Daily Archives: January 16, 2024

The ocean, Earths largest habitat, remains largely unexplored, holding secrets to numerous unidentified species and microorganisms. Recent advancements in ocean DNA research have brought us closer to uncovering these mysteries.

The latest landmark in this journey is the creation of the KMAP Global Ocean Gene Catalog 1.0, a comprehensive database of marine microbial biodiversity.

Elisa Laiolo of the King Abdullah University of Science and Technology (KAUST) in Saudi Arabia, the lead author of the study, shares her excitement.

With over 317 million gene groups from marine organisms globally, the KMAP catalog represents a significant step towards understanding the oceans full diversity. Focusing on marine microbes, this catalog is pivotal for comprehending their influence on ocean health and Earths climate, Laiolo said.

This catalog is a gateway to endless possibilities. Prof Carlos Duarte, KAUST faculty member and the studys senior author, elaborates on its potential.

Hosted on the KAUST Metagenomic Analysis Platform (KMAP), this freely accessible catalog enables scientists to explore diverse ocean ecosystems, assess the effects of pollution and global warming, and even discover biotechnological applications like new antibiotics or methods to degrade plastics.

The quest to map marine biodiversity is centuries old, fraught with challenges, primarily due to the inability to study most marine organisms in a lab setting.

The advent of DNA sequencing technologies revolutionized this field, allowing for direct identification of organisms from ocean water and sediments.

Laiolo simplifies the process, saying, Each species has a unique gene set, enabling us to determine the organisms present in an ocean sample by analyzing its genetic material.

She credits two technological advancements for this large-scale achievement: the rapid development and reduced cost of DNA sequencing technologies, and the emergence of powerful computational and AI technologies.

The research team utilized KMAP to analyze DNA sequences from 2,102 ocean samples collected worldwide.

This cutting-edge computational effort identified 317.5 million gene groups, with over half classified by organism type and gene function.

By correlating this information with sample locations and habitat types, the catalog offers unprecedented insights into the distribution and roles of marine microbes.

This achievement underscores the essence of open science, Duarte remarks. The catalogs creation was possible due to global sailing expeditions for sample collection and the open-access sharing of DNA data. He emphasizes the ongoing collaborative efforts to keep this catalog freely available.

The KMAP catalog has already uncovered significant findings, like differences in microbial activity between the water column and ocean floor, and a notable presence of fungi in the mesopelagic twilight zone.

These discoveries aid in understanding how different habitats microbes shape ecosystems, contribute to ocean health, and affect the climate.

This catalog also serves as a crucial baseline for monitoring the impact of human activities, like pollution and global warming, on marine life. Its a treasure trove of genetic material, ripe for exploration in drug development, energy, and agriculture.

Laiolo highlights the need for continued ocean sampling, especially in under-studied areas like the deep sea. She points out that due to the oceans dynamic nature, the catalog will require regular updates.

However, Duarte warns of the catalogs uncertain future, citing international legislation on benefit-sharing from discoveries in international waters as a major hurdle.

The 2023 Treaty of the High Seas offers some solutions, but it might also hinder research by diminishing investment incentives. Resolving this uncertainty is crucial now that we have the tools for groundbreaking innovation in blue biotechnology, he concludes.

The KMAP Ocean Gene Catalog 1.0 is just the beginning. Its a first step towards developing a comprehensive atlas documenting every gene from every marine species worldwide, from bacteria and fungi to plants and animals.

In summary, as we continue to explore and understand the vast and complex ocean ecosystem, this catalog will be an indispensable resource, guiding us towards a deeper appreciation and better stewardship of our planets greatest natural resource.

The full study was published in the journal Frontiers in Science.

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Largest-ever ocean DNA study uncovers mysteries of marine life - Earth.com

Roughly 2,500-year-old DNA has revealed the first ancient person on record with Turner syndrome, a genetic condition in which a person has just a single X chromosome rather than two, a new study finds.

The individual, who died when they were 18 to 22 years old, likely hadn't gone through puberty, an analysis of the bones revealed. A further investigation of the remains revealed that the individual had mosaic Turner syndrome, as some cells had just one X chromosome while others had two.

The research looked at historical DNA gathered in the Thousand Ancient British Genomes project a database of DNA being collected from skeletons in the U.K. The team identified a total of six people with sex chromosomal conditions, according to a study published Jan. 11 in the journal Communications Biology.

The researchers made the discoveries after developing a computational method to find atypical numbers of chromosomes in DNA from skeletons.

Related: Europeans' ancient ancestors passed down genes tied to multiple sclerosis, Alzheimer's risk

The individual with Turner syndrome, who died in the early Iron Age (750 to 400 B.C.) likely had a partially missing second X chromosome. This condition can often lead to symptoms and characteristics such as shorter-than-average height, cardiac defects and small or absent ovaries, leading to fertility issues.

Of the other five people with aneuploidies, or genetic disorders in which a person doesn't have 46 chromosomes,three individuals showed signs of Klinefelter syndrome a genetic condition in which a person has an XXY set of sex chromosomes. Of these three individuals, one died in the Iron Age (circa 750 B.C. to A.D. 43), one in the high Middle Ages (around A.D. 1050 to 1290) and one in the early 19th century. Klinefelter syndrome often stunts the growth of a person's testicles, leading to lower testosterone levels, lower muscle mass, less body hair and larger breast tissue than typical XY individuals.

The three skeletons identified with this condition were buried in ways typical for their times, according to the study, showing that "their burials did not reveal any differences in how they were perceived by their contemporaries," the researchers wrote.

Another male individual from the early medieval period (eighth century) had an extra Y sex chromosome, known as XYY syndrome. Most people who have XYY chromosomes have no physical features that are different than people with XY chromosomes, other than often being taller than average.

The researchers also identified a male infant from Iron Age Britain who had Down syndrome. This condition can result in neurodevelopmental problems, and identifying skeletons with the syndrome "can provide insights into care within ancient societies, as well as how people with these conditions, which have characteristic physical manifestations, were perceived by their peers," the researchers wrote in the study.

Although the number of people with chromosomal differences revealed in this study is small, the researchers' new method gives them the opportunity to observe genetic diversity to "provide another layer of information that can contribute to a more detailed reconstruction of the human past," they wrote in the study.

In particular, making it easier to study variations in sex chromosomes in ancient DNA can help move the field of skeletal analysis beyond binary sex estimations and into a more complex understanding of social gender.

"It is difficult to know an ancient individual's conception of their own gender identity, and gender norms in the past may not align with those of the present day," the researchers wrote in their study. "It is possible that an elevated proportion would have been seen to transgress gender boundaries."

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1st-ever ancient case of Turner syndrome, with just 1 X chromosome instead of 2, found in ancient DNA - Livescience.com

Felicia Anne Gayle Picus was found dead in her home, the victim of a vicious murder that devastated her family and rattled her neighbors in the gated community of University City, Missouri, just outside St. Louis. Police suspected a burglary gone wrong. The scene was replete with forensic evidence: There were bloody footprints and fingerprints, and the murder weapon a kitchen knife used to stab Picus was left lodged in her neck.

That detail caught the medical examiners attention. Weeks earlier, another woman had been stabbed to death just a couple of miles away, and the weapon was left in the victims body. Days after Picuss murder, the University City police chief told the St. Louis Post-Dispatch that investigators had identified a prime suspect, someone they said had been spotted in the area in recent weeks, whom they believed had killed before.

But whatever became of that lead is unclear. After Picuss family posted a $10,000 reward for information leading to the arrest and conviction of her killer, a jailhouse informant named Henry Cole came forward with a story about how his former cellmate, Marcellus Williams, had confessed to murdering Picus. Soon, police secured a second informant: Laura Asaro, Williamss former girlfriend, also told the cops that Williams was responsible for the killing. There were reasons to be wary of their stories. Both informants were facing prison time for unrelated crimes and stood to benefit. Many of the details they offered shifted over the course of questioning, while others did not match the crime. Nonetheless, Williams was charged with Picuss murder, convicted, and sentenced to death.

Questions about the investigation and Williamss guilt have only mounted in the years since the August 1998 crime. DNA testing on the murder weapon done years after his conviction revealed a partial male profile that could not have come from Williams. On the eve of Williamss scheduled execution in 2017, then-Missouri Gov. Eric Greitens intervened. He issued an executive order that triggered a rarely used provision of Missouri law, empaneling a board to review the evidence, including DNA, that jurors never heard about at trial.

While that review was ongoing for most of the last six years, the board never submitted a final report or recommendation to the governor, as the law requires. Instead, last June, Gov. Mike Parson announced that he was rescinding his predecessors order, effectively dissolving the panel that had been reinvestigating the case.

The question now is whether Missouri law allows the governor to simply disappear an ongoing investigation. Because the law has so rarely been used, its contours have never been fully litigated, prompting the Midwest Innocence Project, which represents Williams, to file a civil lawsuit seeking to invalidate Parsons order. The states attorney general balked, arguing that Williams was trying to usurp the governors independent clemency powers. The AG has asked the Missouri Supreme Court to toss the lawsuit and clear the way for Williamss execution.

Picus spent a decade as a reporter for the St. Louis Post-Dispatch, including on the crime beat, before leaving to focus on philanthropic endeavors. She was an ardent environmentalist and feminist: She persuaded the newspaper to adopt its first recycling program, and a former colleague recalled how shed advocated for using the term personhole instead of manhole in stories.

Diminutive in stature with long hair and a reported fondness for Birkenstocks, Picus was also a dedicated friend. She wrote hundreds of birthday and holiday cards each year the day she was killed, she had more than 30 handmade cards ready to mail. She was like a central switching system on the telephone company of life, a childhood friend and fellow journalist wrote in the Chicago Tribune.

The Post-Dispatch covered the search for Picuss killer as the months without an arrest wore on, publishing a detailed list of items police said had been stolen from her home, among them an old Apple laptop belonging to Picuss husband, Dan. But it wasnt until the $10,000 reward was posted that police secured statements from the informants, Cole and Asaro, claiming that Williams had confessed to the murder. Although the reward was supposed to be paid upon conviction, prosecutors encouraged Dan to pay Cole $5,000 upfront when it appeared that his cooperation might be flagging.

Cole and Asaro were the backbone of the prosecutions case at Williamss trial in the summer of 2001. The state painted a harrowing picture of the attack on Picus and cast Williams as a ruthless killer. There was no physical evidence, however, to back up the informants claims. Asaro claimed that Williams had scratches on his face the day of the murder, yet no foreign DNA was recovered from under Picuss fingernails. Cole said Williamss clothes were bloody and that hed stolen a shirt to cover the stains when he left Picuss house, yet no clothes were missing from the home. Bloody shoeprints found at the scene were a different size than Williamss feet. Fingerprints lifted by investigators were deemed unusable by the state and then destroyed before the defense had a chance to analyze them.

There was, however, the Apple laptop, which police ultimately recovered. According to Asaro, Williams gave his grandfathers neighbor the computer in exchange for crack cocaine. At trial, the man denied that account. Hed paid Williams for the laptop, he said. Williams told him that hed gotten the computer from Asaro and was selling it for her. Prosecutors objected to this testimony, so the jury never heard it. Asaro and the man who received the computer have since died.

Like Cole and Asaro, Williams had a rap sheet. Hed been sentenced to decades in prison for robbery and burglary by the time of the murder trial. According to the Post-Dispatch, the jury deliberated for less than 90 minutes, including lunch, before deciding that Williams should be sentenced to die for Picuss murder.

Marcellus Williams in an undated photo.

Attorneys for Williams sought to conduct DNA testing prior to his trial, but the circuit court judge refused. It wasnt until 2015 that Williams was granted permission to test the murder weapon, which revealed a male DNA profile that did not match Williams. Nonetheless, the Missouri Supreme Court dismissed the new evidence and set Williamss execution for August 22, 2017.

The Midwest Innocence Project turned to Greitens, asking that he halt the execution and convene a board of inquiry to investigate the case. On the day Williams was set to die, Greitens issued an executive order granting the request.

A five-member board would be set up to assess the credibility and weight of all evidence in the case, Greitenss order read. The board was given subpoena power and tasked with keeping the information it collected in strict confidence. The order required the board to make a final report and recommendation to the governor as to whether or not Williams should be executed or his sentence of death commuted.

Greitens appointed five retired judges to the investigation, and they got to work. In the years that followed, the Midwest Innocence Project provided the board with a host of information and suggestions for lines of inquiry continuing well after Greitens resigned amid a swirl of controversies the following year and Parson assumed office.

That is until Parson issued his own executive order on June 29, 2023, rescinding Greitenss order. While Parson acknowledged that his predecessor had required a report from the board of inquiry regarding its investigation, the governor made no mention of any findings.

This board was established nearly six years ago, and it is time to move forward, he said. We could stall and delay for another six years, deferring justice, leaving a victims family in limbo, and solving nothing. This administration wont do that.

In 1963, the Missouri legislature passed several criminal justice reforms, including one aimed at avoiding wrongful executions. The states constitution already empowered the governor to grant reprieves, commutations, and pardons, but lawmakers added new authorities, allowing the governor, in his discretion, to appoint a board of inquiry tasked with gathering information bearing on whether a person condemned to death should in fact be executed. Lawmakers set several specific parameters, including that the board shall issue a final report. The law passed that summer and has never been amended.

Although it has been on the books for 60 years, the provision has only been invoked three times, including in the Marcellus Williams case. In 1997, then-Gov. Mel Carnahan stayed the execution of William Boliek, who had been sentenced to die for murdering a witness to a robbery in Kansas City, and ordered a board of inquiry to look into the case. The board submitted its report to Carnahan, but the governor did not act on it before he was killed in a plane crash meaning the case was never resolved. The Missouri Supreme Court subsequently ruled that Carnahan was the only one who could lift the stay, meaning Boliek could never be executed. He remains on Missouris death row.

In an August 2023 civil lawsuit filed in Cole County, where the state capital is located, the Midwest Innocence Project drew on this history to argue that Parson had violated the law by dissolving Greitenss board before it had fulfilled its statutory duty to provide a report and recommendation in Williamss case.

Once the statute was triggered, the governor was bound to uphold its provisions. Parsons order prematurely dissolving the board exceeded the power granted to his office by the legislature some 60 years ago, the lawyers argued. All Mr. Williams is asking is for the board of inquiry to be able to complete its work and issue a report and recommendation, ensuring that at least one government entity finally hears all the evidence of his innocence, said Tricia Rojo Bushnell, the Midwest Innocence Projects executive director. Once the process is complete, Parson can do what he wants, she added. But until that time, Mr. Williams has a right to this process that was started by Gov. Greitens precisely out of the concern that Missouri may execute an innocent person.

Missouri Attorney General Andrew Bailey during a House Homeland Security Committee hearing on Jan. 10, 2024.

Attorney General Andrew Bailey sought to have the lawsuit dismissed outright, but in November, Circuit Court Judge S. Cotton Walker concluded that it should proceed. The statute didnt expressly give Parson the authority to dissolve the board, and Williams had an interest in the process playing out according to the law, he wrote. There is a fundamental difference between the governors authority to appoint a board in his discretion and the boards ongoing existence being discretionary.

Bailey appealed to the Missouri Supreme Court, arguing that the circuit court couldnt tell the governor what to do in matters of clemency. Since the board of inquiry statute references the governors constitutional powers over clemency, Bailey argued, interfering with his ability to dissolve the board was the same as interfering with his clemency powers. Williams was trying to use the court to hijack Parsons authority, he wrote.

The Midwest Innocence Project argued that Baileys position was a red herring: Williams was not looking to interfere with Parsons authority on matters of clemency; he was merely asking that the governor be required to follow the statute in his decision-making. To find otherwise would be violating the separation of powers in the other direction: allowing the governor to rewrite a decades-old act of the legislature. The governors position, the lawyers wrote, has it backward.

The governors clemency power exists for the public good, not his own, the defense brief reads. As a result, a board of inquiry serves the public, not the governor, and that board shall make a report and recommendation for the governors consideration before he makes a final clemency decision.

There is no timeline for the Missouri Supreme Court to rule.

Meanwhile, the Conviction and Incident Review Unit at the St. Louis County Prosecuting Attorneys Office has also reached out to the court, asking that it refrain from setting a date for Williamss execution for an initial period of six months. The office has also been investigating Williamss case and needs more time to decide whether it will seek to vacate his sentence on its own a power granted to state prosecutors under a newer, but also rarely used, Missouri law.

Marcellus Williams remains grateful to Greitens for staying his execution and invoking the board of inquiry statute. He told the Kansas City Star that he grew up basically like a typical misguided youth, bouncing in and out of juvenile detention. He had just started serving a 20-year sentence for robbing a doughnut shop when he was charged with Picuss killing. He knew he hadnt done it and said that despite his experience with the criminal justice system, he thought the mistake would be discovered and corrected. You still have this naivete right there that youre not really recognizing who youre up against.

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DNA Didn't Match Marcellus Williams. Missouri May Fast-Track Execution Anyway. - The Intercept

Genes that significantly increase risk of developing multiple sclerosis were introduced to northwestern Europe by herders who migrated from the east around 5,000 years ago. SayoStudio

More than 1.8 million people around the world have the autoimmune disease multiple sclerosis (MS). The condition, in which a persons immune system attacks their brain and spinal cord, is most common in northern Europe, but researchers havent been entirely sure why.

A new study of ancient DNA, published Wednesday in the journal Nature, sheds light on this trend, suggesting herders who migrated to Europe from western Eurasia around 5,000 years ago carried genetic variants linked to MS. These variants grew in prevalence at the time and contribute to an increased risk for the disease today, the paper authors write.

This is a tour de force, Llus Quintana-Murci, a population geneticist at the Pasteur Institute in Paris who did not contribute to the findings, tells Nature News Sara Reardon.

The study accompanies three othernewpapers in Nature investigating ancient DNA in Europe and Asia. One of those found that genes linked to an increased risk for diabetes and Alzheimers disease were carried by hunter-gatherers.

Processes that were occurring many thousands of years ago are having these really pronounced and profound effects on the health and longevity of people in the present, Evan Irving-Pease, an author of all four of the studies and a population geneticist at the University of Copenhagen in Denmark, tells the Washington Posts Carolyn Y. Johnson.

Researchers explored this history by sequencing ancient genomes and comparing them to modern DNA. The team examined ancient DNA from bones and teeth dating to the Mesolithic period and Bronze Age, as well as new genomes collected from Medieval times. They studied this data against DNA from 410,000 white British people included in the modern U.K. Biobank.

Major migrations had a strong impact on genetic diversity in western Eurasia, the authors write. Hunter-gatherers entered the picture around 45,000 years ago, farmers came from the Middle East around 11,000 years ago and herders migrated from the Pontic Steppe, a grassland region in the Balkans and western Asia, around 5,000 years ago.

These herders, known as the Yamnaya, rode horses and drove ox-drawn carts, writes Science News Bruce Bower. And they buried their dead with gold and jewelry, per the New York Times Carl Zimmer. Most people in northern Europe today can trace their ancestry to this group.

The researchers found that variants linked to MS arose around 5,000 years ago in the Yamnaya, who spread their genes when they got to northern Europe. These variants increased in prevalence for the steppe population, and later, in the European population, which signaled to the scientists that that they might have provided an evolutionary advantage.

These variants that are causing the high risk of multiple sclerosis today must in the past have had a benefit, Eske Willerslev, a geneticist at the University of Copenhagen and a leader of the research, tells the New York Times.

Such variants could have helped ancient people fight off pathogens, the researchers theorize. The overly active immune system associated with multiple sclerosis could have actually been beneficial for surviving plagues, Willerslev tells Nature News. In particular, the MS-associated variants could have protected the Yamnaya herders against diseases carried by their horses, sheep, cattle and goats.

The situation today is different, because the diseases these variants originally provided protection against are no longer as big a problem as they likely were then, Lars Fugger, a co-author on the MS paper who studies the disease at the University of Oxford in the U.K., said at a news briefing, per Medpage Todays Judy George. Because in the intervening millennia, we have antibiotics, vaccinations and far, far higher standards of hygiene than people had thousands of years ago. The risk genes are now miscast in terms of their original biological role.

Previous studies have found a couple hundred common genetic variants that are linked to MS, and 30 percent of the risk for the disease is thought to come from genetic factors, the study authors write.

Samira Asgari, a computational biologist at the Icahn School of Medicine at Mount Sinai who was not involved in the research, tells the Washington Post the theory that the variants identified in the study protect against infection is reasonable. But she notes that its still a hypothesis.

Thats the part more research is needed to prove, Asgari tells the publication.

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Ancient DNA From Eurasian Herders Sheds Light on the Origins of Multiple Sclerosis - Smithsonian Magazine

Toh Kuyabeh, a new holistic boutique hotel concept in tulum

Spanish architecture practice DNA introduces Toh Kuyabeh, a new concept for a holistic boutique hotel nested amid Tulums lush nature, with a focus on body-mind-soul harmony. Developed for the KUYABEH Sustainable Ecological Community in Mexico, the project draws inspiration from the Toh bird, guided by its shapes, feathers, and radial flight to design a unique structure that embrace the tropical terrain, providing unparalleled panoramic views of the lagoon and a central distribution.

all renders DNA Barcelona

The HotelToh Kuyabeh design by DNA Barcelona (see more here) departs from three volumes containing the architectural program. Thirty-five rooms interconnect in a circular arrangement under a undulating roof recalling bird flight patterns, providing a visual spectacle of the Tohs colors and enhancing movement with reflections in the water. At the center, two levels house different amenities; the first includes a spa and meeting rooms, while the second features a restaurant and terraces. This distribution of standout volumes not only ensures privacy but also offers scenic views from any point in the resort.

Hotel Toh Kuyabeh is an ode to the Toh birds feathers, shape, and flight

In addition to its unique design, the hotel incorporates sustainable practices, namely solar-paneled roofs for renewable energy generation, collecting rainwater, achieving natural ventilation through efficient skin and roof systems. Furthermore, the architects propose a native construction system, adapted to regional traditional techniques, and a dry construction method, to maximize efficiency and green building. The choice of natural and native materials reflects the projects commitment to bio-compatibility and sustainability, comments DNA Barcelona.

a new concept for a holistic boutique resort nested amid Tulums lush nature

using native construction systems as sustainable practices

a pedestrian bridge connecting the different volumes

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DNA's hotel toh kuyabeh mirrors bird flight undulations in tulum - Designboom

Research led by scientists at the Universities of Oxford, Cambridge, Copenhagen, Bristol and California (Berkeley) reveals the evolutionary origins of multiple sclerosis (MS). This new insight into the genetic architecture of this disease changes scientists view of its causes and has implications for its treatment, as well as paving the way for further investigations into other diseases.

Affecting 1 in 1,000 people, multiple sclerosis (MS) is an autoimmune disease in which the body's immune system attacks its own brain and spinal cord. Northern Europe has the highest prevalence of MS in the world.

The new research published in Nature draws on analysis of the DNA of ancient human bones and teeth held in museum collections across Europe and Western Asia. It reveals that a major migration of pastoralist herders known as the Yamnaya people from from the Pontic Steppe (a region spanning parts of what are now Ukraine, South-West Russia and the West Kazakhstan) into Western Europe 5,000 years ago introduced genetic variants into the population.

These new variants provided an advantage to the people carrying them at the time, probably by providing protection against infectious diseases in their domesticated animals. In today's modern environment, however, these same genetic variants increase the risk of developing MS.

To show this, the research team compared data held in a unique gene bank of ancient DNA to the UK Biobank, a large-scale biomedical database and research resource containing genetic, lifestyle and health information and biological samples from half a million UK participants. The research was funded by a 8M grant from the Lundbeck Foundation.

The new insights into the genetic factors behind MS are helping to demystify the disease, which is crucial, stresses co-author Professor Lars Fugger of the MRC Weatherall Institute of Molecular Medicine and Nuffield Department of Clinical Neurosciences at the University of Oxford.

'This is very important from the perspective of both patients and doctors. Because it means that we can do away with the conventional perception of MS, which defines the disease in terms of the impairments it causes, and instead understand and seek to treat MS for what it actually is: the result of a genetic adaptation to certain environmental conditions that occurred back in our prehistory and which has endured in our DNA, even though the environmental conditions have changed hugely in the time between then and now,' Professor Fugger explains.

For more than three decades, as a professor and consultant physician at the Oxford University Hospitals NHS Foundation Trust, Professor Fugger has been conducting research into MS and treating patients with immune-mediated disorders. So far, 233 MS-genetic risk variants have been mapped. The findings presented in the new paper show that many of these genetic variants provided protection against infectious diseases. There is no immediate indication that they held any disadvantage at that time, Fugger explains:

'The situation today is different because the diseases these variants originally provided protection against are no longer as big a problem as they likely were then. Because in the intervening millennia, we have antibiotics, vaccinations and far, far higher standards of hygiene than people had thousands of years ago. Thus, the risk genes are now "miscast" in terms of their original biological role.'

Science so far has 'only an incomplete understanding of why individuals develop MS', co-author Professor Astrid Iversen explains. A professor of virology and immunology at the MRC WIMM and Nuffield Department of Clinical Neurosciences at the University of Oxford, her research concerns the evolutionary processes in the development of the human immune response to challenges from pathogens, meaning the bacteria and viruses that cause disease.

Based on archaeological DNA, Professor Iversen is also investigating how pathogens interacting with environmental and lifestyle factors ever since the the Last Ice Age have impacted the immune system of present-day individuals and their genetic susceptibility to certain diseases, including autoimmune diseases like MS, which have been on the rise over the last 50 years.

'The selection process involving the human immune system is ongoing, meaning it is also happening right now,' explains Professor Iversen, adding: 'The individuals who have immune system genes that allow them to fight off the combination of infectious diseases they are exposed to in life will have children who pass on those same immune system genes. This is why the immune system in all present-day individuals is also, genetically speaking, the product of selection processes our ancestors underwent. But because we now lead very different lives to those of our ancestors in terms of hygiene, diet, medical treatment options for, for example, some parasitic diseases, as a result of our evolutionary history, we may, in some respects be more susceptible to certain diseases than our ancestors were, including autoimmune diseases such as MS.'

Professor Fugger explains how the research findings hold some promise for future treatment: 'MS is an autoimmune disease, and a lot of the drugs we currently use to treat it target the immune system. The downside is that we risk suppressing the immune system so effectively that patients are less well equipped to fight infections.

'What we need is an approach whereby we can learn from more studies on the genetic background of MS how to 'recalibrate' the immune system in patients. This would allow their immune system to play an active role in suppressing the disease. While that's not just around the corner, it's still what we should be aiming for in terms of research.'

This MS study demonstrates that the large ancient human genome data sets, combined with analyses of present-day DNA and input from a number of other research fields, serve as a scientific precision tool capable of providing new insights into diseases.

The international research team now plans to investigate other neurological conditions including Parkinson's and Alzheimer's diseases, and psychiatric disorders including ADHD and schizophrenia.

The paper, 'Elevated genetic risk for multiple sclerosis emerged in steppe pastoralist populations', is published in Nature.

Original post:
Research into ancient DNA sheds new light on cause of Multiple Sclerosis and other neurodegenerative diseases - University of Oxford

Past human gene pools of western Eurasia

In Nature paper (3) the researchers including Morten Allentoft, Professor at Curtin University, Australia and Lundbeck Foundation GeoGenetics Centre at UCPH, Martin Sikora, Associate Professor at the Lundbeck Foundation GeoGenetics Centre at UCPH, andKristian Kristiansen, Professor of Archaeology at the University of Gothenburg, Sweden, show that genetic differences between ancient populations in western Eurasia were substantially higher than previously estimated, and also much higher than observed in present-day populations.

In Nature paper (4) the team reports findings that overturn the commonly-held view that the ancestors of present-day Danes were Stone Age hunter-gatherers.

The team, including Professor Kristian Kristiansen and Dr Anders Fischer, both affiliated with the Lundbeck Foundation GeoGenetics Centre at UCPH, analysed DNA from 100 skeletons of the prehistoric inhabitants of the region now known as Denmark, who lived between 10,000 years ago and 2,700 years ago.

They found that since the last Ice Age around 12,000 years ago, Denmark has experienced two near-total population turnover events, the second of which is still evident in the gene pool of present-day Scandinavia.

Around 5,900 years ago at the dawn of the Neolithic Age, a group of farmers with genetic roots in Anatolia - the Asian part of present-day Turkey brought a new farming culture to Denmark. The resulting changes in diet were clear in analysis of the ancient bones, and show that these farmers completely replaced the hunter-gatherers living in the region.

Then, around 5,000 years ago, the Yamnaya arrived and eliminated the Anatolian farmers. The Yamnaya people are the closest ancestors of present-day ethnic Danes.

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Ancient DNA reveals reason for high MS and Alzheimer's rates in Europe - University of Cambridge news

Sprott, R. L. Biomarkers of aging and disease: introduction and definitions. Exp. Gerontol. 45, 24 (2010).

CAS PubMed Google Scholar

Bell, C. G. et al. DNA methylation aging clocks: challenges and recommendations. Genome Biol. 20, 249 (2019).

PubMed PubMed Central Google Scholar

Horvath, S. & Raj, K. DNA methylation-based biomarkers and the epigenetic clock theory of ageing. Nat. Rev. Genet. 19, 371384 (2018).

CAS PubMed Google Scholar

Schultz, M. B. et al. Age and life expectancy clocks based on machine learning analysis of mouse frailty. Nat. Commun. 11, 4618 (2020).

CAS PubMed PubMed Central Google Scholar

Bobrov, E. et al. PhotoAgeClock: deep learning algorithms for development of non-invasive visual biomarkers of aging. Aging 10, 32493259 (2018).

PubMed PubMed Central Google Scholar

Lehallier, B. et al. Undulating changes in human plasma proteome profiles across the lifespan. Nat. Med. 25, 18431850 (2019).

CAS PubMed PubMed Central Google Scholar

Fleischer, J. G. et al. Predicting age from the transcriptome of human dermal fibroblasts. Genome Biol. 19, 221 (2018).

CAS PubMed PubMed Central Google Scholar

Horvath, S. DNA methylation age of human tissues and cell types. Genome Biol. 14, R115 (2013).

PubMed PubMed Central Google Scholar

Hannum, G. et al. Genome-wide methylation profiles reveal quantitative views of human aging rates. Mol. Cell 49, 359367 (2013).

CAS PubMed Google Scholar

Levine, M. E. et al. An epigenetic biomarker of aging for lifespan and healthspan. Aging 10, 573591 (2018).

PubMed PubMed Central Google Scholar

Petkovich, D. A. et al. Using DNA methylation profiling to evaluate biological age and longevity interventions. Cell Metab. 25, 954960 (2017).

CAS PubMed PubMed Central Google Scholar

Meer, M. V., Podolskiy, D. I., Tyshkovskiy, A. & Gladyshev, V. N. A whole lifespan mouse multi-tissue DNA methylation clock. eLife 7, e40675 (2018).

PubMed PubMed Central Google Scholar

Thompson, M. J. et al. A multi-tissue full lifespan epigenetic clock for mice. Aging 10, 28322854 (2018).

CAS PubMed PubMed Central Google Scholar

Levine, M. et al. A rat epigenetic clock recapitulates phenotypic aging and co-localizes with heterochromatin. eLife 9, e59201 (2020).

CAS PubMed PubMed Central Google Scholar

Robeck, T. R. et al. Multi-species and multi-tissue methylation clocks for age estimation in toothed whales and dolphins. Commun. Biol. 4, 642 (2021).

CAS PubMed PubMed Central Google Scholar

Wilkinson, G. S. et al. DNA methylation predicts age and provides insight into exceptional longevity of bats. Nat. Commun. 12, 1615 (2021).

CAS PubMed PubMed Central Google Scholar

Wang, T. et al. Epigenetic aging signatures in mice livers are slowed by dwarfism, calorie restriction and rapamycin treatment. Genome Biol. 18, 57 (2017).

PubMed PubMed Central Google Scholar

Horvath, S. et al. Epigenetic clock for skin and blood cells applied to Hutchinson Gilford Progeria Syndrome and ex vivo studies. Aging 10, 17581775 (2018).

CAS PubMed PubMed Central Google Scholar

Lu, Y. et al. Reprogramming to recover youthful epigenetic information and restore vision. Nature 588, 124129 (2020).

CAS PubMed PubMed Central Google Scholar

Kerepesi, C., Zhang, B., Lee, S.-G., Trapp, A. & Gladyshev, V. N. Epigenetic clocks reveal a rejuvenation event during embryogenesis followed by aging. Sci. Adv. 7, eabg6082 (2021).

CAS PubMed PubMed Central Google Scholar

Lu, A. T. et al. DNA methylation GrimAge strongly predicts lifespan and healthspan. Aging 11, 303327 (2019).

CAS PubMed PubMed Central Google Scholar

Pidsley, R. et al. Critical evaluation of the Illumina MethylationEPIC BeadChip microarray for whole-genome DNA methylation profiling. Genome Biol. 17, 208 (2016).

PubMed PubMed Central Google Scholar

Meissner, A. et al. Reduced representation bisulfite sequencing for comparative high-resolution DNA methylation analysis. Nucleic Acids Res. 33, 58685877 (2005).

CAS PubMed PubMed Central Google Scholar

Han, Y. et al. Epigenetic age-predictor for mice based on three CpG sites. eLife 7, e37462 (2018).

PubMed PubMed Central Google Scholar

Han, Y. et al. New targeted approaches for epigenetic age predictions. BMC Biol. 18, 71 (2020).

CAS PubMed PubMed Central Google Scholar

Han, Y. et al. Targeted methods for epigenetic age predictions in mice. Sci. Rep. 10, 22439 (2020).

CAS PubMed PubMed Central Google Scholar

Wang, T. et al. Quantitative translation of dog-to-human aging by conserved remodeling of the DNA methylome. Cell Syst. 11, 176185 (2020).

PubMed PubMed Central Google Scholar

Wendt, J., Rosenbaum, H., Richmond, T. A., Jeddeloh, J. A. & Burgess, D. L. Targeted bisulfite sequencing using the SeqCap Epi enrichment system. Methods Mol. Biol. 1708, 383405 (2018).

CAS PubMed Google Scholar

Mulqueen, R. M. et al. Highly scalable generation of DNA methylation profiles in single cells. Nat. Biotechnol. 36, 428431 (2018).

CAS PubMed PubMed Central Google Scholar

Rohland, N. & Reich, D. Cost-effective, high-throughput DNA sequencing libraries for multiplexed target capture. Genome Res. 22, 939946 (2012).

CAS PubMed PubMed Central Google Scholar

Wang, M. & Lemos, B. Ribosomal DNA harbors an evolutionarily conserved clock of biological aging. Genome Res. 29, 325333 (2019).

CAS PubMed PubMed Central Google Scholar

Zullo, J. M. et al. Regulation of lifespan by neural excitation and REST. Nature 574, 359364 (2019).

CAS PubMed PubMed Central Google Scholar

Whitehead, J. C. et al. A clinical frailty index in aging mice: comparisons with frailty index data in humans. J Gerontol. A 69, 621632 (2014).

Google Scholar

Watada, E. et al. Age-dependent ribosomal DNA variations in mice. Mol. Cell. Biol. 40, e00368-20 (2020).

CAS PubMed PubMed Central Google Scholar

Rodriguez-Algarra, F. et al. Genetic variation at mouse and human ribosomal DNA influences associated epigenetic states. Genome Biol. 23, 54 (2022).

CAS PubMed PubMed Central Google Scholar

Seligman, B. J., Berry, S. D., Lipsitz, L. A., Travison, T. G. & Kiel, D. P. Epigenetic age acceleration and change in frailty in MOBILIZE Boston. J. Gerontol. A 77, 17601765 (2022).

CAS Google Scholar

Zhou, W. et al. DNA methylation dynamics and dysregulation delineated by high-throughput profiling in the mouse. Cell Genom. 2, 100144 (2022).

CAS PubMed PubMed Central Google Scholar

Lee, M. B., Hill, C. M., Bitto, A. & Kaeberlein, M. Antiaging diets: separating fact from fiction. Science 374, eabe7365 (2021).

CAS PubMed PubMed Central Google Scholar

Baur, J. A. et al. Resveratrol improves health and survival of mice on a high-calorie diet. Nature 444, 337342 (2006).

CAS PubMed PubMed Central Google Scholar

Ocampo, A. et al. In vivo amelioration of age-associated hallmarks by partial reprogramming. Cell 167, 17191733 (2016).

CAS PubMed PubMed Central Google Scholar

Gill, D. et al. Multi-omic rejuvenation of human cells by maturation phase transient reprogramming. eLife 11, e71624 (2022).

CAS PubMed PubMed Central Google Scholar

Matsuyama, M., WuWong, D. J., Horvath, S. & Matsuyama, S. Epigenetic clock analysis of human fibroblasts in vitro: effects of hypoxia, donor age, and expression of hTERT and SV40 largeT. Aging 11, 30123022 (2019).

CAS PubMed PubMed Central Google Scholar

Matsuyama, M. et al. Analysis of epigenetic aging in vivo and in vitro: factors controlling the speed and direction. Exp. Biol. Med. 245, 15431551 (2020).

CAS Google Scholar

Liu, Z. et al. Underlying features of epigenetic aging clocks in vivo and in vitro. Aging Cell 19, e13229 (2020).

CAS PubMed PubMed Central Google Scholar

Gu, H. et al. Preparation of reduced representation bisulfite sequencing libraries for genome-scale DNA methylation profiling. Nat. Protoc. 6, 468481 (2011).

CAS PubMed Google Scholar

Lehallier, B., Shokhirev, M. N., Wyss-Coray, T. & Johnson, A. A. Data mining of human plasma proteins generates a multitude of highly predictive aging clocks that reflect different aspects of aging. Aging Cell 19, e13256 (2020).

CAS PubMed PubMed Central Google Scholar

Bruinsma, S. et al. Bead-linked transposomes enable a normalization-free workflow for NGS library preparation. BMC Genomics 19, 722 (2018).

PubMed PubMed Central Google Scholar

Mulqueen, R. M. et al. High-content single-cell combinatorial indexing. Nat. Biotechnol. 39, 15741580 (2021).

CAS PubMed PubMed Central Google Scholar

Nguyen Ba, A. N. et al. Barcoded bulk QTL mapping reveals highly polygenic and epistatic architecture of complex traits in yeast. eLife 11, e73983 (2022).

PubMed PubMed Central Google Scholar

Krueger, F. & Andrews, S. R. Bismark: a flexible aligner and methylation caller for bisulfite-seq applications. Bioinformatics 27, 15711572 (2011).

CAS PubMed PubMed Central Google Scholar

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TIME-seq reduces time and cost of DNA methylation measurement for epigenetic clock construction - Nature.com

A jolt of java enjoyed by accused Long Island serial killer Rex Heuermann's daughter gave authorities a boost in building their case against him, according to court papers filed Tuesday.

New evidence disclosed by prosecutors following Heuermann's indictment in a fourth slaying included DNA testing on a beverage can that investigators allegedly saw his daughter drink from last year.

Heuermann, who was arrested in July, has pleaded not guilty to all charges and his lawyer has suggested authorities charged the wrong person.

Victoria Heuermann, who worked at her father's architectural firm in New York City, was trailed by undercover investigators as she boarded a commuter train to the family's suburban hometown of Massapequa Park on Long Island, on May 25, 2023, according to court papers.

During the trip, Victoria Heuermann, then 26, was seen sipping from a gold-colored can of "Monster Java" energy drink. A legal filing includes a photo of her with her face blacked out, holding the can with one hand and a cellphone with the other.

When the train arrived in Massapequa Park, she got off, tossed the can into a trash barrel and walked away from the station.

Investigators retrieved the can and took it to the Suffolk County Crime Laboratory in Hauppauge, where scientists later concluded that a female DNA profile obtained from the can matched one from a cheek swab of Victoria Heuermann, prosecutors wrote.

An unidentified forensic lab also generated DNA sequencing data from a hair on Amber Costello one of Rex Heuermann's four alleged victims and "conducted a one-to-one autosomal nuclear DNA comparison" between that profile and Victoria Heuermann's which linked them, according to court papers.

Victoria Heuermann's profile allegedly includes her single nucleotide polymorphisms, or SNPs, which are the most common type of genetic variation among people, according to the National Library of Medicine.

A report from the lab said the hair found on Costello was 4.654 times 10 to the power of 63 "more likely to have come from a person genetically identical to Victoria Heuermanns SNP Genotype File than from an unrelated individual," prosecutors wrote.

Court papers said Victoria Heuermann was "almost one-month shy of her 14th birthday" when Costello disappeared and was killed, and prosecutors have previously said she was out of town at the time, suggesting that Rex Heuermann allegedly transferred her hair to Costello by accident.

In addition to Costello, Heuermann previously faced murder charges in the deaths of Melissa Barthelemy and Megan Waterman, and he was charged Tuesday in the slaying of Maureen Brainard-Barnes.

The women, known as the "Gilgo Four," were sex workers who disappeared between 2007 and September 2010 and were found in December 2010 along Ocean Parkway near Gilgo Beach in Babylon, on Long Island's South Shore.

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Gilgo Serial Killer Suspect Rex Heuermann Tied to Slaying by DNA From Daughter's Can of Coffee: Prosecutors - The Messenger

Following a multi-year sexual assault investigation, a man has been arrested and indicted in two Denton Police Department cases where DNA evidence connected him to the offenses, according to a Denton PD news release.

On March 8, 2020, a woman reported a man entered her home in the 2400 block of Charlotte Street and tried to force her on the bed. The suspect fled after the victim resisted. Items of evidence were collected and analyzed at a lab, and an unknown DNA profile was entered into the Combined DNA Index System (CODIS) law enforcement database, according to police.

On Nov. 7, 2020, a man knocked on a womans door in the 2500 block of Charlotte Street. The suspect engaged the victim in casual conversation before forcing his way into her apartment and sexually assaulting her, according to the news release. A forensic examination kit was completed, and an unknown male DNA profile was obtained.

In December 2022, Denton PD was notified that the DNA profiles generated in these two cases were linked. Denton PD requested Dallas FBIs assistance with further DNA testing. In November 2023, these efforts resulted in the identification of a relative of the unknown suspect. Subsequent investigation into the family lineage led to the identification of 38-year-old Jason Warren, a current Marshall resident who previously lived in Denton.

With the assistance of the FBI and the Joint Harrison County Violent Crime and Narcotics Task Force, an additional DNA sample was obtained from Warren in December 2023. The DNA was taken to a lab for analysis, where it was concluded that Warrens DNA profile could not be excluded as a contributor to the DNA samples collected, according to the news release.

On Tuesday, Warren was indicted on two counts of sexually motivated Burglary of a Habitation Intend Other Felony, a first-degree felony. He was arrested two days later on the two Denton PD warrants, as well as a Criminal Trespass of a Habitation warrant from the Waco Police Department, according to police. He was booked into the Harrison County Jail on a total $210,000 bond before being transported to the Denton County Jail.

The investigation is ongoing. Anyone with information relating to these cases, or any unreported incidents, is encouraged to contact Detective Marqui Curtis at (940) 349-7727.

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DNA evidence leads to arrest of Denton sexual assault suspect - The Cross Timbers Gazette