Category Archives: Transhuman News

LEIPZIG, GERMANYAccording to a CNNreport, new analysis of ancient DNA samples from the Avars, a population of nomads from the Eurasian Steppe who dominated eastern central Europe for 250 years from the mid-sixth to early ninth century A.D, is shedding light on Avar social and marriage practices. Originating in eastern-central Asia as part of a coalition of tribes known as the Rouran khaganate, which was defeated in A.D. 550 by the Turks, the Avars traveled from Mongolia to Caucasus and settled in the Carpathian Basin of present-day Hungary in A.D. 567568. While hundreds of thousands of lavish burials of Avar menwhich included horses, saddles, and harnesseshave been excavated, no written historical records remain that document their lifestyle. In the study, researchers led by Guido Alberto Gnecchi Ruscone of the Max Planck Institute for Evolutionary Anthropology examined DNA from more than 300 peoplewho were buried in four Avar-period cemeteries in Hungary across a span of nine generations. They determined that these Avars practiced a system of patrilineal kinship. This included patrilocality, a system where men remained in their communities following marriage, and female exogamy, whereby women typically married outside of their own groups and maintained social cohesion between communities. Analysis of identity-by-descent DNA connections demonstrated a high level of variability in the female lineage. This suggests that women who married into the Avar community were from far-flung places, but retained a shared steppe ancestry, indicating they were not likely a local people conquered by the Avars. That finding was also substantiated by a lack of interbreeding. In many cases, men were found to have multiple partners, and closely related men often had offspring with the same women partners, in which case widows were likely required to marry male family members to bear sons. According to the researchers, these patterns, in which children belong to their fathers family and ancestry is traced father to son, correspond with previous evidence of Eurasian steppe societies. Read the original scholarly article about this research in Nature. To read more about the archaeology of the Avars, go to The Avars Advance.

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Ancient DNA Reveals Kinship Structure of Eurasia's Avars - Archaeology Magazine

Mitchell Gaff was booked on murder, arson, burglary, rape and kidnapping charges.

EVERETT, Wash. A man was arrested Wednesday in connection to the killing of an Everett woman nearly 40 years ago.

On June 2, 1984, 42-year-old Judith "Judy" Weaver was killed inside her home on Rucker Avenue, according to the Everett Police Department (EPD). Officials initially responded to her home for a report of a fire and found her inside.

The suspect, Mitchell Gaff, 61, was booked on charges of first-degree murder, first-degree arson, first-degree burglary, first-degree rape and first-degree kidnapping. A Snohomish County judge found probable cause to hold Gaff on the charges without bail.

According to EPD, Gaff was identified from "new DNA evidence" and was taken into custody by police in Olympia.

KING 5 does not typically name suspects until they are formally charged. However, Gaff's criminal record shows many similarities to Weaver's killing. His past convictions show a trend of him tying women up and then assaulting them.

He was convicted of assaulting a woman in 1979 but she was able to escape. Then, five years later, he was convicted of raping two teenage girls in Everett.

After his conviction, Gaff was incarcerated on McNeil Island, a prison housing people the state deems to be the most violent sex offenders. In 2006, he was granted release into a halfway house in Seattle.

Two of Weaver's surviving family members attended court Thursday afternoon and declined to speak on camera. Gaff faces the possibility of life in prison without parole if convicted.

Weaver co-owned a business on Hewitt Avenue and had walked home alone the night she was killed, according to EPD. She was a mother, grandmother and sister.

My heart is with Judys family and friends as they continue grieving this difficult loss," Everett Mayor Cassie Franklin said in a press release. "I also want to commend our police department and our partner agencies for their continued focus on cold cases like this."

Court documents revealed how a DNA sample collected in 1984 and tested in 2023 led to Gaff's arrest Wednesday.

A DNA profile lifted from a piece of fabric used to bind Weaver's wrists resulted in a match in the state's CODIS system, a database used to store the DNA profiles of convicted criminals, and samples from unsolved crimes and missing persons.

The database identified Gaff as a possible contributor to the DNA, but law enforcement needed to get another sample to confirm the match.

In January, Everett police detective Susan Logothetti and other undercover officers "surreptitiously" collected Gaff's DNA through a ruse. That profile was used to confirm the match made by the CODIS system in the fall.

Everett police chief John DeRousse praised Logothetti for her work, which led to Gaff's arrest.

The Washington State Patrol Crime Lab matched the DNA sample to samples from a vaginal swab taken off of Weaver's body, three pieces of clothing the victim was wearing on the night of the murder and from the ligatures Gaff allegedly used to strangle her.

This is a developing story. Check back for updates.

Download our free KING 5 appto stay up-to-date on news stories from across western Washington.

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New DNA evidence leads to arrest in 1984 cold case homicide of Everett woman - KING5.com

___ Investigators hope new DNA evidence could get them closer to solving a decade-old murder case.

The FBIand the Putnam County Sheriff's office confirmed on Thursday that additional DNA has been found in connection with the murders of Shirley and Russell Dermond.

The evidence has been sent to a private DNA lab for further testing.

The couple waskilled nearly 10 years ago. On May 6, 2014 Russell Dermondwas found dead in his home in Eatonton. Authorities say he had been decapitated. Ten days later, his wife Shirley Dermond's body was found by fishermen in Lake Oconee.The grisly crime shocked their Lake Oconee community.

Putnam County Sheriff Howard Sills is working with Andy Smith, special agent with the FBI on the case.

"This is a a crime that has really had an effect on a wonderful community in Middle Georgia, and it has had an effect on the sheriff's office there," he said in audio released from the FBI. "The investigators, the it's it was such a horrific crime. It's really a convergence of events that have caused this case to go unsolved. "Earlier this week,investigatorsupped the reward for information in the case from $5,000 to $20,000.

The agency says that is in addition to $5,000 dollars offered by local authorities.

"This is the first time we have confirmation of a sample that did not belong to Russell or Shirley Dermond, Smith said.

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New DNA evidence found in connection with 2014 Georgia murders of Shirley and Russell Dermond - GPB News

Joel Embiids son, Arthur, was born on Sept. 17, 2020, about three months before the first COVID-19 vaccine became available. The world was a cauldron of civic unrest and pandemic turmoil. Embiids NBA career largely had been a disappointment. He named his son after his little brother, who, six years earlier at the age of 13, had been killed by a passing truck while walking home from school in Cameroon.

A month earlier, in the NBAs COVID bubble in a playoff run delayed by the pandemic, Embiid had averaged 30 points and 12.3 rebounds in a first-round sweep at the hands of the Boston Celtics. The Sixers played without injured point guard Ben Simmons, and Embiid was not as good as his numbers.

Everything changed when he became a dad a month later.

He began to eat better, sleep more, beef on social media less. He began to refine all aspects of his game. He began to study opponents. By the end of last season, Embiid was the NBA MVP, and he thanked his son for the inspiration.

Losing my brother, and then giving his name to my son meant a lot. My son is the reason why Im really sitting here, Embiid said at the time. When I found out we were having a kid, I just remember I was like, Ive got to be a great role model and Ive got to set a good example. I want him to understand that his dad not only was pretty good, but he also worked hard and he went and took everything he wanted.

My whole mindset just changed. Everything about me just changed. The way I went about my business, my life, everything changed because I wanted to be a great father, set a good example.

Were seeing the effects of that change now.

It took a decade since he left Kansas and four years since the birth of his son, but Embiid finally understands what it takes to be a champion. It means ignoring the pain and soreness of a surgically repaired knee. It means ignoring fear and discomfort. It means, no matter how much you hurt and no matter how tired you are, you grab moments by the throat and pull the lesser players along.

Embiids left knee hurt. Embiids left eye was impaired due to a bout with Bells palsy hes been dealing with for more than a week. Youd never have known it.

Trailing the series 2-0, in a sport that has never seen a comeback from a 3-0 hole, Embiid scored 50 points, his best postseason output by 10, and saved the Sixers season.

READ MORE: Joel Embiid powers through Bells palsy for 50 as Sixers smack Knicks in the head. Literally.

This is what Michael Jordan and Dwayne Wade did. This is what Kobe did. This is what LeBron and Steph and Timothy Theodore Duncan did. This is how Hakeem Olajuwon, Embiids closest comp, won twice. They played through pain and injury and illness. That group of seven players account for 27 of the last 33 NBA championships.

Embiid had little in common with them before Arthurs birth. Five years ago, theres no way hed be playing. On Tuesday, in Game 3 of the first round of the Eastern Conference playoffs, he came closer to them than he ever has been before. Can he do it again on Sunday afternoon? He will try.

I want to play as much as possible. I only have about, maybe, eight years left. So I have to enjoy this as much as possible and I want to win, Embiid said. Im just trying to keep pushing. Im not going to quit. If its on one leg, Im still going to go out there and try, but thats not an excuse. Got to keep playing better, and better, and better.

Thats what a champion says.

Embiid underwent surgery 2 1/2 months ago to repair a torn meniscus in his left knee. He irritated the joint when he landed after a self-pass slam dunk in in the first half of Game 1 in on Saturday. In the same arena in which Willis Reed became the games emblem of toughness, Embiid emerged from the locker room just before the third quarter resumed. He stunk, and the Sixers lost, but he returned. He played better Monday night, but again faded in the second half. Thursday in Philly was a different story.

Embiid scored 33 points on 8-of-10 shooting in the second half. He made all five of his three-pointers. He flummoxed double-teams; he had three assists. He had three rebounds, but he dominated the paint.

He was, for one night, everything the Sixers could hope for him to be.

Big fella came out and was just ballin for us tonight, said Tobias Harris, Embiids longest-tenured teammate. Everybody down the line was able to figure their role.

Harris joined the Sixers in 2019, perhaps Embiids worst hour. A virus and knee tendinitis led to an average of 17.6 points and 8.7 rebounds in a seven-game second-round loss to eventual-champion Toronto on a Sixers team that, with Jimmy Butler, Harris, and JJ Reddick, was the best combination of talent since Josh Harris bought the team in 2011. Infamously, after the Game 7 loss in Toronto, outside the locker room just after the game, he wept in the arms of his fiance. Hall of Fame big men Shaquille ONeal and Charles Barkley, the foremost NBA analysts on the planet, questioned Embiids hunger and leadership. The points they made were fair ... until Arthur arrived.

Embiid tore the meniscus in his right knee in the first round of the 2021 playoffs. His effectiveness diminished as the second round advanced, and when the Hawks won Game 7, Embiid told us that the game turned when Simmons refused to dunk the basketball in the games final minutes. This was the first glimmer of leadership; he never criticized teammates. Simmons never played another game for the Sixers.

Embiid, already playing with a thumb that needed surgery, fractured his right orbital bone in the first round of the 2022 playoffs. He missed the first two games of the second round and the Sixers and new point guard James Harden could not overcome the toughness of Miami. Embiid got tougher.

Last year, he sprained his right knee in Game 3 of the first round and missed the first game of the second round. He rallied, but by the end of the second round against the Celtics hed run out of gas.

Every single year you start asking yourself questions: Why? Embiid said. Gotta keep putting my body on the line, for my family. ... Im not going to quit. When Im done Im going to be proud of myself, and my people are going to be proud of me.

Sure enough, this year has been different. For the first time in eight trips to the postseason hes averaging more points in the playoffs than in the regular season. Hes also playing more minutes than in any regular season or playoff run.

And hes done it with one eye, on one leg. Give him a patch and a parrot and hed be Long John Silver.

Legends are born of such moments as Thursday. Jordans 38-point flu game in the 1997 NBA Finals. Isiah Thomas 45-point ankle game in the 1988 Finals. Reed playing with a torn thigh muscle in Game 7 of the 1970 Finals, the Knicks first title.

Granted, we might be making too much of a single game, but lord, what a game: a must-win 50-piece, on a bad leg, with a frozen face, and the heart of a champion.

Original post:
Joel Embiid finally discovers he has the DNA of a champion. Down 2-1, can he lead the Sixers past the Knicks? - The Philadelphia Inquirer

From movies set in dystopian futures to real-life courtroom dramas, DNA, or deoxyribonucleic acid, has fueled storytellers imaginations for decades. The molecule responsible for shaping our understanding of biological inheritance has inspired everything from comic book tales about the birth of mutants to blockbuster films about resurrecting dinosaurs in a theme park, each captivating audiences worldwide.

Today (April 25) is National DNA Day, a day commemorating the completion of the Human Genome Project in 2003 and the discovery of DNAs double helix in 1953. To find out more about this remarkable molecules impact on pop culture and society, The Daily sat down with Divita Mathur, assistant professor in the Department of Chemistry at Case Western Reserve University.

Read on to learn more from Mathur about how DNA intertwines with our daily lives.

Namor, the original Aquaman from the Marvel universe, was first conceived in the comic world before World War II and can be considered the first mutant being to be created in American pop culture. Mutants are born from what DNA naturally doesgenetic recombination and mutations. Now we have some very popular universes of mutants, including the Spider-Verse, Teenage Mutant Ninja Turtles, and X-Men.

When a very animated cartoon DNA in the 1993 movie Jurassic Park explained that a 66-million-year-old mosquito fossilized in a drop of amber was about to be squeezed to harvest dinosaur blood/DNA (spoiler alert!), audiences across the globe immediately came on board with having dinosaurs walk amongst men again. Even an asteroid that wiped the giant beasts off the planet could not fry natures hard-drive for storing genetic information: DNA. The movie went on to skip a few steps and took liberal creative license with others, but we learned that DNA is pretty resilient. Fifteen years later and after improved CGI effects, Avatars Navi in 2009 were infiltrated by humans who stole Navi DNA to become one of themand gave us another record-smashing movie franchise.

The movie that gave DNA most street cred is Gattaca (1997). What a clever name that uses DNAs four-letter alphabetA, T, C, G! Gattaca is the leader of the dystopian movie genre that espouses control over humankind using the most unique fingerprint we possessour DNA code. Subsequently, DNA databasesor Denabasesare adopted by other movies such as Blade Runner 2049 to register every citizen using their DNA, kind of like your drivers license, fingerprint, social security number, and retina scan all rolled into one. Dystopian worlds with DNA-reading machines as IDs are pretty ironclad in their control over the masses, until artificial intelligence-driven organic robot humanoids go rogue.

Evidently, 40+ drops of blood sampled from the murder scene of Nicole Brown Simpson and Ron Goldman were screened and presented as DNA evidence in the all-consuming trial: The People v. O.J. Simpson. Believing that DNA evidence gets the final word, both sides of the aisle somehow leveraged the evidence in their favor, leading to the famous acquittal and a larger debate over the role of such forensic evidence in highly televised trials. Before the turn of the century, DNA evidence revealed President Bill Clintons perjury and the media and publics gross prejudice against Monica Lewinsky, adding fuel to an already eyeball-grabbing scandal involving a U.S. president.

Benign (or so we thought) versions of Denabases exist now, thanks to the democratization of DNA sequencing to find out ones ancestry by simply mailing ones spit to a company. Trace amounts of a killers DNA from a crime scene can end up matching a growing family tree on a genealogy database and can be used to track them down. It has spawned a new genre of crime-solving documentaries that have brought serial killers to justice because their distant cousins innocuously and voluntarily submitted their spit/DNA to an ancestry database. The Golden State Killer is one such popular victim of the genetic genealogy fad and the protagonist of a gripping documentary.

Looking to dive into genetics in pop culturespecifically in literature? Marie Vibbert has you covered. Vibbert is the webmaster for the College of Arts and Sciences at Case Western Reserveand also a science fiction author, having written more than 90 short stories and three novels.

Vibbert recommends the following books with genetics in their plots:

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Unraveling DNA's role in pop culturefrom superheroes to crime scenes - The Daily | Case Western Reserve University

As we celebrate World DNA Day, I am living proof of DNAs profound impact on our criminal legal system.

My name is Michelle Murphy. I am one of 15 women exonerated in the United States with the help of post-conviction DNA testing and I am the first and only woman in Oklahoma to be exonerated by DNA testing.

In 1994, at just 17, I was a single mother of two, navigating a challenging world, dreaming of a better future for my children and myself. But my life took a tragic turn when my infant son was murdered, a crime for which I was wrongly accused of committing. My coerced confession during a distressing police interrogation was used to convict me, and I was sentenced to life without parole. Falsely confessing to a crime I did not commit is not a unique phenomenon, and one of the leading causes of wrongful conviction.

It was clear that DNA evidence, crucial in my case due to the presence of blood at the crime scene, would be pivotal. Although lab tests conducted by the prosecution proved my DNA wasnt present at the crime scene, this crucial information was kept from my defense team. However, during the trial, the prosecution misleadingly suggested to the jury that the blood from the scene was mine, using this to claim I was guilty.

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DNA Testing Proved My Innocence of My Son's Murder - Innocence Project

Generative A.I. technologies can write poetry and computer programs or create images of teddy bears and videos of cartoon characters that look like something from a Hollywood movie.

Now, new A.I. technology is generating blueprints for microscopic biological mechanisms that can edit your DNA, pointing to a future when scientists can battle illness and diseases with even greater precision and speed than they can today.

Described in a research paper published on Monday by a Berkeley, Calif., startup called Profluent, the technology is based on the same methods that drive ChatGPT, the online chatbot that launched the A.I. boom after its release in 2022. The company is expected to present the paper next month at the annual meeting of the American Society of Gene and Cell Therapy.

Much as ChatGPT learns to generate language by analyzing Wikipedia articles, books and chat logs, Profluents technology creates new gene editors after analyzing enormous amounts of biological data, including microscopic mechanisms that scientists already use to edit human DNA.

These gene editors are based on Nobel Prize-winning methods involving biological mechanisms called CRISPR. Technology based on CRISPR is already changing how scientists study and fight illness and disease, providing a way of altering genes that cause hereditary conditions, such as sickle cell anemia and blindness.

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Generative A.I. Arrives in the Gene Editing World of CRISPR - The New York Times

Schrer, O. D. Nucleotide excision repair in Eukaryotes. Cold Spring Harb. Perspect. Biol. 5, a012609 (2013).

Article PubMed PubMed Central Google Scholar

Marteijn, J. A., Lans, H., Vermeulen, W. & Hoeijmakers, J. H. J. Understanding nucleotide excision repair and its roles in cancer and ageing. Nat. Rev. Mol. Cell Biol. 15, 465481 (2014).

Article CAS PubMed Google Scholar

Mu, H., Geacintov, N. E., Broyde, S., Yeo, J. E. & Schrer, O. D. Molecular basis for damage recognition and verification by XPC-RAD23B and TFIIH in nucleotide excision repair. DNA Repair 71, 3342 (2018). vol.

Article CAS PubMed PubMed Central Google Scholar

Sugasawa, K. Molecular mechanisms of DNA damage recognition for mammalian nucleotide excision repair. DNA Repair (Amst.) 44, 110117 (2016).

Article CAS PubMed Google Scholar

Lans, H., Hoeijmakers, J. H. J., Vermeulen, W. & Marteijn, J. A. The DNA damage response to transcription stress. Nat. Rev. Mol. Cell Biol. 20, 766784 (2019).

Article CAS PubMed Google Scholar

Jia, N. et al. Dealing with transcription-blocking DNA damage: Repair mechanisms, RNA polymerase II processing and human disorders. DNA Repair (Amst.) 106, 103192 (2021).

Article CAS PubMed Google Scholar

Theil, A. F., Hckes, D. & Lans, H. TFIIH central activity in nucleotide excision repair to prevent disease. DNA Repair (Amst.) 132, 103568 (2023).

Article CAS PubMed Google Scholar

Bernardes de Jesus, B. M., Bjrs, M., Coin, F. & Egly, J. M. Dissection of the Molecular Defects Caused by Pathogenic Mutations in the DNA Repair Factor XPC. Mol. Cell. Biol. 28, 72257235 (2008).

Article CAS PubMed PubMed Central Google Scholar

Okuda, M., Nakazawa, Y., Guo, C., Ogi, T. & Nishimura, Y. Common TFIIH recruitment mechanism in global genome and transcription-coupled repair subpathways. Nucleic Acids Res. 45, 1304313055 (2017).

Article CAS PubMed PubMed Central Google Scholar

Oksenych, V., De Jesus, B. B., Zhovmer, A., Egly, J. M. & Coin, F. Molecular insights into the recruitment of TFIIH to sites of DNA damage. EMBO J. 28, 29712980 (2009).

Article CAS PubMed PubMed Central Google Scholar

van der Weegen, Y. et al. The cooperative action of CSB, CSA, and UVSSA target TFIIH to DNA damage-stalled RNA polymerase II. Nat. Commun. 11, 116 (2020).

Google Scholar

Ribeiro-Silva, C. et al. Ubiquitin and TFIIH-stimulated DDB2 dissociation drives DNA damage handover in nucleotide excision repair. Nat. Commun. 11, 4868 (2020).

Article CAS PubMed PubMed Central Google Scholar

Coin, F., Oksenych, V. & Egly, J. M. Distinct Roles for the XPB/p52 and XPD/p44 Subcomplexes of TFIIH in Damaged DNA Opening during Nucleotide Excision Repair. Mol. Cell 26, 245256 (2007).

Article CAS PubMed Google Scholar

Sugasawa, K., Akagi, Jichi, Nishi, R., Iwai, S. & Hanaoka, F. Two-step recognition of DNA damage for mammalian nucleotide excision repair: directional binding of the XPC complex and DNA strand scanning. Mol. Cell 36, 642653 (2009).

Article CAS PubMed Google Scholar

Li, C. L. et al. Tripartite DNA lesion recognition and verification by XPC, TFIIH, and XPA in nucleotide excision repair. Mol. Cell 59, 10251034 (2015).

Article CAS PubMed PubMed Central Google Scholar

De Laat, W. L. et al. DNA-binding polarity of human replication protein A positions nucleases in nucleotide excision repair. Genes Dev. 12, 25982609 (1998).

Article PubMed PubMed Central Google Scholar

Matsunaga, T., Park, C. H., Bessho, T., Mu, D. & Sancar, A. Replication protein A confers structure-specific endonuclease activities to the XPF-ERCC1 and XPG subunits of human DNA repair excision nuclease. J. Biol. Chem. 271, 1104711050 (1996).

Article CAS PubMed Google Scholar

Sugitani, N., Sivley, R. M., Perry, K. E., Capra, J. A. & Chazin, W. J. XPA: A key scaffold for human nucleotide excision repair. DNA Repair 44, 123135 (2016).

Article CAS PubMed PubMed Central Google Scholar

Kokic, G. et al. Structural basis of TFIIH activation for nucleotide excision repair. Nat. Commun. 10, 2885 (2019).

Article PubMed PubMed Central Google Scholar

Coin, F. et al. Nucleotide Excision Repair Driven by the Dissociation of CAK from TFIIH. Mol. Cell 31, 920 (2008).

Article CAS PubMed Google Scholar

Staresincic, L. et al. Coordination of dual incision and repair synthesis in human nucleotide excision repair. EMBO J. 28, 11111120 (2009).

Article CAS PubMed PubMed Central Google Scholar

Fagbemi, A. F., Orelli, B. & Schrer, O. D. Regulation of endonuclease activity in human nucleotide excision repair. DNA Repair (Amst.) 10, 722729 (2011).

Article CAS PubMed Google Scholar

Muniesa-Vargas, A. et al. XPG: a multitasking genome caretaker. Cell. Mol. Life Sci. 79, 120 (2022).

Article Google Scholar

van Toorn, M. et al. Active DNA damage eviction by HLTF stimulates nucleotide excision repair. Mol. Cell 82, 13431358.e8 (2022).

Article PubMed PubMed Central Google Scholar

Ogi, T. et al. Three DNA polymerases, recruited by different mechanisms, carry out NER repair synthesis in human cells. Mol. Cell 37, 714727 (2010).

Article CAS PubMed Google Scholar

Ferri, D., Orioli, D. & Botta, E. Heterogeneity and overlaps in nucleotide excision repair disorders. Clin. Genet. 97, 1224 (2020).

Article CAS PubMed Google Scholar

Lehmann, A. R., McGibbon, D. & Stefanini, M. Xeroderma pigmentosum. Orphanet J. Rare Dis. 6, 70 (2011).

Article PubMed PubMed Central Google Scholar

Natale, V. A comprehensive description of the severity groups in Cockayne syndrome. Am. J. Med. Genet. A 155A, 10811095 (2011).

Article PubMed Google Scholar

Natale, V. & Raquer, H. Xeroderma pigmentosum-Cockayne syndrome complex. Orphanet J. Rare Dis. 12, 65 (2017).

Article PubMed PubMed Central Google Scholar

Kraemer, K. H. et al. Xeroderma pigmentosum, trichothiodystrophy and Cockayne syndrome: A complex genotype-phenotype relationship. Neuroscience 145, 13881396 (2007).

Article CAS PubMed Google Scholar

Theil, A. F., Hoeijmakers, J. H. J. & Vermeulen, W. TTDA: big impact of a small protein. Exp. Cell Res. 329, 6168 (2014).

Article CAS PubMed Google Scholar

Stefanini, M., Botta, E., Lanzafame, M. & Orioli, D. Trichothiodystrophy: From basic mechanisms to clinical implications. DNA Repair 9, 210 (2010).

Article CAS PubMed Google Scholar

Rahbar, Z. & Naraghi, M. De Sanctis-Cacchione syndrome: A case report and literature review. Int. J. Womens Dermatol. 1, 136139 (2015).

Article Google Scholar

Karikkineth, A. C., Scheibye-Knudsen, M., Fivenson, E., Croteau, D. L. & Bohr, V. A. Cockayne syndrome: Clinical features, model systems and pathways. Ageing Res. Rev. 33, 317 (2017).

Article CAS PubMed Google Scholar

Wang, Y. et al. Dysregulation of gene expression as a cause of cockayne syndrome neurological disease. Proc. Natl Acad. Sci. Usa. 111, 1445414459 (2014).

Article CAS PubMed PubMed Central Google Scholar

Vlez-Cruz, R. & Egly, J. M. Cockayne syndrome group B (CSB) protein: At the crossroads of transcriptional networks. Mech. Ageing Dev. 134, 234242 (2013).

Article PubMed Google Scholar

Sabatella, M. et al. Repair protein persistence at DNA lesions characterizes XPF defect with Cockayne syndrome features. Nucleic Acids Res. 46, 95639577 (2018).

Article CAS PubMed PubMed Central Google Scholar

Lans, H. & Vermeulen, W. Tissue specific response to DNA damage: C. elegans as role model. DNA Repair (Amst.) 32, 141148 (2015).

Article CAS PubMed Google Scholar

Hoogstraten, D. et al. Rapid switching of TFIIH between RNA polymerase I and II transcription and DNA repair in vivo. Mol. Cell 10, 11631174 (2002).

Article CAS PubMed Google Scholar

Vermeulen, W. Dynamics of mammalian NER proteins. DNA Repair (Amst.) 10, 760771 (2011).

Article CAS PubMed Google Scholar

Fassihi, H. et al. Deep phenotyping of 89 xeroderma pigmentosum patients reveals unexpected heterogeneity dependent on the precise molecular defect. Proc. Natl Acad. Sci. Usa. 113, E1236E1245 (2016).

Article CAS PubMed PubMed Central Google Scholar

Kashiyama, K. et al. Malfunction of nuclease ERCC1-XPF results in diverse clinical manifestations and causes Cockayne syndrome, xeroderma pigmentosum, and Fanconi anemia. Am. J. Hum. Genet. 92, 807819 (2013).

Article CAS PubMed PubMed Central Google Scholar

Sijbers, A. M. et al. Xeroderma pigmentosum group F caused by a defect in a structure-specific DNA repair endonuclease. Cell 86, 811822 (1996).

Article CAS PubMed Google Scholar

Ahmad, A. et al. Mislocalization of XPF-ERCC1 nuclease contributes to reduced DNA repair in XP-F patients. PLoS Genet 6, e1000871 (2010).

Article PubMed PubMed Central Google Scholar

Jia, N. et al. A rapid, comprehensive system for assaying DNA repair activity and cytotoxic effects of DNA-damaging reagents. Nat. Protoc. 10, 1224 (2015).

Article CAS PubMed Google Scholar

Llerena Schiffmacher, D. A. et al. Live cell transcription-coupled nucleotide excision repair dynamics revisited. DNA Repair (Amst.) 130, 103566 (2023).

Article CAS PubMed Google Scholar

Geijer, M. E. et al. Elongation factor ELOF1 drives transcription-coupled repair and prevents genome instability. Nat. Cell Biol. 23, 608619 (2021).

Article CAS PubMed PubMed Central Google Scholar

Kim, D. E. et al. Deficiency in the DNA repair protein ERCC1 triggers a link between senescence and apoptosis in human fibroblasts and mouse skin. Aging Cell 19, e13072 (2020).

Article MathSciNet CAS PubMed Google Scholar

Harada, Y.-N. et al. Postnatal Growth Failure, Short Life Span, and Early Onset of Cellular Senescence and Subsequent Immortalization in Mice Lacking the Xeroderma Pigmentosum Group G Gene. Mol. Cell. Biol. 19, 2366 (1999).

Article CAS PubMed PubMed Central Google Scholar

Niedernhofer, L. J. et al. A new progeroid syndrome reveals that genotoxic stress suppresses the somatotroph axis. Nature 444, 10381043 (2006).

Article CAS PubMed Google Scholar

Excerpt from:
Persistent TFIIH binding to non-excised DNA damage causes cell and developmental failure - Nature.com

In July 1957, 22 prominent scientists gathered quietly at a private lodge in Pugwash, a small town in Canadas Nova Scotia province. They had answered a call to action by Albert Einstein, inviting scientists to shape guardrails that would contain the danger of nuclear weapons. The Pugwash Conference earned a Nobel Peace Prize, and more importantly, it laid the foundations for the nuclear non-proliferation treaties, which saved our world from risks of annihilation.

Today, governments and businesses are frantically searching for ways to limit the many feared perils of AIespecially those from Artificial General Intelligence (AGI), the next phase of AI evolution. AGI will perform a wide range of cognitive tasks with an efficiency and accuracy far superior to current AI systems. This next stage of A.I., often referred to by Silicon Valley enthusiasts as God-like, is expected to surpass human intelligence and efficiency by a substantial margin. It is rumored that an internal report on the risks of AGI may be what ignited the recent board drama at OpenAI, the maker of ChatGPT. But while the race to build AGI is still in progress, we can be certain that whoever controls it will have enormous sway on society and the economy, potentially exerting influence on the lives of humans everywhere.

In the past year, numerous and uncoordinated efforts by government and business to contain AI sprang across the world, in the U.S., China, the EU, and the U.K. Businesses have been pleading with governments to regulate their AI creations, whilst knowing full well that governments will never succeed in regulating effectively at the speed of A.I. evolution. The EU recently completed a multi-year effort to deliver the AI Act. However, the shifts in generative AI capabilities mean that by the time it is enacted in 2025, the new AI Act may already be outdated.

Governments are not equipped to outgallop fast-moving technologies with effective rules and policiesespecially in the early hyperfast stages of development. Moreover, AI technologies have a transnational borderless reach, limiting the effectiveness of national and regional rule systems to govern them. As for businesses, they are in intense competition to dominate and profit from these technologies. In such a race, fueled by billions of investments, safety guardrails are inevitably a low priority for most businesses.

Ironically, governments and businesses are in fact the two stakeholders who are most in need of guardrails to prevent them from misusing A.I. in surveillance, warfare, and other endeavors to influence or control the public.

A careful analysis of how prior technologies and scientific innovations were tamed in the 20th century offers a clear answer to this dilemma. Guardrails were designed by scientists who know their own creations and understand (better than most) how they might evolve.

At Pugwash, influential scientists came together to develop strategies to mitigate the risks of nuclear weapons, significantly contributing to the formulation of arms control agreements and fostering international dialogue during the tense Cold War era.

In February 1975, at the Asilomar Conference in California, it was again scientists who met and successfully established critical guidelines for the safe and ethical research of DNA, thereby preventing potential biohazards. The Asilomar guidelines not only paved the way for responsible scientific inquiry but also informed regulatory policies worldwide. More recently, it was again the scientists and inventors of the Internet, led by Vint Cerf, who convened and shaped the framework of guardrails and protocols that made the Internet thrive globally.

All these successful precedents are proof that we need businesses and governments to first make space and let A.I. scientists shape a framework of guardrails that contain the risks without limiting the many benefits of A.I. Businesses can then implement such a framework voluntarily, and only when necessary, governments should step in to enforce the implementation by enacting policies and laws based on the scientists framework. This proven approach worked well for nuclear technology, DNA, and the Internet. It should be a blueprint to build safer AI.

A Pugwash Conference for AI scientists is therefore urgently needed. The conference should include no more than two dozen scientists, in the mold of Geoffrey Hinton who chose to quit Google in order to speak his mind on AIs promise and perils.

Like Pugwash, the scientists should be chosen from all the key countries where advanced A.I. technologies are developing, in order to at least strive for a global consensus. Most importantly, the choice of the participants at this seminal A.I. conference must reassure the public that the conferees are shielded from special interests, geopolitical pressures, and profit-centric motives.

While hundreds of government leaders and business bosses will cozy up to discuss A.I. at multiple annual international events, thoughtful and independent A.I. scientists must urgently get together to make A.I. good for all.

Fadi Chehad is chairman, cofounder, and managingpartner of Ethos Capital. He founded several software companies and was a fellow at Harvard and Oxford. From 2012 to 2016 he led ICANN, the technical institution that sets the global rules and policies for the internets key resources.

The opinions expressed in Fortune.com commentary pieces are solely the views of their authors and do not necessarily reflect the opinions and beliefs ofFortune.

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Scientists inspired the right guardrails for nuclear energy, the internet, and DNA research. Let them do the same for AI - Fortune

Strelitzia is a genus of five species of perennial plants, native to South Africa. It belongs to the plant family Strelitziaceae. A common name of the genus is bird of paradise flower/plant, because of a resemblance of its flowers to birds-of-paradise. In South Africa, it is commonly known as a crane flower. Wikipedia

The most up-to-date understanding of the flowering plant tree of life is presented in a new study published today in the journal Nature by an international team of 279 scientists, including three University of Michigan biologists.

Using 1.8 billion letters of genetic code from more than 9,500 species covering almost 8,000 known flowering plant genera (ca. 60%), this achievement sheds new light on the evolutionary history of flowering plants and their rise to ecological dominance on Earth.

Led by scientists at the Royal Botanic Gardens, Kew, the research team believes the data will aid future attempts to identify new species, refine plant classification, uncover new medicinal compounds, and conserve plants in the face of climate change and biodiversity loss.

The major milestone for plant science, involving 138 organizations internationally, was built on 15 times more data than any comparable studies of the flowering plant tree of life. Among the species sequenced for this study, more than 800 have never had their DNA sequenced before.

The sheer amount of data unlocked by this research, which would take a single computer 18 years to process, is a huge stride toward building a tree of life for all 330,000 known species of flowering plantsa massive undertaking by Kews Tree of Life Initiative.

Analyzing this unprecedented amount of data to decode the information hidden in millions of DNA sequences was a huge challenge. But it also offered the unique opportunity to reevaluate and extend our knowledge of the plant tree of life, opening a new window to explore the complexity of plant evolution, said Alexandre Zuntini, a research fellow at Royal Botanic Gardens, Kew.

Tom Carruthers, postdoctoral researcher in the lab of U-M evolutionary biologist Stephen Smith, is co-lead author of the study with Zuntini, who he previously worked with at Kew. U-M plant systematist Richard Rabeler is a co-author.

All 64 orders, all 416 families and 58% (7,923) of genera are represented. The young tree is illustrated here (maximum constraint at the root node of 154Ma), with branch colours representing net diversification rates. Black dots at nodes indicate the phylogenetic placement of fossil calibrations based on the updated AngioCal fossil calibration dataset. Note that calibrated nodes can be older than the age of the corresponding fossils owing to the use of minimum age constraints. Arcs around the tree indicate the main clades of angiosperms as circumscribed in this paper. ANA grade refers to the three consecutively diverging orders Amborellales, Nymphaeales and Austrobaileyales. Plant portraits illustrating key orders were sourced from Curtiss Botanical Magazine (Biodiversity Heritage Library). These portraits, by S. Edwards, W. H. Fitch, W. J. Hooker, J. McNab and M. Smith, were first published between 1804 and 1916 (for a key to illustrations see Supplementary Table 2). A high-resolution version of this figure can be downloaded from https://doi.org/10.5281/zenodo.10778206 (ref. 55).

Flowering plants feed, clothe and greet us whenever we walk into the woods. The construction of a flowering plant tree of life has been a significant challenge and goal for the field of evolutionary biology for more than a century, said Smith, co-author of the study and professor in the U-M Department of Ecology and Evolutionary Biology. This project moves us closer to that goal by providing a massive dataset for most of the genera of flowering plants and offering one strategy to complete this goal.

Smith had two roles on the project. First, members of his labincluding former U-M graduate student Drew Larsontraveled to Kew to help sequence members of a large and diverse plant group called Ericales, which includes blueberries, tea, ebony, azaleas, rhododendrons and Brazil nuts.

Second, Smith supervised the analyses and construction of the project dataset along with William Baker and Felix Forest of the Royal Botanic Gardens, Kew, and Wolf Eisenhardt of Aarhus University.

One of the biggest challenges faced by the team was the unexpected complexity underlying many of the gene regions, where different genes tell different evolutionary histories. Procedures had to be developed to examine these patterns on a scale that hadnt been done before, said Smith, who is also director of the Program in Biology and an associate curator in biodiversity informatics at the U-M Herbarium.

As co-leader of the study, Carruthers main responsibilities included scaling the evolutionary tree to time using 200 fossils, analyzing the different evolutionary histories of the genes underlying the overall evolutionary tree, and estimating rates of diversification in different flowering plant lineages at different times.

Hebarium speciment from 1832 Trepocarpus aethusae RBG Kew

Constructing such a large tree of life for flowering plants, based on so many genes, sheds light on the evolutionary history of this special group, helping us to understand how they came to be such an integral and dominant part of the world, Carruthers said. The evolutionary relationships that are presentedand the data underlying themwill provide an important foundation for a lot of future studies.

The flowering plant tree of life, much like our own family tree, enables us to understand how different species are related to each other. The tree of life is uncovered by comparing DNA sequences between different species to identify changes (mutations) that accumulate over time like a molecular fossil record.

Our understanding of the tree of life is improving rapidly in tandem with advances in DNA sequencing technology. For this study, new genomic techniques were developed to magnetically capture hundreds of genes and hundreds of thousands of letters of genetic code from every sample, orders of magnitude more than earlier methods.

A key advantage of the teams approach is that it enables a wide diversity of plant material, old and new, to be sequenced, even when the DNA is badly damaged. The vast treasure troves of dried plant material in the worlds herbarium collections, which comprise nearly 400 million scientific specimens of plants, can now be studied genetically.

In many ways this novel approach has allowed us to collaborate with the botanists of the past by tapping into the wealth of data locked up in historic herbarium specimens, some of which were collected as far back as the early 19th century, said Baker, senior research leader for Kews Tree of Life Initiative.

Our illustrious predecessors, such as Charles Darwin or Joseph Hooker, could not have anticipated how important these specimens would be in genomic research today. DNA was not even discovered in their lifetimes. Our work shows just how important these incredible botanical museums are to groundbreaking studies of life on Earth. Who knows what other undiscovered science opportunities lie within them?

Across all 9,506 species sequenced, more than 3,400 came from material sourced from 163 herbaria in 48 countries.

Sampling herbarium specimens for the study of plant relationships makes broad sampling from diverse areas of the world much more feasible than if one had to travel to get fresh material from the field, said U-Ms Rabeler, a research scientist emeritus and former collection manager at the U-M Herbarium.

For the tree of life project, Rabeler helped verify the identity of herbarium specimens selected for sampling and analyzed the resulting data.

Flowering plants alone account for about 90% of all known plant life on land and are found virtually everywhere on the planetfrom the steamiest tropics to the rocky outcrops of the Antarctic Peninsula. And yet, our understanding of how these plants came to dominate the scene soon after their origin has baffled scientists for generations, including Darwin.

Flowering plants originated more than 140 million years ago after which they rapidly overtook other vascular plants including their closest living relativesthe gymnosperms (nonflowering plants that have naked seeds, such as cycads, conifers and ginkgo).

Darwin was mystified by the seemingly sudden appearance of such diversity in the fossil record. In an 1879 letter to Hooker, his close confidant and director of the Royal Botanic Gardens, Kew, he wrote: The rapid development as far as we can judge of all the higher plants within recent geological times is an abominable mystery.

Using 200 fossils, the authors scaled their tree of life to time, revealing how flowering plants evolved across geological time. They found that early flowering plants did indeed explode in diversity, giving rise to more than 80% of the major lineages that exist today shortly after their origin.

However, this trend then declined to a steadier rate for the next 100 million years until another surge in diversification about 40 million years ago, coinciding with a global decline in temperatures. These new insights would have fascinated Darwin and will surely help todays scientists grappling with the challenges of understanding how and why species diversify.

Assembling a tree of life this extensive would have been impossible without Kews scientists collaborating with many partners across the globe. In total, 279 authors were involved in the research, representing many different nationalities from 138 organizations in 27 countries.

The plant community has a long history of collaborating and coordinating molecular sequencing to generate a more comprehensive and robust plant tree of life. The effort that led to this paper continues in that tradition but scales up quite significantly, said U-Ms Smith.

The flowering plant tree of life has enormous potential in biodiversity research. This is because, just as one can predict the properties of an element based on its position in the periodic table, the location of a species in the tree of life allows us to predict its properties. The new data will thus be invaluable for enhancing many areas of science and beyond.

To enable this, the tree and all of the data that underpin it have been made openly and freely accessible to both the public and scientific community, including through the Kew Tree of Life Explorer.

Open access will help scientists to make the best use of the data, such as combining it with artificial intelligence to predict which plant species may include molecules with medicinal potential.

Similarly, the tree of life can be used to better understand and predict how pests and diseases are going to affect plants in the future. Ultimately, the authors note, the applications of this data will be driven by the ingenuity of the scientists accessing it.

Phylogenomics and the rise of the Angiosperms, Nature (open access)

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