Fishing for phages in Lund University’s Botanical Gardens

Lund University

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Vasili Hauryliuk

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Credit: Kennet Ruona

Kompetensportalen, Lucat, Lupin, Lubas and LUCRIS. Those are the names of some of Lund University’s administrative systems. They are now also the names of five new bacteriophages that have recently been discovered in the ponds of Lund University’s Botanical Gardens.

Bacteriophages – often abbreviated to phages – are viruses that attack bacteria. Phages are astonishingly effective assassins – these viruses wipe out 20 percent of all bacteria on Earth every day. The ongoing battle with bacteria has made phages humanity’s natural ally when it comes to treating bacterial infections The growing urgency of combating antibiotic resistance has made phage research – particularly the development of phage-basered therapies – more relevant than ever.

“Bacteria are under constant attack from phages. Phages are picky about their prey – different phages infect different species of bacteria, sometimes only a specific strain. The challenge lies in assembling the right “collection” of phages, each one a precision weapon calibrated to infect and obliterate only the intended strain of bacteria,” says Vasili Hauryliuk, professor of medical biochemistry at Lund University.

Finding the right bacteriophage for the right bacterial strain is a major challenge. Natural bacterial strains are also constantly changing, thanks to mutations among other things. This means that a phage that has previously been effective may become ineffective.

At Lund University, Sweden’s first international course in phage biology has been completed. Doctoral students from across Europe came to attend lectures by leading phage researchers, exchange ideas, and, of course, to hunt for new phages and find the right precision weapons with which to attack various bacteria. Phages thrive wherever bacteria are found, which often means ponds and watercourses that are rich in organic material. The ponds in Lund University’s Botanical Gardens – both indoors and out – therefore proved to be perfect locations for phage fishing. However, to catch phages requires the right “bait”, which means the right bacterial strain to attract the virus.

“Collecting phages is like fishing in that you never know what you will end up with on the hook. Since it is fairly simple to isolate bacteriophages from ponds – and Lund has several – we combined research and education and went fishing for phages,” says Marcus Johansson, associate researcher at Lund University and one of the course coordinators. He is also last author on the study.

The researchers used a strain of E. coli, a common gut bacterium that can become a lethal pathogen. When a laboratory E. coli strain is grown in flasks without shaking, it becomes motile by developing a so-called flagellum – a “tail” that the bacterium uses to propel itself and explore the environment. Some phages specifically recognise the “tail” to infect. Using a motile E. coli strain, researchers managed to catch a new “tail-loving” phage from the Botanical Gardens’ ponds. Remarkably, this phage can kill not only E. coli, but also another motile bacterial species –Salmonella.

“One fun part about phage fishing is that you can name the new viruses – and phage names can be pretty weird! We wanted our phages to have names that were linked to Lund University and the tail-loving phage was named “Kompetensportalen”. We named two other phages Lucat and Lupin, after the University’s staff directory and its purchasing and invoicing tool, respectively” explains Vasili Hauryliuk.

The total of five newly-discovered bacteriophages from the Botanical Gardens are now serving as ambassadors for Lund University in the world of international phage research. The phage, “Kompetensportalen” has quickly attracted attention and phage researchers from outside Sweden have already expressed an interest in it.

“The diversity of bacteriophages discovered in the Botanical Gardens’ ponds is particularly fascinating as the Gardens’ greenhouses are currently being renovated. It underlines the great diversity in biology and our role as a centre for education and research. It is exciting to discover that our ponds are home to more than just plants,” says Allison Perrigo, director of Lund University’s Botanical Gardens.

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Journal

Microbiology Spectrum

DOI

10.1128/spectrum.02274-25 

Method of Research

Experimental study

Subject of Research

Not applicable

Article Title

Characterization of five environmental phages infecting Escherichia coli K-12 isolated during a phage biology training course

Article Publication Date

26-Nov-2025

 

Evidence suggests early developing human brains are preconfigured with instructions for understanding the world

University of California - Santa Cruz

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Sharf holds a CMOS-based microelectrode array chip used to precisely locate the electrical activity of single neurons within millimeter-sized organoid tissue. 
 

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Credit: Carolyn Lagattuta/ UC Santa Cruz

Humans have long wondered when and how we begin to form thoughts. Are we born with a pre-configured brain, or do thought patterns only begin to emerge in response to our sensory experiences of the world around us? Now, science is getting closer to answering the questions philosophers have pondered for centuries. 

Researchers at the University of California, Santa Cruz, are using tiny models of human brain tissue, called organoids, to study the earliest moments of electrical activity in the brain. A new study in Nature Neuroscience finds that the earliest firings of the brain occur in structured patterns without any external experiences, suggesting that the human brain is preconfigured with instructions about how to navigate and interact with the world.

“These cells are clearly interacting with each other and forming circuits that self-assemble before we can experience anything from the outside world,” said Tal Sharf, assistant professor of biomolecular engineering at the Baskin School of Engineering and the study’s senior author. “There's an operating system that exists, that emerges in a primordial state. In my laboratory, we grow brain organoids to peer into this primordial version of the brain's operating system and study how the brain builds itself before it's shaped by sensory experience.”

In improving our fundamental understanding of human brain development, these findings can help researchers better understand neurodevelopmental disorders, and pinpoint the impact of toxins like pesticides and microplastics in the developing brain. 

Studying the developing brain

The brain, similar to a computer, runs on electrical signals—the firing of neurons. When these signals begin to fire, and how the human brain develops, are challenging topics for scientists to study, as the early developing human brain is protected within the womb.

Organoids, which are 3D models of tissue grown from human stem cells in the lab, provide a unique window into brain development. The Braingeneers group at UC Santa Cruz, in collaboration with researchers at UC San Francisco and UC Santa Barbara, are pioneering methods to grow these models and take measurements from them to gain insights into brain development and disorders. 

Organoids are particularly useful for understanding if the brain develops in response to sensory input—as they exist in the lab setting and not the body—and can be grown ethically in large quantities. In this study, researchers prompted stem cells to form brain tissue, and then measured their electrical activity using specialized microchips, similar to those that run a computer. Sharf’s background in both applied physics, computation, and neurobiology form his expertise in modelling the circuitry of the early brain. 

“An organoid system that's intrinsically decoupled from any sensory input or communication with organs gives you a window into what's happening with this self-assembly process,” Sharf said. “That self-assembly process is really hard to do with traditional 2D cell culture—you can’t get the cell diversity and the architecture. The cells need to be in intimate contact with each other. We're trying to control the initial conditions, so we can let biology do its wonderful thing.”

Pattern production

The researchers observed the electrical activity of the brain tissue as they self-assembled from stem cells into a tissue that can translate the senses and produce language and conscious thought. They found that within the first few months of development, long before the human brain is capable of receiving and processing complex external sensory information such as vision and hearing, its cells spontaneously began to emit electrical signals characteristic of the patterns that underlie translation of the senses. 

Through decades of neuroscience research, the community has discovered that neurons fire in patterns that aren’t just random. Instead, the brain has a “default mode” — a basic underlying structure for firing neurons which then becomes more specific as the brain processes unique signals like a smell or taste. This background mode outlines the possible range of sensory responses the body and brain can produce.

In their observations of single neuron spikes in the self-assembling organoid models, Sharf and colleagues found that these earliest observable patterns have striking similarity with the brain’s default mode. Even without having received any sensory input, they are firing off a complex repertoire of time-based patterns, or sequences, which have the potential to be refined for specific senses, hinting at a genetically encoded blueprint inherent to the neural architecture of the living brain 

“These intrinsically self-organized systems could serve as a basis for constructing a representation of the world around us,” Sharf said. “The fact that we can see them in these early stages suggests that evolution has figured out a way that the central nervous system can construct a map that would allow us to navigate and interact with the world.”

Knowing that these organoids produce the basic structure of the living brain opens up a range of possibilities for better understanding human neurodevelopment, disease, and the effects of toxins in the brain. 

“We’re showing that there is a basis for capturing complex dynamics that likely could be signatures of pathological onsets that we could study in human tissue,” Sharf said. “That would allow us to develop therapies, working with clinicians at the preclinical level to potentially develop compounds, drug therapies, and gene editing tools that could be cheaper, more efficient, higher throughput.”

This study included researchers at UC Santa Barbara, Washington University in St. Louis, Johns Hopkins University, the University Medical Center Hamburg-Eppendorf, and ETH Zurich.
 

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Journal

Nature Neuroscience

DOI

10.1038/s41593-025-02111-0 

Article Title

Preconfigured neuronal firing sequences in human brain organoids

Article Publication Date

24-Nov-2025

METAL ALCHEMY

Absolutely metal: scientists capture footage of crystals growing in liquid metal

University of Sydney

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Image of rods of platinum crystals in a droplet of liquid metal.

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Credit: Widjajana et al.

Researchers have successfully grown platinum crystals in liquid metal, using a powerful X-ray technique giving rare insight into how these delicate crystals form and grow.

More than a beautiful curiosity, liquid metal-grown crystals could be the key to creating new materials. They are potentially a vital ingredient in new technology being developed to extract hydrogen from water and in quantum computing applications.  

Published in Nature Communications, the University of Sydney led team used metallic crystals to build an electrode that can efficiently produce hydrogen from water.

Liquid metals like Gallium are curious elements. They shimmer on the surface like solid metals but can also be fluid. For instance, Gallium at room temperature resembles solid blocks of metal, but when warmed to body temperature it transforms into liquid metallic puddles.

“Witnessing the formation of crystals inside liquid metals like Gallium is a challenging task. Gallium is a very dense element whose atoms are tightly packed and is so opaque it is impossible for most microscopes to pass through a thick layer of Gallium. It was a really special moment to be able to develop a method to do this,” said Professor Kourosh Kalantar-Zadeh, from the School of Chemical and Biomolecular Engineering, University of Sydney, who led the research.

The team used X-ray computed tomography, equipment commonly used in medical imaging, to map internal organs.

The machinery revealed the internal details of the metallic crystals in 3D. It showed crystals blooming in liquid metal, revealing distinctive rod or frostlike structures developing over minutes and hours.

“To see how liquid metals can be harnessed to shape the future of smart materials and identify those that play important roles in energy sources, we need to understand their metallic and chemical properties, inside and out,” said Professor Kalantah-Zader.

“With X-ray computed tomography, we can now truly see what we are working with and design liquid metal grown crystals to grow more precisely.”

The contradictory nature of liquid metals, which contain both metallic and liquid properties, makes them desirable in the material science world. Researchers like Professor Kalantar- Zadeh have long eyed liquid metals as the future of industrial chemical processes. His research team specialises in pushing the chemical and technical boundaries of liquid metals to create new materials and ‘green’ catalysts, to make chemical reactions faster.    

“Liquid metals are also very good solvents, with a powerful ability to dissolve other metallic elements, like sugar in water,” said Professor Kalantah-Zader.  

Excess metallic elements form crystals, in the same way crystals form when there is too much sugar in water.

In this study, researchers dissolved platinum beads in Gallium or Gallium-indium liquid metal at 500 degrees Celsius, then cooled them to kickstart the crystal growing process.

X-ray computed tomography then imaged a droplet of the platinum and Gallium alloy (a material with two metals) in cross-sections, which were then stitched together to re-create a 3D image. This allowed the researchers to map the crystal formation process. While the platinum and Gallium alloy cooled, tiny crystal rods began to rapidly form.

“We observed with fascination how metallic particles of various crystal orientations grew inside liquid metals by changing the temperature and environmental conditions,” said study co-author PhD student Ms Moonika Widjajana.

“This study illustrated how X-ray computed tomography can overcome the challenge of observing crystal growth within liquid metal – an opaque material that is usually impossible to penetrate with light and electrons.” 

Current technology means the crystals observed can be imaged at low resolution only, but advancements in X-ray computed tomography mean researchers will soon be able to understand more about what happens when metallic crystals form.

X-ray computed tomography of crystals in Gallium [VIDEO] 

X-ray computed tomography reveal delicate frostlike structures in Gallium

Credit

Credit: Widjajana et al.

Crystals growing in liquid metal 

Credit

Credit: Widjajana et al.

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Journal

Nature Communications

Method of Research

Imaging analysis

Subject of Research

Not applicable

Article Title

Observing growth of metallic crystals inside liquid metal solvents

COI Statement

Declaration: The authors declare no competing interests. The work was supported by the Australian Research Council (ARC) Laureate Fellowship grant and the ARC discovery grant. The research was conducted with the scientific and technical assistance at Sydney Microscopy and Microanalysis, at the University of Sydney node of Microscopy Australia.