Wednesday, April 16, 2025

 

Cornell researchers explore plant-environment interactions with grapevines in 3 states


Cornell University





ITHACA, N.Y. – A new project led by Cornell University researchers will explore how genetically identical grapevines adapt to differences in temperature, humidity, soils and other environmental factors in New York, Missouri and South Dakota.

The $2.3 million project, funded by the National Science Foundation, will aid grape growers and winemakers as they cope with increasingly erratic climate conditions by uncovering the most adaptable varieties.

“A chardonnay vine in New York and a chardonnay vine in France are genetic twins, which means you can specifically explore how the plant genome interacts with its environment,” said Jason Londo, associate professor. “There are lots of different species we could use to do this study, but grapes are the perfect plant to use because, in winemaking, we already have a cultural passion around this concept of how the environment influences the way genes are expressed: terroir.”

From the French for “lands,” terroir refers to the various ways that a vineyard’s climate, farming practices, soil composition and other factors influence a wine’s flavor.

“Scientifically, we call terroir ‘plasticity’ – the ability for a species to adapt to many different environments and climate conditions,” Londo said. “Those who enjoy wine usually think of terroir in terms of the juice or wine itself, but in truth, the leaves are optimizing, the roots are optimizing, the branches are optimizing – there’s terroir everywhere.”

The project will also look at which genes and gene clusters can be modified under different environmental pressures and influence how an organism’s DNA is expressed. These findings could inform research and plant breeding on any crop that reproduces asexually, including apples, cherries, peaches, potatoes, bananas and strawberries.

“We want to know which components of the genome are under the greatest manipulation by the environment,” Londo said. “With that information, you could think about how to stimulate the genome with certain pressures, or maybe you could breed for those components that are more sensitive or more resistant to environmental pressures, depending on the outcome you want to achieve in the vineyard, such as drought resistance or heat tolerance.”

Londo is leading the project at Cornell but working with colleagues at Pennsylvania State University, South Dakota State University, Missouri State University and the nonprofit Donald Danforth Plant Science Center in Olivette, Missouri.

The researchers created a nursery of Marquette grapevines grafted onto five different commercial rootstocks and 220 newly developed rootstocks. Those young vines have been cloned and transplanted in three different locations, in New York, Missouri and South Dakota.

Assessing how genetically identical plants perform in the cold and wet climate of New York, the hot and wet environment of Missouri, and the cold and dry environment of South Dakota will enable researchers to make recommendations tailored to grape growers in each location.

For additional information, read this Cornell Chronicle story.

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Microbes in Brooklyn Superfund site teach lessons on fighting industrial pollution



NYU Tandon School of Engineering-led research team discovers unprecedented genetic adaptations in Gowanus Canal organisms, revealing a potential new approach for cleaning contaminated waters and recovering valuable resources



NYU Tandon School of Engineering







Using advanced DNA sequence analysis, a research team led by NYU Tandon School of Engineering's Assistant Professor Elizabeth Hénaff has discovered that tiny organisms in Brooklyn's highly contaminated Gowanus Canal have developed a comprehensive collection of pollution-fighting genes.

The findings were published in the Journal of Applied Microbiology on April 15, 2025.

The team identified 455 species of microorganisms wielding 64 different biochemical pathways to degrade pollutants and 1,171 genes to process heavy metals. This suggests the potential of a cheaper, more sustainable, and less disruptive method for cleaning contaminated waterways than the current oft-used dredging operations. 

The researchers also discovered 2,300 novel genetic sequences that could enable microbes to produce potentially valuable biochemical compounds for medicine, industry, or environmental applications.

"We found what amounts to nature's own toxic cleanup manual, but with a crucial warning," said Hénaff, who sits in NYU Tandon's Technology, Culture and Society Department and is a member of Tandon's Center for Urban Science + Progress. "These microbes have stories to tell that go beyond scientific data."

To communicate these stories effectively, Hénaff and colleagues created CHANNEL, an immersive installation at BioBAT Art Space in Brooklyn, New York featuring sculpture, prints, sound, and projections alongside over 300 gallons of native Gowanus sediment and water that has been growing over the last 9 months. The Living Interfaces Lab, Hénaff's research group, uses methods from sciences and arts to address pressing urban issues.

"While more research is needed to understand how to cooperate with these organisms effectively, the discovery of such genetic tools for pollution cleanup may offer valuable lessons for environmental restoration worldwide," Hénaff said. "I consider artistic research to be a key component in not just illustrating but also informing our scientific research." The work is on view at the exhibit’s closing event on April 18, 2025. 

The team discovered genes for resistance to eight different classes of antibiotics in the canal microbes, with some coming from human gut bacteria that enter the canal during Combined Sewer Overflows – when heavy rainfall causes stormwater and untreated sewage to discharge directly into waterways. Other resistance genes were found in native aquatic species.

“The long-term coexistence of microbial communities from sewage and the natural canal environment is expected to enhance the rates of horizontal transfer of a wide array of genetic elements, and as such merits our attention for public health monitoring and surveillance as environmental ‘superbug’ reservoirs,” said Sergios-Orestis Kolokotronis, a study co-author and assistant professor of epidemiology and infectious diseases at SUNY Downstate Health Sciences University.

Despite these concerns, the study also reveals promising potential benefits. While the pollutant-degrading microbes in the canal can break down contaminants, their natural processes are too slow for practical cleanup. Understanding their genetic adaptations could help scientists develop faster methods, either by isolating specific microbes for treatment or enhancing their abilities. 

Some classes of contaminants such as heavy metals are also valuable materials for industry, and bioremediation methods could be adapted to resource recovery for re-use, not just removal. 

To make its discoveries, the team collected samples from 14 locations along the canal's 1.8-mile length, gathering both surface sediment and deep core samples reaching 11.5 feet below the canal floor. They found microbes capable of breaking down many historical pollutants, including petroleum products, PCBs, and industrial solvents.

The findings come as the Environmental Protection Agency continues its $1.5 billion dredging and capping operation at the canal, removing contaminated sediment and sealing remaining pollution under clean material.

The team's current study builds on prior research spanning a decade to understand the Gowanus Canal microbiome. The project began in 2014 when the current study’s co-authors Ian Quate of Fruit Studio and Matthew Seibert of the University of Virginia led the first sediment sampling, processing samples at community bio lab Genspace with study co-author Ellen Jorgensen of Biotech without Borders. 

The DNA was sequenced in the lab of study co-author Christopher Mason – WorldQuant Professor of Genomics and Computational Biomedicine at Weill Cornell Medicine – as part of the Pathomap Project, now expanded to cities around the world in the metagenomics of subways and urban biomes (MetaSUB) project.

“The hardy microbial organisms of the Gowanus Canal have a unique genetic catalog of survival, which provides a roadmap for adaptation and directed evolution that we can use in polluted sites around the world,” said Mason, who serves as co-founder and Director of the MetaSUB Consortium. 

Later, lead author Hénaff's team collected more samples through the BKBioReactor project while study co-author Kolokotronisgathered core samples. Bioinformatic approaches implemented by study co-authors Chandrima Bhattacharya of Weill Cornell Medicine and Rupobrata Panja of Rutgers University allowed the team to identify microbes breaking down industrial pollutants in the canal's thick sediment.

This research was supported by funding from WorldQuant Foundation, the Pershing Square Foundation, National Aeronautics and Space Administration, National Institutes of Health, National Science Foundation and NYU Tandon.

 CSI

Researchers introduce a brand-new method to detect gunshot residue at the crime scene



Crime scene investigation may soon become significantly more accurate and efficient




Universiteit van Amsterdam

Photoluminescent lead detection in gunshot residue 

image: 

Photoluminescent lead detection in gunshot residue. (A) Shooting firearms produces gunshot residue that typically contains lead particulates. (B) Methyl ammonium bromide in the reagent reacts with lead in gunshot residue to form perovskite, which emits bright green light upon illumination with UV light. (C) Typically, the combustion plume and bullet wipe contaminate objects such as clothing, hands, and targets with gunshot residue, which is rapidly visualized with photoluminescent lead detection to assess suspect involvement and to assist crime scene reconstruction. Image provided by AMOLF.

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Credit: AMOLF




Crime scene investigation may soon become significantly more accurate and efficient thanks to a new method for detecting gunshot residues. Researchers from the groups of Wim Noorduin (AMOLF / University of Amsterdam) and Arian van Asten (University of Amsterdam) developed the technique that converts lead particles found in gunshot residue into a light-emitting semiconductor. The method, published last month in 'Forensic Science International', is faster, more sensitive, and easier to use than current alternatives. Forensic experts at the Amsterdam police force are already testing it in actual crime scene investigations.

Gunshot Residue Clues
The innovative light-emitting lead analysis method offers exciting opportunities for crime scene investigations. When a weapon is fired, it leaves gunshot residue containing lead traces on the surrounding environment, including clothing and skin. Bente van Kralingen, a forensic expert at the Amsterdam Police, explains: "Obtaining an indication of gunshot residue at the crime scene is a major advantage, helping us answer key questions about shooting incidents. For instance, determining whether the damage found could have been caused by a bullet and determining the relative position of a person who might have been involved in a shooting incident. We test for lead traces on possible bullet holes and a suspect’s or a victim’s clothing or hands."

Currently, police send all samples to the lab for analysis. However, the methods used there are often time-consuming, labor-intensive, and require expensive equipment. "We’re excited about the tests we’re conducting, and hopefully this will allow us to use the light-emitting method soon in actual court cases as evidence," says Bente.

Semiconductor Technology
The new analysis method builds on recent advances in perovskite research. Perovskites are a promising material used in applications ranging from solar cells to LEDs. A few years ago, the research group of Wim Noorduin developed an easy-to-use lead detection method based on perovskite technology. In this method a reagent converts lead containing surfaces into a perovskite semiconductor. Shining with a UV lamp will make the newly formed semiconductor emit a bright green glow visible to the naked eye—making even small traces of lead easily detectable. 

In 2021, Wim Noorduin and Lukas Helmbrecht (formerly PhD student in the group) established a start-up company to develop this lead testing method into a practical lead detection kit: Lumetallix. Over the past years, many people worldwide have been investigating their surroundings using the Lumetallix test kit. They report positive tests in all sorts of objects, for example: dinner plates, beer glasses, but also in paint dust at construction sites. 

Lukas Helmbrecht developed an altered version of the Lumetallix reagent for the forensic application: one that reacts especially well with lead atoms in gunshot residue and produces a long-lasting green glow. 

At the shooting range
To validate the effectiveness of this method, the researchers conducted a series of controlled experiments. PhD students Kendra Adelberg and Arno van der Weijden (AMOLF/UvA) visited a shooting range in Amsterdam. Kendra: "We used standard 9 mm full metal jacket bullets and fired them from two different pistols at cotton cloth targets placed at various distances. After applying the reagent, we visualized the gunshot residue patterns. The results revealed well-defined luminescent patterns that were clearly visible to the naked eye, even at extended distances," says Kendra.

During their experiments, Kendra and her colleagues made two other remarkable discoveries. Firstly, unlike other methods, the new light-emitting technique remains effective even after extensive washing of the shooter’s hands. This is important for forensic investigations, as suspects often try to tamper with or remove evidence of their involvement. Secondly, bystanders standing approximately two meters away from the shooter also tested positive for lead traces on their hands. "These findings provide valuable pieces of the puzzle when reconstructing a shooting incident. But, a positive test also needs to be carefully interpreted, it does not automatically mean that you fired a gun." says Kendra.

Who Will Benefit?
The researchers believe this new method will be especially beneficial to first responders, such as police officers, who can use it to rapidly screen potential suspects and witnesses to secure crucial evidence.
Beyond forensic applications, the team is also exploring the potential of this light-emitting method to detect lead contamination in environmental samples such as water and soil. Since lead is toxic and harmful to the environment, this research could have broader implications for environmental monitoring and public health.

Reference 
Kendra Adelberg, Arno van der Weijden, Lukas Helmbrecht, Diede Blaauw, Arian C. van Asten, Willem L. Noorduin, Perovskite-based photoluminescent detection of lead particles in gunshot residue, Forensic Science International, 370, 112415, March 9th (2025). https://doi.org/10.1016/j.forsciint.2025.112415


(A) Color marked areas for gunshot residue testing. (B) Direct lead testing on shooter’s hand showing bright green luminescence. (C) Lead testing on the hand of bystander after shooting showing moderate luminescence, and (D) weak luminescence after washing with water and soap. (E) Bystander’s hand after thorough washing still showing clear green luminescence on nails. (F) Indirect lead testing by wiping glass fiber cloth over clothing of a bystander shows bright luminescence. (G) Indirect testing of bystander’s shoe sole. (H) SEM stub after stubbing shooter’s hand showing green luminescence where lead is present. Image provided by AMOLF.

Credit

AMOLF

The new method for detecting g [VIDEO] 

 

Our DNA is at risk of hacking - warn scientists



First comprehensive review of cyber-biosecurity risks released


University of Portsmouth




Next-generation DNA sequencing (NGS)  - the same technology which is powering the development of tailor-made medicines, cancer diagnostics, infectious disease tracking, and gene research - could become a prime target for hackers.

study, published in IEEE Access, highlights growing concerns over how this powerful sequencing tool - if left unsecured - could be exploited for data breaches, privacy violations, and even future biothreats.

Led by Dr Nasreen Anjum from the University of Portsmouth’s School of Computing, it is the first comprehensive research study of cyber-biosecurity threats across the entire NGS workflow.

NGS is a cornerstone of modern biotechnology, enabling rapid and cost-effective DNA and RNA sequencing that supports important advances in cancer research, drug development, agricultural innovation and forensic science.

The sequencing process within NGS workflow involves a series of complex, interdependent steps - from sample preparation and sequencing to data analysis and interpretation - each involving highly specialised instruments, technologies, software, and connected systems.

While the steps are essential for generating accurate results, they also open up multiple points of vulnerability. As many DNA datasets are openly accessible online, the study warns it is possible for cybercriminals to misuse the information for surveillance, manipulation, or malicious experimentation.

Dr Anjum said: "Our work is a wake-up call. Protecting genomic data isn’t just about encryption - it’s about anticipating attacks that don’t yet exist. We need a paradigm shift in how we secure the future of precision medicine."

The research was carried out in collaboration with colleagues from the Department of Computer Science at Anglia Ruskin University in Cambridge, the University of Gloucestershire’s Department of Cyber Security and ComputingNarjan University’s Department of Computer Science and Emerging Research Laboratory, and the Department of Microbiology at Shaheed Benazir Bhutto Women University.

Dr Mahreen-Ul-Hassan, microbiologist and co-author from the Shaheed Benazir Bhutto Women University, said: "Genomic data is one of the most personal forms of data we have. If compromised, the consequences go far beyond a typical data breach.”

The research team identified new and emerging methods that hackers and those with malicious intent could use to exploit or attack systems, such as synthetic DNA-encoded malware, AI-driven manipulation of genome data, and identity tracing through re-identification techniques. These threats go beyond typical data breaches, posing risks to individual privacy, scientific integrity, and national security.

Dr Anjun added: “Despite its importance, cyber-biosecurity remains one of the most neglected and poorly understood research disciplines and is leaving a critical gap in global biosecurity. To make sure our DNA information stays safe and is used only for good, we’re urging more research and collaboration to find ways to keep this powerful technology secure.

“Governments, regulatory bodies, funding agencies, and academic institutions must prioritise this field and invest in dedicated research, education, and policy development before it’s too late.

“Without coordinated action, genomic data could be exploited for surveillance, discrimination, or even bioterrorism. Current protections are fragmented, and vital collaboration between disciplines is lacking. Key to successful prevention will be interdisciplinary cooperation between computer scientists, bioinformaticians, biotechnologists, and security professionals - groups that rarely work together but must align.

“Our research lays the foundations for improving biosecurity by providing a single, clear list of all the possible threats in the entire next-generation sequencing process.”

The paper also recommends practical solutions, including secure sequencing protocols, encrypted storage, and AI-powered anomaly detection, creating a foundation for much stronger cyber-biosecurity.

The study was funded by the British Council’s UK-Saudi Challenge Fund and a Quality Related Research Grant from the University of Portsmouth. 

 

Climate-related trauma can have lasting effects on decision-making, study finds



Researchers found that wildfire survivors were less likely to stick with choices that offered greater long-term rewards.



University of California - San Diego





A new study from University of California San Diego suggests that climate trauma — such as experiencing a devastating wildfire — can have lasting effects on cognitive function. The research, which focused on survivors of the 2018 Camp Fire in Northern California, found that individuals directly exposed to the disaster had difficulty making decisions that prioritize long-term benefits. The findings were recently published in Scientific Reports, part of the Nature portfolio of journals.

“Our previous research has shown that survivors of California’s 2018 Camp Fire experience prolonged symptoms of post-traumatic stress disorder, anxiety and depression alongside hyper-distractibility,” said Jyoti Mishra, Ph.D., senior author and an associate professor at UC San Diego’s School of Medicine and co-director of the University of California Climate Resilience Initiative. “This new study suggests that climate trauma may also impact important cognitive abilities of decision-making and underlying brain function.”

Wildfires, which have become increasingly frequent due to climate change, are known to affect both physical and mental health. This study provides new evidence that cognitive function — particularly decision-making — is also impacted.

The study involved 75 participants, divided into three groups:

  • Directly exposed to the fire (n=27)
  • Indirectly exposed (witnessed the fire but were not directly affected, n=21)
  • Non-exposed controls (n=27)

All participants completed a decision-making task with monetary rewards while undergoing Electroencephalogram (EEG) brain recordings. Researchers evaluated their Win-Stay behavior, measuring how often they continued selecting the option with the highest long-term rewards.

Researchers found that wildfire survivors were significantly less likely to stick with choices that offered long-term rewards, a behavior they tracked with a choice metric known as “Win-Stay.” Brain recordings revealed a possible reason why. EEG brain scans taken while participants engaged in the decision-making tasks showed heightened activity in the parietal brain region, and localized to the posterior cingulate cortex (PCC) — a brain region associated with deep thought and rumination.

“It was clear that brains of study participants directly exposed to wildfires — as opposed to those not exposed — became significantly hyper-aroused when trying to make proper decision choices but they were still unable to execute the task well,” said Jason Nan, a UC San Diego bioengineering graduate student and study first author. “We interpret this to mean that their brain was attempting to focus on making sound decisions, but they were unable to.”

Understanding how climate trauma affects decision-making could lead to new diagnostic tools and personalized treatments for those impacted. One potential intervention is mindfulness and compassion training, which has shown promise in suppressing ruminating thoughts and thereby, mitigating the effects of trauma. Mobilizing early post-disaster intervention resources is a key priority of the California Climate Resilience Initiative.

As climate disasters become more frequent and more severe, researchers emphasize the need to: study pre- vs. post-disaster cognitive changes, investigate long-term effects of repeated exposure to climate trauma and develop scalable mental health interventions for affected communities.

Co-authors include: Satish Jaiswal and Dhakshin Ramanathan from UC San Diego, and Mathew C. Withers from Utah Valley University. 

The study was funded, in part, by the Tang Prize Foundation, the Hope for Depression Research Foundation and the CA CARES (Climate Action, Resilience, and Environmental Sustainability) proof of concept funds.

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