Category Archives: DNA

A DNA test kit revealed to a Chicago woman that she is a distant relative of Catherine O'Leary, an Irishwoman who was blamed for starting the Great Chicago Fire.

According to the Chicago Tribune, results from a DNA test done by Chicago local Cindy OGara, have shown that her biological father was the great-grandson of Catherine OLearys eldest child, Mary OLeary Scully.

O'Gara eventually connected with her birth fathers two sisters, who recalled family stories theyd grown up with and the 150-year-old tale that has haunted several generations of the OLearys, making their name synonymous with the citys destruction.

Their family story goes back to the 1800s when Patrick OLeary from County Kerry, Ireland married Catherine Donegan from County Cork.

After the birth of their first child, the family immigrated to America and Patrick enlisted in the Civil War. Soon after the war ended, the OLearys arrived in Chicago, where the couples last three children were born.

There are several versions of the legend of the Great Fire, but the most common one is that on October 8, 1871, Catherine OLeary went into a barn on a dry night with a lantern to milk one of her cows for oyster stew. OLeary left the lantern in the barn and the cow kicked it over and started the fire.

Chicago at that time was still a new city. Founded a mere 30 years before it was believed to be the fastest-growing city in the entire world. Most of it had been constructed in haste - and poorly at that - almost everything was made of wood and tightly packed together. Tragically the aftermath of the two-day blaze left 300 dead and 100,000 homeless.

The O'Leary family of the time long maintained that they were in bed that evening when the fire started. The cause of the fire still remains a mystery, with many agreeing now that a poor Irish emigrant was the perfect scapegoat. Catherine O'Leary was vilified for the rest of her life and would eventually die "heartbroken".

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The fire remained a taboo subject within the O'Leary family for generations and the shame of the incident was passed down.

People would come from all over to throw rocks at the house, explained Peggy Knight, a great-great-granddaughter of Catherine and Patrick OLeary.

Now approaching the anniversary year of the familys biggest tragedy, descendants say theyre embracing their Irish heritage and want to finally put an end to the old rumor.

"Kate and Patrick OLeary were these strong people. Its hard to get out of Ireland during the Potato Famine, and then the shame heaped upon us, Knight said

I think its time for closure...I wish she would have [spoken to reporters], but there was no option. There was no social media. All that was written [on the incident] is what was written in the newspapers and it wasnt the gospel truth.

Reflecting on the discovery of her family and her connection to the O'Leary name, Cindy O'Gara said,

Obviously growing up in Chicago, I was very familiar with the story, but I always kept a distance from it, she said. But not now, because now I know. Its my blood. I know who I am now. Im an OLeary.

Read more:
How a DNA test led a Chicago woman to find family ties to Mrs OLeary of the Great Fire fame - IrishCentral

I lost three out of my four grandparents when I was just a kid in the early 70s, so it was hardly on my radar to quiz them about the good old days, when I was wrapped up in more important matters like Whos better The Osmonds or The Jackson 5?

I would have had the chance with my last remaining grandparent, Grandma Charlotte, who died when I was 28. But I didn't take it. Charlotte, better known by us as "Mommygan," was an old Southern lady, a mad good knitter who also liked to drink bourbon while watching Jeopardy.

She was kind of a character.

Once when I was a kid snacking on sunflower seeds and drinking a Mountain Dew, Mommygan said, in her luxurious Southern drawl, Why, back in Nashville, Mountain Dew was moonshine and we only gave sunflower seeds to the birds. The woman had flair and Im sure stories to spare.

I just didnt really get to hear them.

Fortunately, the same cant be said for Alice Bjorklund Gunness grandchildren.

Alice, at the age of 88, has just released her second book of stories and memories, Nurtured by Nature Book II. And it's simply delightful.

I first met Alice in 2018 when she achieved her lifelong dream of becoming a published author with her first Nurtured by Nature book she wrote at the age of 85. But apparently the writing itch had not been sufficiently scratched, and the pandemic allowed Alice even more time to write her stories.

Photographer Dave Samson and I caught up with Alice a couple of weeks ago as she was hosting a book signing for her fans at Riverview Place in Fargo where she lives. Dressed in beautiful florals, she softly read some of the passages from her book. Most of the chapters are about her ancestors and the hardships they endured as they settled in Otter Tail County, Minn.

Alice Gunness reads a from "Nurtured by Nature II" at Riverview Place in south Fargo. David Samson / The Forum

My dad came over from Sweden and got married in 1917. Prices for land were high at the time, so my dad had to chop down so many trees to make enough money to buy the land. Then the stock market crashed and the Depression hit. It was tough, she says.

But Alice says her ancestors overcame the hardships, and thats what she wants her five children, eight grandchildren and three (soon to be six) great-grandchildren to remember.

I think it's so important that they know the struggles their ancestors went through and while times might be difficult for them now, they can get through it.

Alice starts to tear up when she talks about how her stories might help her grandchildren and great-grandchildren, who live far away, to navigate their own lives.

Theyre going to have hard times too and they better be prepared. We all have struggles and life isnt always easy. I want them to know that times might be different, but some things dont change, she says.

Alice says shes so happy to hear that her homespun tales have proven comforting to people shes not even related to. She says one woman told her she reads her stories every night before bed.

Alice and her family are quick to point out the many people who helped her publish the book, including Karla Smart-Morstad, David Morstad, Terry Sinner and more.

Her daughter, Sarah Ostrem, is grateful to all of the people whove made her moms dreams come true.

Its Gods miracle that she was given so many wonderful helpers, Ostrem says.

Alice Gunness discusses her new book, "Nurtured by Nature II," at Riverview Place in south Fargo. David Samson / The Forum

Her son, Arthur Gunness, once said of his mothers writings, Well, Mom, I think you found your passion.

Alice just smiles at that.

But the best part of finding that passion is that Alices descendants won't have to search for their family stories the way so many of us have had to.

Way to go, Alice! Thanks for the memories!

Ill leave you with this plea: Grandmothers and grandfathers, follow Alices lead. While you dont necessarily need to write your stories down in a book, make sure to share them with loved ones. And grandchildren, listen and soak it all in. I promise you wont regret it.

For more information about Alice and her books, email her at dakgunn@rrt.net.

Grandparents: Have you shared stories with your grandchildren?Grandchildren: Have you asked your grandparents to share stories? Thank you for voting!

Yes, we have shared a lot

0%

No, not at all

0%

Maybe a few, but we should share more

100%

Readers can reach Forum reporter and "Back Then with Tracy Briggs" columnist Tracy Briggs at tracy.briggs@forumcomm.com.

The rest is here:
Lessons for the grandkids that there's strength in your DNA - INFORUM

A new study suggests that modern Japanese have descended from three ancestral populations, including people in the Kofun Period between the third and seventh century.

According to current mainstream theory, Japanese have mixed origins in the Jomon people known for their distinctive pottery culture (c. 14500 B.C.-1000 B.C.) and the Yayoi people with their own pottery culture (1000 B.C.-A.D. 250).

However, a DNA analysis of human bones from about 1,500 years ago during the Kofun Period showed genetic characteristics unique to East Asians, which are found in present-day Japanese but not in prehistoric Jomon and Yayoi people, researchers said.

This is the first evidence that Japanese have descended from three ancestral populations of Jomon, Yayoi and Kofun people, said Takashi Gakuhari, an assistant professor of archaeological science at Kanazawa Universitys Center for the Study of Ancient Civilizations and Cultural Resources.

An international team of researchers from Kanazawa University, Tottori University and other institutions published their findings in the U.S. journal Science Advances on Sept. 18.

According to the widely accepted dual structure model theory announced in 1991 by Kazuro Hanihara, who was a professor emeritus at the University of Tokyo at the time, modern Japanese have mixed origins in indigenous Jomon hunter-gatherers and succeeding Yayoi farmers.

The Jomon people inhabited across the Japanese archipelago, and they eventually became the Yayoi people after immigrant groups arrived from the Asian continent.

The research team analyzed DNA of 12 remains, including a Jomon person from about 9,000 years ago and a Kofun individual from about 1,500 years ago and compare the data with those from two Yayoi people whose DNA had been previously examined.

The researchers studied which one of the ancient populations was genetically close to modern Japanese based on traces of small differences caused by mutations when genetic information was passed from the parent to the child.

They confirmed that the Yayoi people had genetic characteristics commonly found in people in Northeast Asia, including areas along the Liao River in northeastern China, and that they admixed with the Jomon people.

The Kofun people had genetic characteristics widely found among East Asians but not in the Yayoi people. They also shared genetic characteristics almost identical to modern Japanese.

Large-scale migrations from the continent date back to about 3,000 years ago during the Yayoi Period. The researchers said additional immigrant groups, such as Han Chinese, came to Japan, handing down textile, civil engineering and other technologies during the Kofun Period.

The researchers said they need to analyze more remains from the Kofun Period to confirm the new theory. The latest analysis covered bones of only three Kofun individuals excavated in Kanazawa.

We want to close in on the mystery of the origins of Japanese by studying the genomes of other Kofun and Yayoi people, Gakuhari said.

To read the paper, go to (https://www.science.org/doi/10.1126/sciadv.abh2419).

Read more here:
DNA study points to three ancestral populations for modern Japanese | The Asahi Shimbun: Breaking News, Japan News and Analysis - Asahi Shimbun

Significance

Structural sophistication in nature would not be possible without hierarchical assembly: the concept that an initial building block (e.g., polypeptide) contains all necessary structural and chemical information to determine its assembly along a multistep pathway to generate a complex architecture (e.g., viral capsid). Translating this concept to synthetic systems is an outstanding challenge. Here, we use DNAthe blueprint of lifeto direct the hierarchical assembly of proteins. Through DNA design, we can change the directionality of protein assembly and pathway by which proteinDNA conjugates will assemble as well as realize distinct structures by directing assembly along different pathways. These findings will facilitate the assembly of proteinDNA materials with structural complexity more closely approaching that observed in nature.

The structural and functional diversity of materials in nature depends on the controlled assembly of discrete building blocks into complex architectures via specific, multistep, hierarchical assembly pathways. Achieving similar complexity in synthetic materials through hierarchical assembly is challenging due to difficulties with defining multiple recognition areas on synthetic building blocks and controlling the sequence through which those recognition sites direct assembly. Here, we show that we can exploit the chemical anisotropy of proteins and the programmability of DNA ligands to deliberately control the hierarchical assembly of proteinDNA materials. Through DNA sequence design, we introduce orthogonal DNA interactions with disparate interaction strengths (strong and weak) onto specific geometric regions of a model protein, stable protein 1 (Sp1). We show that the spatial encoding of DNA ligands leads to highly directional assembly via strong interactions and that, by design, the first stage of assembly increases the multivalency of weak DNADNA interactions that give rise to an emergent second stage of assembly. Furthermore, we demonstrate that judicious DNA design not only directs assembly along a given pathway but can also direct distinct structural outcomes from a single pathway. This combination of protein surface and DNA sequence design allows us to encode the structural and chemical information necessary into building blocks to program their multistep hierarchical assembly. Our findings represent a strategy for controlling the hierarchical assembly of proteins to realize a diverse set of proteinDNA materials by design.

Author contributions: O.G.H., B.E.P., and C.A.M. designed research; O.G.H. and B.E.P. performed research; O.G.H. and B.E.P. contributed new reagents/analytic tools; O.G.H. and B.E.P. analyzed data; and O.G.H., B.E.P., and C.A.M. wrote the paper.

The authors declare no competing interest.

This article is a PNAS Direct Submission.

This article contains supporting information online at https://www.pnas.org/lookup/suppl/doi:10.1073/pnas.2106808118/-/DCSupplemental.

All study data are included in the article and/or SI Appendix.

Read the original here:
Encoding hierarchical assembly pathways of proteins with DNA - pnas.org

Have you ever wondered about your family history and ancestry? Living in such a globalized world where people are constantly moving to new countries and cultures are mixing and evolving, it can be tough to track down exactly where your ancestors came from. Lucky for you, your family secrets are hidden in your DNA, waiting to be analyzed.

Using the latest technological advances in genealogy, you are now able to send in a spit sample from you or even your pet, and in a few weeks, discover what percentage of French or Nigerian you really are, or what breed your pet dog or cat is. These kits can even give you clues about your health, and they're all discounted by 15% during our VIP Sale. Use promo code VIP15 at checkout to save more on these already discounted test kits.

We all know our bodies are unique, yet so many of us waste our time with cookie-cutter diets and trendy workouts. With Vitagene, all it takes is a simple cheek swab to access key information about your body to guide a healthy lifestyle designed for you. Vitagene can provide you with actionable health plans based on your DNA, lifestyle, and goals. You can learn how your genetics influence your diet, understand which supplements and workouts are best for you, and discover how your genes inform your global ancestry.

Vitagenes premium DNA ancestry test kit and health plan voucher give you all of the benefits of the standard kit and more. Along with learning how your genetics influence your diet, understanding which supplements and workouts are best for you, and discovering how your genes inform your global ancestry, the premium kit allows you to discover your genetic risk for common skin conditions with detailed reports. The kit also gives you continuous updates to your reports as genetic research emerges.

Understand your favorite four-legged friend on a whole new level. Simply swab your dog's cheek, mail in the DNA sample, and in two weeks or less you'll get detailed reports breaking down your dog's unique characteristics: personality traits, DNA composition, breed mix, predisposition to disease, and much more. Sample collection is fast, easy, and painless.

Alternatively, this upgraded kit determines the breeds in your dog AND screen your dog for over 100 of the most common breed diseases through a simple, at-home cheek swab. Results include a report on all of the breeds found in your dog's DNA by percentage and a custom results certificate PLUS a comprehensive report of your dog's genetic health risks and physical traits. This test is easy, painless, and takes less than 2 minutes with results that have 99.97% accuracy.

Living DNA offers advanced DNA reports, delivering an enriching view of your ancestry from 80,000 years ago until recent times. The full ancestry experience is the most advanced in the industry, offering a complete view of your ancestry, delivered through an intuitive interactive online platform. The kit percentage results for over 150 regions including sub-regional ancestry breakdowns, detailed reports, maternal & paternal haplogroups & back in time covering up to 80,000 years.

Gain the benefits of both the Well-being kit and Ancestry kit. Using the unique DNA Constellations method, you'll be able to explore 500 years of your family ancestry from all over the world and even delve deeper into the unique sub-regional breakdown. On the other hand, you'll discover the genetic variants that can impact the way your body metabolizes vitamins and minerals while maximizing what you eat, with tips on foods that provide you with the nutrients you need.

This test kit helps cat owners learn about their cat's breed, health, traits, and habits all with just a bit of DNA collected at home. With a gentle, painless swab of your cat's cheek, you can get a comparison of 4 main breed groups and 21 individual breeds, Chromosome Map, Wild Cat Index, 39 genetic markers associated with 17 diseases, and more.

Orivet's proprietary dog DNA test will reveal your furry friend's true breed. Gain a deeper understanding of your dog with a percentages report specifying the exact breed percentages of your dog, from just a simple DNA swab. You'll also receive a LifePlan including your pet's very own personalized wellness plan based on their breed, age, weight, gender, geographic location, and lifestyle. The Orivet LifePlan also includes a schedule you may follow with your veterinarian to implement a customized wellness plan for your dog.

Ever wondered if your dog was part wolf? Now you can know. With DNA My Dog, you can test for any wolf or coyote hybrid DNA in your dog and determine the breeds in your dog through a simple, at-home cheek swab. Receive an in-depth report on all of the breeds found in your dog's DNA by percentage and a custom results certificate. This test is easy, painless, and takes less than 2 minutes with results that have 99.97% accuracy.

Ship your DNA to the moon! Lifeship will extract your genetic code from a sample and preserve it in synthetic amber. It's stored in a time capsule with the DNA of other humans, plus the DNA of various plant and animal species, and an archive of human knowledge. The capsule gets sent to the Moon on a lunar lander shared with NASA missions. The kit comes with the saliva collection swab and prepaid mailer for returning your sample to LifeShip's lab. You'll also receive invitations to watch the rocket launch and lunar landing live streams, as well as a personalized digital mission certificate showing your location on the Moon.

Read more:
Discover your and your pet's DNA story with these kits that are now 15% off - Boing Boing

Scientists used DNA analysis of mummies from ancient Egypt to reconstruct the faces of three men buried more than 2,000 years ago. Parabon NanoLabs

In a feat seemingly straight out of The Mummy movies, DNA is helping researchers reanimate the faces of people who lived more than 2,000 years ago. As Mindy Weisberger reports for Live Science, scientists used genetic information taken from three ancient Egyptian mummies to produce digital images of what the men might have looked like at age 25.

Residents of Abusir el-Meleq, an ancient Egyptian city south of Cairo, the men died between 1380 B.C.E. and 450 C.E. A team from Parabon NanoLabs presented the trios facial reconstructions at the International Symposium on Human Identification in September.

[T]his is the first time comprehensive DNA phenotyping has been performed on human DNA of this age, says Parabon, a Virginia-based company that typically uses genetic analysis to help solve cold cases, in a statement.

To approximate the mens faces, researchers used DNA phenotyping, which predicts individuals physical appearance based on genetic markers. (Phenotyping can suggest subjects skin, hair and eye color, but as Caitlin Curtis and James Hereward wrote for the Conversationin 2018, the process has its limitations.) The team determined the mummies other characteristics through examination of their physical remains, reports Hannah Sparks for the New York Post.

Parabon used DNA taken from the mummies in 2017 to create the 3-D images. Thatearlier study, led by scientists at the Max Planck Institute for the Science of Human History in Germany, marked the first time researchers successfully extracted DNA from ancient mummiesa tantalizing prospect long considered more myth than science, wrote Ben Panko for Smithsonian magazine at the time.

[Scholars] were generally skeptical about DNA preservation in Egyptian mummies, due to the hot climate, the high humidity levels in tombs and some of the chemicals used during mummification, which are all factors that make it hard for DNA to survive for such a long time, study co-author Stephan Schiffels told Tracy Staedter of Live Science in 2017.

The images released by Parabon show faces similar to modern Mediterranean and Middle Eastern individuals rather than modern Egyptians. Based on phenotyping, the team suggests that the mummies had light brown skin with dark hair and eyes.

According to the statement, Parabons 3-D facial reconstructions are highly consistent with the earlier genome analysis, which concluded that ancient Egyptians shared more ancestry with Near Easterners than present-day Egyptians, who received additional sub-Saharan admixture in more recent times.

In 2017, study co-author Johannes Krause, a paleogeneticist at the University of Tbingen in Germany, told the Washington Posts Ben Guarino that the assessment showed complete genetic continuity across 1,300 years. In other words, though their kingdom was conquered by a succession of outside powers, the ancient Egyptians included in the analysis didnt really intermix with invaders.

After predicting the three mens likely phenotypes, the Parabon team searched the companys database for people whose DNA closely aligned with the ancient Egyptians, reports Leslie Katz for CNET. Drawing on information pulled from the database, the researchers modeled the probable width, height and depth of the mummies heads and facial features. A forensic artist took over the process from there.

Its great to see how genome sequencing and advanced bioinformatics can be applied to ancient ... samples, says Parabons director of bioinformatics, Ellen Greytak, in the statement.

Speaking with CNET, Greytak adds, This study was an exciting proof-of-concept of how much we can learn about ancient people from their DNA.

Read more here:
3-D Reconstruction Reveals the Faces of Three Ancient Egyptian Mummies - Smithsonian

The fossilized skeleton of a dinosaur outside a Brazilian research center.Photo: CARL DE SOUZA/AFP (Getty Images)

Dinosaur researchers working on extremely well-preserved remains from the Jehol Biota in northeastern China recently reported that they had detected fossilized biomolecules in a feathered dinosaur from the Early Cretaceous.

The intriguing microscopic material was found in the femur of a Caudipteryx, a feathered, turkey-looking dino that lived between about 125 million and 113 million years ago. The team put cartilage from the femur under a microscope and stained it with chemicals called hematoxylin and eosin, which are used to highlight cell nuclei and cytoplasm in modern cells.

They also stained the cartilage of a chicken and found that the dinosaur and chicken cartilage lit up in the same way. The researchers say that nuclei and chromatin, the material our chromosomes are made of, were visible. The teams research was published last week in the Nature journal Communications Biology.

Geological data has accumulated over the years and shown that fossil preservation in the Jehol Biota was exceptional due to fine volcanic ashes that entombed the carcasses and preserved them down to the cellular level, said study co-author Li Zhiheng, a vertebrate paleontologist at the Institute of Vertebrate Paleontology and Paleoanthropology of the Chinese Academy of Sciences, in an academy press release.

Members of this research team also described finding genetic material in another specimen last year; as Gizmodo reported at the time, some scientists were similarly skeptical of their claims that traces of genetic material were preserved in the fossilized Hypacrosaurus skull. The Caudipteryx fossil in the new work is about 50 million years older that the Hypacrosaurus.

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They were identified using completely different methods than in the Hypacrosaurus, wrote Alida Bailleul, lead author of the new paper, in an email to Gizmodo. But what was striking was the hematoxylin staining of the cell nucleus in Caudipteryxit was comparable to the staining seen in a chicken cell nucleus, said Bailleul, a paleobiologist at the Institute of Vertebrate Paleontology and Paleoanthropology in Beijing.

If this fossil did reveal the same structures that were highlighted in the modern chicken, itd be a remarkable demonstration of how well biological material can preserve and how mercifully the cartilage was treated by Earths often-destructive processes. But not everyone is so convinced about what exactly was showing up in the stains.

I dont really see how much has changed here, said Evan Saitta, a researcher from the Integrative Research Center at the Field Museum of Natural History in Chicago. The change in time were interested in here is not between the hypacrosaur and this new specimen; the difference is the amount of time between well-supported DNA preservation and any of these fossils.

The oldest-yet sequenced DNA was described in a paper this February and came out of the teeth of a roughly 1-million-year-old woolly mammoth. All dinosaurs (besides birds) went extinct some 65 million years ago. That makes the dinosaur materials absurdly older than the spectacular results from the woolly mammoth remains, Saitta said.

So what exactly was reacting to the dyes and stains the recent team applied to the dinosaur cartilage? According to Saitta, it could be microbes that set up shop in the dinosaur remains or mineral infill of the space vacated by deteriorated genetic material. The latter is the opinion of Nic Rawlence, the director of the paleogenetics laboratory at the University of Otago in New Zealand.

The current limit of ancient DNA is 1.2 million years ago, and we dont expect to be able to go much further back in time, certainly not to the Age of Dinosaurs, Rawlence said in an email to Gizmodo. While these fossilised cells and DNA in this new dinosaur may look like those from a modern chicken, they are a stone copy, where the cells and DNA have been replaced by minerals, in the same way a dinosaur bone is a mineralised version of modern bone.

When bones fossilize, they do so from the obvious macroscopic features to the smallest elements of their structure. That allows paleontologists to do things like learn about the growth rates of T. rex, for example, as holes appear in the bone where blood vessels used to be. But genetic material is quick to deteriorateone team estimated that DNA would cease to be readable after 1.5 million years, making the mammoth tooth find trepidatiously close to the materials upper limit. And the mammoth remains were only so well-preserved thanks to their encasement in permafrost.

Chemically speaking, you deal with a completely different set-up of compounds here, compared to when you look at permafrost material thats pretty much comparable to frozen turkey in your freezer, to some extent, said Jasmina Wiemann, a molecular paleobiologist at Yale University, in a video call.

That makes the situation of that million-year-old mammoth fundamentally different from that of the 125-million-year-old Caudipteryx. Though the mammoth teeth did undergo diagenesisthe process by which organic compounds are gradually replaced by inorganic things like mineralsthey were cooled by the Siberian climate, preserving the biomolecules to the modern day. (This is also the reason you occasionally read about Ice Age researchers being able to eat what they studied, like steppe bison.)

A woolly mammoth skeleton. The oldest sequenced DNA is from the teeth of a 1.2-million-year-old mammoth.Photo: PHILIP FONG/AFP (Getty Images)

When it comes to actual DNA molecules, I think it is pretty much impossible that such molecules remain in dinosaur material, wrote Love Daln, a paleogeneticist at the Centre for Palaeogenetics who was on the mammoth tooth team, in an email to Gizmodo. We know from both massive empirical studies and theoretical models that even under completely frozen conditions, DNA molecules will not survive more than ca 3 million years.

Just because different dyes or stains react with parts of a fossilised remain does not mean that any actual DNA molecules remain in the fossil, Daln added.

Whats more, just because a bone fossilizes doesnt mean that every component of the once-living creature is exchanged, tit-for-tat, for any specific mineral or metal compound. Every dead dinosaur in every deposit around the world means a unique set of conditions are brought together, so no two fossils are really the same chemically. That means that a Hypacrosaur bone from Montana will have undergone a different sort of fossilization than a Caudipteryx in China, making the work of molecular biologists, geochemists, and paleontologists that much more complicated.

It goes through, like, a grinder, but what comes out ends up looking very similar, Wiemann said. Were missing a foundational understanding of how fossilization works. I think thats the whole challenge here.

The mammoth DNA could be sequenced because it was more deep-frozen than it was fossilized. That is, the DNA wasnt given an opportunity to interact with the molecular environment around it, and particularly with water, which causes the DNA to break down, as one co-author of the mammoth paper told Gizmodo.

So besides the question of what exactly was preserved in the Caudipteryx, its important to recognize that dinosaur DNA cant be sequenced, at least not yet. The molecules have simply undergone so much change that they do not resemble the animals they were a part of. But ancient biomolecules can persist: dinosaur proteins were seemingly found on 200-million-year-old bone, though as a research team including Saitta pointed out in one paper, decaying dinosaur bones are a happy home for microbes, which can cosplay as dinosaur genetic material.

Part of the problem with the recent paper, several scientists said, was the staining method used to compare the Caudipteryx and chicken nuclei. Hematoxylin and eosin can bind to all sorts of things, not just genetic material, the researchers said, making the results pretty general. I think it is tricky to apply a staining protocol that is not very specific at all to something like fossil materials that we dont even understand what they actually represent, Wiemann said.

A helpful step to address such ambiguity would be to cross-reference the staining results with additional, independent methods of looking at the cartilage. Such triangulation would help put the tissue issue to rest, Saitta said. Wiemann suggested using mass spectroscopy to look at the entire bone, and seeing if the material that was stained could be mapped to any nucleobases or DNAs sugar-phosphate backbone. Its an incredibly exciting avenue of research, Wiemann added, saying these additional methods would help home in on exactly whats preserved in the fossil.

I am a firm believer that if you dabble in deep time molecular bio, you MUST incorporate as many methods as you possibly can, AND you must consider and rule out, with data, any alternatives, such as invasion by microbes, either ancient or modern, Mary Schweitzer, a molecular paleontologist at North Carolina State University and the Museum of the Rockies in Montana, told Gizmodo in an email. Schweitzer co-authored the hypacrosaur paper alongside Bailleul, who worked in Schweitzers lab. For me, the ultimate goal is to obtain sequence information, so anything we can learn about diagenetic alterations to these recovered molecules becomes critical.

Two fossils, 50 million years apart, turn up a biomolecular quandary in the span of two years. If that timeline is anything to go on, more data could come soon, hopefully bringing more clarity to this exciting new area of paleontology.

Correction: A previous version of this article incorrectly referred to the recent fossil as duck-billed (actually, it was the earlier find, the hypacrosaur, that had a duckbill). Thanks to commenter artiofab for pointing out the error.

More: How Do We Know Birds Are Dinosaurs?

Read more from the original source:
Some Paleontologists Think They've Found Fossilized Dinosaur DNA. Others Arent So Sure - Gizmodo

And data leaks are always a possibility.

Your DNA, a long, slender molecule that contains your unique genetic code, belongs solely to you. But it's also most likely in a database somewhere, without your knowledge or consent.

Countries around the world are collecting genetic material from millions of citizens in the name of fighting crime and terrorism. This is crucial since, if you were to get robbed, you would like the government to have some type of system that's able to identify the thief. In today's world, the thief leaving a bit of their DNA could easily solve the problem since law enforcement could search it in their database to identify them.

However, with the possibility of leaks in surveillance programs, some critics say this goes into an uncharted ethical territory with data collection going possibly too far. In this video, Derek Muller of the YouTube channel Veritasium goes into greater detail about it, and while you may want to skip it if you don't want to hear serious crimes discussed, it's definitely worth a watch if you don't mind.

See original here:
Your DNA Is Probably In a Database Without Your Consent - Interesting Engineering

How does our DNA relate to our personality and appearance? Emma, age 9, Sydney

Hi Emma. Thank you for this great question!

Our body is made up of trillions of cells, each of which has a nucleus that holds our DNA.

Our DNA is made up of more than 20,000 genes. You can think of genes as the the instructions which help decide what we look like, how our bodies work and even our personalities.

We get half our genes from our biological mother and the other half from our father. Thats why we dont look exactly like our parents, but we may look a bit like them and may also think and act similarly to them.

That said, each of us still has a unique collection of genes overall. That means no two people carry exactly the same genes, not even brothers and sisters. And thats why each of us has a unique appearance and personality.

Our genes help explain many parts of our appearance, like how tall we are and the colour of our eyes.

They also have a hand in our other skills, such as how fast we can run, how good we are at solving problems, and whether we enjoy talking to new people (rather than if we feel shy).

By studying a persons genes, scientists can tell whether that person is more likely to have blue or brown eyes, without even seeing them.

They may also be able to tell that person how likely they are to develop certain medical conditions later in life, such as cancer or myopia (when you cant see far-off objects as clearly).

Read more: Curious Kids: Why do people get cancer?

Although genes are important, theyre not the only reason for why we look, think, feel and act as we do or why were more likely to have certain diseases. While some traits such as eye colour are mainly determined by our genes, an eye injury can change someones eye colour.

Our habits, such as how much we eat and exercise, also have a big impact on who we are and what we look like. If you eat too much junk, youll probably get chubby and start running slower, regardless of the genes your parents gave you.

Our environment at home, school and/or work play a key role in shaping us, too. Take myopia. Before the discovery of the more than 400 genes for myopia, scientists noticed children are at least three times more likely to be myopic if either one or both parents are. They realised if someone has trouble seeing far-off objects, theres a decent chance this is related to genetics.

At the same time, however, there is currently a surge in myopia happening around the world, with more people becoming myopic even though their parents are not!

Researchers discovered our environments and habits play a huge role in myopia development. For instance, they found myopia (and the need to wear glasses) is more likely to happen among people living in cities rather than the country, and those who spend less time outdoors.

The way we perceive colour is also influenced by both our genes and environment. You might remember the social media trend of #thedress that went viral back in 2015.

The world was torn over whether the dress (below) is actually blue and black, or white and gold. Researchers later found the way we see colour in this dress is 34% related to our genes and 66% linked to environmental factors.

Read more: Curious Kids: why are people colour blind?

Personality describes the relatively stable ways in which people think, feel and act. And again, genes do a pretty good job of explaining why some people are more outgoing and energetic, while others tend to be more moody and anxious.

Our genes also help explain how smart we are. But one surprising finding is our genes have more of an effect on us as we age. Among children, about 40% of the differences in intelligence scores are explained by genes. In young adults, this increases to about 60%, even though its the same genes that continue to affect intelligence.

This is most likely because our genes can impact which environments we prefer, and adults often act on their preferences.

For example, most adults do not get told when to go to bed at night! And adults who enjoy learning new things can choose to spend their time in libraries and art museums, or taking classes. In other words, adults can choose the environments and activities that best express their genes.

You can think of your genes as a way to understand yourself but not as a way to make decisions. For example, just because someones parents may not have been able to go to university, they themselves can if they study hard.

Or, a persons parents may be overweight, but that doesnt mean they have to be. They can still join a sprint team if theyre willing to put in the effort.

Even though your DNA and genes shape a lot of your personality and appearance, remember: they do not determine your life story.

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Curious Kids: how does our DNA relate to our personality and appearance? - The Conversation AU

India last month began boasting that it has created and its regulatory body approved the worlds first DNA vaccine, ZyCoV-D.

The vaccine, developed by a company called Zydus Cadila, expects to have it available for use as early as next month, giving hope to a country that has suffered more than 447,000 deaths at the hand of the virus.

What is a DNA vaccine and could this new class of vaccination become the next tool in the worlds fight against COVID-19?

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A DNA vaccine is a form of a software vaccine, explained Tel Aviv Universitys Prof. Jonathan Gershoni.

A software vaccine is one in which scientists vaccinate with the blueprint of the virus just the DNA or the RNA corresponding to the genes that code for the spike protein injecting it in a palatable and effective way into the body. The cells then synthesize the viral protein, which leads to the production of antibodies against the viral spike.

This is as opposed to a hardware vaccine, which actually contains hardware, that is physical bits and pieces of the virus protein.

You can have a hardware vaccine that consists of a killed virus, for example, or an attenuated virus, Gershoni explained. Or you can have a subunit vaccine as well, such as the vaccine for Hepatitis B, which is just purified spike protein.

The immune system identifies the presence of the viral protein and that stimulates the immune system to respond and make highly specific targeted antibodies that inactivate the virus.

All of the traditional childhood vaccines that exist today are hardware vaccines.

However, since the late 1980s, scientists began playing with the idea that there could be applications for injecting DNA or RNA directly first, in trying to develop gene therapy, and more recently, in the development of what Gershoni calls software vaccines.

We know that the information flow in biology goes like this: the genetic material is stored in a very stable molecule, double-stranded DNA, Gershoni said. However, the information that flows from the gene needs to be transcribed to create a disposable and intermediate genetic material in the form of RNA. So, RNA in the traditional sense, is simply a disposable copy of the DNA gene.

However, it is the RNA and not the DNA that is able to interact with the protein manufacturing machinery, known as ribosomes. The ribosomes are what recognize the RNA and systematically translate the genetic material, which is written in the language of RNA, into the hardware that is to say, the protein.

The hardware is the protein and the instruction manuals, the recipes that tell us how to make these proteins, can be either in DNA or RNA, he said. DNA or RNA, therefore, fall under the category of software vaccines.

Injecting RNA in some respects is more efficient, Gershoni said.

Both the Pfizer and the Moderna vaccines, for example, are RNA vaccines.

Despite the claims coming from India, there are other DNA vaccines already on the market. They are just packaged differently.

The AstraZeneca, Sputnik V and Johnson & Johnson vaccines all contain DNA of the spike protein as their active ingredient. These vaccines, Gershoni explained, take the DNA of the coronavirus spike protein and package it inside the DNA of a safe virus called Adenovirus.

These vaccines deliver the gene for the spike protein via the Adenovirus that infects human cells but does not cause any noticeable or harmful disease.

If we take a virus like that and manipulate its genes and swap some of the genes of the viral vector with the gene for the coronavirus spike, when such viral vectors infect our cells they are manipulated and produce the coronavirus spike protein, which then stimulates the production of antibodies against coronavirus, Gershoni further explained.

So what is the difference, given that the India vaccine also contains DNA and is a DNA virus?

What differentiates the Indian vaccine is that it contains much less DNA and is not packaged in a viral vector. The Indian DNA stands alone.

What they have done is taken a small, circular piece of DNA called a plasmid and incorporated into this plasmid a piece of DNA that corresponds to the 1,200 amino acids of the coronavirus spike protein, Gershoni said.

The plasmid that they are using in ZyCoV-D is a plasmid from the 1990s called pVAX1 a commercially available plasmid DNA whose total size is only about 3,000 letters (nucleotide base pairs).

In this case, the DNA is not wrapped or packaged in anything but directly injected into the arm, something referred to as naked DNA.

This is the first plasmid DNA vaccine that has been authorized for human use. Gershoni said that there have been veterinary applications of plasmid DNA used in the past.

It is also different from the other vaccines because it is delivered intradermally, meaning it is injected without a needle via a high-pressure stream of liquid containing the DNA.

The ZyCoV-D regimen is three shots, each 28 days apart. The phase III trial found the vaccines efficacy to be less than 70%.

Gershoni said that although some people have expressed concern with DNA vaccines, which must enter the nucleus of the cell to be transcribed and generate the RNA and therefore could theoretically impact a persons chromosomes, there is no obvious mechanistic reason why this should occur.

He said that an effort was made to streamline the DNA, make it as compact, clean and mean and with as little extra DNA as possible.

Whereas people around the world may be concerned and debating whether this DNA vaccine is a good idea, Gershoni continued, we have been blessed in Israel with RNA vaccines. So under no circumstances should theoretical arguments about DNA safety be used in Israel. They are simply not relevant.

Read more here:
Could DNA vaccines be the next tool in the worlds battle against COVID? - The Jerusalem Post