Press releases 鈥� August 2025
Aug
28
2025
09:03
Technology developed by a team led by researchers from 看片软件 Frankfurt helps in the search for genes with certain functions
How plants rot: New method decodes hidden decomposers of wood and leaves
When millions of tiny organisms decompose dead plant material, they keep the global carbon cycle going. Together with colleagues from the Senckenberg 鈥� Leibniz Institution for Biodiversity and Earth System Research (SGN) and Justus Liebig University (JLU) in Giessen, researchers from 看片软件 Frankfurt have developed a new method to identify the molecular tools that different species use for this process. Their analysis of over 18,000 species brought surprising discoveries to light: In addition to fungi and bacteria, some invertebrates also evidently have a whole range of such tools at their disposal, while the one or other fungus lost them when it became parasitic.
FRANKFURT. When a tree dies, it forms the foundation for new life: In a slow, invisible process, leaves, wood and roots are gradually decomposed 鈥� not by wind or weather but by millions and millions of tiny organisms. Fungi thread their way through the dead wood and degrade cell walls. Tiny animals such as insect larvae and mites gnaw through the tissue. And something very important happens in the process: The carbon stored in the plant is released, ultimately placing it at the disposal of plants again for the purpose of photosynthesis. But what exactly is responsible for performing this task in the global carbon cycle? And which molecular tools do the organisms use for it? To answer these questions, the researchers have developed a new bioinformatics-based method, which they have now presented in Molecular Biology and Evolution.
18,000 species in the spotlight
This method, called fDOG (Feature architecture-aware directed ortholog search), makes it possible to search in the genetic material of various organisms for genes that have evolved from the same precursor gene. It is assumed that these genes, known as 鈥渙rthologs鈥�, encode proteins with similar functions. For the current study, the scientists searched for the genes of plant cell wall-degrading enzymes (PCDs). Unlike previous methods, fDOG not only searches through masses of genomic information but also analyzes the architecture of the proteins found 鈥� i.e. their structural composition, which reveals a lot about an enzyme鈥檚 function.
鈥淲e start with a gene from one species, referred to as the seed, and then trawl through tens of thousands of species in the search for orthologous genes,鈥� explains Ingo Ebersberger, Professor for Applied Bioinformatics at 看片软件 Frankfurt. 鈥淚n the process, we constantly monitor whether the genes we find perhaps differ from the seed in terms of function and structure 鈥� for example, through the loss or gain of individual areas relevant for function.鈥�
The research team used this method to search for more than 200 potential PCD candidates in over 18,000 species from all three domains of life 鈥� bacteria, archaea and eukaryotes (plants, animals, fungi). The result is a detailed global map 鈥� with unprecedented accuracy 鈥� of enzymes capable of degrading plant cell walls.
Surprising discoveries among fungi and animals
The researchers devised special visualization methods to analyze the vast amounts of data and detect patterns. This revealed characteristic changes in the enzyme repertoire of the fungi under study, indicating a change in lifestyle of certain fungal species: From a decomposing lifestyle 鈥� i.e. the degradation of dead plants 鈥� to a parasitic lifestyle in which they infest living animals. Such evolutionary transitions are mirrored in characteristic patterns of enzyme loss.
A special surprise in the animal kingdom was the discovery that some arthropods possess an unexpectedly wide range of plant cell wall-degrading enzymes. These enzymes presumably originated from fungi and bacteria and entered the genome of invertebrates via direct gene transfer between different organisms 鈥� i.e. horizontal gene transfer. This suggests that they might be able to degrade plant material independently and are not reliant on the bacteria in their intestines, as was previously assumed. In another case, however, it emerged that the potential PCD genes in the analyzed sequence could be ascribed to microbial contamination 鈥� an important sign that such data need to be checked very carefully.
New insights into the global carbon cycle
The study shows how fDOG can be used to systematically map biological capabilities across the entire tree of life 鈥� from broad-scale overviews to detailed investigations of individual species. With this method, it is possible both to track evolutionary trajectories and to identify players previously overlooked in the global carbon cycle. Since soils contain large amounts of dead plant material and therefore constitute the largest terrestrial carbon sink, the decomposition of plant material is an important driver of the global carbon cycle. 鈥淥ur method gives us a fresh view of how metabolic capacities are distributed across the tree of life,鈥� says Ebersberger. 鈥淲e can now conduct multi-scale analyses and in the process detect both recent evolutionary changes and large patterns.鈥�
Publication: Vinh Tran, Felix Langschied, Hannah Muelbaier, Julian Dosch, Freya Arthen, Miklos Balint, Ingo Ebersberger: Feature architecture-aware ortholog search with fDOG reveals the distribution of plant cell wall-degrading enzymes across life. Molecular Biology and Evolution (2025) https://doi.org/10.1093/molbev/msaf120
Picture download:
Caption: A recent bioinformatics-based study conducted by 看片软件 Frankfurt has investigated which organisms possess the enzymatic tools necessary for degrading cellulose in dead wood and leaves. (Photo: Markus Bernards)
Further Information:
Professor Ingo Ebersberger
Head of Working Group for Applied Bioinformatics
Institute of Cell Biology and Neuroscience
看片软件 Frankfurt, Germany
Tel. +49 (0)69 798-42112
ebersberger@bio.uni-frankfurt.de
Editor: Dr. Markus Bernards, Science Editor, PR & Communications Office, Theodor-W.-Adorno-Platz 1, 60323 Frankfurt, Tel: +49 (0) 69 798-12498, bernards@em.uni-frankfurt.de
Aug
8
2025
09:06
Frankfurt physicists observe coupled quantum zero-point motion of a molecule鈥檚 atoms
Molecules in the Spotlight: Snapshots Reveal the Eternal Dance of Particles
Researchers at 看片软件 Frankfurt have, for the first time, directly visualized the so-called quantum zero-point motion in a larger molecule. This motion is exhibited by particles even at absolute zero temperature. In a collaborative experiment with the Max Planck Institute for Nuclear Physics, the University of Hamburg, the European XFEL, and other partners, they managed to make this 鈥渆ternal dance" of the atoms visible. The discovery was made possible by the COLTRIMS reaction microscope developed in Frankfurt, which is capable of reconstructing molecular structures. The findings have now been published in the journal Science.
FRANKFURT. Most of us find it difficult to grasp the quantum world: According to Heisenberg's uncertainty principle, it's like observing a dance without being able to see simultaneously exactly where someone is dancing and how fast they're moving 鈥� you always must choose to focus on one. And yet, this quantum dance is far from chaotic; the dancers follow a strict choreography. In molecules, this strange behavior has another consequence: Even if a molecule should be completely frozen at absolute zero, it never truly comes to rest. The atoms it is made of perform a constant, never-ending quiet dance driven by so-called zero-point energy.
First direct measurement of correlated zero-point motion
For a long time, these patterned zero-point movements were considered impossible to measure directly. However, scientists at 看片软件 Frankfurt and partner institutions have now succeeded in doing precisely that at the world's largest X-ray laser, the European XFEL in Hamburg, Germany. They captured the 鈥渄ance of the atoms" by shining a 鈥渟potlight" on individual molecules and taking snapshots of their atoms 鈥� revealing each atom's precise choreography.
Professor Till Jahnke from the Institute for Nuclear Physics at 看片软件 Frankfurt and the Max Planck Institute for Nuclear Physics in Heidelberg explains: 鈥淭he exciting thing about our work is that we were able to see that the atoms don't just vibrate individually, but that they vibrate in a coupled manner, following fixed patterns. We directly measured this behavior for the first time in individual medium-sized molecules that were also in their lowest energy state. This zero-point motion is a purely quantum mechanical phenomenon that cannot be explained classically." Instead of choreography, physicists speak of vibrational modes. While the motion patterns of molecules with two or three atoms are fairly easy to follow, it quickly becomes complex with medium-sized molecules 鈥� like the studied iodopyridine, which consists of eleven atoms. Iodopyridine features a whole repertoire of 27 different vibrational modes 鈥� from ballet to tango to folk dance.
鈥淭his experiment has a long history," says Jahnke. 鈥淲e originally collected the data in 2019 during a measurement campaign led by Rebecca Boll at the European XFEL, which had an entirely different goal. It wasn't until two years later that we realized we were actually seeing signs of zero-point motion. The breakthrough came through collaboration with our colleagues from theoretical physics from the Center for Free-Electron Laser Science in Hamburg. Beno卯t Richard and Ludger Inhester, in particular, came up with new analysis methods that elevated our data interpretation to an entirely new level. Looking back, many puzzle pieces had to come together perfectly."
Explosion reveals molecular structure
But how can you capture an image of dancing particles? Using a technique called Coulomb Explosion Imaging, molecules are triggered to undergo a controlled explosion by ultrashort, high-intensity X-ray laser pulses, allowing high-resolution images of their structure to be generated. The X-ray pulse knocks many electrons out of the molecule, causing the atoms 鈥� now positively charged 鈥� to repel each other and fly apart in a fraction of a trillionth of a second. The fragments are recorded by a special apparatus that measures their time and position of impact, enabling the reconstruction of the molecule's original structure. This COLTRIMS reaction microscope has been developed over the past decades by 看片软件's Atomic Physics group. A version tailored specifically to the European XFEL was built by Dr. Gregor Kastirke during his PhD work. Seeing the device in action is something special, Kastirke says: 鈥淲itnessing such groundbreaking results makes me feel a little proud. After all, they only come about through years of preparation and close teamwork."
New insights into the quantum world
The results provide entirely new insights into quantum phenomena. For the first time, researchers can directly observe the complex patterns of zero-point motion in more complex molecules. These findings demonstrate the potential of the Frankfurt-developed COLTRIMS reaction microscope. 鈥淲e're constantly improving our method and are already planning the next experiments," says Jahnke. 鈥淥ur goal is to go beyond the dance of atoms and observe in addition the dance of electrons 鈥� a choreography that is significantly faster and also influenced by atomic motion. With our apparatus, we can gradually create real short films of molecular processes 鈥� something that was once unimaginable."
Publication: Beno卯t Richard, Rebecca Boll, Sourav Banerjee, Julia M. Sch盲fer, Zoltan Jurek, Gregor Kastirke, Kilian Fehre, Markus S. Sch枚ffler, Nils Anders, Thomas M. Baumann, Sebastian Eckart, Benjamin Erk, Alberto De Fanis, Reinhard D枚rner, Sven Grundmann, Patrik Grychtol, Max Hofmann, Markus Ilchen, Max Kircher, Katharina Kubicek, Maksim Kunitski, Xiang Li, Tommaso Mazza, Severin Meister, Niklas Melzer, Jacobo Montano, Valerija Music, Yevheniy Ovcharenko, Christopher Passow, Andreas Pier, Nils Rennhack, Jonas Rist, Daniel E. Rivas, Daniel Rolles, Ilme Schlichting, Lothar Ph. H. Schmidt, Philipp Schmidt, Daniel Trabert, Florian Trinter, Rene Wagner, Peter Walter, Pawel Ziolkowski, Artem Rudenko, Michael Meyer, Robin Santra, Ludger Inhester, and Till Jahnke: Imaging collective quantum fluctuations of the structure of a complex molecule. Science (2025) DOI: 10.1126/science.adu2637
Images for download:
Caption: Ultrashort, high-intensity X-ray laser pulses trigger controlled explosions of molecules 鈥� making it possible to capture high-resolution images of molecular structures (image: Till Jahnke).
Further information
Prof. Dr. Till Jahnke
Max Planck Institute for Nuclear Physics Heidelberg
and
Institute for Nuclear Physics
看片软件 Frankfurt
+49 (0)69 798 47023
till.jahnke@xfel.eu
Editor: Dr. Phyllis Mania, Science Editor, PR & Communications Office, Theodor-W.-Adorno-Platz 1, 60323 Frankfurt am Main, Tel +49-(0)69 798-13001, Fax 069 798-763-12531, mania@physik.uni-frankfurt.de