The sea off the west coast of South America is one of the most vital and productive fishing grounds on earth. Around eight percent of the global catch of marine species comes from the areas off the coasts of Peru, where the near-surface Humboldt Current provides a high nutrient supply and thus sufficient food for commercially exploited fish species such as the anchovy. Ten percent of the total global catch of anchovies alone comes from the region. Much of it is processed into fish meal and oil and used primarily for aquacultures in China and Norway. However, catches of anchovy in the Humboldt upwelling system are currently declining. The causes of species shifts are mainly due to climate change according to the results of the new study.

Researchers from the Institute of Geosciences at Kiel University, together with colleagues from GEOMAR Helmholtz Centre for Ocean Research and international partners, have for the first time investigated the relationships between temperature, oxygen, nutrient supply and the occurrence of individual fish species using paleo-oceanographic data from the Humboldt Current region. The scientists focused on the warm period about 125,000 years ago (Eemian interglacial). During this time, conditions were similar to those predicted by climate projections (e.g., the IPCC report) for the end of the 21st century at the latest: comparable primary production but water temperatures two degrees Celsius higher than today and increased oxygen deficiency in mid-depth water masses.

For their paleo-oceanographic studies, the researchers at Kiel University primarily analyzed small fish vertebrae that they were able to isolate from the sediment cores. According to the results, smaller, goby-like fish predominated in coastal waters during the ancient warm period, while anchovies made up only a small proportion. Fish with smaller body sizes can adapt better to warmer temperatures. They retain their high activity even in less oxygenated waters thanks to their larger gill surface area relative to their body volume.

“The conditions of this past warm period that we were able to reconstruct from our samples can definitely be compared to the current development and put in context with future scenarios,” says first author of the study, Dr. Renato Salvatteci, who is currently working at the Center for Ocean and Society of the Kiel Marine Science (KMS) priority research area at Kiel University and in the BMBF-funded Humboldt-Tipping project. “According to this, there is a clear regime shift towards smaller fish that feel more comfortable in the warm, lower-oxygen conditions. We conclude from our results that the effects of human-induced climate change may have a stronger influence on the evolution of stocks in the region than previously thought,” Salvatteci added. Smaller fish are harder to catch and less palatable. According to the report, the impact on the Peru region, local fisheries income and global trade in anchovies could be far-reaching — potentially affecting global food security.

“Our studies using sediment cores can give us fairly accurate information about the changes and their dynamics in highly productive coastal waters around the world that have occurred in the wake of different climate states and over different time scales,” explains Professor Ralph Schneider, a paleoclimate researcher at the Institute of Geosciences at Kiel University and co-author of the study.

The results indicate that due to increasing warming in the Humboldt Current upwelling area, the ecosystem is heading towards a tipping point beyond which anchovy will begin to retreat and not continue to dominate nearshore fishing grounds. “Despite a flexible, sustainable and adaptive management strategy, anchovy biomass and landings have declined, suggesting that we are closer to the ecological tipping point than suspected,” summarizes lead author Renato Salvatteci.

The results of the study help to better assess the extent to which a warming ocean can provide sufficient food for the world’s population and what changes should be expected for the development of important fish species such as the anchovy.

The study was funded by the Collaborative Research Center (SFB) 754 “Climate-Biogeochemical Interactions in the Tropical Ocean,” a collaborative project of Kiel University (CAU) and GEOMAR Helmholtz Centre for Ocean Research Kiel. Additional support came from the BMBF project Humboldt-Tipping, coordinated at the Center for Ocean and Society, as well as funding from the Emmy-Noether Junior Research Group ICONOX at GEOMAR. First author Renato Salvatteci was further supported by a fellowship from the Alexander von Humboldt Foundation.

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“Red dwarfs” are small stars and thus much cooler than our Sun. Around stars like these, liquid water is possible on planets much closer to the star than in our solar system. The distance between an exoplanet and its star is a crucial factor in its detection: the closer a planet is to its host star, the higher the probability that it can be detected.

In a study recently published in the journal Astronomy & Astrophysics, researchers led by Dr. Nicole Schanche of the Center for Space and Habitability CSH of the University of Bern report the discovery of the exoplanet TOI-2257 b orbiting a nearby red dwarf. Nicole Schanche is also a member of the National Center of Competence in Research PlanetS, which the University of Bern runs together with the University of Geneva.

A special telescope is part of the solution

Exoplanets that are very far from our solar system cannot be observed directly with a telescope — they are too small and reflect too little light. However, one way to detect such planets is the transit method. This involves using telescopes to look for dips in the star’s brightness that occur when planets pass in front of the star. Repeated observations of the dips in the star’s brightness give precise measurements of the planet’s orbital period around the star, and the depth of the transit allows researchers to determine the planet’s diameter. When combined with planet mass estimates from other methods, such as using radial velocity measurements, the planet density can be calculated.

Planet TOI-2257 b was initially identified by data from NASA’s Transiting Exoplanet Survey Satellite TESS space telescope. The small star was observed for a total of four months, but the gaps between observations meant that it was not clear whether the decrease in brightness could be explained by the transit of a planet with an orbit of 176, 88, 59, 44 or 35 days.

Observation of the star with the Las Cumbres Observatory Global Telescope subsequently ruled out the possibility that a planet with a 59-day orbital period was causing the drop in brightness. “Next, we wanted to find out if the 35-day orbital period could be possible,” explains Nicole Schanche.

The Mexico-based SAINT-EX telescope, co-operated by the CSH and the NCCR PlanetS, is purpose-built to study red dwarfs and their planets in more detail. SAINT-EX is an acronym that stands for Search And characterIsatioN of Transiting EXoplanets. The project was named in honor of Antoine de Saint-Exupéry (Saint-Ex), the famous writer, poet and aviator. SAINT-EX observed a partial transit of TOI-2257 b and was able to confirm the exoplanet’s exact orbital period around its star, 35 days. “Another 35 days later, SAINT-EX was able to observe the entire transit, which gave us even more information about the properties of the system,” says co-author Robert Wells from the CSH, who was involved in the data processing.

A temperate planet with an irregular orbit

With its 35-day orbital period, TOI-2257 b orbits the host star at a distance where liquid water is possible on the planet, and therefore conditions favorable for the emergence of life could exist. Planets in this so-called “habitable zone” near a small red dwarf star are easier to study because they have shorter orbital periods and can therefore be observed more often. The radius of TOI-2257 b (2.2 times larger than Earth’s) suggests that the planet is rather gaseous, with high atmospheric pressure not conducive to life.

“We found that TOI-2257 b does not have a circular, concentric orbit,” explains Nicole Schanche. In fact, it is the most eccentric planet orbiting a cool star ever discovered. “In terms of potential habitability, this is bad news,” Nicole Schanche continues. “While the planet’s average temperature is comfortable, it varies from -80°C to about 100°C depending on where in its orbit the planet is, far from or close to the star.” A possible explanation for this surprising orbit is that further out in the system a giant planet is lurking and disturbing the orbit of TOI 2257 b. Further observations measuring the radial velocity of the star will help confirm the eccentricity and search for possible additional planets that could not be observed in transit.

Candidate for observation with JWST

The James Webb Space Telescope (JWST), which successfully launched on December 25, will revolutionize research into exoplanet atmospheres. In order to prioritize good candidates for observations with the JWST, a transmission spectroscopy metric (TSM) was developed that rates different system properties. TOI-2257 b is well positioned with respect to TSM and is one of the most attractive sub-Neptune targets for further observations. “In particular, the planet could be studied for signs of features such as water vapor in the atmosphere,” Nicole Schanche concludes.

In a study published this month in The International Journal of High Performance Computing Applications, a research team led by the University of Tsukuba describes a highly efficient method for simulating light-matter interactions at the atomic scale.

What makes these interactions so difficult to simulate? One reason is that phenomena associated with the interactions encompass many areas of physics, involving both the propagation of light waves and the dynamics of electrons and ions in matter. Another reason is that such phenomena can cover a wide range of length and time scales.

Given the multiphysics and multiscale nature of the problem, light-matter interactions are typically modeled using two separate computational methods. The first is electromagnetic analysis, whereby the electromagnetic fields of the light are studied; the second is a quantum-mechanical calculation of the optical properties of the matter. But these methods assume that the electromagnetic fields are weak and that there is a difference in the length scale.

“Our approach provides a unified and improved way to simulate light-matter interactions,” says senior author of the study Professor Kazuhiro Yabana. “We achieve this feat by simultaneously solving three key physics equations: the Maxwell equation for the electromagnetic fields, the time-dependent Kohn-Sham equation for the electrons, and the Newton equation for the ions.”

The researchers implemented the method in their in-house software SALMON (Scalable Ab initio Light-Matter simulator for Optics and Nanoscience), and they thoroughly optimized the simulation computer code to maximize its performance. They then tested the code by modeling light-matter interactions in a thin film of amorphous silicon dioxide, composed of more than 10,000 atoms. This simulation was carried out using almost 28,000 nodes of the fastest supercomputer in the world, Fugaku, at the RIKEN Center for Computational Science in Kobe, Japan.

“We found that our code is extremely efficient, achieving the goal of one second per time step of the calculation that is needed for practical applications,” says Professor Yabana. “The performance is close to its maximum possible value, set by the bandwidth of the computer memory, and the code has the desirable property of excellent weak scalability.”

Although the team simulated light-matter interactions in a thin film in this work, their approach could be used to explore many phenomena in nanoscale optics and photonics.

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Biofilms are prevalent in the living world, inhabiting sewer pipes, kitchen counters and even the surface of our teeth. A previous research study demonstrated that these biofilms employ sophisticated systems to communicate with one another, while another proved biofilms have a robust capacity for memory.

Süel’s laboratory, along with researchers at Stanford University and the Universitat Pompeu Fabra in Spain, has now found a feature of biofilms that reveal these communities as far more advanced than previously believed. Biological Sciences graduate student Kwang-Tao Chou, former Biological Sciences graduate student Daisy Lee, Süel and their colleagues discovered that biofilm cells are organized in elaborate patterns, a feature that previously only had been associated with higher-level organisms such as plants and animals. The findings, which describe the culmination of eight years of research, are published Jan. 6 in the journal Cell.

“We are seeing that biofilms are much more sophisticated than we thought,” said Süel, a UC San Diego professor in the Division of Biological Sciences’ Section of Molecular Biology, with affiliations in the San Diego Center for Systems Biology, BioCircuits Institute and Center for Microbiome Innovation. “From a biological perspective our results suggest that the concept of cell patterning during development is far more ancient than previously thought. Apparently, the ability of cells to segment themselves in space and time did not just emerge with plants and vertebrates, but may go back over a billion years.”

Biofilm communities are made up of cells of different types. Scientists previously had not thought that these disparate cells could be organized into regulated complex patterns. For the new study, the scientists developed experiments and a mathematical model that revealed the genetic basis for a “clock and wavefront” mechanism, previously only seen in highly evolved organisms ranging from plants to fruit flies to humans. As the biofilm expands and consumes nutrients, a “wave” of nutrient depletion moves across cells within the bacterial community and freezes a molecular clock inside each cell at a specific time and position, creating an intricate composite pattern of repeating segments of distinct cell types.

The breakthrough for the researchers was the ability to identify the genetic circuit underlying the biofilm’s ability to generate the biofilm community-wide concentric rings of gene expression patterns. The researchers were then able to model predictions showing that biofilms could inherently generate many segments.

“Our discovery demonstrates that bacterial biofilms employ a developmental patterning mechanism hitherto believed to be exclusive to vertebrates and plant systems,” the authors note in the Cell paper.

The study’s findings offer implications for a multitude of research areas. Because biofilms are pervasive in our lives, they are of interest in applications ranging from medicine to the food industry and even the military. Biofilms as systems with the capability to test how simple cell systems can organize themselves into complex patterns could be useful in developmental biology to investigate specific aspects of the clock and waveform mechanism that functions in vertebrates, as one example.

“We can see that bacterial communities are not just globs of cells,” said Süel, who envisions research collaborations offering bacteria as new paradigms for studying developmental patterns. “Having a bacterial system allows us to provide some answers that are difficult to obtain in vertebrate and plant systems because bacteria offer more experimentally accessible systems that could provide new insights for the field of development.”

Coauthors of the paper include: Kwang-Tao Chou (UC San Diego graduate student), Dong-yeon Lee (former UC San Diego graduate student, now a postdoctoral scholar at Stanford University), Jian-geng Chiou (UC San Diego postdoctoral scholar), Leticia Galera-Laporta (UC San Diego postdoctoral scholar), San Ly (former UC San Diego researcher), Jordi Garcia-Ojalvo (Universitat Pompeu Fabra Professor) and Gürol Süel (UC San Diego Professor).

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The study published in Cell Stem Cell therefore establishes senescence as a potentially targetable mechanism for future treatment of Down syndrome, said Hiruy Meharena, a new assistant professor at the University of California San Diego who led the work as a Senior Alana Fellow in the Alana Down Syndrome Center at MIT.

“There is a cell-type specific genome-wide disruption that is independent of the gene dosage response,” Meharena said. “It’s a very similar phenomenon to what’s observed in senescence. This suggests that excessive senescence in the developing brain induced by the third copy of chromosome 21 could be a key reason for the neurodevelopmental abnormalities seen in Down syndrome.”

The study’s finding that neural progenitor cells (NPCs), which develop into major cells in the brain including neurons, have a senescent character is remarkable and novel, said senior author Li-Huei Tsai, but it is substantiated by the team’s extensive work to elucidate the underlying mechanism of the effects of abnormal chromosome number, or aneupoloidy, within the nucleus of the cells.

“This study illustrates the importance of asking fundamental questions about the underlying mechanisms of neurological disorders,” said Tsai, Picower Professor of Neuroscience, director of the Alana Center, and of The Picower Institute for Learning and Memory at MIT. “We didn’t begin this work expecting to see senescence as a translationally relevant feature of Down syndrome, but the data emerged from asking how the presence of an extra chromosome affects the architecture of all of a cell’s chromosomes during development.”

Genomewide changes

Meharena and co-authors spent years measuring distinctions between human cell cultures that differed only by whether they had a third copy of chromosome 21. Stem cells derived from volunteers were cultured to turn into NPCs. In both the stem cells and the NPCs, the team examined 3D chromosome architecture, several metrics of DNA structure and interaction, gene accessibility and transcription, and gene expression. They also looked at the consequences of the gene expression differences on important functions of these developmental cells, such as how well they proliferated and migrated in 3D brain tissue cultures. Stem cells were not particularly different, but NPCs were substantially affected by the third copy of chromosome 21.

Overall, the picture that emerged in NPCs was that the presence of a third copy causes all the other chromosomes to squish inward, not unlike when people in a crowded elevator must narrow their stance when one more person squeezes in. The main effects of this “chromosomal introversion,” meticulously quantified in the study, are more genetic interactions within each chromosome and less interactions among them. These changes and differences in DNA conformation within the cell nucleus lead to changes in how genes are transcribed and therefore expressed, causing important differences in cell function that affect brain development.

Treated as senescence

For the first couple of years as these data emerged, Meharena said, the full significance of the genomic changes were not apparent, but then he read a paper showing very similar genomic rearrangement and transcriptional alterations in senescent cells.

After validating that the Down syndrome cells indeed bore such a similar signature of transcriptional differences, the team decided to test whether anti-senolytic drugs could undo the effects. They tested a combination of two: dasatinib and quercetin. The medications improved not only gene accessibility and transcription, but also the migration and proliferation of cells.

That said, the drugs have very significant side effects — dasatinib is only given to cancer patients when other treatments have not done enough — so they are not appropriate for attempting to intervene in brain development amid Down syndrome, Meharena said. Instead an outcome of the study could be to inspire a search for medications that could have anti-senolytic effects with a safer profile.

Senescence is a stress response of cells. At the same time, years of research by former MIT biology professor Angelika Amon, who co-directed the Alana Center with Tsai, has shown that aneuploidy is a source of considerable stress for cells. A question raised by the new findings, therefore, is whether the senescence-like character of Down syndrome NPCs is indeed the result of an aneuploidy induced stress and if so, exactly what that stress is.

Another implication of the findings is how excessive senescence among brain cells might affect people with Down syndrome later in life. The risk of Alzheimer’s disease is much higher at a substantially earlier age in the Down syndrome population than among people in general. In large part this is believed to be because a key Alzheimer’s risk gene, APP, is on chromosome 21, but the newly identified inclination for senescence may also accelerate Alzheimer’s development.

The Alana Foundation, the LuMind Foundation, Burroughs Wellcome Fund, UNCF-Merck and the National Institutes of Health funded the research.

“People may wonder why our team is working on fingerprints,” says Sijia Wang, a geneticist at the Shanghai Institute of Nutrition and Health, of Chinese Academy of Sciences, and co-senior author on the paper. “We started the work purely out of curiosity. But later it turns out fingerprint pattern is associated with genes for limb growth, which are critical for fetal development. This provides another classic example of pleiotropy, when multiple phenotypes are interrelated to each other and are affected by the same genes.”

While fingerprints are unique to individuals, they are generally categorized into three types: arch, loop, and whorl. These furrows and ridges begin to form on a fetus’ fingers and toes after the third month of pregnancy. Scientists have suspected that fingerprints have potentially evolved to help grab objects and sense their textures, but exactly how these patterns are formed remains unknown.

Wang and colleagues scanned the DNA of more than 23,000 people across ethnic groups and found that at least 43 regions on the genome are associated with fingerprint patterns. One of the most influential regions appeared to be regulating the expression of a gene called EVI1, which is known for its role in embryonic limb development.

To test their finding, the team modified the DNA of mice so their expression of EVI1 was turned down. They found that mice with downregulated EVI1 developed abnormal skin patterns on their digits compared with wild-type mice.

Analysis of human data revealed that fingerprint patterns are genetically correlated with finger length. For example, people with whorl-shaped fingerprints on both of their little fingers tend to have longer little fingers than those who do not, and this correlation is strongly linked to genes involved ini limb development.

“We don’t know exactly how the genes shape fingerprint patterns, but it could be determined by the amount of strength from growth that’s put on an embryonic tissue called volar pads that plays an important role in the formation of different patterns of fingerprint,” says Jinxi Li, a geneticist at the Human Phenome Institute at Fudan University in Shanghai, and a co-first author on the paper. She explains that as a fetus’ hands grow, the palms and fingers would stretch and elongate. These forces could turn a whorl into a loop, for example.

Notably, previous research has suggested that EVI1 is linked to risk of leukemia, and some studies have observed that people with more whorl patterns are more susceptible to the disease,” Wang says.

“Many congenital genetic disorders are related to different dermatoglyphic patterns, such as fingerprints,” he says. For example, children with Down’s syndrome are more likely to have a single crease running across the palm of their hands. “Our study suggests that dermatoglyphic patterns are affected by crucial development genes, which provides a strong theoretical basis for this kind of pleiotropy.”

The research is part of the International Human Phenome Project led by Fudan University in Shanghai that aims to map how the human phenotypical traits are correlated with each other. Next, the team plans to conduct more research on how dermatoglyphic patterns are related to diseases and the underlying pleiotropic mechanism.

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