The new approach uses samples from infected humans to allow real-time monitoring of pathogens circulating in human populations, and enable vaccine-evading bugs to be quickly and automatically identified. This could inform the development of vaccines that are more effective in preventing disease.

The approach can also quickly detect emerging variants with resistance to antibiotics. This could inform the choice of treatment for people who become infected — and try to limit the spread of the disease.

It uses genetic sequencing data to provide information on the genetic changes underlying the emergence of new variants. This is important to help understand why different variants spread differently in human populations.

There are very few systems in place to keep watch for emerging variants of infectious diseases, apart from the established COVID and influenza surveillance programmes. The technique is a major advance on the existing approach to these diseases, which has relied on groups of experts to decide when a circulating bacteria or virus has changed enough to be designated a new variant.

By creating ‘family trees’, the new approach identifies new variants automatically based on how much a pathogen has changed genetically, and how easily it spreads in the human population — removing the need to convene experts to do this.

It can be used for a broad range of viruses and bacteria and only a small number of samples, taken from infected people, are needed to reveal the variants circulating in a population. This makes it particularly valuable for resource-poor settings.

The report is published today in the journal Nature.

“Our new method provides a way to show, surprisingly quickly, whether there are new transmissible variants of pathogens circulating in populations — and it can be used for a huge range of bacteria and viruses,” said Dr Noémie Lefrancq, first author of the report, who carried out the work at the University of Cambridge’s Department of Genetics.

Lefrancq, who is now based at ETH Zurich, added: “We can even use it to start predicting how new variants are going to take over, which means decisions can quickly be made about how to respond.”

“Our method provides a completely objective way of spotting new strains of disease-causing bugs, by analysing their genetics and how they’re spreading in the population. This means we can rapidly and effectively spot the emergence of new highly transmissible strains,” said Professor Julian Parkhill, a researcher in the University of Cambridge’s Department of Veterinary Medicine who was involved in the study.

Testing the technique

The researchers used their new technique to analyse samples of Bordetella pertussis, the bacteria that causes whooping cough. Many countries are currently experiencing their worst whooping cough outbreaks of the last 25 years. It immediately identified three new variants circulating in the population that had been previously undetected.

“The novel method proves very timely for the agent of whooping cough, which warrants reinforced surveillance, given its current comeback in many countries and the worrying emergence of antimicrobial resistant lineages,” said Professor Sylvain Brisse, Head of the National Reference Center for whooping cough at Institut Pasteur, who provided bioresources and expertise on Bordetella pertussis genomic analyses and epidemiology.

In a second test, they analysed samples of Mycobacterium tuberculosis, the bacteria that causes Tuberculosis. It showed that two variants with resistance to antibiotics are spreading.

“The approach will quickly show which variants of a pathogen are most worrying in terms of the potential to make people ill. This means a vaccine can be specifically targeted against these variants, to make it as effective as possible,” said Professor Henrik Salje in the University of Cambridge’s Department of Genetics, senior author of the report.

He added: “If we see a rapid expansion of an antibiotic-resistant variant, then we could change the antibiotic that’s being prescribed to people infected by it, to try and limit the spread of that variant.”

The researchers say this work is an important piece in the larger jigsaw of any public health response to infectious disease.

A constant threat

Bacteria and viruses that cause disease are constantly evolving to be better and faster at spreading between us. During the COVID pandemic, this led to the emergence of new strains: the original Wuhan strain spread rapidly but was later overtaken by other variants, including Omicron, which evolved from the original and were better at spreading. Underlying this evolution are changes in the genetic make-up of the pathogens.

Pathogens evolve through genetic changes that make them better at spreading. Scientists are particularly worried about genetic changes that allow pathogens to evade our immune system and cause disease despite us being vaccinated against them.

“This work has the potential to become an integral part of infectious disease surveillance systems around the world, and the insights it provides could completely change the way governments respond,” said Salje.

Rapid detection of dangers and threats is important for personal safety. Since our ancestors first appeared, snakes have posed a deadly danger to primates, including humans. Even monkeys and human infants who have never encountered a snake react to pictures of them, demonstrating our innate fear of these creatures.

Kawai’s first experiment demonstrated that monkeys exhibited an immediate response to images of snakes but not to images of salamanders, implying a specific fear of snakes. On the basis of this observation, he wondered what would happen if he edited the images of the salamanders to have snakeskin without changing anything else. Would monkeys respond to the skin, or would they recognize the harmless salamander in snake clothing?

To answer this question, Kawai presented monkeys that had never seen a real snake with nine images on a board and trained them to find the one that was different to receive a reward. When presented with a single snake amidst a group of salamanders, monkeys exhibited a faster response time to locate the snake compared to identifying a salamander among snakes. This observation suggests that the monkeys had a strong response to the potentially dangerous reptile.

However, when Kawai showed the edited images of salamanders with snakeskin to monkeys, they reacted to the altered images of the harmless creature equally fast, or even faster, than to the snake.

“Previously we demonstrated that humans and primates can recognize snakes quickly; however, the critical visual feature was unknown,” Kawai said. “The monkeys did not react faster to salamanders, a species that shares a similar elongated body and tail with snakes, until the images were changed to cover them with snakeskin.” This suggests that the monkeys were most threatened by the scales.

“This may be because during evolution our primate ancestors evolved a visual system to identify scales, which are characteristic of snakes,” he continued. “These insights into primate evolution will likely improve our understanding of vision and brain evolution in animals, including ourselves.”

Humans create a lot of waste, but when you throw something away, how much do you know about where it goes or how it’s handled? This article is the second in a five-part series that explores what happens to the tons of materials we discard.

Around half of the garbage generated in the United States ends up in the landfill — and these days, more than a little of the recycling gets rerouted there as well.

Thinking about all that waste going to the dump can be depressing, but it’s is not quite the environmental nightmare many environmentalists think. Here’s some background on the modern sanitary landfill and how it works.

The Dump

Humans have been dumping their garbage for as long as they have been generating it.

Prehistoric middens are important sources of information to archaeologists and anthropologists. Ancient Rome had municipal waste collection. But the first municipal sanitary landfill was built in Fresno in the late 1930s.

Dumps proliferated in the U.S. throughout the mid-20^th century. Some of them, like the one in Fresno, were true sanitary landfills — that is, they layered refuse and dirt in trenches, compacted them both, and then covered the filled areas each day to minimize rodent and debris problems. Some of them lined the holes or trenches with clay before filling them in order to minimize leaching. However, many of them were no more than an open hole in the ground that was covered with dirt only when filled — they were real dumps.

Sanitary Landfills

In 1965, the federal government established an office to manage garbage with the Solid Waste Disposal Act. This act, with many subsequent emendations, still governs waste disposal in the U.S.

By the mid-1970s, states were required to establish waste management regulations. Today, the Resource Conservation and Recovery Act (RCRA) creates the framework for the proper management of all types of solid waste. Subtitle D of RCRA establishes the stringent design, operation, and closure requirements for sanitary landfills. Subtitle D does not allow new landfills to be built in environmentally sensitive areas.

A modern sanitary landfill is a complex structure that isolates trash from the surrounding environment until it becomes inert. Landfills comprise a bottom liner made from clay and durable synthetic plastic; a leachate collection system to remove liquids; a stormwater management system that keeps surface water from flowing into the garbage; and a methane collection system that removes landfill gas as it is generated.

The leachate, stormwater, and gas collection systems are constantly monitored. Landfills are required to budget for monitoring and maintenance for decades after closure to ensure that no harmful chemicals escape.

How Landfills Work

Landfills are divided into sections, called cells, that are filled and closed sequentially. Cells can be anywhere from 2,500 square feet up to 20 acres or more, depending on the size of the landfill. Nowadays, the tendency is toward larger cells and landfills.

When a new cell is built, the hole is lined with 2 feet of compacted clay, a durable plastic liner, and a nonporous geotextile membrane. That outliner lining is covered with a layer of granular material that helps funnel liquids into a leachate collection system. Up to two feet of soil is layered on top of that before garbage is added. Often, the first layer of garbage will comprise special materials such as old mattresses, to further protect the lining.

Once the cell is constructed, municipal solid waste is dumped inside and run over by compacting tractors. At the end of each day, the garbage must be completely covered to minimize odors, deter pests, limit rainwater runoff, prevent waste fires, and discourage scavenging. Daily cover most often consists of six inches of soil. This can fill up a cell more quickly, so alternate daily covers, such as geotextile cloth or even certain types of waste like ash or tires, are sometimes used to maximize efficiency. Wells and trenches for collecting landfill gas are installed at regular intervals as the landfill fills.

This diagram from Advanced Disposal illustrates the elements of a modern sanitary landfill:

When the cell is completely full, it receives a final cover, or cap, much like the bottom liner. The cap will be further covered by topsoil, which will be seeded with vegetation for the duration of the decades-long post-closure monitoring period.

Landfill Gas

By far the largest environmental impact of landfilling is the production of landfill gas (LFG).

Although landfills are designed to minimize decomposition, organic materials do eventually break down in a landfill. When they do, LFG is the byproduct. LFG is roughly half methane and half carbon dioxide, and as such, it is a powerful greenhouse gas. All landfills are required to collect LFG. At most landfills, the collected gas is burned off at flare stations, making landfills the third-largest source of human-related methane emissions in the United States.

Nevertheless, LFG can be utilized to make landfills greener. Instead of burning it, some landfills are converting the LFG they collect into usable energy. Sometimes the collected gas is used to power boilers or furnaces, or it can be refined into renewable natural gas. Most often, it is used to generate electricity.

Whatever the end use, LFG-to-energy projects can capture 60% to 90% of the LFG generated at a landfill and displace the same amount of energy from nonrenewable sources.

Limitations of Landfilling

Old landfills, which were unlined or only lined with clay, which could crack, also did not set aside money for post-closure monitoring. As a result, many continue to leach chemicals into nearby soil and groundwater. Current landfills are much better at containing and monitoring their contents. But there is always a risk of future failure, and there is some evidence that all landfills leak.

Modern landfills are huge and are constantly improving their ability to compact waste, but eventually, even the largest, most efficient landfills will be full. When existing landfills run out of room, finding space for new ones may be impossible.

Landfills must be sited in areas with safe hydrogeological features — that is, away from faults, wetlands, flood plains, and other sensitive areas. They require vast rural sites and few communities are enthusiastic hosts to waste disposal sites of any kind.

When it comes to disposing of waste, the modern sanitary landfill is hard to beat. But it still has environmental impacts. No disposal method can ever be perfect, because however cleanly we dispose of things, all disposal is waste.

The dump may not be the dirty place we imagine, but it is still impossible to ever truly throw something away.

Read part three of this five-part series, How Commercial Composting Works. 

Editor’s Note: Originally published on October 22, 2019, this article was updated in December 2024.

Electron transfer, critical to processes such as cellular respiration and energy harvesting in plants, has long posed challenges to scientists due to the complex quantum interactions involved. Current computational techniques often fall short of capturing the full scope of these processes. The multidisciplinary team at Rice, including physicists, chemists and biologists, addressed these challenges by creating a programmable quantum system capable of independently controlling the key factors in electron transfer: donor-acceptor energy gaps, electronic and vibronic couplings and environmental dissipation.

Using an ion crystal trapped in a vacuum system and manipulated by laser light, the researchers demonstrated the ability to simulate real-time spin dynamics and measure transfer rates across a range of conditions. The findings not only validate key theories of quantum mechanics but also pave the way for novel insights into light-harvesting systems and molecular devices.

“This is the first time that this kind of model was simulated on a physical device while including the role of the environment and even tailoring it in a controlled way,” said lead researcher Guido Pagano, assistant professor of physics and astronomy. “It represents a significant leap forward in our ability to use quantum simulators to investigate models and regimes that are relevant for chemistry and biology. The hope is that by harnessing the power of quantum simulation, we will eventually be able to explore scenarios that are currently inaccessible to classical computational methods.”

The team achieved a significant milestone by successfully replicating a standard model of molecular electron transfer using a programmable quantum platform. Through the precise engineering of tunable dissipation, the researchers explored both adiabatic and nonadiabatic regimes of electron transfer, demonstrating how these quantum effects operate under varying conditions. Additionally, their simulations identified optimal conditions for electron transfer, which parallel the energy transport mechanisms observed in natural photosynthetic systems.

“Our work is driven by the question: Can quantum hardware be used to directly simulate chemical dynamics?” Pagano said. “Specifically, can we incorporate environmental effects into these simulations as they play a crucial role in processes essential to life such as photosynthesis and electron transfer in biomolecules? Addressing this question is significant as the ability to directly simulate electron transfer in biomolecules could provide valuable insights for designing new light-harvesting materials.”

The implications for practical applications are far-reaching. Understanding electron transfer processes at this level could lead to breakthroughs in renewable energy technologies, molecular electronics and even the development of new materials for quantum computing.

“This experiment is a promising first step to gain a deeper understanding of how quantum effects influence energy transport, particularly in biological systems like photosynthetic complexes,” said Jose N. Onuchic, study co-author, the Harry C. and Olga K. Wiess Chair of Physics and professor of physics and astronomy, chemistry and biosciences. “The insights we gain in this type of experiment could inspire the design of more efficient light-harvesting materials.”

Peter G. Wolynes, study co-author, the D.R. Bullard-Welch Foundation Professor of Science and professor of chemistry, biosciences and physics and astronomy, emphasized the broader significance of the findings: “This research bridges the gap between theoretical predictions and experimental verification, offering an exquisitely tunable framework for exploring quantum processes in complex systems.”

The team plans to extend its simulations to include more complex molecular systems such as those involved in photosynthesis and DNA charge transport. The researchers also hope to investigate the role of quantum coherence and delocalization in energy transfer, leveraging the unique capabilities of their quantum platform.

“This is just the beginning,” said Han Pu, co-lead author of the study and professor of physics and astronomy. “We are excited to explore how this technology can help unravel the quantum mysteries of life and beyond.”

The study’s other co-authors include graduate students Visal So, Midhuna Duraisamy Suganthi, Abhishek Menon, Mingjian Zhu and research scientist Roman Zhuravel.

This research was made possible thanks to the Welch Foundation Award C-2154, the Office of Naval Research Young Investigator Program (No. N00014-22-1-2282), a National Science Foundation CAREER Award (No. PHY-2144910), the Army Research Office (W911NF22C0012), the Office of Naval Research (No. N00014-23-1-2665), the NSF (PHY-2207283, PHY-2019745 and PHY-2210291) and the D. R. Bullard-Welch Chair at Rice (No. C0016). The authors acknowledge that this material is based upon work supported by the U.S Department of Energy, Office of Science, Office of Nuclear Physics under the Early Career Award No. DE-SC0023806. The isotopes used in this research were supplied by the U.S. Department of Energy Isotope Program managed by the Office of Isotope R&D and Production.