorders like all psychiatric conditions are complex in their pathophysiology. We don't know exactly what causes them, and therefore, our knowledge on how to treat them is somewhat incomplete. A variety of pharmacological and non-pharmacological treatment options are available; however, they are often limited in success and may only benefit certain individuals.

An increasing amount of research is focusing on the contribution of genetics to the development of mental health conditions. Murray Stein, San Diego VA staff psychiatrist and Distinguished Professor of Psychiatry and of family medicine and public health at UCSD points out "While there have been many studies on the genetic basis of depression, far fewer have looked for variants linked to anxiety, disorders of which afflict as many as one in ten Americans."

Stein is the senior author of a new study, published in the American Journal of Psychiatry, that explores the contribution of certain genetic variants to the development of anxiety disorders.

The research, a genome wide association study (GWAS), analyzed the genomes of approximately 200,000 military veterans from the Million Veteran Program (MVP). From the data, they discovered six genetic variants linked to anxiety. Five were identified in European Americans and one was identified in African Americans.

A selection of these variants has also been previously linked to other conditions such as bipolar disorder, schizophrenia and posttraumatic stress disorder.

"This is the richest set of results for the genetic basis of anxiety to date," said co-lead author Joel Gelernter, the Foundations Fund Professor of Psychiatry, professor of genetics and of neuroscience at Yale. "There has been no explanation for the comorbidity of anxiety and depression and other mental health disorders, but here we have found specific, shared genetic risks."

The MVP offers the opportunity to study a large data set that would otherwise be difficult to gather and collate. Thus far, several studies have utilized the MVP data to make interesting discoveries relating to genetics and psychiatric disorders. Gelernter says, "This is a rich vein we have just begun to tap."

Also of note is the fact that some of the genetic variants identified were linked to genes that regulate hormonal activity, specifically in relation to the sex hormone estrogen. As more females are affected by an anxiety disorder than males, this is an intriguing finding. However, the scientists emphasize that the research sample from the MVP largely consists of men, which could be considered a study limitation.

Nonetheless, the research serves as a contributor to the pool of research expanding our knowledge of the molecular underpinnings of psychiatric disorders.

"One of the goals of this research is to find important risk genes that are associated with risk for many psychiatric and behavioral traits for which we don't have a good explanation," Yale's Daniel Levey, a postdoctoral associate and co-lead author of the study, concludes.

Reference: Leveyet al. (2020). Reproducible Genetic Risk Loci for Anxiety: Results from ~200,000 Million Veteran Program Participants. The American Journal of Psychiatry. DOI:https://doi.org/10.1101/540245.

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Richest Set of Results to Date Pinpoint Six Genes That Are Linked to Anxiety Disorders - Technology Networks

Are humans basically good kind, generous and peaceful? Or are we essentially evil cruel, selfish and aggressive? Evolutionary science is uncovering the answer, and it provides important guidance about how we can best live together.

But it should not be oversimplified.

In a recent column on evolution (Could our real advantage be survival of the friendliest? Nov. 28), Cass Sunstein discussed the human self-domestication theory. Summarizing a recent article by Duke anthropologist Brian Hare and a book by Hares former teacher, Harvards Richard Wrangham, Sunstein presents their findings that we homo sapiens are a domesticated version of earlier, more aggressive, human species, just as dogs are a docile version of wolves.

Like dogs, we evolved to have lower levels of reactive aggression toward those around us, which enabled the cooperation and communication that have propelled our species to world domination.

Sunsteins column was a feel-good piece about how we are hard-wired to get along with each other. Thats great and ought to be celebrated.

The story of human domestication is much more interesting than Sunstein let on, however, and it has troublesome implications.

Hares and Wranghams answer to the age-old puzzle about human nature is that we have separate neurological pathways for good and evil, and they come to the fore in different contexts and for different reasons. Hitler was kind to his secretary and inconsolable at the death of his dog.

Hare shows that whether people are helpful or hurtful to others depends on how similar the others in question seem to themselves. Instinctive antagonism toward outsiders co-evolved through the same biological mechanisms that molded group solidarity. Think of parents, who are the soul of gentleness with their own children, but would readily kill to protect them.

Thus, armed conflict with neighbors usually sneaky night raids and ambushes is a feature of nearly every human society ever studied. And recent brain imaging studies confirm that we literally think differently about infractions committed by members of our group than about those committed by an out-group.

Wranghams book isnt called Human Goodness but The Goodness Paradox. The paradox is that domestication has a dark side it evolved through lethal violence against bullies, nonconformists and outsiders. Once language developed, coalitions of subordinate males could plot to oust the aggressive alpha males of the kind that dominate groups of apes. And once male coalitions discovered their overwhelming power, they could employ it against all kinds of troublemakers.

Some 12,000 generations of capital punishment that is, homicide systematically culled from the gene pool the tendencies to domineer or deviate.

Indeed, in nomadic hunter-gatherer societies people have been killed by male coalitions for a wide range of social transgressions things as seemingly trivial as a woman treading on the mens secret path. The moral sense itself could be considered the instinct to look over our shoulders we survivors of this culling process have a healthy vigilance about who might be watching. Simply putting up a picture of human eyes has been shown to deter bicycle theft and littering.

Sunstein briefly acknowledges that while domestication reduced reactive aggression, it did not affect our unique capacity for proactive aggression. But he implies that sort of behavior consists only of aggression that involves a lot of advance planning. In fact, it is the threat of aggression by groups of males that underlies all the coercive, hierarchical institutions of human history.

Thus, the truth is far from Sunsteins rosy picture: We evolved to be nervous conformists who get together to murder troublemakers and outsiders.

Heres the important thing. Genes dont determine behavior, they create tendencies that can be countermanded by culture and choice. Recognizing our dark tendencies, there are things we can do to curb and control them.

To start with, the self-domestication theory provides a lens through which to see more clearly our nations important challenges.

Take immigration. We must recognize that our views on immigrants are not entirely rational but are subtly influenced by a genetically based hostility toward outsiders.

Or consider the intolerance toward unpopular speakers that is infecting college campuses. We need to be alert that our instinctive, nervous herd mentality may be operating there.

And anyone who listened to any of the congressional deliberations on impeachment has to have seen that the adversaries were literally thinking with different parts of their brains.

Be aware that nationalism is a mixed bag. It brings out our best instincts for loyalty and service, but it will always stimulate a genetic threat to international peace.

The thought experiment for how group solidarity is forged in response to an adversary is to imagine what would happen if hostile alien spaceships appeared over major cities. Those sneaky Russians and monolithic Chinese would quickly start to feel like our kin. Climate change is another kind of worldwide threat which, depending on how we address it, could forge bonds across boundaries or could lead to the mind-set of every man for himself.

As for our nations history of persecuting nonconformists and reformers, we need to take to heart the language of a case that new law students study, Papachristou v. City of Jacksonville.

Back in 1972, Jacksonville had a vagrancy ordinance so broad that it allowed the police to sweep up just about anyone they considered undesirable. Supreme Court Justice William Douglas, a bit of a nonconformist himself, would have none of it. He wrote that the choices to be a nightwalker or a loafer are unwritten amenities of American life that have dignified the right of dissent and have honored the right to be nonconformists and the right to defy submissiveness. They have encouraged lives of high spirits, rather than hushed, suffocating silence.

Dare I offer the best vision for the future for a domesticated species? It would be a time when we are all citizens of the world with robust protections for individuality and nonconformity.

Evolution built us. All in the service of promoting the most base reproductive success, it engineered beings capable of great love and loyalty, works of beautiful creativity and worldwide collaboration, and awe and wonder at the mysteries of the universe. But it also endowed us with the pain of guilt and shame, anxiety about our reputations, insatiable acquisitiveness and the potential for intolerance and cruelty.

Still, the story can be more empowering than discouraging. Knowledge is power. We are finally at the point in history where we can start to see our own evolution. And seeing it, we can refuse to be its slaves and start being its master.

Bruce Peterson is a senior district court judge who teaches a course on Lawyers as Peacemakers at the University of Minnesota Law School.

Go here to see the original:
OPINION EXCHANGE | We mustn't be naive about evolution - Minneapolis Star Tribune

Childhood exposure to the air pollutant nitrogen dioxide (NO2) is associated with an increased risk of developing schizophrenia, according to the findings of a recent study which appeared in JAMA Network Open.

This population-based cohort study comprised of 23,355 individuals (51.3% male) with schizophrenia and a randomly selected sub-cohort.Using national registry data, all individuals born in Denmark between May 1, 1981, and December 31, 2002, were followed up from their 10th birthday until the first occurrence of schizophrenia (the primary endpoint), emigration, death, or December 31, 2012, whichever came first. Statistical analyses were conducted between October 24, 2018, and June 17, 2019 using adjusted hazard ratios (AHRs) for schizophrenia with 95% Cis according to NO2 exposure. Polygenic risk scores were calculated as the weighted sum of risk alleles at selected single-nucleotide polymorphisms based on genetic material obtained from dried blood spot samples from the Danish Newborn Screening Biobank and on the Psychiatric Genomics Consortium genome-wide association study summary statistics file.

According to the results of the study, during the period of the study, 3,531 subjects were diagnosed with schizophrenia. The researchers observed that higher polygenic risk scores were linked with higher childhood NO2 exposure (=0.0782; 95% CI, 0.065 to 0.091; P <.001). Moreover, they found that a 10-g/m3increase in childhood daily NO2 exposure (AHR, 1.23; 95% CI, 1.15 to 1.32) along with a 1-SD increase in polygenic risk score (AHR, 1.29; 95% CI, 1.23 to 1.35) were both independently correlated with an augmented risk of developing schizophrenia.

Potential biological mechanisms for the association between air pollution and schizophrenia remain uncertain, but air pollutants have been purported to cause inflammation of the tissue of the nervous system, oxidative stress, microglial activation, protein aggregation, subclinical cerebrovascular disease, and disruption of the blood-brain barrier, the study authors wrote.

With the complex clinical features of schizophrenia, it is likely that genetic variation may play a role in determining an individuals susceptibility to the damaging effects of air pollution. However, our findings suggest that a polygenic risk score based on common variants related to schizophrenia cannot account for the association between childhood NO2 exposure and schizophrenia.

They added that these results demonstrate the utility of including polygenic risk scores in epidemiologic studies.

Read the rest here:
Childhood Exposure to Air Pollution Linked to Increased Risk of Schizophrenia - DocWire News

Its not King Herod decreeing that male children should be killed, but it certainly is eyebrow-raising: Chinas ever-growing, totalitarian surveillance state is now requiring blood samples from boys in provinces across the nation.

This is according to Bitter Winter (BW), a magazine on religious liberty and human rights in China. BW reports that one explanation given to concerned parents of schoolboys was that the program was designed to prevent children from being lost or abducted. Of course, though, since girls can be abducted, too, this excuse only further raises suspicions.

Providing background, BW wrote yesterday that since the beginning of 2016, the government ofXinjiangUyghurAutonomous Regionhas been collecting DNA samples fromUyghursand other Muslims to build databases fortracking and monitoring them. As this measure in the name of maintaining social stabilityspreads across mainland China, theCCP [Chinese Communist Party]is collecting biometric data on an ever-increasing scale. All males, including young children, are now mandated to give blood samples.

BW continues:

Residents of Guigang, Guilin, Hechi, and Cenxi cities in southern Chinas Guangxi Zhuang Autonomous Region reported toBitter Winterthat local police uniformly collected blood samples from primary and middle school boys in November. This has been done without informing their guardians.

Isnt it the doctors duty to take blood? Why did the police do it? a parent of a primary school student asked. Blood samples have been taken from students in many schools, as part of the governments massive operation. No notice or written communication has been issued to parents. We felt very unsafe.

When parents demanded to know the reasons for the collection of blood samples from their children, the schools explained that it was needed to prevent children from being lost or abducted and sold.

If it is to prevent children from being lost or abducted, why have samples been taken only from boys and not girls? Because girls wont be lost? Its really strange!

Reporting on the program in October, shortly after a government announcement relating to it was made, the Epoch Times wrote that China is building a massiveDNAdatabase on its citizens.

The announcement stated that the effort is part of the public securitys basic information work to improve the precision and controllability of population management, and the samples would be collected either by group or door-to-door, the Times related.

The program is just one of the most recent compulsory DNA collection initiatives, which critics of Chinese authorities say are a gross violation of privacy and serve to further the regimes plan to control the genetic makeup of its population, the Times continued.

The Times also informs that the goal of the male-oriented program is to develop a comprehensive Y-STR database. Y-STR stands for Y-chromosome short tandem repeat analysis, which relates to DNA information passed down along the male descendants of families, the Times tells us.

Bitter Winter reports on the most plausible explanation for the current program, quoting a teacher from Guilin. The collection of blood samples is demanded in a government-issued document, which proclaims that they will be used by law enforcement to find criminals, related BW. No matter where they escape, the police can locate them.

Since boys and men are not only more likely to commit violent crimes but, note, are also more likely to be the revolutionaries opposing state tyranny the current focus on a Y-STR database may make sense.

On an even darker note, BW writes that because schools were secretive and couldnt provide adequate explanation for the blood-collection program, some parents worried thatDNA samples will be used for organ harvesting.

(Note: It could occur to a person that since Chinas recently scrapped one-child policy led to a sex imbalance in which males notably outnumber females, the Beijing government may view boys as more expendable. Just a wild thought.)

This said, the latest initiative is apparently just part of a wider effort to collect DNA on Chinas entire population. The purposes, though, would still largely be nefarious.

Bitter Winter writes that one motivation is to facilitate religious persecution. For example, In July, the police harassed the parents of a member ofThe Church of Almighty Godwho has been on the run to escape persecution and forcibly collected their blood samples, claiming that this will help them to track down the believer, the site relates.

As to another motivation, Steven Mosher, an expert in population control [and] president of U.S.-based think tank Population Research Institute said the term population control has always had an eugenics element, the Epoch Times reports.

The regime wants to ensure quality births, Mosher told The Epoch Times, adding that one way to achieve that is by tracing who is related to whom, so authorities can eliminate those carrying recessive genes that produce birth defects.

With the advent of genetic testing, [this practice] is about to get a high-tech boost and become much more comprehensive, he said, the site further related.

Eugenics, the science of improving the human gene pool via selective breeding (and now genetic engineering), gained much credence in the early 1900s, especially in Britain and the United Sates. It was later discredited when the Nazis in Germany pursued it, killing innocents and violating human rights in the process.

The Chinese authorities are similarly disposed, using deception, threats, and even physical force to collect reluctant subjects blood. Yet this is just part of Beijings wider development of an all-encompassing surveillance state that seems to mistake George Orwells 1984 for an instruction manual. As Sarah Cook, a senior China analyst at U.S. human rights advocacy group Freedom House, put it while addressing the massive DNA collection program, the fascistic Beijing regime treats the Chinese population as nothing more than slaves, with whom you can do exactly as you please.

Yet is this surprising? China is not only the worlds most irreligious country, but atheism is its governments official position. This matters because atheism has a certain corollary: that we have no souls and then are, essentially, mere organic robots, some pounds of chemicals and water.

And, of course, what could be wrong with altering an organic robots software (social engineering) or, more to the point here, its hardware (genetic engineering)? For that matter, what could be immoral about terminating an organic robots function? Material things are there to be used, after all and discarded when no longer needed.

It really is no surprise that men who believed our rights come from God forged the United States and that a godless state proceeds as if people are objects that have no rights.

Selwyn Duke (@SelwynDuke) has written for The New American for more than a decade. He has also written for The Hill,Observer,The American Conservative, WorldNetDaily, American Thinker, and many other print and online publications. In addition, he has contributed to college textbooks published by Gale-Cengage Learning, has appeared on television, and is a frequent guest on radio.

More:
Bleed the Males? China Currently Demanding DNA from Boys and ONLY Boys - The New American

If it looks like a duck and quacks like a duck, then its probably...Brad Pitt.

The Once Upon A Time...In Hollywood star and genetic experiment in perfection has done the remarkable. Hes taken a hairstyle associated with 60-year-old male radio show hosts and college freshman who dont yet know how to make their own barber appointments and made it red carpet-worthy.

Frazer Harrison

The ducktail hairstyle, also known as the ducks ass, peaked in popularity in the late 1950s with the rise of the bad-boy Greaser look (Think: Elvis Presley and Sodapop from The Outsiders.) It's styled by slicking back shaggy hair on both sides of your head to create a ridge at the back, allowing the bottom edges to subtly flip out at the ends. Its almost moving into mullet territory, with a bit of Donald Trump at the edges. Joe Dirt would find the style aspirational.

Carl Iwasaki

Beautiful Brad wasnt alone in his efforts at the Golden Globes Sunday night. Famous men like Ansel Elgort, Adam Driver, and Joaquin Phoenix added to the hairsanity. We're a mere week into 2020, and several Hollywood dudes have started sporting the style, with a slight update: the new version includes less duck and more tail, creating a neck curtain of sorts. These are men of flair, drama, and panache: the curtain rises and falls even on their distinguished necks.

Daniele Venturelli

Daniele Venturelli

Steve Granitz

Michael Kovac

This is the kind of hair that makes you believe if you went home with these grown men, you might wake up on a futon. It's a style for men who think basketball shorts are formal wear, who eat from the communal nuts at a bar, rub their noses, then grabs another handful. It is, in short, the hair of men who used to fart and claim Safety immediately after. It is not at all the 'do of a movie star, which is perhaps exactly its point: We dare you to still find us attractive, Pitt and his A-list cohorts seem to be saying. Unfortunately, in spite of their best efforts, we do.

Read this article:
Are Male Celebrities Trying to Ruin Their Hotness With Bad Hair? 'Cuz It's Not Working - ELLE.com

This is not a good time to be a wolverine.

The infamously scrappy, snow-adapted mustelid a relation of badgers, martens and otters is barely hanging on in the contiguous United States, where its population has dipped to mere hundreds. Decades of habitat loss and trapping reduced the wolverines numbers, and now diminishing snowpack from climate change is adding insult to injury.

And we can add one more surprising threat to the list: roads.

Yes, even though wolverines (Gulo gulo) thrive in remote, snowy wildernesses, roads can still pose a problem but perhaps not in the way you might think.

Researchers studying wolverine populations in Canada found that roads serve to diminish the animals genetic diversity, because females refuse to cross them, although young males still readily disperse and find new territories.

This has important consequences for U.S. wolverines, which may depend on Canadian travelers for their genetic health and future population growth.

Anthony (Tony) Clevenger, a scientist at Montana State Universitys Western Transportation Institute and an expert in the field of road ecology, was one of three researchers involved in the study.

We talked to him about the challenges facing wolverines and whats being done to boost their recovery.

What attracted you to the field of road ecology?

Pure chance. I was out of work, living in Europe where I did my Ph.D. on a small population of brown bears in northern Spain, and I heard Banff National Park was hiring a conservation biologist to study underpasses and overpasses for wildlife. I got the job [in 1996] and became fascinated with studying how roads affect nature around us. It opened up a new world for me.

Your recent study focused on wolverines and the Trans-Canada Highway. What prompted this? What were you hoping to learn?

The final twinning [from two to four lanes] of the Trans-Canada Highway ends at the Continental Divide. This stretch of the highway enters subalpine areas home to wolverine and lynx species that we knew very little about.

We knew in the lower 48 some 2-lane highways limited wolverine movement. Little was known about wolverines in the Canadian Rockies and much less about how a major 4-lane highway may affect movements and gene flow.So this was a unique opportunity given the number of interstate highways and expanding roads in the southern part of wolverine range.

What did you find out about how roads affect wolverines, and is it different from how roads affect other animals?

After three years of noninvasive genetic sampling within our 3,088 square-mile study area [around Banff, Kootenay and Yoho national parks], we found that the Trans-Canada Highway is not a barrier to male wolverine movement but is a strong barrier to female wolverine movement.Females are more sensitive todisturbance, particularly human activity.

This is important since females need to cross the highway, survive and breed for there to be functional connectivity.

This is the same response that others have found for grizzly bear movements and genetic structure across highways, and also jaguars in Central America. Getting breeding females to cross and connect subpopulations is key, and we hope that crossing structures can help that function.

What are the implications for wolverine populations in North America, and specifically in the United States, where numbers are low?

The prospects are not good in the lower 48 where the population is [currently] estimated at 300 but we all believe that is far too high. Habitats are highly fragmented, unlike wolverine range in southern Canada (Alberta and British Columbia). The population in Canada is in the thousands.

Trapping still occurs in southern Canada and we published a paper recently that demonstrates that the trapping of wolverines in southeast British Columbia and southwest Alberta is not sustainable. Governments there are starting to change trapping regulations.

These populations are the lifeline for wolverine populations in the United States. We lose that and we lose everything.

What is being done or can be done to help? Are there particular kinds of crossing structures that would be most beneficial for wolverines?

Crossing structures have been built in the Canadian Rockies along the Trans-Canada Highway, which will help the mountain park wolverines. The critical piece of the puzzle is located in multi-use lands between the mountain national parks and the United States border (near Glacier and Waterton Lakes national parks).

This area is still trapped for wolverines, and forest cutting and motorized recreation are extensive and in some places there is oil and gas exploration activities that limit wolverine movement, reproductive success and survival. The provincial government of British Columbia is changing trapping regulations and we hope Alberta will follow suit its a good thing and necessary.

Overpasses and underpasses are also being planned for the British Columbia section of Highway 3, a critical linkage zone in the Yellowstone-to-Yukon ecoregion. The public is more informed of the plight of wolverines in this critical area, as are trappers.

Working together we can help provide a more viable future for one of our icons of wilderness and intact ecosystems.

Originally posted here:
Road to Nowhere: Highways Pose Existential Threat to Wolverines - The Revelator

Cincinnati's thousand-pound toddler turns 3 years old this January, overcoming every obstacle thrown her way.Fiona the hippo will celebrate her third birthday this month. It's a big deal for the half-ton of pure hippo sass, considering she weighed a fifth of what a normal baby hippo should weigh when she was born Jan. 24, 2017."Fiona is remarkable for being unremarkable now," said Cincinnati Zoo curator of mammals Christina Gorsuch. "She's just like most other 2-year-old hippos, except for the fact that she's a celebrity in Cincinnati and beyond!"Fiona weighed 29 pounds when she was born, which is about 25 pounds lighter than the lowest recorded birth weight for this species. The normal range is 55-120 pounds.She has become an ambassador for her species and a great example of why zoos exist. She survived because of her animal care team's tireless efforts to save her and has inspired many to care about her species and wildlife, which is Cincinnati Zoo's mission.She now weights well over 1,000 pounds. Once Cincinnati's little baby, the hippo has reached a certain level of maturity as she nears three as her tusks begin to come in.But don't worry, Cincinnati. She's not old enough to date yet.She needs to be at least 5 before she starts thinking about boys, according to Wendy Rice, the head keeper at Cincinnati Zoo's Africa Department.And although she has hippo admirers across the country, Rice said Fiona is still a few years away from picking up a boyfriend.Of those hippo admirers, one such hippo is still laying it on thick. Timothy, a 3-year-old hippo from San Antonio, still pens Fiona weekly love notes on Facebook.But what ultimately will decide Fiona's potential future romance? It may not be cute love notes."The genetics are basically what's going to matter most," Rice said. "If and when Fiona were to get a breeding recommendation someday, it would be based entirely on who was genetically the best match for her -- that may or may not be Timothy."Fiona's genes are valuable in the world of Nile hippopotamuses. And eventually, Rice said the goal is to have Fiona breed if she can. But we're talking way down the road, when Fiona is at least 5 years old.What happens then?"We obviously don't want her going anywhere," Rice said. "We love her. She's our baby and this hometown loves her. We're fairly certain people would riot if we said Fiona was leaving. We're hopeful that if she gets a breeding recommendation, that a male would be brought here for her so she wouldn't have to leave Cincinnati."

Cincinnati's thousand-pound toddler turns 3 years old this January, overcoming every obstacle thrown her way.

Fiona the hippo will celebrate her third birthday this month. It's a big deal for the half-ton of pure hippo sass, considering she weighed a fifth of what a normal baby hippo should weigh when she was born Jan. 24, 2017.

"Fiona is remarkable for being unremarkable now," said Cincinnati Zoo curator of mammals Christina Gorsuch. "She's just like most other 2-year-old hippos, except for the fact that she's a celebrity in Cincinnati and beyond!"

Fiona weighed 29 pounds when she was born, which is about 25 pounds lighter than the lowest recorded birth weight for this species. The normal range is 55-120 pounds.

She has become an ambassador for her species and a great example of why zoos exist. She survived because of her animal care team's tireless efforts to save her and has inspired many to care about her species and wildlife, which is Cincinnati Zoo's mission.

She now weights well over 1,000 pounds. Once Cincinnati's little baby, the hippo has reached a certain level of maturity as she nears three as her tusks begin to come in.

But don't worry, Cincinnati. She's not old enough to date yet.

She needs to be at least 5 before she starts thinking about boys, according to Wendy Rice, the head keeper at Cincinnati Zoo's Africa Department.

And although she has hippo admirers across the country, Rice said Fiona is still a few years away from picking up a boyfriend.

Of those hippo admirers, one such hippo is still laying it on thick. Timothy, a 3-year-old hippo from San Antonio, still pens Fiona weekly love notes on Facebook.

But what ultimately will decide Fiona's potential future romance? It may not be cute love notes.

"The genetics are basically what's going to matter most," Rice said. "If and when Fiona were to get a breeding recommendation someday, it would be based entirely on who was genetically the best match for her -- that may or may not be Timothy."

Fiona's genes are valuable in the world of Nile hippopotamuses. And eventually, Rice said the goal is to have Fiona breed if she can. But we're talking way down the road, when Fiona is at least 5 years old.

What happens then?

"We obviously don't want her going anywhere," Rice said. "We love her. She's our baby and this hometown loves her. We're fairly certain people would riot if we said Fiona was leaving. We're hopeful that if she gets a breeding recommendation, that a male would be brought here for her so she wouldn't have to leave Cincinnati."

Excerpt from:
Fiona's greatest hits: 3 years of sassy hippo bliss - WLWT Cincinnati

The clotting disorder hemophilia A may become the third gene therapy that the US Food and Drug Administration approves, joining treatments for a form of retinal blindness in 2017, and spinal muscular atrophy in 2019.

Biomarin Pharmaceutical Inc. has submitted a biologics license application to FDA and documentation of clinical trial results to the European Medicines Agency, with reviews slated to begin early this year at both organizations.

An article in the January 2 New England Journal of Medicine from a UK research team presents the findings of a phase 3 analysis of continuing success of a phase 1/2 trial (instead of a new phase 3 trial). The hemophilia gene therapy called valoctocogene roxaparvovec for now can mean a one-time infusion that replaces the more than 100-150 infusions of clotting factor a patient takes each year, and can also alleviate the painful joint bleeding that is the hallmark of the disease.

The different clotting disorders result from mutations in different genes in the pathway that knits a clot from protein fibrils. Hemophilia A is a deficiency of clotting factor VIII, and is also called classic hemophilia. It accounts for 80 percent of people with the disease. The clotting disorder that threaded through the royal families of Europe was hemophilia B, which is a deficiency of factor IX.

Both hemophilias are transmitted by genes on the X chromosome, and therefore affect only males. One in 10,000 males has hemophilia A, and it arises as a new mutation (rather than being inherited), in about a third of cases.

The world focused on hemophilia A with the sad case of Ryan White. Born in 1971, Ryan was diagnosed at 3 days of age when his circumcision wound wouldnt stop bleeding.

Like many people with hemophilia A at the time, Ryan received weekly factor VIII pooled from donors. That would prove tragic, as President Reagan was late to the game of testing the blood supply for viruses. He refused to even utter the word AIDS until actor Rock Hudson died of it in 1985.

That was too late for Ryan White.

HIV as the cause of the mysterious new epidemic was identified in 1983, although for a time it was known by different names.

In 1984, Ryan had a lung biopsy to diagnose severe pneumonia that revealed that he was HIV positive. Nearly 90% of people with hemophilia who received clotting factors from pooled donor blood between 1979 and 1984 contracted HIV and/or hepatitis C.

Ryan survived longer than predicted, until the end of 1990. In the intervening years he catalyzed AIDS activism when he was denied admittance to school, and he and his family fought the discrimination and ignorance.

Hemophilia A gene therapy has been twenty years in the making.

By the end of the decade that began with Ryan Whites death, the first gene therapy for hemophilia A was being tested in a clinical trial in Pittsburgh. I was fortunate to interviewthe first patient soon after he received the gene therapy.

Like Ryan White, Don Miller had nearly bled to death when he was circumcised. He recalled other frightening incidents.

I fell at my grandmothers house and had a one-inch-long cut on the back of my leg. It took five weeks to stop bleeding. It leaked slowly, so I didnt need whole blood replacement. But if I moved a little the wrong way, it would open and bleed again.

Millers treatments paralleled the history of countering hemophilia, from whole blood infusions, to plasma replacement, to cryoprecipitate (a frozen plasma product containing clotting factors). Then he injected pooled factor VIII three times a month. But somehow he never contracted HIV, and thats what got him into the gene therapy clinical trial.

I lucked out, Miller told me. Besides his good fortune at dodging the HIV bullet, he was in the right place at the right time. Hed been a librarian at the University of Pittsburgh, where the clinical trial was to take place.

On June 1, 1999, Don Miller received the first of three injections of retroviruses engineered to carry factor VIII. Chiron Corp., one of the original wave of big biotech companies that was absorbed into Novartis in 2006, designed and manufactured the vector.

The goal of this first round of hemophilia A gene therapy wasnt to cure the disease, but to boost factor VIII levels a scant 2 to 7 percent, which was expected to dampen bleeds.

Don Miller hadnt had any side effects when I spoke with him, but I dont know how he fared. At the time, he spoke freely to the media, but I contacted his physician and she couldnt provide an update due to HIPAA regulations.

But that first hemophilia A gene therapy was safe. Some patients had transient increases in factor VIII, and for 5 of the 13, bleeds became less frequent.

When the gene therapy field emerged from several setbacks that began with the death of Jesse Gelsinger in 1999, the hemophilia strategy changed to a safer and more efficient vector. The clinical trial leading to the current FDA submission began with 15 patients who received the factor VIII gene delivered in adeno-associated virus serotype 5, starting in June 2015. A year later, 13 of the men treated with a single infusion had normal or near-normal levels of factor VIII.

The AAV5 vector coaxes greater expression of the gene than does the retrovirus used in the earlier trial. Plus, an added bit of control DNA (a promoter) directs the vector to the types of cells that normally make the factor in the liver and to white blood cells.

AAV5s capacity is only about 4,700 DNA bases, so the big factor VIII gene is trimmed a bit (as it was for the earlier trial too). Still, it had to be delivered in two viral shipments, with some assembly required, like sending a cell phone and its charger in separate Amazon prime boxes.

Unlike other vectors (lentivirus and retroviruses), AAV remains separate from the cells chromosomes, forming a DNA circle called an episome.

Two of the 15 patients received doses too low (6 or 20 trillion viruses per kilogram of body weight) to have an effect. But six men receiving an intermediate dose of 40 trillion viruses had no bleeding events; the annual number of needed factor VIII infusions for the three-year study period fell from 155 to 0.5, and only one man had a bleed in a large joint.

The high-dose (60 trillion viruses) men did the best: none required factor VIII infusions, bleeding events, or large joint bleeds.

Analysis of factor VIII levels and various biomarkers of the gene indicated that of the 13 men who responded, one is considered to no longer have hemophilia, eleven have mild disease, and one has moderate disease.

It all adds up to what the researchers call a sustained, clinically relevant benefit. Said lead author John Pasi, from the Royal London Haemophilia Centre, Barts Health NHS Trust:

Our 2017 paper showed that gene therapy could significantly boost factor VIII levels in men with hemophilia A. Our new data are critical in helping the scientific and medical communities understand this pioneering technology. This latest study confirms both safety and long-term beneficial impact. A long-term treatment that effectively ends the life-long regular injections can transform care and massively improve the quality of life of hundreds of thousands of people born with this challenging genetic condition.

Once an advisory committee to FDA agrees, valoctocogene roxaparvovec will debut with a catchier brand name. It may cost in the $400,000 to $1 million range (or higher) of other gene therapies in the US and Europe, but considering that current therapies for hemophilia A are about $270,000 annually without complications and can exceed $1 million if there are, a one-and-done gene therapy for hemophilia A sounds like a good deal.

Ricki Lewis is the GLPs senior contributing writer focusing on gene therapy and gene editing. She has a PhD in genetics and is a genetic counselor, science writer and author of The Forever Fix: Gene Therapy and the Boy Who Saved It, the only popular book about gene therapy. BIO. Follow her at her website or Twitter @rickilewis

Read the rest here:
Will 2020 see the debut of promising gene therapy for hemophilia A? It's up to the FDA. - Genetic Literacy Project

Changing landscapes, habitat loss, fragmentation, and global climate change have been listed as the main reasons for biodiversity decline worldwide. Now, a new study from the National Centre for Biological Sciences (NCBS), Bengaluru, has added to the growing knowledge that anthropogenic activities can impact genetic connectivity or the movement among habitat patches usually resulting in mating and genetic exchange.

In several mammalian carnivores, juveniles disperse away from their mother's territory to establish their own territory. Males are known to travel longer distances than females. Isolation of habitat patches (due to habitat destruction and fragmentation) can restrict animal movement among habitat patches and thus reduce genetic exchange and increase the probability of extinction. Hence maintaining connectivity is critical to ensure long term persistence of a species, Prachi Thatte explains. Dr. Thatte is the first author of the paper published in Diversity and Distributions and now works with WWF-India on connectivity conservation

Four wide-ranging mammals Jungle cats, leopards, sloth bears, tigers were investigated for the genetic differentiation in central India, which is a critical landscape for several species. The DNA extracted from faecal samples were used for understanding genetic connectivity. The samples were collected from nine protected areas during the period 2012-2017.

The team looked at how land-use, human population density, nearby roads and traffic affected the genetic structure. The paper notes that tigers were impacted the most by high human footprint. Although known to travel long distances and move through agricultural fields to some extent, tigers in central India do not have equally high genetic exchange throughout the landscape. Some protected areas like Bandhavgarh tiger reserve seem to be getting relatively isolated (the 2014 tiger census report also shows the same), explains Dr. Thatte.

Jungle cats were found to be the least impacted. That is likely because in central India, they occupy a variety of habitats including forests, scrublands, grasslands and even irrigated agricultural fields close to the forests, she explains.

Despite being the least impacted by human activity, the team encountered several jungle cat road-kills while carrying out fieldwork. She explains that with increasing infrastructure and traffic, systematically studying the impact of roads on smaller species like jungle cat and jackals and ensuring the presence of mitigation structures like underpasses and overpasses would be crucial to ensure that we don't fragment the currently well-connected populations.

IIndia has also started paying attention to wildlife corridors and encouraging engineering reforms to promote wildlife movements. Last year, the Ministry of Environment along with the Wildlife Institute of India released a document that lays out the regulatory requirements for developing roads, railways, powerlines while recognising the impacts on wildlife and people. NHAI and all PWDs have been instructed to follow the guidelines.

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How humans affect genetic connectivity of four mammals - The Hindu