Category Archives: DNA

John Gurda| Milwaukee Journal Sentinel

As summer ends and we put away the beach toys, our focus shifts to more sedentary pursuits, things we can do on rainy days and in the cold calm of the approaching winter. For millions of Americans, that means genealogy. Since the 1960s, probing our roots has been one the nations most popular hobbies, and interest in the field has only grown since then, the result of a sea change in technology.

For centuries, family history was largely the province of African griots and European royalty, whose privilege depended on pedigree. The past has been radically democratized in recent years. Genealogists once had to scroll through miles of microfilm to unearth census tables, naturalization records, birth certificates, obituaries, military recordsand other rich archival ore. Now those sources are as close to the surface as the nearest computer.

But digitized vital records arent the whole story. Perhaps the most astounding development in the entire history of family history is the recent use of DNA to establish ancestry a tool that has been in popular use for little more than a decade. It turns out that each of us bears in our own cells, in the fiber of our physical being, every step in the evolution of our families and in fact of our entire species. The biological pageant of humanity is recorded in every strand of our hair and every particle of our skin. We may move freely and widely throughout the world, but we carry with us the traceable imprint of uncounted earlier generations.

More: DNA testing can share all your family secrets. Are you ready for that?

More: Could DNA tests bring home missing kids? Lack of diversity in databases hinders searches

The portal to the past is comparison. All of todays ancestry services rely on voluminous databases of DNA drawn from individuals around the world whose families have lived in one place for centuries, before the mobility revolution of the 1800s. Until fairly recently, most humans rarely ventured beyond the confines of their own valley or forest or plain, which severely limited their choices of a mate. Intermarriage was inevitable, and the result over thousands of years was a gene pool unique to each region. The descendants of those earlier generations who have remained in place carry a book of DNA that sets their locale apart from every other volume in the worlds ethnic library.

I was intrigued with genetic genealogy from the beginning, even though my own ethnic story seemed straightforward. I come from peasant stock on both sides of my family. My Norwegian ancestors tilled the stony soil north of Oslo, and my Polish forebears worked more tractable land near the Baltic Sea. Both of my grandfathers, John Johnson and John Gurda, were born in Europe (my first name was a given), and their wives were second-generation Americans of matching stock.

But physical corroboration of that story was irresistible. In 2015 I spit into a tube and sent it off with $89.95 to AncestryDNA, the company with the largest DNA reference database. The results, I must say, surprised me. The first broad strokes confirmed my family narrative: 50%Scandinavian and 42%Eastern European. But I also came up as 6%Irish. How did that happen? Who was this person wanderer or settler, lover or slave who introduced a touch of the Celt to my bloodline? A sailor washed up in Gdansk? A Dublin girl carried home by a Viking?

The revelation didnt make me feel any different. My hair wasnt curlier or thicker. My accent was the same innocuous Midwestern dialect Ive always had, without a trace of brogue. And I didnt feel either more or less interested in potatoes and cabbage. But I longed to learn more. First of all, was that Irish ancestor on my mothers side or my fathers? Equipped with only an English majors understanding of DNA and a diploma from a Catholic high school that didnt offer biology, I prevailed upon my dads sistermy last aunt or uncle by genes on either side to take the spit test. She was analyzed as 86%Eastern European, with a minor element of Scandinavian and barely a trace of Irish.

My Celtic forebear was evidently not on the Polish side, but the results, I learned, couldnt possibly be as precise as Id imagined. Each of us gets exactly half of our DNA from each parent, but the composition of each half is absolutely random, a genetic shuffle that can produce lopsided ancestry results. But there were apparently Irish genes somewhere in there.

Then, just as I was recalibrating my self-image and wondering if we should have named our sons Seamus and Declan, Ancestry sent me (at no additional charge) an update based on new information from its ever-evolving DNA database. My revised ethnic mix was 41%Swedish and Danish, 32%Norwegian, and only 18%Eastern European not even close to what my family had always assumed. Goodbye, Ireland, and, for that matter, goodbye, Poland.

Such a radical shift in results over just a few years turned on my skeptical gene. If the same DNA could have that many interpretations, perhaps the whole concept was flawed. A 2022 update slightly eased my doubts, estimating my ancestry as 43%Norwegian and 31%Eastern European, with smaller proportions of Swedish, Danishand Baltic. But its clear that describing my results as imprecise would be an understatement.

On admittedly scant evidence, I suspect that part of the problem is an inherent limitation of the process. The standard autosomal test doesnt date-stamp your DNA; different periods in the evolution of an ancestral line can be conflated and confused. Our actual migration stories disappear into the mists of time, going back into the preliterate, even prehistoric past that starts, for every one of us, in Africa.

Not everyones test results are as muddled as mine. My wife, Sonja, who has always prided herself on being a purebred Norwegian, turns out to be a purebred Norwegian. The first results from AncestryDNA pegged her as 3% Micronesian, to her amazement and amusement, but the companys updates confirmed that all of her ancestors are from Norway. The most recent estimates even correctly identified her familys counties of origin in the southwestern part of the country.

Although most of us are hoping to find our roots when we take the test, AncestryDNA has started offering, for an extra fee, information about inherited traits that have nothing to do with ancestral geographies. The company carefully avoids worrisome markers like those for cancer, depression, addiction, heart diseaseand other maladies, testing instead for more innocuous qualities. I ponied up my 20 bucks and found that Im genetically predisposed to be lousy at remembering dreams (false), a good sprinter (once upon a time), a devotee of caffeine (false), blue-eyed (true), cleft-chinned (sort of), freckled (false), wavy-haired (in days gone by), and unibrowed (false). Oh, and my urine has a distinctive smell after I eat asparagus. Hardly earth-shaking, and just as imprecise as my estimated ethnic origins.

Even if its nowhere close to definitive, DNA testing is an interesting exercise. My own results demonstrate that the road back can have as many twists and turns as the road ahead. I will never make his acquaintance, but I cherish the thought of some peasant ancestor long gone to dust, a Peder or a Janek, known in his village as a near-sighted fellow with a decent memory and a penchant for solitude or perhaps as the serious one who would rather read than plow but still liked his tankard of beer. That familiar personage is one of countless characters who reside in my familys indeterminate past, and he lives on today, however mutely, in every strand of my DNA.

John Gurda writes a column on local history for the Ideas Lab on the first Sunday of every month. Email:mail@johngurda.com

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It may be in the genes, but DNA testing offers a bumpy ride to the past - Milwaukee Journal Sentinel

ABSTRACT breaks down mind-bending scientific research, future tech, new discoveries, and major breakthroughs.

Death is a universal fact of life, unless you're a jellyfish. As explained in a new study, the jellyfish Turritopsis dohrnii "is the only species able to rejuvenate repeatedly after sexual reproduction, becoming biologically immortal," and its DNA might hold the answer to the secret of eternal life.

T. dohrnii pulls off an amazing biological feat to cheat death. Every member of the species is an identical clone, and starts life as a polyp that becomes a mature organism called a medusa. This isn't particularly unique, but what's amazing about T. dohrnii is that if the medusas get injured, sick, or old, they don't throw in the towel. Instead, they become a "cyst" that turns back into a polyp and restarts the whole process, churning out more clones. While it might be a bit different from the idea of living forever in a vampire story, it is, strictly speaking, biological immortality. You can also call it, as scientists do, "life cycle reversal." It would be like if a person got old and turned back into a fetus, or a chicken into an egg.

In a study published on Monday in the journal PNAS by researchers at the University of Oveidas in Spain, the authors describe how they compared the DNA of T. dohrnii to another closely-related jellyfish species that is not immortal to determine what makes it special.

Specifically, they compared "genes involved in aging and DNA repair, together with the transcriptome [mRNA] analysis of life cycle reversal (LCR) of T. dohrnii," which has now "provided new insights into the molecular mechanisms underlying Turritopsis plasticity, which may contribute to the immortal phenotype of T. dohrnii," they wrote in the study.

Indeed, the researchers found several differences that they pinned as likely having an effect contributing to the jellyfish's immortality. Overall, these changes "suggest that T. dohrnii may have more efficient replicative mechanisms and repair systems" than other species, the authors write.

For example, they found more copies of POLD1 and POLA2 geneswhich encode different proteinsin T. dohrnii than in its mortal relatives, which "suggest enhanced replicative capabilities in this species," the study notes. The species also had more copies of genes governing DNA repair, and those that govern telomerase, which are enzymes that replenish the telomeres on DNA that shorten with age. This "may contribute to a reduced telomere attrition and as a consequence to an enhanced cellular plasticity," the authors write, and "may indicate that telomerase activity could be enhanced or more finely regulated in this species."

While this knowledge isn't going to let humans become "biologically immortal" like T. dohrniiand even if it could, would we want it?it is an astounding jump forward in our understanding of age and how some species defeat it entirely.

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Scientists Analyzed DNA of Immortal Jellyfish to Find Secret to Eternal Life - VICE

COVID and monkeypox seem to have come out of nowhere and exploded across continents. But the phenomenon of natural selection acting on genetic variants of viruses or organisms that have an advantage in a certain place and time is ages old. The rabbits of Australia provide a powerful example of natural selection run amok, favoring a particularly robust mix of domestic and wild traits against an environmental backdrop of plenty of food and a paucity of predators.

The animals that have overrun the continent eat almost any plant, their appetites reverberating along food webs, costing an estimated $200 million a year. Over decades, interventions to control their numbers from rabbit-proof fences to intentional infections with nasty viruses to shooting have all failed. In Australia, the rabbit has survived drought, fire, flood, diseases, predators, poisons and other stratagems devised by man and remains this countrys most serious vertebrate pest, wrote Brian Coman in Tooth and Nail: The Story of the Rabbit in Australia.

Now researchers from the University of Cambridge and CIBIO Institute in Portugal have wed genetics to history to illuminate the precise source of Australias problem. Their report is in the Proceedings of the National Academy of Sciences.

The colonisation of Australia by the European rabbit is one of the most iconic and devastating biological invasions in recorded history. Here, we show that despite numerous introductions over a 70-year period, this invasion was triggered by a single release of a few animals that spread thousands of kilometres across the continent, the researchers write.

Feral rabbits once-domestic animals relocated, where novel behaviors emerge remain a problem in Australia, where they number more than 150 million. Its an interesting mammal, in terms of the relationships to us. The rabbit has, in various times and places, been a treasured pet, a commercial farm animal, a valued subject of the hunt, a major ecological force and an economic pest, wrote Coman, to which Id add a valuable model organism in the lab.

Thirteen Rascally Rabbits

The rabbit invasion of Australia began with a mixing of genomes sex among 13 animals shipped from England in 1859. But those werent the first rabbits just the first to take over.

Historical records trace the pioneer rabbits to 1788, when the First Fleet of 11 ships six convict transports, three ships of goods, and two Royal Navy vessels brought the founding European and African settlers from Portsmouth, England, to Botany Bay, New South Wales. Among the 1400 humans were five silver grey domestic bunnies. These pets were taken to Sydney, supposedly never released into the wild.

At least 90 times after that, domestic rabbits came to Australia, but the populations stayed small. Then in 1859 wild rabbits nosed into a shipment of domestics and all hell broke loose.

The animals spread 100 kilometers a year for the next half-century, munching their way through native plants and starving the indigenous herbivores and then carnivores that had evolved there over millions of years. The new genetic analysis reveals that it was specific genes that spawned the fastest colonization rate for an introduced mammal ever recorded.

What happened in and after 1859 to propel these particular wild rabbits into reproductive overdrive? DNA provides the answer. But first, more backstory.

Local lore as well as the historical record trace the origin of Australias rabbit plague to Thomas Austin, master of the Barwon Park estate Winchelsea, southwest of Melbourne.

On October 6, 1859, Thomass brother William, who lived at the family estate in Baltonsborough, Somerset, England, sent the 13 rabbits to Australia. It was a mixed bunch. Wild rabbits were by no means common round Baltonsborough. It was only with great difficulty that he managed to get six; these were half-grown specimens taken from their nests and tamed. To make up the number he bought seven grey rabbits that the villagers had kept in hutches, either as pets or to eat, recalled Williams granddaughter Joan Palmer. Eighty days later, on Christmas, two dozen rabbits arrived in Australia theyd clearly bred on the journey.

The domestic and wild rabbit genomes mixing on this particular trip from England brewed a gene combination that enabled the animals to explode in numbers once let loose into the vast new land full of food from the new pastoral practices. One such trait from the domestic camp was the colored coat that provided protection across the land, and the burgeoning rabbit population came to be called the grey blanket.

Within three years, the animals had expanded to thousands. In 1865, Austin killed 20,000 rabbits at his estate, alarmed by the extraordinary fecundity of the English rabbit. A year later, hunters bagged 14,000 more there.

Austins rabbits spread, finding plentiful food and no predators. From 1880 to 1894, they took over New South Wales, Queensland, and Western Australia. An article from the National Museum Australia provides context: It took rabbits 700 years to spread throughout Britain, but 50 years to colonize two-thirds of Australia, which is about 25 times larger.

By the late 1940s the animals numbered 600 million, despite many people eating them during the depression and war years. Robust harvests following abundant rainfall fed the rabbits, while men who could build more fences were in short supply.

DNA Analysis Reveals 5 Founding Females Echoing History

The researchers sequenced the exomes (the protein-encoding parts of the genome) of 187 rabbits. Most were wild, from Australia, Tasmania, and New Zealand, but a few were from France and Britain. The analysis included nearly 2 million gene variants.

The animals had been caught between 1865 and 2018. Theyd become pests in New Zealand and Tasmania in the decades following their introduction too. The common denominator among the Australian, New Zealand, and Tasmanian rabbits, the investigators conclude, was the arrival of a new genotype that was better adapted to the natural environment, which is arid and semi-arid.

We managed to trace the ancestry of Australias invasive population right back to the South-West of England, where Austins family collected the rabbits in 1859. Our findings show that despite the numerous introductions across Australia, it was a single batch of English rabbits that triggered this devastating biological invasion, the effects of which are still being felt today, said lead author Joel Alves.

The genetic diversity of the rabbits fell as the animals migrated away from Barwon Park and natural selection favored the gene variants that accelerated growth and fitness. In the lexicon of Darwin, fitness means reproductive success.

If an environmental change beginning in 1859 was the only force that had spurred the rabbit population explosion, such as agriculture, then several small rabbit populations would have expanded across the continent. But the petering out of pre-1859 rabbits and the new DNA evidence argue against that explanation, pointing to a single event that led to a hardy, adaptive genome.

What traits could have propelled the rabbits success? Animals introduced earlier had the hallmarks of pets: floppy ears, complex coat coloring, and tameness. But Austins rabbits also brought in a combination of traits that conferred a changed body shape that enabled the animals to withstand a much greater temperature range which enabled them to take over and eat nearly any plant. The historical record indicates that Austins rabbit shipment was the only one to include wild animals.

Even more compelling evidence comes from analysis of mitochondrial DNA, which is passed from mothers to all offspring. Remember mitochondrial Eve from 1987? She was the theoretical most recent woman from whom all living humans descend, deduced from comparing mitochondrial DNA from 147 people from 5 diverse populations. Similar analysis of rabbit mitochondrial DNA indicated 5 female rabbits having seeded the millions of invasive descendants and that matches, precisely, the historical record of Austins original 13 rabbits, which included 5 wild females.

In all my years of science writing, I cant think of a more elegant example of converging genetic and historical evidence.

What happened after Austins rabbits reached Australia was a phenomenon called allele surfing. An allele is an older term for gene variant. When the alleles conferring grey color and a svelte body came to Australia, the geographic expansion triggered a sudden amplification of the alleles conferring these traits because the characteristics were, and continue to be, so adaptive. In other words, alleles that were rare in the ancestral British population exploded under the environmental conditions in Australia.

Summed up Alves:

More than 150 years have passed since Thomas Austin asked his brother to send him some wild rabbits from their family property in England. Unbeknown to him, this request caused a cascade of events that changed forever the landscape of an entire continent and resulted in the greatest pastoral pest of the 20th century.

These findings matter because biological invasions are a major threat to global biodiversity and if you want to prevent them you need to understand what makes them succeed. Environmental change may have made Australia vulnerable to invasion, but it was the genetic makeup of a small batch of wild rabbits that ignited one of the most iconic biological invasions of all time. This serves as a reminder that the actions of just one person, or a few people, can have a devastating environmental impact.

Read more:
DNA Analysis Solves the Mystery of the Rabbit Invasion of Australia - DNA Science - PLOS

Neanderthals have served as a reflection of our own humanity since they were first discovered in 1856. What we think we know about them has been shaped and moulded to fit our cultural trends, social norms and scientific standards. They have changed from diseased specimens to primitive sub-human lumbering cousins to advanced humans.

We now know Homo neanderthalensis were very similar to ourselves and we even met them and frequently interbred. But why did they go extinct, while we survived, flourished and ended up taking over the planet?

Neanderthals evolved over 400,000 years ago, most likely from an earlier ancestor Homo heidelbergensis. They were extremely successful and spread across an area from the Mediterranean to Siberia. They were highly intelligent, with brains on average bigger than Homo sapienss.

They hunted for big game, collected plants, fungi, and seafood, controlled fire to cook, made composite tools, made clothes from animal skins, made beads from shells, and were able to carve symbols on to cave walls. They took care of their young, old and weak, created shelters for protection, lived through harsh winters and warm summers, and they buried their dead.

Neanderthals did meet our ancestors on several occasions over the course of tens of thousands of years and the two species shared the European continent for at least 14,000 years. They even mated with each other.

The most significant difference between Neanderthals and ourselves is that they went extinct about 40,000 years ago. The precise cause of their demise still eludes us, but we think it was probably the result of a combination of factors.

First the climate of the last ice age was very variable, shifting from cold to warm and back again, which put pressure on animal and plant food sources and meant Neanderthals constantly had to adapt to environmental change. Second there were never that many Neanderthals, with the overall population never exceeding the tens of thousands.

They lived in groups of five to 15 individuals, compared with Homo Sapiens that had groups of up to 150 individuals. These small isolated Neanderthal populations may have been increasingly genetically unsustainable.

Third there was competition with other predators, particularly the groups of modern humans that emerged from Africa about 60,000 years ago. We speculate that many Neanderthals may have been assimilated into the larger bands of Homo sapiens.

Neanderthals left numerous traces for us to examine tens of thousands of years later, much of which can be seen at the special exhibition we have helped curate at the Natural History Museum of Denmark. Over the past 150 years we have collected fossil bones, stone and wooden tools, found trinkets and jewellery they left behind, uncovered burials, and now mapped their genome from ancient DNA. It seems that 99.7% of Neanderthal and modern human DNA is identical and they are our closest extinct relatives.

Perhaps the most surprising fact was evidence of interbreeding that has left traces of DNA in living humans today. Many Europeans and Asians have between 1% and 4% Neanderthal DNA while African people south of the Sahara have almost zero. Ironically, with a current world population of about 8 billion people, this means that there has never been more Neanderthal DNA on Earth.

The Neanderthal genome also helps us understand more of what they looked like, as there is evidence that some Neanderthals evolved pale skin and red hair long before Homo sapiens. The many genes that are shared between Neanderthals and modern humans are linked to anything from the ability to taste bitter foods to the capacity to speak.

We have also increased our knowledge of human health. For instance, some Neanderthal DNA that might have been beneficial to humans tens of thousands of years ago now seems to cause issues when combined with a modern western lifestyle.

There are links to alcoholism, obesity, allergies, blood clotting, and depression. Recently, scientists suggested an ancient gene variant from Neanderthals might increase the risk of serious complications from contracting COVID-19.

Like the dinosaurs, the Neanderthals didnt know what was coming. The difference is that the dinosaurs disappeared suddenly following a giant meteorite hit from outer space. To the Neanderthals extinction happened gradually. They eventually lost their world, a comfortable home they had successfully occupied for hundreds of thousands of years that slowly turned against them, until existence itself was unsustainable.

In that sense, Neanderthals now serve a different purpose. We see our reflection in them. They didnt know what was happening to them and they had no choice but to continue down the road that eventually led to extinction. We on the other hand are painfully aware of our situation and the impact we have on this planet.

Human activity is changing the climate and is leading straight into a sixth mass extinction. We can reflect on the mess we have landed ourselves in and we can do something about it.

If we dont want to end up like the Neanderthals, we better get our act together and collectively work for a more sustainable future. Neanderthal extinction reminds us that we should never take our existence for granted.

Link:
Neanderthals died out 40,000 years ago, but there has never been more of their DNA on Earth - The Conversation Indonesia

The largest RNA study ever conducted in hereditary cancer analyzed more than 43,000 patients who received Ambrys +RNAinsight testing and found that 1 in 950 had an elusive clinically actionable result that would have been missed by DNA-only testing.

Combined DNA and RNA testing identified cancer risk in an additional 1 out of 79 patients compared to DNA-only testing.

ALISO VIEJO, Calif., August 29, 2022--(BUSINESS WIRE)--Ambry Genetics, a leader in clinical diagnostic testing and a subsidiary of REALM IDx, Inc., announced today the findings of a study that showed paired RNA and DNA genetic testing, conducted at the same time, detected elusive pathogenic variants in 1 of every 950 patients that were missed by DNA testing alone. The findings, published in npj Genomic Medicine, highlight the importance of combining RNA and DNA analysis in hereditary cancer testing to give clinicians and their patients the most accurate and comprehensive genetic data needed to inform patient care and achieve the best outcomes.

According to the National Library of Medicine, as of August 2017, there were approximately 75,000 genetic tests on the market, representing 10,000 unique test types. Unfortunately, many of these DNA-only tests exclude large portions of DNA such as introns, a sequence of DNA that is spliced out before an RNA molecule is translated into a protein. In addition to omitting large portions of introns, DNA-only testing lacks the functional context to determine whether a variant increases cancer risk, which can lead to inconclusive results. These limitations may prevent patients and their families from getting accurate results to inform their preventative or therapeutic care.

Concurrent RNA and DNA testing helps identify more patients at risk by determining if an uncertain result from DNA testing is normal or disease-causing, and expands the range of genetic testing to identify mutations that DNA-only testing misses.

"With our +RNAinsight test we were the first company to offer upfront paired DNA and RNA sequencing to give clinicians and their patients the most accurate and comprehensive information about their cancer risk," said Tom Schoenherr, CEO, Ambry Genetics. "This study confirms that conducting RNA and DNA testing together is critical to help identify high-risk individuals who would have been missed by DNA-only testing."

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Previously, published evidence of the value of RNA sequencing has been limited by studies with small sample sizes and enriched cohorts. This study by Ambry is the largest to examine the impact of paired DNA and RNA analysis in hereditary cancer testing. In the study, tests from 43,524 patients who underwent paired DNA-RNA genetic testing using Ambrys +RNAinsight from March 2019 through April 2020 were examined to determine if the paired sequencing detected more pathogenic variants than DNA testing alone. The analysis identified patients who had disease-causing alterations that DNA testing alone would have misinterpreted. Examining the RNA data resolved variant findings in 549 patients (1 in 79 patients) by providing the required functional data for more accurate interpretation of splicing variants. In addition, the analysis showed that 1 of every 950 patients had a pathogenic deep intronic variant that would not have appeared in DNA testing alone.

The results from the study may underestimate the total clinical impact because some of the patients families who are now eligible for genetic testing were not tested. In addition, the ripple effect created by these updated results extends to past and future patients. These downstream benefits were not quantified in the current study.

"This is the largest study of its kind to show the importance of RNA testing in predicting cancer risk," said Carrie Horton, senior clinical research specialist for oncology and first author of the study. "Its clear that RNA analysis has the potential to become a standard practice for genetic testing to improve hereditary cancer care."

A webinar, open to the media, genetic counselors, clinicians and other interested parties, will be conducted on Thursday, September 15 at 10 a.m. PT to review the study findings. Registration information is here.

Ambrys +RNAinsight was the first test to provide comprehensive gene coverage for RNA analysis to help classify and detect DNA variants associated with a variety of cancers including breast, ovarian, prostate, colon, pancreatic and uterine. +RNAinsight enables more accurate identification of patients with increased genetic risks for cancer, finds actionable results that may otherwise be missed and decreases the frequency of inconclusive results.

About Ambry Genetics

Ambry Genetics, a subsidiary of REALM IDx, Inc., translates scientific research into clinically actionable test results based upon a deep understanding of the human genome and the biology behind genetic disease. It is a leader in genetic testing that aims to improve health by understanding the relationship between genetics and disease. Its unparalleled track record of discoveries over 20 years, and growing database that continues to expand in collaboration with academic, corporate and pharmaceutical partners, means Ambry Genetics is first to market with innovative products and comprehensive analysis that enable clinicians to confidently inform patient health decisions.

View source version on businesswire.com: https://www.businesswire.com/news/home/20220829005605/en/

Contacts

Media Contact

Brad LottermanCommunications DirectorREALM IDx949-401-0465blotterman@realmidx.com

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Ambry Genetics Publishes 43,000 Patient Study Showing Combined RNA and DNA Analysis Identifies Patients Who Are High-Risk for Cancer but Would Have...

Examples of photographs of virtual doubles (with similar facial features, but without family ties) used in the research published in the journal 'Cell Reports'FRANOIS BRUNELLE

Our faces, at first glance, are what differentiate us from one another. Sometimes, though, people can look virtually identical, even if they dont have any shared blood. Spanish researchers have discovered that these lookalikes actually have more than superficial features in common in fact, they may even have genetic similarities.

What unites lookalikes the most is their DNA sequence, says lead scientist Manel Esteller, who has published his groups findings in the scientific journal Cell Reports. Genomics groups them together.

The study reveals that genetic similarities may not only result in facial resemblances, but also in similar habits or behaviors. The results will likely have long-term implications within the forensic sciences.

The researchers identified pairs of virtual doppelgangers by looking through the works of photographer Franois Brunelle, a Canadian artist who has spent more than 20 years taking images of lookalikes around the world. The researchers subsequently passed them through facial recognition programs so that algorithms could verify the similarities. The 32 pairs that were eventually recruited ended up having confirmed resemblances in three recognition systems, with scores similar to those obtained by identical twins. Biological samples were then taken from the 64 participants, who were then subjected to exhaustive questionnaires about their habits and lifestyles.

In 2005, we discovered that identical twins, called monozygotes, had the same DNA. I then decided to look at people who looked alike, but werent twins. I wanted to know how much [of that resemblance] came from nature or from the environment that surrounded them, explains Esteller.

The researchers looked at the genome, but also at the epigenome, which can attach to DNA and cause functional changes, like a kind of switch that conditioned by environments or habits turns off or turns on the activity of genes. The scientists also analyzed the microbiome of the participants, or the ecosystem of microorganisms that populate a human being.

We found that what binds [each pair of virtual doubles] the most is their DNA sequence, their genomes. By chance, similar genomes end up being produced [in unrelated people]. Thats because there are so many people in the world that DNA is repeated, explains Esteller. They are not identical, but they share similarities, the researcher specifies: Similarities in their genomes explain the similarity of these pairs; however, the different composition of their epigenomes helps to differentiate them.

The research offers clues about the genetic environment associated with facial appearance. For example, genetic variations shared by the doubles were associated with physical characteristics, such as lip or eye color, hip circumference, height, body mass index or hair. But the research suggests that these molecular similarities found influence beyond the construction of the face. The study points out a facial correlation with certain physical attributes, habits and behaviors:

We saw that there is greater genetic determination in whether [the participants] are left-handed or right-handed, or prone to addictions like smoking.

Through the lifestyle questionnaires and biometric parameters, the article points out that, in matters such as height, weight, level of education or smoking habits, those who are superficially similar have more in common than those who do not look alike.

The researchers admit that there are some limitations in their study, such as the small number of participants, the fact that the majority were European, or that the photos were in black-and-white, resulting in a lack of definition of skin tone and features. But Esteller is confident that, despite all of this, the study opens a new door in the scientific community and points to two possible derivatives:

It may have forensic implications, because from an unknown genome, you can start to construct a face. And, on the other hand, by looking at a face, we can also begin to deduce the genome of the person. For example, if they have a certain kind of face, they may be more or less at risk of cardiovascular disease,

ngel Carracedo, a geneticist at the Institute of Forensic Sciences of the University of Santiago de Compostela who did not participate in the study notes that, while the results are interesting, they do not currently have direct application in the forensic field. It is, for now, an exploratory work

but the study broadens perspectives in the forensic field, which uses some biomarkers, he says, such as the biological witnesses in police investigations.

At the moment, the physical characteristics that can be determined with a good level of prediction for forensic purposes are pigmentation (especially eye and skin color), hair type and little else new genes are very important to explore other facial and physical characteristics.

Carracedo who leads a project to design techniques that determine the physical characteristics, biographical origins and ages of people based on their DNA agrees, however, that all of this must continue to be studied, replicated and validated, while meeting the highest forensic standards.

Read more:
Similar faces share similar DNA - EL PAS USA

Scientists around the world are racing to record the genetic blueprints of every known species on the planet. The effort comes as the United Nationswarns that an estimated one million plant and animal species are at risk of becoming extinct within the coming decades.

"This is absolutely urgent," researcher Joanna Harley told CBS News correspondent Roxana Saberi. "It's really important to protect species on this planet. They share with us and they keep us going and the more we erode away at the world, the less there will be."

Around 5,000 scientists across the globe are part of the Earth BioGenome Project. Over the next decade, teams will digitize DNA of the 1.8 million named plant, animal, fungi and single-celled eukaryote species on the planet. By the end of 2022, the scientists plan on sequencing 3,000 genomes.

By DNA sequencing life on Earth, the researchers have goals of benefitting human welfare, protecting biodiversity and better understanding ecosystems.

"Everything's interconnected," Mark Blaxter, who leads a group working under the Earth BioGenome Project, told Saberi. "We need the services that these plants and animals and fungi give us...so by understanding how they do it, we can help humans as well."

So far, researchers in Britain have recorded the genetic blueprints of nearly 400 of the country's 70,000 known species.

The lengthy process begins with researchers like Harley who help search for species. The collected specimens are then sent for sorting before they're shipped off to sequencing labs. The data is then shared online.

"We'll be able to look at a species and work out whether it's endangered or not, and we'll know what to do to keep it going," Blaxter said.

The scientists added that decoding DNA won't save endangered plants and animals alone, but that it can be beneficial as more species are on the track of extinction.

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Tori B. Powell is a breaking news reporter at CBS News. Reach her at tori.powell@viacomcbs.com

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Scientists race to digitize DNA of every known species on the planet - CBS News

Experiments from the UNC School of Medicine lab of Nobel Prize-winning scientist Aziz Sancar, MD, PhD, show how a common molecular tool for DNA labeling also has anticancer properties worthy of further investigation, especially for brain cancers.

CHAPEL HILL, NC Scientists at the UNC School of Medicine have made the surprising discovery that a molecule called EdU, which is commonly used in laboratory experiments to label DNA, is in fact recognized by human cells as DNA damage, triggering a runaway process of DNA repair that is eventually fatal to affected cells, including cancer cells.

The discovery, published in the Proceedings of the National Academy of Sciences, points to the possibility of using EdU as the basis for a cancer treatment, given its toxicity and its selectivity for cells that divide fast.

The unexpected properties of EdU suggest it would be worthwhile to conduct further studies of its potential, particularly against brain cancers, said study senior author Aziz Sancar, MD, PhD, the Sarah Graham Kenan Professor of Biochemistry and Biophysics at the UNC School of Medicine and member of the UNC Lineberger Comprehensive Cancer Center. We want to stress that this is a basic but important scientific discovery. The scientific community has much work ahead to figure out if EdU could actually become a weapon against cancer.

EdU (5-ethynyl-2-deoxyuridine) is essentially a popular scientific tool first synthesized in 2008 as an analog, or chemical mimic, of the DNA building block thymidine which represents the letter T in the DNA code of adenine (A), cytosine (C), guanine (G) and thymine (T). Scientists add EdU to cells in lab experiments to replace the thymidine in DNA. Unlike other thymidine analogs, it has a convenient chemical handle to which fluorescent probe molecules will bond tightly. It thus can be used relatively easily and efficiently to label and track DNA, for example in studies of the DNA replication process during cell division.

Since 2008, scientists have used EdU as a tool in this way, as published in thousands of studies. Sancar, who won the 2015 Nobel Prize for Chemistry for his seminal work on DNA repair, is one such scientist. When his lab began using EdU, his team unexpectedly observed that EdU-labeled DNA triggered a DNA repair response even when it wasnt exposed to DNA-damaging agents, such as ultraviolet light.

That was quite a shock, Sancar said. So we decided to explore it further.

Following up on the strange observation, the team discovered that EdU, for reasons that are still unclear, alters DNA in a way that provokes a repair response called nucleotide excision repair. This process involves the removal of a short stretch of damaged DNA and re-synthesis of a replacement strand. This is the mechanism that repairs most damage from ultraviolet light, cigarette smoke, and DNA-altering chemo drugs. The researchers mapped EdU-induced excision repair at high resolution and found that it occurs across the genome, and it apparently occurs again and again, since each new repair strand includes EdU and thus provokes the repair response anew.

It had been known that EdU is moderately toxic to cells, though the mechanism of its toxicity had been a mystery. The teams findings strongly suggest that EdU kills cells by inducing a runaway process of futile excision repair, which ultimately leads the cell to terminate itself through a programmed cell-death process called apoptosis.

That discovery was interesting in its own right, Sancar said, because it suggested that researchers using EdU to label DNA need to take into account its triggering of runaway excision repair.

As we speak, hundreds and maybe thousands of researchers use EdU to study DNA replication and cell proliferation in lab experiments without knowing that human cells detect it as DNA damage, Sancar said.

Sancar and colleagues also realized that EdUs properties might make it the basis for an effective brain cancer drug because EdU becomes incorporated into DNA only in cells that are actively dividing, whereas, in the brain, most healthy cells are non-dividing. Thus, in principle, EdU could kill fast-dividing cancerous brain cells while sparing non-dividing, healthy brain cells.

Sancar and his team hope to pursue follow-up collaborations with other researchers to investigate EdUs properties as an anticancer agent.

Prior studies have already found evidence that EdU kills cancer cells, including brain cancer cells, but strangely, no one has ever followed up on those results, Sancar said.

Nucleotide excision repair removes thymidine analog 5-ethynyl-2-deoxyuridine from the mammalian genome was co-authored by Li Wang, Xuemei Cao, Yanyan Yang, Cansu Kose, Hiroaki Kawara, Laura Lindsey-Boltz, Christopher Selby, and Aziz Sancar. Funding was provided by the National Institutes of Health (GM118102, ES02755).

Media contact: Mark Derewicz, UNC School of Medicine, 919-923-0959

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Scientists Discover Surprise Anticancer Properties of Common Lab Molecule | Newsroom - UNC Health and UNC School of Medicine

If you're looking for a multi-bagger, there's a few things to keep an eye out for. One common approach is to try and find a company with returns on capital employed (ROCE) that are increasing, in conjunction with a growing amount of capital employed. Ultimately, this demonstrates that it's a business that is reinvesting profits at increasing rates of return. With that in mind, the ROCE of Denbury (NYSE:DEN) looks great, so lets see what the trend can tell us.

If you haven't worked with ROCE before, it measures the 'return' (pre-tax profit) a company generates from capital employed in its business. To calculate this metric for Denbury, this is the formula:

Return on Capital Employed = Earnings Before Interest and Tax (EBIT) (Total Assets - Current Liabilities)

0.24 = US$378m (US$2.1b - US$539m) (Based on the trailing twelve months to June 2022).

So, Denbury has an ROCE of 24%. That's a fantastic return and not only that, it outpaces the average of 16% earned by companies in a similar industry.

Check out our latest analysis for Denbury

roce

In the above chart we have measured Denbury's prior ROCE against its prior performance, but the future is arguably more important. If you're interested, you can view the analysts predictions in our free report on analyst forecasts for the company.

Denbury has not disappointed in regards to ROCE growth. We found that the returns on capital employed over the last five years have risen by 450%. That's a very favorable trend because this means that the company is earning more per dollar of capital that's being employed. Interestingly, the business may be becoming more efficient because it's applying 61% less capital than it was five years ago. If this trend continues, the business might be getting more efficient but it's shrinking in terms of total assets.

On a side note, we noticed that the improvement in ROCE appears to be partly fueled by an increase in current liabilities. The current liabilities has increased to 25% of total assets, so the business is now more funded by the likes of its suppliers or short-term creditors. Keep an eye out for future increases because when the ratio of current liabilities to total assets gets particularly high, this can introduce some new risks for the business.

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In the end, Denbury has proven it's capital allocation skills are good with those higher returns from less amount of capital. And investors seem to expect more of this going forward, since the stock has rewarded shareholders with a 29% return over the last year. So given the stock has proven it has promising trends, it's worth researching the company further to see if these trends are likely to persist.

Like most companies, Denbury does come with some risks, and we've found 1 warning sign that you should be aware of.

If you'd like to see other companies earning high returns, check out our free list of companies earning high returns with solid balance sheets here.

Have feedback on this article? Concerned about the content? Get in touch with us directly. Alternatively, email editorial-team (at) simplywallst.com.

This article by Simply Wall St is general in nature. We provide commentary based on historical data and analyst forecasts only using an unbiased methodology and our articles are not intended to be financial advice. It does not constitute a recommendation to buy or sell any stock, and does not take account of your objectives, or your financial situation. We aim to bring you long-term focused analysis driven by fundamental data. Note that our analysis may not factor in the latest price-sensitive company announcements or qualitative material. Simply Wall St has no position in any stocks mentioned.

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We Think Denbury (NYSE:DEN) Might Have The DNA Of A Multi-Bagger - Yahoo Finance

STUNNED BY veteran leader Ghulam Nabi Azads resignation and his attack on Rahul Gandhi, the Congress initially questioned the timing of his decision, and then launched a scathing counter-attack, accusing him of being in cahoots with the BJP. Several Congress leaders, including its two chief ministers, Ashok Gehlot and Bhupesh Baghel, attacked Azad.

It is most unfortunate and most regrettable that this has happened when Congress president Sonia Gandhi, Rahul Gandhi and the entire Congress party organisation across the country is engaged in confronting, combating and fighting the BJP on public issues of price rise, unemployment and polarisation, Jairam Ramesh, AICC general secretary in charge of communication, said at a press conference.

The Congress had earlier scheduled a press conference to be addressed by Ajay Maken, to target the AAP government in Delhi on the liquor policy. But it cancelled this, and a short statement was read out by Maken and Ramesh on Azads resignation instead.

The entire Congress party organisation has been involved in preparing for the Mehangai Par Hallo Bol rally in New Delhi on September 4 which would be addressed by Rahul Gandhi. Twenty-two press conferences have been scheduled across the country on August 29. The launch of the Bharat Jodo Yatra will take place on September 7 in Kanyakumari; finalisation of that launch is also underway and 32 press conferences have been scheduled across the country to project the message of the Bharat Jodo Yatra, Ramesh said.

So, at a time when every Congressman and every Congresswoman is involved in ensuring that the rally is a success, and wants to be a Bharat yatri and walk along with Rahul Gandhi it is most unfortunate and most regrettable that we have had to read this letter that has been released to the press, Ramesh said.

Launching an all-out attack soon after, Ramesh tweeted: A man who has been treated with the greatest respect by the Congress leadership has betrayed it by his vicious personal attacks which reveal his true character. GNAs DNA has been modi-fied First Modis tears in Parliament, then Padma Vibhushan, then the extension for residence. Yeh sanyog nahi, sahyog hai (Its not a coincidence, its a collaboration).

Ramesh said the contents of Azads resignation letter were not factual and its timing was awful.

The partys media department head, Pawan Khera, linked Azads resignation to the end of his Rajya Sabha tenure. As soon as your Rajya Sabha term got over, you became restless, you cannot stay without a post even for a second. It is a challenging time, everyone is fighting together and the party is being strengthened under Rahul Gandhis leadership, he said, adding that the people who had contributed to weakening the party were now saying that the party has been weakened.

Claiming that every party worker was aware of this betrayal, Khera said his (Azads) remote control is in the hands of Modi. We have seen the love between Narendra Modi and Ghulam Nabi Azad, it was also seen in Parliament. That love has been manifested in this letter, he said.

It is very clear. Perhaps you have joined hands with those people who have scrapped Article 370 in Kashmir. Ho sakta hai kuch aapke unke saat madhur sambandh ho gaye honge (It is possible that you have a warm relationship with them). But I want to tell you one thing. You have written in the letter that it is time to unite the Congress. And in the same letter you are saying there is no need for Bharat jodo. Instead of uniting the Congress, I condemn the step that you have taken to divide the Congress, said senior party leader Digvijaya Singh.

And that at a time when Sonia Gandhi, whose family had given you everything, is abroad for medical treatment. I did not expect this from you. The Congress had given you everything. At such a time of crisis, you should have stood firmly with the Congress, he said.

Gehlot said Rahul would have his own ideas on taking the Congress forward. I am aghast. I am shocked. We have been together for 42 years. The party gave him every opportunity be it Indira Gandhi or Sanjay Gandhi they even went to attend Azads wedding in Srinagar. From there it all started they wanted to promote the young man for the last 42 years, he got all the posts, all the opportunities Union minister, AICC general secretary, chief minister The Congress never hesitated in giving him opportunities, Gehlot said.

Today, his identity in the country is because of the Congress, because of Indira Gandhi, Rajiv Gandhi, P V Narasimha Rao and Sonia Gandhi. I do not think the way he has expressed his sentiment can be called proper Whatever our identity is today is due to the faith the Congress high command had in us. How many people get a chance? No one in the country expected that Azad saab would now write such a letter, he said.

Questioning the timing of the decision, at a time when Sonia is abroad for a medical check-up, Gehlot said: This, I believe, is against human nature, against sensitivity.

Baghel said Azad was constantly trying to harm the party. The party had given him full respect. He was made a cabinet minister and chief minister. His exit will cause no loss to the party, he said.

Leader of the Opposition in Rajya Sabha Mallikarjun Kharge said Azads remarks against Rahul were not in good taste. He enjoyed everything, power and authority, for a long time and is now finding fault, he said.

Link:
Cong's reply: His DNA is modi-fied, remote in Modi hands - The Indian Express