Cabernet sauvignon’s long memory revealed

UC Davis study finds wine grape still carries a molecular memory of its ancestry after 400 years

University of California - Davis

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About 400 years ago, a cross between cabernet franc and sauvignon blanc gave birth to cabernet sauvignon. Today, cabernet sauvignon is the world’s most-planted wine grape, dominating vineyards from Napa to Bordeaux. New research from the University of California, Davis, reveals that the grape still carries a kind of gene memory of its parents.

Clones over the centuries

Unlike annual crops such as corn or wheat, grapevines are propagated from cuttings, not seeds. Each new vine is essentially a clone of its ancestor. That means every cabernet sauvignon vine grown today is genetically nearly identical to the original 17th-century plant.

“When you think about it, it’s unusual compared to most crops, which are continuously improved through breeding,” said Professor Dario Cantù, of the UC Davis Department of Viticulture and Enology. “We still cultivate plant material selected hundreds of years ago simply because cabernet sauvignon is so beloved.”

Scientists have long wondered whether chemical “switches” that help control how genes turn on and off, known as epigenetic marks, remain stable across hundreds of years of clonal reproduction. A new study led by Cantù and published in the journal Genome Biology shows they do.

“These are modifications that don’t alter the genetic code itself, but sit on top of it,” Cantù explained. “They can be inherited from your parents, but also change as you develop, as you interact with the environment or as you’re challenged by stress or disease.”

The team used advanced genome sequencing to assess the stability of these epigenetic modifications, which can influence traits like fruit quality and stress tolerance. The study is the first to show that this kind of molecular memory can persist for centuries in a clonally-propagated crop.

“It’s like sequencing identical twins at 90 and still detecting the parental signatures they inherited, even though their experiences — and much of their epigenome — has changed with age,” Cantù said.

New genetic analysis tools

To uncover this, scientists assembled highly detailed genome maps of cabernet sauvignon and its parent varieties, cabernet franc and sauvignon blanc. They analyzed multiple clones of each cultivar and developed a sophisticated genomic model, called a phased sequence graph, that captures subtle genetic and epigenetic variations more accurately than traditional reference genomes.

This new framework allowed researchers to trace how epigenetic marks are inherited along with DNA, and to understand how those marks affect gene activity. The study showed clonal plants may show minor differences from one vine to another, but their core epigenetic patterns or “gene memory” remain remarkably stable, even across centuries of clonal propagation.

Clues for climate resilience

This discovery could help scientists understand how long-lived crops adapt to their environments and whether those adaptations leave stable molecular marks. Cantù noted that if some epigenetic responses to heat, drought or other stresses prove to be stable, they could become targets in breeding. 

“If we know which stress-induced epigenetic changes persist, we could potentially introduce them by exposing plants to specific conditions and select vines that retain those beneficial marks over the long term — without altering their genetic makeup and preserving the defining traits of varieties like cabernet sauvignon.”

The framework developed for this research can be applied to many other perennial crops. By identifying which inherited markers endure, scientists hope to guide breeding programs for resilience and quality.

The discovery also carries a historical resonance for UC Davis. In 1997, UC Davis professor and geneticist Carole Meredith first identified cabernet franc and sauvignon blanc as the parents of cabernet sauvignon. Nearly three decades later, Cantù’s team has shown that the grape still bears molecular traces of that ancestral pairing.

“This work connects a UC Davis classic to a UC Davis first,” Cantù said. “It shows that even after centuries, cabernet sauvignon still holds the molecular memory of where it came from.”

Other authors include Noé Cochetel, Amanda M. Vondras and Rosa Figueroa-Balderas of UC Davis; Joel Liou and Paul Peluso of Pacific Biosciences.

This research was partially supported by the National Science Foundation, the U.S. Department of Agriculture National Institute of Food and Agriculture, the E. & J. Gallo Winery and the Ray Rossi Endowment in Viticulture and Enology.

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Journal

Genome Biology

DOI

10.1186/s13059-025-03858-2 

Article Title

Phased epigenomics and methylation inheritance in a historical Vitis vinifera hybrid

Article Publication Date

17-Nov-2025

 

Advanced ion-beam analysis reveals age variations in disputed Jordan codices

University of Surrey

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Jordan codices sample

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Credit: University of Surrey

Scientists have delivered the most detailed assessment yet of a set of disputed lead books known as the Jordan codices. With debate centred on whether they could date back to the early Christian period, a study led by the University of Surrey’s Ion Beam Centre has now shed new light on their origin. 

The study, published in Elsevier’s Nuclear Instruments and Methods in Physics Research B:  Beam Interactions with Materials and Atoms, finds that while some of the external pages of one of the books have been found to be contaminated by interactions with the environment, giving ambiguous age determination, inside pages are less contaminated and give clear scientific readings showing they are at least 200 years old, and possibly older. 

Working in collaboration with the University of Glasgow, the Scottish Universities Environmental Research Centre and the University of Vienna, researchers applied four analytical techniques to samples from the books. These included trace-element analysis, lead-isotope measurements, alpha-particle tests and radiogenic helium analysis to assess the composition and likely age of the lead. No single method could determine a definitive age, but together they provide a more detailed picture of how different parts of the codices were made.  

Tests run to date do not allow for a definitive date older than 200 years, but do not rule out that possibility, opening the door to further analysis with even more accurate future testing. Although the study could not determine that the codices were created in the early Christian period, it was also not possible to show that they were of modern origin. However, a truly definitive test to determine the true age of the manufacture of the books requires further investigation due to substantial non-uniformity of the samples and a much higher degree of background contamination than was expected.  

Professor Roger Webb, Director of Surrey’s Ion Beam Centre and lead author of the study, said: 

“Our aim throughout this work has been to bring rigorous, objective science to a subject that has attracted a great deal of speculation. I have been examining these materials since 2011, and as our analytical techniques have become more advanced, the picture has become more nuanced. Some parts of the codices appear modern, while others show characteristics of older lead that we cannot explain using contemporary materials. We have been unable to prove that they are truly ancient, but we have also not been able to prove that all of the objects are modern. We have seen some codices that have tested to be modern, but others clearly test as older than 200 years – thus as far back as our currently successful tests can go.” 

The Surrey Ion Beam Centre is the lead site for the UK National Ion Beam Centre and is equipped with state-of-the-art ion implanters and analysis facilities used across disciplines ranging from quantum technologies to materials science and biosciences.  

As part of its mission, the centre also applies ion-beam techniques to cultural heritage and art conservation, including studies of timbers from the Cutty Sark and analyses used to assess whether a ‘Leonardoesque’ painting could be attributed to Leonardo Da Vinci. These capabilities allow researchers to investigate materials at microscopic and atomic scales, providing the precision needed for studies such as this. 

Professor Webb added: 

“At the Surrey Ion Beam Centre, we routinely apply these techniques to everything from quantum devices to cultural heritage objects, and our study shows just how powerful ion-beam analysis can be. The fact that some key samples cannot be shown to be modern provides a strong scientific basis for scholars to take the codices seriously and for further, more advanced testing to be carried out.” 

The study was funded by the European Union’s Horizon 2020 research and innovation programme and by the EPSRC National Research Facility. As the results point to the need for deeper analysis, the research team is now looking to secure further investment and collaboration for the next phase of testing. 

[ENDS] 

Notes to editors 

• Professor Roger Webb is available for interview; please contact mediarelations@surrey.ac.uk to arrange. 

• The findings from the paper will be formally launched at an event in the House of Commons at 10:30am on 21 November, hosted by Brian Matthews MP, and with Professor Webb appearing as the keynote scientific speaker. For more information and to request an invitation, please contact Lara Alexander, Executive Officer, from the Numen Society, the event’s organisers, on: 

Scientists study a sample from the Jordan codices

Credit

University of Surrey

Journal

Nuclear Instruments and Methods in Physics Research

DOI

10.1016/j.nimb.2025.165947 

Article Title

On the analysis of lead objects in an attempt to determine their age

Article Publication Date

18-Nov-2025

MIT researchers use CT scans to unravel mysteries of early metal production

The team adapted the medical technique to study slag waste that was a byproduct of ancient copper smelting.

Massachusetts Institute of Technology

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Around 5,000 years ago, people living in what is now Iran began extracting copper from rock by processingore, an activity known as smelting. This monumental shift gave them a powerful new technology and may have marked the birth of metallurgy. Soon after, people in different parts of the world were using copper and bronzes (alloys of copper and tin, or copper and arsenic) to produce decorative objects, weapons, tools, and more.

Studying how humans produced such objects is challenging because little evidence still exists, and artifacts that have survived are carefully guarded and preserved.

In a paper published in PLOS One, MIT researchers demonstrated a new approach to uncovering details of some of the earliest metallurgical processes. They studied 5,000-year-old slag waste, a byproduct of smelting ore, using techniques including X-ray computed tomography, also known as CT scanning. In their paper, they show how this noninvasive imaging technique, which has primarily been used in the medical field, can reveal fine details about structures within the pieces of ancient slag.

“Even though slag might not give us the complete picture, it tells stories of how past civilizations were able to refine raw materials from ore and then to metal,” says postdoc Benjamin Sabatini. “It speaks to their technological ability at that time, and it gives us a lot of information. The goal is to understand, from start to finish, how they accomplished making these shiny metal products.”

In the paper, Sabatini and senior author Antoine Allanore, a professor of metallurgy and the Heather N. Lechtman Professor of Materials Science and Engineering, combined CT scanning with more traditional methods of studying ancient artifacts, including cutting the samples for further analysis. They demonstrated that CT scanning could be used to complement those techniques, revealing pores and droplets of different materials within samples. This information could shed light on the materials used by and the technological sophistication of some of the first metallurgists on Earth.

“The Early Bronze Age is one of the earliest reported interactions between mankind and metals,” says Allanore, who is also director of MIT’s Center for Materials Research in Archaeology and Ethnology. “Artifacts in that region at that period are extremely important in archaeology, yet the materials themselves are not very well-characterized in terms of our understanding of the underlying materials and chemical processes. The CT scan approach is a transformation of traditional archaeological methods of determining how to make cuts and analyze samples.”

A new tool in archaeology

Slag is produced as a molten hot liquid when ores are heated to produce metal. The slag contains other constituent minerals from the ore, as well as unreacted metals, which are commonly mixed with additives like limestone. In the mixture, the slag is less dense than the metal, so it can rise and be removed, solidifying like lava as it cools.

“Slag waste is chemically complex to interpret because in our modern metallurgical practices it contains everything not desired in the final product — in particular, arsenic, which is a key element in the original minerals for copper,” says Allanore. “There’s always been a question in archaeometallurgy if we can use arsenic and similar elements in these remains to learn something about the metal production process. The challenge here is that these minerals, especially arsenic, are very prone to dissolution and leaching, and therefore their environmental stability creates additional problems in terms of interpreting what this object was when it was being made 6,000 years ago.”

For the study, the researchers used slag from an ancient site known as Tepe Hissar in Iran. The slag has previously been dated to the period between 3100 and 2900 BCE and was loaned by the Penn Museum to Allanore for study in 2022.

“This region is often brought up as one of the earliest places where evidence of copper processing and object production might have happened,” Allanore explains. “It is very well-preserved, and it’s an early example of a site with long-distance trade and highly organized society. That’s why it’s so important in metallurgy.”

The researchers believe this is the first attempt to study ancient slag using CT scanning, partly because medical-grade scanners are expensive and primarily located in hospitals. The researchers overcame these challenges by working with a local startup in Cambridge that makes industrial CT scanners. They also used the CT scanner on MIT’s campus.

“It was really out of curiosity to see if there was a better way to study these objects,” Sabatini said.

In addition to the CT scans, the researchers used more conventional archaeological analytical methods such as X-ray fluorescence, X-ray diffraction, and optical and scanning electron microscopy. The CT scans provided a detailed overall picture of the internal structure of the slag and the location of interesting features like pores and bits of different materials, augmenting the conventional techniques to impart more complete information about the inside of samples.

They used that information to decide where to section their sample, noting that researchers often guess where to section samples, unsure even which side of the sample was originally facing up or down.

“My strategy was to zero in on the high-density metal droplets that looked like they were still intact, since those might be most representative of the original process,” Sabatini says. “Then I could destructively analyze the samples with a single slice. The CT scanning shows you exactly what is most interesting, as well as the general layout of things you need to study.”

Finding stories in slag

In previous studies, some slag samples from the Tepe Hissar site contained copper and thus seemed to fit the narrative that they resulted from the production of copper, while others showed no evidence of copper at all.

The researchers found that CT scanning allowed them to characterize the intact droplets that contained copper. It also allowed them to identify where gases evolved, forming voids that hold information about how the slags were produced.

Other slags at the site had previously been found to contain small metallic arsenide compounds, leading to disagreements about the role of arsenic in early metal production. The MIT researchers found that arsenic existed in different phases across their samples and could move within the slag or even escape the slag entirely, making it complicated to infer metallurgical processes from the study of arsenic alone.

Moving forward, the researchers say CT scanning could be a powerful tool in archaeology to unravel complex ancient materials and processes.

“This should be an important lever for more systematic studies of the copper aspect of smelting, and also for continuing to understand the role of arsenic,” Allanore says. “It allows us to be cognizant of the role of corrosion and the long-term stability of the artifacts to continue to learn more. It will be a key support for people who want to investigate these questions.”

This work was supported, in part, by the MIT Human Insight Collaborative (MITHIC).

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Written by Zach Winn, MIT News

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Journal

PLOS One

DOI

10.1371/journal.pone.0336603 

Article Title

“A novel application of X-ray computed tomography towards the characterization and interpretation of phase formations, mineral parageneses, and internal features in ancient copper slag from Tepe Hissar, Iran”

Manure digesters on farms carry limited benefits and potential harms

Review of scientific literature highlights technology’s shortcomings and risks

Johns Hopkins Bloomberg School of Public Health

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Manure digesters, touted as eco-friendly solutions for managing agricultural waste and reducing greenhouse gases, have limited capacity to reduce livestock-related greenhouse gas emissions, and entail potential hazards that may outweigh their benefits, according to a new paper from researchers at the Johns Hopkins Bloomberg School of Public Health.

Manure digesters are covered lagoons or large, sealed tanks that use bacteria to break down animal manure and other organic farm waste. The process yields methane-rich “biogas,” which can be a source of energy and a nutrient-rich “digestate” that can be applied as fertilizer. Critics, including environmental nonprofits and rural community advocates, have argued that digesters worsen pollution hazards and incentivize industrial animal agriculture with no meaningful climate benefit. 

The researchers evaluated the literature relevant to claims made by proponents and opponents, and found the benefits of manure digesters were overstated and risks and harms understated.

The paper was published online November 8 in Current Environmental Health Reports.

“Based on available evidence, we conclude that manure digesters should not be subsidized and promoted as a pro-environment, pro-public-health technology,” says study senior author Keeve Nachman, PhD, MHS, the Robert S. Lawrence Professor in Environmental Health and Engineering at the Bloomberg School and associate director of the Johns Hopkins Center for a Livable Future.

According to data from the Environmental Protection Agency, 460 manure digesters were in use or under construction on farms in the U.S. as of June 2024. Their rapid adoption has been supported by state and federal financing and subsidy programs. 

The digesters have been promoted as a “green” technology that reduces agricultural greenhouse gas emissions and serves as a renewable source of energy and fertilizer. The technology is particularly widespread in the dairy industry in California, where the state provides grants and other incentives to support digester construction and subsidizes the sale of biogas digesters.

For the study, the researchers reviewed the literature relating to manure digesters and their impacts.

“We didn’t come to this with a bias against manure digesters,” Nachman says. “We started with what was being said about them, which is that they may be a sustainable climate solution, and we went through the claims and did our best to figure out what evidence exists to support or refute them.”

The authors concluded that manure digesters are not a climate solution. Methane emissions from untreated manure only accounted for about 11% of total U.S. agricultural greenhouse gas emissions, and even in the best case, digesters reduce just a portion of that fraction. As the scientists note, even that minor impact could be diminished by biogas leaks and increases in nitrous oxide, another potent greenhouse gas.

The authors also note that digesters may often end up “pollution swapping”—for example, reducing methane emissions while increasing ammonia emissions, toxic byproducts from biogas flaring, and other pollutant releases into the environment.

“Digesters don’t appear to be the solution for agricultural contaminants that proponents would have everyone believe,” says Brent Kim, MHS, an assistant scientist at the Johns Hopkins Center for a Livable Future and one of the study’s authors.

The researchers observed that any sustained economic viability of digesters is likely possible only in large livestock operations. Promotion of digester technology, including with government subsidies, effectively incentivizes industrial-scale agriculture, which has been widely demonstrated in prior studies to pose elevanted risks from air and water pollution, animal-to-human disease transmission, and other public health hazards to rural populations.

The authors also note that promoting manure digesters may represent a missed opportunity to protect the environment and public health.

“When we adopt a measure to address a problem, even an ineffective measure, society and policymakers tend to move on as if the problem has been solved,” says Kim. “Evaluating the state of scientific evidence surrounding newly purported ‘solutions’ is a critical step when we’re dealing with complex, systemic problems for which silver bullets rarely exist.”

“Deconstructing the Livestock Manure Digester and Biogas Controversy” was written by co-first authors Allie Wainer, David Love, and Brent Kim; and by Jamie Harding, Qinfan Lyu, D’Ann Williams, Christopher Heaney, Benjamin Hobbs, and Keeve Nachman.

Funding for the study was provided by the Silicon Valley Community Foundation.

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Journal

Current Environmental Health Reports