Daily Archives: June 21, 2020

A man buried in a huge, roughly 5,200-year-old Irish stone tomb was the product of incest, a new study finds.

DNA extracted from the ancient mans remains displays an unusually large number of identical versions of the same genes. That pattern indicates that his parents were either a brother and sister or a parent and child, a team led by geneticists Lara Cassidy and Daniel Bradley of Trinity College Dublin reports June 17 in Nature.

That new DNA discovery combined with the monumental tomb suggests that ruling families who wielded enough power to direct big building projects emerged among some early European farming communities, the researchers contend.

The mans bones had previously been found in the Newgrange passage tomb, an earthen mound covering more than 4,000 square meters near the River Boyne. A rooftop opening in a 19-meter-long stone passage allows sunlight to reach deep into a chamber inside the mound on the shortest days of the year, suggesting the structure held astrological and religious significance (SN: 6/29/74). It may have been built this way to mark a new year in dramatic fashion, perhaps while winter solstice ceremonies were conducted.

Cassidy and Bradleys team studied DNA from 44 individuals buried in various Irish tombs and graves dating to between roughly 6,600 and 4,500 years ago. Only the Newgrange man, who was interred in the largest and most impressive structure, had inherited genetic markers of incest.

Socially sanctioned incest tends to be rare throughout history but is known from instances of royal inbreeding. Mating between brothers and sisters, for example, occurred in some ancient societies with ruling families headed by men regarded as gods not subject to human incest taboos. Ancient Egypts King Tutankhamun, whose rule began 3,352 years ago, was the son of a brother and sister. So finding the offspring of inbreeding in such an impressive stone structure is highly suggestive of a practice of inbreeding among elites, even if not conclusive, the researchers say.

The rest is here:
DNA from a 5,200-year-old Irish tomb hints at ancient royal incest - Science News

The impetus for the campaign can be traced back to a crime spree in the northern Chinese region of Inner Mongolia. For nearly three decades, the police there investigated the rapes and murders of 11 women and girls, one as young as 8. They collected 230,000 fingerprints and sifted through more than 100,000 DNA samples. They offered a $28,000 reward.

Then, in 2016, they arrested a man on unrelated bribery charges, according to the state news media. Analyzing his genes, they found he was related to a person who had left his DNA at the site of the 2005 killing of one of the women. That person, Gao Chengyong, confessed to the crimes and was later executed.

Mr. Gaos capture spurred the state media to call for the creation of a national database of male DNA. The police in Henan Province showed it was possible, after amassing samples from 5.3 million men, or roughly 10 percent of the provinces male population, between 2014 and 2016. In November 2017, the Ministry of Public Security, which controls the police, unveiled plans for a national database.

China already holds the worlds largest trove of genetic material, totaling 80 million profiles, according to state media. But earlier DNA gathering efforts were often more focused. Officials targeted criminal suspects or groups they considered potentially destabilizing, like migrant workers in certain neighborhoods. The police have also gathered DNA from ethnic minority groups like the Uighurs as a way to tighten the Communist Partys control over them.

The effort to compile a national male database broadens those efforts, said Emile Dirks, an author of the report from the Australian institute and a Ph.D. candidate in the department of political science at the University of Toronto. We are seeing the expansion of those models to the rest of China in an aggressive way that I dont think weve seen before, Mr. Dirks said.

In the report released by the Australian institute, it estimated that the authorities aimed to collect DNA samples from 35 million to 70 million men and boys, or roughly 5 percent to 10 percent of Chinas male population. They do not need to sample every male, because one persons DNA sample can unlock the genetic identity of male relatives.

The rest is here:
China Is Collecting DNA From Tens of Millions of Men and Boys, Using U.S. Equipment - The New York Times

Gardenias newly sequenced genome highlights how evolutionary tinkering transforms plants into some of natures great chemical-makers.

Plants are some of natures most extraordinary chemists. Unlike animals, they cant run from predators or pathogens. They cant uproot themselves to seek out a mate or spread their seeds.

So instead, they manufacture chemicals: toxins to kill bacteria. Bitter alkaloids to ward off herbivores. Sweet nectar and jewel-colored pigments to draw in pollinators or birds that can help disperse seeds.

Chemicals, you could say, are one of a plants ways of making love and war.

But how did trees, shrubs and flowers obtain these capabilities?

In a new study, scientists explore this question through the evolution of the gardenia, Gardenia jasminoides, an evergreen shrub with white flowers thats planted as an ornamental in the tropics.

In a new study, researchers report sequencing the species genome. Credit: YW Low

Researchers sequenced the genome of the gardenia for the first time. Then, they looked in-depth at how the plant makes a compound called crocin. This brightly colored chemical,which gives saffron its vermillion hue, is also responsible for the red-orange shade of the gardenias ripened fruits.

The study identified the genes involved in making crocin and used them to create the compound in the lab. This work which included deciphering the step-by-step process that gardenias use to synthesize crocin lays the foundation for large-scale production of the chemical, which is thought to have medicinal properties as an antioxidant.

The research also explored the origins of crocin in gardenias. The findings, which will be published on June 18 inBMC Biology,highlight the power of an evolutionary process called tandem gene duplication, in which accidental copying of DNA gives organisms flexibility to expand the arsenal of genetic tools they have at their disposal. Its just one way that plants can evolve new capabilities, but its a crucial one.

The important principle is that plants can reinvent things, says study co-author Victor Albert, PhD, a University at Buffalo biologist. They can duplicate some parts of their genetic toolkit and twiddle the functions a little. So lets say you have a screwdriver, but the head is a super-big one. Imagine you could duplicate that screwdriver, but you could grind the head to make it smaller and useful for little screws, but you also still have the original one with the big head to handle large ones. Thats what these plants are doing.

A chemical compound called crocin gives the fruits their red-orange hue. Credit: YW Low

It was exciting to uncover these molecular tricks of the trade while researching the genome of a plant so important to traditional Chinese medicine, and now to modern biomedical research as well, says the studys co-corresponding author, Jingyuan Song, PhD, from the Engineering Research Center of Chinese Medicine Resource in China, who is also affiliated with the Chinese Academy of Medical Sciences and Peking Union Medical College.

The project was led by Song and Shilin Chen, PhD, from the Engineering Research Center of Chinese Medicine Resource and China Academy of Chinese Medical Sciences, and by Giovanni Giuliano, PhD, of the Italian National Agency for New Technologies, Energy and Sustainable Economic Development (ENEA). The first authors were Zhichau Xu, PhD, and Xiangdong Pu, both of the Chinese Academy of Medical Sciences and Peking Union Medical College. Xu is also affiliated with the Engineering Research Center of Chinese Medicine Resource.

Albert, professor of biological sciences in the UB College of Arts and Sciences and a visiting professor at Nanyang Technological University in Singapore, and his students made important contributions, conducting bioinformatics research that helped unravel the evolutionary history of crocin and caffeine synthesis in the gardenia and coffee plants, respectively.

In a tandem duplication event, a single gene gets replicated by mistake during reproduction. Then, as a species evolves over time, the excess DNA is free to mutate and take on new functions.

In Gardenia jasminoides, tandem duplication led to the evolution of a gene that is needed for crocin synthesis, the study concludes. This form of genetic replication also enabled a close relative of the gardenia the coffee plant Coffea canephora to develop caffeine-producing genes, according to the research, which compared the gardenias DNA to that of Coffea canephora and a few other plants.

This is a case where we see the same underlying evolutionary mechanism generating these tandem duplicates to create two different biosynthetic pathways of interest in two plants, Albert says. We have coffee and gardenia, which evolved from a close common ancestor, and in one case tandem duplicates formed and went crazy in coffee to make caffeine. And in the other, they formed and went crazy in gardenia to make crocins.

Made by plants, but useful for humans, too

Crocin is found not just in gardenias, but also in the crocus plant, which produces saffron. These species didnt inherit the ability to make crocin from a common ancestor: They evolved their arsenal of genes independently. The same goes for caffeine genes in coffee, tea and chocolate plants.

Plants are playing games with multiple evolutions of interesting phytochemicals, Albert says. And, of course, all of these phytochemicals are useful to the plants, maybe in fighting against pathogens or serving as attractants to insects.

When it comes to gardenias, the fiery color of the plants fruit helps to extend the species range, helping to attract animals that eat the fruits and expel the seeds in new locations.

But while plants perform chemistry for their own good, the compounds they produce can benefit humans too. Aspirin is closely related to a compound found in willow bark. Digoxin, used sparingly to treat heart problems, comes from the foxglove plant. Crocins antioxidant properties are of interest to researchers, and now, scientists have the knowledge they need to make that chemical in the lab.

Its a known fact that the same chemical (for instance, caffeine, or crocin) can appear again and again in distant plant species, says co-corresponding author Giuliano. One outstanding question was: How do the genes involved in the biosynthesis of such chemicals appear all at once in these different species? The work we published not only describes for the first time the complete pathway to crocin biosynthesis in any plant, but also shows that the pathway evolved in gardenias through the appearance of just one gene that acts early in the pathway, while the later ones were pre-existing, and were hitchhiked for making crocin. This is an elegant demonstration, at the biochemical level, of how nature reuses and adapts pre-existing mechanisms, rather than creating completely novel ones.

Reference: Tandem gene duplications drive divergent evolution of caffeine and crocin biosynthetic pathways in plants by Zhichao Xu, Xiangdong Pu, Ranran Gao, Olivia Costantina Demurtas, Steven J. Fleck, Michaela Richter, Chunnian He, Aijia Ji, Wei Sun, Jianqiang Kong, Kaizhi Hu, Fengming Ren, Jiejie Song, Zhe Wang, Ting Gao, Chao Xiong, Haoying Yu, Tianyi Xin, Victor A. Albert, Giovanni Giuliano, Shilin Chen and Jingyuan Song, 18 June 2020, BMC Biology.DOI: 10.1186/s12915-020-00795-3

See the article here:
DNA Shows Plants Are Extraordinary Chemists Making Love and War - SciTechDaily

COLD SPRING HARBOR, N.Y., June 17, 2020 /PRNewswire/ -- An expansive new analysis of genetic variation among tomatoes has uncovered 230,000 previously hidden large-scale differences in DNA between 100 different varieties. As tomato plants evolved, segments of DNA were deleted, duplicated, or rearranged. These genomic "structural variations" underpin the vast diversity among tomatoes, changing flavors, altering yield, and shaping other important traits.

Tomatoes come in many sizes, colors, and flavors. CSHL Professor Zach Lippman, JHU Professor Mike Schatz, and colleagues around the world described the genetic underpinnings of 100 different types of tomatoes, including those in this photograph. Credit: Lippman lab/CSHL, 2020.

The study, a collaborative effort led by Cold Spring Harbor Laboratory (CSHL) Professor and Howard Hughes Medical Institute Investigator Zachary Lippman and Johns Hopkins University (JHU) Professor Michael Schatz, is the most comprehensive analysis of structural genome variation for a major crop. Breeders and scientists will be able to apply the information to breed or engineer new, more desirable plants with greater efficiency.

Large-scale differences between genomes, known collectively as structural variants, are likely responsible for a wide range of plant features that breeders care about, but these elements have been notoriously difficult to study, leaving much of the genetic origins of tomato diversity unexplained, says Xingang Wang, a postdoctoral researcher in Lippman's lab. New DNA sequencing technology along with powerful new genome editing technology has recently made structural variants easier to detect and study how they affect crop traits. Lippman's team, in collaboration with scientists at JHU, the University of Georgia, the Boyce Thompson Institute, and others, seized the opportunity to investigate.

Together, the group sequenced and compared the genomes of 100 different varieties of tomato, including robust varieties suitable for industrial agriculture, succulent heirlooms, and wild relatives of cultivated tomato.

To gain a better understanding of structural variants' role in diversity, the team showed that thousands of genes were changed by the structural variations. Then they used CRISPRthe genome editing tool that can make targeted changes in DNAto show that duplication of a particular gene causes a plant's tomatoes to increase in size by about 30 percent. Investigating another variant, they tracked down a gene that contributes to a smoky flavor in some tomatoes. And in another set of experiments, the researchers uncovered a complex interaction involving four structural variants that eliminates a trade-off between a feature that simplifies tomato harvesting and another that reduces productivity.

Understanding how these and other structural variants influence tomatoes gives breeders new power to improve the properties of tomatoes, a $190 billion global industry, and shows how structural variants that can enhance breeding are likely hidden in the complex genomes of many other important crops, like corn, rice, and soybeans.

About Cold Spring Harbor Laboratory

Founded in 1890, Cold Spring Harbor Laboratory has shaped contemporary biomedical research and education with programs in cancer, neuroscience, plant biology and quantitative biology. Home to eight Nobel Prize winners, the private, not-for-profit Laboratory employs 1,100 people including 600 scientists, students and technicians. For more information, visit http://www.cshl.edu.

About Johns Hopkins

Johns Hopkins is America's first research institution and a premier university and health system with campuses around the world.

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SOURCE Cold Spring Harbor Laboratory

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The DNA tricks that gave us 100 different kinds of tomatoes - Yahoo Finance

To 10-year-old Katie Krall, it just made sense. Her dad, who coached her softball team, should put his best hitter at leadoff and second-best hitter second. She figured if the best hitters were at the top of the order, theyd come to the plate the most and thats what youd want.

This was after the book Moneyball came out, but before the movie was released, so those kinds of thoughts, along with the importance of on-base percentage over batting average, had been in the ether but had yet to find their way to pee-wee softball. Shed read the book several years later, but at the time, Krall was just like many other 10-year-olds who liked to ask why and refused to accept the status quo just because itd always been that way. It portended a new type of baseball executive, a path that Krall, 23, would later find herself.

Krall swayed her dad, Darryl, and found herself batting second in the lineup behind her twin...

The rest is here:
Baseball's in her DNA: Reds operations analyst Katie Krall living a dream - The Athletic

I must have looked like hell.

I was walking across the grounds of Kennedy Meadows Resort Sunday just having come off the trail on my 15-mile day hike to Kennedy Lake and back. It is a hike most opt to do in two days so they can enjoy the lake in a setting surrounded by 9,000- to 11,000-foot peaks.

Two guys in their 20s that had been fishing nearby who had passed me up and were loading their gear in their pickup truck when I caught up asked if I wanted a lift to the trailhead parking lot still about a half mile away.

I thought about it for about a second and told them I appreciated the offer but no thanks. My right foot and right leg on the next step let me know what they thought of my turning the ride down.

A few minutes later a couple in a golf cart made the same offer. I again politely turned them down

When I got back to the car taking off my hiking boots was an adventure in pain. Due to two bunions that would make Paul Bunyan wince and a hammertoe that would spook Babe the Blue Ox, I have to cut up and apply a small fortune in moleskin to my toes as well as a nice pair of matching ankle spurs before I take off on Sierra hikes. They normally due to the trick but stretches of extremely muddy trails around the lake had managed to get both feet soaking wet.

That in its self would have made for an interesting return trip.

But even before I stepped out of the car that morning I knew I was going to be in for fun. Ive been walking from time-to-time with a slight limp during the past 10 months. Thats because a nice 15-foot semi-tumble downhill while scrambling at the end of last summer had aggravated a hereditary issue with my right leg. The need to cancel my annual trip to Death Valley last November due to work meant the only hikes with any degree of elevation gain and distance were ones I did tackling Mt. Diablo and nearby peaks which were nowhere tough enough to test my limits.

I was starting to hurt perhaps three miles shy of the turnaround point. My body was telling me to stop and go back. But I wasnt willing to do so.

I am clearly not athletic, coordinated or anywhere close to being someone who moves fast whether Im hiking or doing what passes for running. That said I can keep going.As for pain, its all relative. And given in my case it is more like a first cousin than something that is a stranger I tend to just deal with it.

As such I like to tell myself I have a high threshold of pain. But on Sunday I was beginning to think I was lying to myself.

It got to the point I had to slow my pace due to my leg hurting.

This is where most people will probably start thinking I am nuts. But unless something was broken or I was incapacitated in some manner I cant accept pain winning.

It is not mind over matter as much as understanding ones self.

I was fortunate enough to get a chance to explore pushing my limits 32 years ago in a research project a medical professional at Roseville Community Hospital was doing for his doctorate at the University of California, Davis.

Originally he had hoped to get athletic males from the hospital staff to severe as the six participants for a study to see the impacts on the body for someone who goes from rest to pushing it as hard as they can and sustaining it at the most strenuous predetermined level for five minutes.

Why he wasnt able to secure the number of participants he needed from the hospital staff for the nine-week project that required a once a week testing was the fact it required having eight spots on your chest shaved to connect you to all sorts of monitoring devices.

Although Im a candidate for the missing link, the shaving part did not bother me as I do not take by shirt off for fear of blinding pilots and causing planes to crash.

The hospital PR folks mentioned that I might by a good candidate given they knew I was bicycling 10,000 miles a year back then.

I agreed because quite frankly it sounded like a good story plus I was able to get a free platinum level physical complete with a cardiologist, water immersion body fat test, spot body fat measuring and assorted other prods and tests.

The treadmill test was interesting. The goal was to get my heart rate up to a sustained level at 85 percent of my maximum and stay there for two minutes. The goal was to do this within a 15-minute period.

I warned the cardiologist I sweat like theres no tomorrow. He said I probably wouldnt as I should hit the 85 percent threshold in six or so minutes. Seven minutes later I was dripping all over the place including on his work surface next to the treadmill when he handed me a tissue. Meanwhile he kept increasing the incline. It ended up taking the full 15 minutes before he got my heart rate where he wanted it.

The weekly tests involved using a Stairmaster. The length of the test was only five minutes max. Initially the weekly tests started with a minute warm-up before they started increasing the resistance. By the ninth week, you got no warm-up and the entire 5 minutes was spent on the highest setting for difficulty.

Afterwards, I was told they assumed Id be the weakest given how my body fat testing and general build stacked up against the others.

The other five were all active as runners or played basketball three or four times a week. All had played sports in high school.

It was then that I understood physical fitness and the ability to deal with or push through pain has nothing to do with being athletic or having been blessed with DNA that puts you in Greek god status.

It really is a matter of constantly pushing your limits.

In was tempted to accept a lift on Sunday but didnt. That wasnt because of pride but because I had to finish what I started. If Im by myself in the Sierra wilderness or in remote Death Valley canyon my mindset has to be I will get back to where I started under my own power.

That means listening to your body and making sure what it is telling you doesnt blind you from what you are capable of doing.

The real test, of course, is how you recover. My feet wanted to mutiny, my quads felt like I had just finished a double century cycling, and my right calf made a Charlie horse feel like a good thing later that night.

But 14 hours after completing the hike, I was able to take a 2 mile run and do so with no pain. That said sitting and simply walking for a few says after was anything but pain free.

The point of all this is simple. Pain shouldnt control your life.

See more here:
One doesn't have to win the DNA lottery to learn to deal with pain - Manteca Bulletin