Cells must precisely control which of the many genes contained in the genome they use. This is done in so-called transcription factories, molecular assemblies in the cell nucleus. Researchers at the Karlsruhe Institute of Technology (KIT), at the Friedrich Alexander University Erlangen-Nuremberg (FAU) and at the Max Planck Center for Physics and Medicine (MPZPM) have now found that the formation of transcription factories resembles the condensation of liquids. Their findings may contribute to the understanding of disease causes in the future, as well as advance the development of DNA-based data storage. The researchers report in Molecular Systems Biology.
The human genome contains more than 20,000 different genes. However, each cell accesses only a fraction of the information stored in this genome. Cells must therefore precisely control which genes they use – otherwise, for example, cancer may develop or embryonic growth may be disturbed. A central role in the selection of active genes is played by so-called transcription factories.
“These factories are molecular assemblies in the cell nucleus that combine the correct selection of active genes and the readout of their sequence at a central location.”
– Lennart Hilbert, assistant professor
Set up and running in a matter of seconds
How transcription factories are built and specifically started up within a few seconds has occupied cell and molecular biologists for decades. Results from recent years indicate the relevance of processes that were previously only known from industrial and technical polymer and liquid materials. Currently, research is particularly investigating phase separation as a central mechanism. In everyday life, phase separation is evident, for example, in the separation of oil and water. Until now, however, it was not clear how exactly phase separation contributes to the construction of transcription factories in living cells.
Researchers at the Institute of Biological and Chemical Systems (IBCS), the Zoological Institute (ZOO), the Institute of Applied Physics (APH), and the Institute of Nanotechnology (INT) of KIT, together with scientists at the Friedrich Alexander University Erlangen-Nuremberg (FAU), the Max Planck Center for Physics and Medicine (MPZPM) in Erlangen, and the University of Illinois at Urbana-Champaign/USA, have gained new insights into the formation of transcription factories: It happens in a similar way to the condensation of liquids. The scientists show this in a publication in the journal Molecular Systems Biology. First authors are Agnieszka Pancholi from KIT’s IBCS-BIP and ZOO, and Tim Klingberg from FAU and MPZPM.
State-of-the-art light microscopy combined with computer simulations
In their publication, the researchers show that condensation during the formation of transcription factories is similar to fogging up a pair of glasses or a window pane: Liquid only condenses in the presence of a receptive surface, but then very rapidly. In the living cell, specially marked areas of the genome serve as condensation surfaces. The fluid-coated areas allow the attachment of relevant gene sequences as well as additional molecules that eventually activate the attached genes.
These findings were achieved through an interdisciplinary collaboration. For example, the researchers observed zebrafish embryos with state-of-the-art light microscopes developed in Professor Gerd Ulrich Nienhaus’ team at APH. These observations were combined with computer simulations at the Department of Mathematics in the Life Sciences at FAU and at MPZPM, which is headed by Professor Vasily Zaburdaev. The combination of observations and simulations makes the condensation process comprehensible and explains how living cells can quickly and reliably build transcription factories.
In recent years, the new understanding of condensed fluids in living cells has provided fundamentally new approaches to the therapy of cancer and nervous system diseases. These approaches are already being pursued by recently formed companies to develop new drugs. Other research is looking at the use of DNA sequences as digital data storage devices.
The feasibility in principle of DNA-based data storage has now been demonstrated by several research groups. However, reliably storing and reading information in such DNA storage media is still a challenge. “Our research shows how the biological cell organizes such processes quickly and reliably at the same time.
Pulsed electric fields caused by lightning strikes make themselves felt as voltage spikes and represent a destructive hazard for electronic components. They cause considerable damage. A team from the Helmholtz-Zentrum Dresden-Rossendorf (HZDR) has now discovered that such voltage spikes can have quite useful properties. In the journal Physical Review Research (DOI: 10.1103/PhysRevResearch.3.033153), the scientists report how, for example, nuclear fusion processes can be significantly enhanced by extremely strong and fast pulsed electric fields. Nuclear fusions, such as those that take place in the sun, are made possible by the quantum mechanical tunnel effect.
“One consequence of the tunnel effect is that similarly charged particles can overcome their mutual repulsion, even if their energy is not actually sufficient to do so – at least not according to the laws of classical mechanics. We can observe something like this, for example, in the fusion of two light atomic nuclei: The closer one nucleus approaches the other, the greater the repulsion, which we can imagine figuratively as a mountain piling up in front of the nucleus, the so-called potential barrier. Instead of taking the more energy-consuming path over the top, the laws of quantum mechanics allow the nucleus to penetrate or ‘tunnel’ straight through this mountain in a much more energetically favorable way – and finally to fuse.”
– Prof. Ralf Schützhold, Head of the Department of Theoretical Physics
Although the tunneling effect plays an important role in many areas of physics and was first described nearly one hundred years ago, our understanding of the process is still incomplete today. “Various facets of the influence of electric fields on tunneling processes were already known. For example, electric fields can additionally accelerate particles, helping them to gain more energy. They can also deform the potential barrier and increase the tunneling probability in this way,” says Dr. Christian Kohlfürst, outlining the situation at the beginning of their research.
His colleague Dr. Friedemann Queisser briefly sums up their results: “Our calculations now show for the first time a special feature of pulsed electric fields that change rapidly in time: they can ensure that the particles are pushed out of the potential barrier, figuratively speaking, and thus tunnel more easily.” The calculations of the HZDR team show this quite concretely in various examples, including a fusion reaction of interest for possible energy generation: the fusion of a proton with the isotope boron-11.
Fusion reaction with advantages
It is interesting primarily because of the relatively readily available fuel. Three alpha particles, each with a double positive charge, are produced in the process. What is remarkable about this reaction is that the energy is released in the form of charged particles and not as neutron radiation as in the most well-known fusion reactions at present. This has advantages: For one thing, the problems associated with neutron flux would be significantly reduced, such as the dangers of dealing with ionizing radiation. For another, the energy of charged particles can be converted directly, and thus much more easily, into electricity.
However, the conditions required to use the reaction are even more extreme than those of the deuterium-tritium fusion favored in the current ITER fusion reactor experiment. Igniting the proton-boron reaction is more difficult by comparison, and scientists are still searching for viable ways to do so. Schützhold’s team now points to one possibility: “According to our calculations, a sufficiently fast and strong pulsed electric field can significantly enhance not only deuterium-tritium fusion but also the proton-boron reaction.”
However, generating such fields is very difficult. “In principle, we can think of it as being like a thunderstorm, where the energy stored in huge cloud formations is discharged in the form of a lightning strike in a very short time and in a very confined space. Facilities are being built or planned around the world that are intended to concentrate ever higher energies into ever shorter periods of time and ever smaller spatial areas,” says Schützhold. Unfortunately, the facilities available today are not yet quite capable of generating such fast and powerful “artificial lightning.”
But there is a possible way out: The electric field of an alpha particle flying fast and, above all, close to the proton can act like such a pulsed electric field and strike so strongly that the proton can tunnel through the potential barrier of boron-11 and trigger the fusion reaction. Alpha particles with the necessary pulse energy are actually generated in the proton-boron reaction, but they can also be injected from outside.
Therapeutics and bioinsecticides: production by spider venom
The venom of a single spider can contain up to 3000 components. The components, mostly peptides, can be used to develop promising active ingredient candidates for the treatment of diseases. Spider venom can also be used in pest control – as a biological pesticide. A team of researchers from the Fraunhofer Institute for Molecular Biology and Applied Ecology IME and the Justus Liebig University Giessen is focusing on native spiders and their venom mix, which have received little attention to date. The research results on the biology of the toxins – especially on the venom of the wasp spider – have been published in scientific journals.
Spiders make many people uncomfortable, and some are even afraid of the eight-legged creatures. At the Fraunhofer Institute for Molecular Biology and Applied Ecology IME in Giessen, however, they are welcome. Here, biochemist Dr. Tim Lüddecke and his team are conducting research on spider toxins.
“Spider toxins are a largely untapped resource, this is partly due to the sheer diversity – some 50,000 species are known. There is a lot of potential in spider venom for medicine, for example in researching disease mechanisms.”
– Dr. Tim Lüddecke, head of the new “Animal Venomics” research group
For example, it is possible to study in the laboratory how individual toxins act on pain receptors of nerve cells. The venom cocktail of the Australian funnel web spider is particularly promising. It is assumed that it can be used to treat neuronal damage after strokes and to make hearts for organ transplants last longer. Other drug candidates are of interest for use as antibiotics or painkillers. “This is a very young field of research. The substances have been discovered and described, but they are not yet in the preclinical stage,” Lüddecke said. Pesticide research is a different story. Spiders stun insects with their venom and then eat them. Because the toxins are very effective against insects, they provide a good basis for biopesticides; they are suitable for crop pest control.
Research to date has focused on the toxins of the very large or potentially dangerous species that live in the tropics. The native, small and harmless spiders have not been in focus. “Most spiders in Central Europe are no more than two centimeters in size, and their venom levels were not sufficient for experiments. But now we have precise analytical methods to study even the small amounts of the previously neglected majority of spiders,” explains Lüddecke. The working group at the Giessen Bioresources branch of the Fraunhofer IME is devoting itself to these species as part of a research project. In the process, they are collaborating with research teams from the Justus Liebig University in Giessen, among others. The work is funded by the LOEWE Center for Translational Biodiversity Genomics (LOEWE-TBG) in Frankfurt am Main.
The scientists are paying particular attention to the wasp spider (Argiope bruennichi), which owes its name to its striking wasp-like coloration. They have succeeded in decoding its venom, identifying numerous novel biomolecules. The research findings were published in the journal Biomolecules.
New biomolecules from wasp spider venom
Spider venoms are highly complex, they can contain up to a maximum of 3000 components. The venom of the wasp spider, on the other hand, contains only about 53 biomolecules. It is heavily dominated by high-molecular-weight components, including so-called CAP proteins and other enzymes. As in other spider venoms, knottins are present – but these make up only a small part of the total mixture.
Knottins represent a group of neurotoxic peptides that are robust to chemical, enzymatic, and thermal degradation due to their nodal structure. One could therefore administer these molecules orally as a component of drugs without digesting them in the gastrointestinal tract. They can therefore exert their effects very well, which is why they offer great potential for medicine. In addition, knottins bind specifically to ion channels. “The more specifically a molecule docks onto its target molecule, attacking only a single type of ion channel, the fewer side effects it triggers,” explains Lüddecke. Moreover, even in small amounts, the knottins affect the activity of the ion channels, i.e., they are effective at low concentrations. As a result, derived drugs can be administered in low doses. The combination of these properties is what makes spider venoms so interesting for science.
The project partners also discovered molecules in the wasp spider’s venom that are similar in structure to neuropeptides, which are responsible for transporting information between nerve cells. “We have found novel families of neuropeptides that we have not previously seen in other spiders. We suspect that the wasp spider uses them to attack the nervous system of insects. It has been known for some time that neuropeptides in the animal kingdom are frequently converted into toxins in the course of evolution,” says the researcher.
Replicating toxins in the lab
Since the toxin yield is low in small spiders, the researchers extract the toxin glands and sequence the mRNA from them. Based on the gene structure, the toxins can be decoded. The venom profile of the wasp spider is now available in its entirety, and the next step is to produce the relevant components. For this, the gene sequence is incorporated into a bacterial cell using biotechnology, which then produces the toxin. “We are building quasi genetically modified bacteria that produce the toxin on a large scale.” Lüddecke and his team have been able to mass produce the main component of the wasp spider toxin, the CAP protein. The first functional studies will start soon.
Venom of male and female spiders differs
In another review paper, the biochemist, in cooperation with colleagues at the Justus Liebig University of Giessen and researchers at the Australian University of the Sunshine Coast, was able to deduce that spider venoms are very dynamic and that many influences shape their composition and functionality. “The dynamics of spider venom have been completely underestimated. The biochemical repertoire is critically influenced by life stage, habitat, and especially sex. Even the venom cocktail of juveniles and adults is not necessarily identical. It is rather the interaction of the many components that makes spider venom so effective than the effect of a single toxin. Through their interactions, the components increase their effectiveness,” the researcher sums up.
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