New Discovery By SMART Allows Early Detection of Shade Avoidance Syndrome in Plants (Botany)

Researchers use Raman spectroscopy for early detection of SAS, which can help farmers better monitor plant health and lead to improved crop yield.

  • Negative effects of shade avoidance syndrome (SAS), where plants reach for more light to overcome shaded conditions, are irreversible and early detection is crucial for sustainable agricultural practices
  • Study found Raman spectroscopy can detect SAS in plants within a few hours, while conventional methods rely on morphological changes that can take one to three days
  • New method can be widely applied across various plant species and crops

Singapore, 25 November 2020 – Researchers from the Disruptive & Sustainable Technologies for Agricultural Precision (DiSTAP) Interdisciplinary Research Group (IRG) of Singapore-MIT Alliance for Research and Technology (SMART), MIT’s research enterprise in Singapore and Temasek Life Sciences Laboratory (TLL) have discovered a way to use Raman spectroscopy for early detection of shade avoidance syndrome (SAS) in plants. The discovery can help farmers with timely intervention against SAS, leading to better plant health and crop yield.

Raman spectroscopy and the carotenoid Raman peak allows for early detection of Shade Avoidance Syndrome (SAS) in the (a) model plant Arabidopsis thaliana and (b) leafy vegetables Kai Lan and Choy Sum. Diagrams adapted from Sng et al., 2020. Plant Methods 16: 144. ©Singapore-MIT Alliance for Research and Technology

SAS is an adaptive response and an irreversible phenomenon, where plants reach for more light to overcome shaded conditions. It is commonly seen in plants experiencing vegetative shade which is detrimental to plant health, as it leads to a number of issues including hindrance of leaf development, early flowering and weakening of the plant’s structure and immune system.

Thus, early detection of SAS is key for sustainable agriculture and improved crop yield. However, existing methods for detection of SAS in plants are restricted to observing structural changes, making it difficult to detect SAS early.

In a paper titled “Rapid metabolite response in leaf blade and petiole as a marker for shade avoidance syndrome” published in the prestigious journal Plant Methods, SMART DiSTAP and TLL scientists explain their new way of detecting SAS early on, allowing farmers to intervene in time to prevent the irreversible effects of SAS. The team built a tabletop Raman spectroscopy instrument that allows measurement of carotenoid levels in plants, which can indicate whether a plant has SAS.

“Our experiments with Raman spectroscopy detected a decrease in the carotenoid contents of plants that have SAS,” said Dr Gajendra Pratap Singh, co-first author of the paper and Scientific Director and Principal Investigator at DiSTAP. “While plants with longer exposure to shade developed more severe SAS, these morphological changes were only seen after one to three days. However, changes in the carotenoid peak intensities were detected much earlier, from just four hours of shade treatment.”

Using Raman spectroscopy, the scientists are able to non-destructively measure carotenoid content in the plant leaves, and have discovered its correlation to the severity of SAS and as a peak biomarker for early diagnosis. This cuts down the time taken to detect SAS from days to a matter of hours. The method can also be used to detect SAS in plants due to high-density planting and can be particularly useful to improve urban farming practices.

“We conducted our experiments on a number of edible plants, including frequently consumed Asian vegetables like Kai Lan and Choy Sum,” said Mr Benny Jian Rong Sng, the paper’s co-first author and PhD student from Dr In-Cheol Jang’s group at TLL and Department of Biological Sciences, National University of Singapore. “Our results showed that Raman spectroscopy can be used to detect SAS, induced by shade as well as high-density planting. Regardless of the food crop, this technology can be applied to improve agriculture and to meet the nutritional demands of today’s growing populations.”

Dr In-Cheol Jang, Principal Investigator at TLL and DiSTAP, who led the project said the novel discovery can go a long way in assisting farmers to improve urban farming practices. “We look forward to helping urban farmers achieve higher crop yields by detecting SAS within shorter time periods. By adopting scalable, precision agri-technologies like Raman spectroscopy-enabled sensors, we can better position cities like Singapore to grow more produce with less resources, while achieving desirable nutritional profiles for global food security.”

References: Sng, B.J.R., Singh, G.P., Van Vu, K. et al. Rapid metabolite response in leaf blade and petiole as a marker for shade avoidance syndrome. Plant Methods 16, 144 (2020).

Provided by Singapore-MIT Alliance for Research and Technology (SMART)

Space Travel Can Adversely Impact Energy Production in a Cell (Planetary Science)

Studies of both mice and humans who have traveled into space reveal that critical parts of a cell’s energy production machinery, the mitochondria, can be made dysfunctional due to changes in gravity, radiation exposure and other factors, according to investigators at Georgetown Lombardi Comprehensive Cancer Center. These findings are part of an extensive research effort across many scientific disciplines to look at the health effects of travel into space. The research has implications for future space travel as well as how metabolic changes due to space travel could inform medical science on earth.

Georgetown researcher Evagelia C. Laiakis, PhD, and dozens of other scientists described recent findings about the impact of space travel on health as part of a large compendium of work that appears concurrently in Cell, Cell Reports, Cell Systems, Patterns, and IScience. ©Jerry Angdisen/Georgetown University

The findings appeared November 25, 2020, in Cell and are part of a larger compendium of research into health aspects of space travel that appears concurrently in Cell, Cell Reports, Cell Systems, Patterns, and iScience.

“My group’s research efforts centered around muscle tissue from mice that were sent into space and were compared with analyses by other scientists who studied different mouse tissue,” says Evagelia C. Laiakis, PhD, an associate professor of oncology at Georgetown. “Although we each studied different tissue, we all came to the same conclusion: that mitochondrial function was adversely impacted by space travel.”

In addition to studying the effects of space travel on cellular function, the scientists used a trove of data from decades of NASA human flight experiments to correlate their outcomes in animals with those from 59 astronauts. They were also able to access data derived from NASA’s repository of biospecimens that had flown in space to do further comparisons. Data from NASA’s Twin Study of Mark and Scott Kelly was particularly informative as it allowed for a comparison of the health effects seen in an astronaut in space, Scott, with his earth-bound brother, Mark, who is a retired astronaut. Comparing their studies of mice with human data, Laiakis and the team of researchers were able to determine that space travel led to certain metabolic effects:

  • Isolated cells were adversely impacted to a higher degree than whole organs
  • Changes in the liver were more noticeable than in other organs
  • Mitochondrial function was impacted

Because space travel almost always exposes people to higher levels of radiation than would be found on earth, the scientists knew that such an exposure could harm mitochondria. This aspect of radiation exposure translates to health outcomes here on earth for cancer patients who undergo radiotherapy. With this knowledge of radiation’s impact on mitochondria, clinicians might tailor radiation therapy in different ways in the future to protect normal tissue. The implications for travel to Mars are especially concerning, the researchers say, as that would involve a much longer time in space and hence lengthy exposure to radiation.

“The launch of SpaceX earlier this month was very exciting,” says Laiakis. “From this, and other planned ventures to the moon, and eventually Mars, we hope to learn much more about the effects that spaceflight can have on metabolism and how to potentially mitigate adverse effects for future space travelers.”

Provided by Georgetown University Medical Center

Quantum Nanodiamonds May Help Detect Disease Earlier (Medicine)

The quantum sensing abilities of nanodiamonds can be used to improve the sensitivity of paper-based diagnostic tests, potentially allowing for earlier detection of diseases such as HIV, according to a study led by UCL researchers in the i-sense McKendry group.

An artist’s conception of nanodiamonds used for in vitro diagnostics. ©Ella Maru Studio/ UCL

Paper-based lateral flow tests work the same way as a pregnancy test in that a strip of paper is soaked in a fluid sample and a change in colour – or fluorescent signal – indicates a positive result and the detection of virus proteins or DNA. They are widely used to detect viruses ranging from HIV to SARS-CoV-2 (lateral flow tests for Covid-19 are currently being piloted across England) and can provide a rapid diagnosis, as the results do not have to be processed in a lab.

The new research, published in Nature, found that low-cost nanodiamonds could be used to signal the presence of an HIV disease marker with a sensitivity many thousands of times greater than the gold nanoparticles widely used in these tests.

This greater sensitivity allows lower viral loads to be detected, meaning the test could pick up lower levels of disease or detect the disease at an earlier stage, which is crucial for reducing transmission risk of infected individuals and for effective treatment of diseases such as HIV.

The research team are working on adapting the new technology to test for COVID-19 and other diseases over the coming months. A key next step is to develop a hand-held device that can “read” the results, as the technique was demonstrated using a microscope in a laboratory. Further clinical evaluation studies are also planned.

Lead author Professor Rachel McKendry, Professor of Biomedical Nanotechnology at UCL and Director of i-sense EPSRC IRC, said: “Our proof-of-concept study shows how quantum technologies can be used to detect ultralow levels of virus in a patient sample, enabling much earlier diagnosis.

“We have focused on the detection of HIV, but our approach is very flexible and can be easily adapted to other diseases and biomarker types. We are working on adapting our approach to COVID-19. We believe that this transformative new technology will benefit patients and protect populations from infectious diseases.”

The researchers made use of the quantum properties of nanodiamonds manufactured with a precise imperfection. This defect in the highly regular structure of a diamond creates what is called a nitrogen-vacancy (NV) centre. NV centres have many potential applications, from fluorescent biomarking for use in ultra-sensitive imaging to information processing qubits in quantum computing.

The NV centres can signal the presence of an antigen or other target molecule by emitting a bright fluorescent light. In the past, fluorescent markers have been limited by background fluorescence, either from the sample or the test strip, making it harder to detect low concentrations of virus proteins or DNA that would indicate a positive test. However, the quantum properties of fluorescent nanodiamonds allow their emission to be selectively modulated, meaning the signal can be fixed at a set frequency using a microwave field and can be efficiently separated from the background fluorescence, addressing this limitation.

The optical results showed up to a five orders of magnitude (100,000 times) improvement in sensitivity compared to gold nanoparticles (that is, a much lower number of nanoparticles were required to generate a detectable signal). With the inclusion of a short 10-minute constant-temperature amplification step, in which copies of the RNA were multiplied, the researchers were able to detect HIV RNA at the level of a single molecule in a model sample.

The work was demonstrated in a laboratory setting but the team hopes to develop the tests so that the results could be read with a smartphone or portable fluorescence reader. This means that the test could, in future, be performed in low-resource settings, making it more accessible to users.

First author Dr Ben Miller (i-sense Postdoctoral Research Associate at the London Centre for Nanotechnology at UCL) said: “Paper-based lateral flow tests with gold nanoparticles do not require laboratory analysis, making them particularly useful in low resource settings and where access to healthcare is limited. They are low cost, portable, and user friendly.

“However, these tests currently lack the sensitivity to detect very low levels of biomarkers. By replacing commonly used gold nanoparticles with fluorescent nanodiamonds in this new design, and selectively modulating their (already bright) emission of light, we have been able to separate their signal from the unwanted background fluorescence of the test strip, dramatically improving sensitivity.”

Co-author Professor John Morton, Director of UCL’s Quantum Science and Technology Institute (UCLQ), said: “This interdisciplinary collaboration between UCLQ and the i-sense team in the LCN is a fantastic illustration of how foundational work on quantum systems, such as NV centre in diamond, can evolve from the lab and play a crucial role in real-world applications in sensing and diagnostics. Researchers at UCLQ are exploring and enabling the impact of these and other quantum technologies by working with industry and other academic research groups.”

The study was carried out by an interdisciplinary team of i-sense researchers from UCL, UCLH, and University of Oxford, led by the London Centre for Nanotechnology at UCL. i-sense is an Interdisciplinary Research Collaboration (IRC) funded by the UK Engineering and Physical Sciences Research Council (EPSRC).

This work was funded by the UK EPSRC, Royal Society, London Centre for Nanotechnology, H2020 European Research Council, the UCLH NHS Foundation Trust and supported by the National Institute for Health Research University College London Hospitals Biomedical Research Centre.


Provided by University College London

Specific Bacterium in The Gut Linked to Irritable Bowel Syndrome (IBS) (Medicine)

Researchers at the University of Gothenburg have detected a connection between Brachyspira, a genus of bacteria in the intestines, and IBS — especially the form that causes diarrhea. Although the discovery needs confirmation in larger studies, there is hope that it might lead to new remedies for many people with irritable bowel syndrome.

Graphical summary of the study design. Schematic representation of the different phases of the study. In-depth profiling of clinical, histological and molecular characteristics (phase 4) was performed in participants where Brachyspira colonisation could be confirmed/rejected with high confidence, typically based on consistent results from two different methods. Quantification of mucosal immune cells by histology was performed in a representative subset of participants with good-quality biopsy sections, whereas analysis of the human mucus proteome was largely restricted to participants from the explorative cohort. The figure was created with

The pathogenic bacterial genus, Brachyspira, is not usually present in human gut flora. A new study links the bacterium to IBS, particularly the form with diarrhea, and shows that the bacterium hides under the mucus layer protecting the intestinal surface from fecal bacteria.

Attached to intestinal cells

To detect Brachyspira, analyses of fecal samples — which are routinely used for studying the gut flora — were insufficient. Instead, the scientists analyzed bacterial proteins in mucus from biopsies taken from the intestine.

“Unlike most other gut bacteria, Brachyspira is in direct contact with the cells and covers their surface. I was immensely surprised when we kept finding Brachyspira in more and more IBS patients, but not in healthy individuals,” says Karolina Sjöberg Jabbar, who gained her doctorate at Sahlgrenska Academy, University of Gothenburg, and is the first author of the article.

Results inspire hope

Globally, between 5 and 10 percent of the adult population have symptoms compatible with IBS (irritable bowel syndrome). The condition causes abdominal pain and diarrhea, constipation, or alternating bouts of diarrhea and constipation. People with mild forms of IBS can often live a fairly normal life, but if the symptoms are more pronounced it may involve a severe deterioration in quality of life.

“Many questions remain to be answered, but we are hopeful that we might have found a treatable cause of IBS in at least some patients,” says Karolina Sjöberg Jabbar.

Bacterium found in 19 out of 62

The study was based on colonic tissue samples (biopsies) from 62 patients with IBS and 31 healthy volunteers (controls). Nineteen of the 62 IBS patients (31 percent) proved to have Brachyspira in their gut, but the bacterium was not found in any samples from the healthy volunteers. Brachyspira was particularly common in IBS patients with diarrhea.

“The study suggests that the bacterium may be found in about a third of individuals with IBS. We want to see whether this can be confirmed in a larger study, and we’re also going to investigate whether, and how, Brachyspira causes symptoms in IBS. Our findings may open up completely new opportunities for treating and perhaps even curing some IBS patients, especially those who have diarrhea,” says Magnus Simrén, Professor of Gastroenterology at Sahlgrenska Academy, University of Gothenburg, and Senior Consultant at Sahlgrenska University Hospital.

Several possible therapies

In a pilot study that involved treating IBS patients with Brachyspira with antibiotics, the researchers did not succeed in eradicating the bacterium.

“Brachyspira seemed to be taking refuge inside the intestinal goblet cells, which secrete mucus. This appears to be a previously unknown way for bacteria to survive antibiotics, which could hopefully improve our understanding of other infections that are difficult to treat,” Sjöberg Jabbar says.

However, if the association between Brachyspira and IBS symptoms can be confirmed in more extensive studies, other antibiotic regimens, as well as probiotics, may become possible treatments in the future. Since the study shows that patients with the bacterium have a gut inflammation resembling an allergic reaction, allergy medications or dietary changes may be other potential treatment options. The researchers at the University of Gothenburg plan to investigate this in further studies.

“This is another good example of the importance of free, independent basic research that, in cooperation with healthcare, results in unexpected and important discoveries that may be beneficial to many patients. All made without the primary purpose of the study being to look for Brachyspira,” says Professor Gunnar C Hansson, who is a world leading authority in research on the protective mucus layer in the intestines.

The study is published in the journal Gut.

References: Karolina S Jabbar, Brendan Dolan et al., “Association between Brachyspira and irritable bowel syndrome with diarrhoea”; Gut, 2020.

Provided by University of Gothenburg

Fruit Flies Reveal New Insights Into Space Travel’s Effect on the Heart (Planetary Science)

Scientists at Sanford Burnham Prebys Medical Discovery Institute have shown that fruit flies that spent several weeks on the International Space Station (ISS)–about half of their lives–experienced profound structural and biochemical changes to their hearts. The study, published today in Cell Reports, suggests that astronauts who spend a lengthy amount of time in space–which would be required for formation of a moon colony or travel to distant Mars–could suffer similar effects and may benefit from protective measures to keep their hearts healthy. The research also revealed new insights that could one day help people on Earth who are on long-term bed rest or living with heart disease.

©Stanley walls

“For the first time, we can see the cellular and molecular changes that may underlie the heart conditions seen in astronaut studies,” says Karen Ocorr, Ph.D., assistant professor in the Development, Aging and Regeneration Program at Sanford Burnham Prebys and co-senior author of the study. “We initiated this study to understand the effects of microgravity on the heart, and now we have a roadmap we can use to start to develop strategies to keep astronaut hearts strong and healthy.”

Past studies have shown that under microgravity conditions, the human heart shifts from an oval to a more spherical shape. Space flight also causes the heart muscle to weaken (atrophy), reducing its ability to pump blood throughout the body. However, until now, human heart studies–completed using ultrasounds performed on the ISS–have been limited to a relatively small number of astronauts. While important, these studies didn’t reveal the cellular and molecular changes that drive these transformations–information needed to develop countermeasures that will keep astronauts safe on prolonged flights.

“As we continue our work to establish a colony on the moon and send the first astronauts to Mars, understanding the effects of extended time in microgravity on the human body is imperative,” says Sharmila Bhattacharya, Ph.D., senior scientist at NASA and a study author. “Today’s results show that microgravity can have dramatic effects on the heart, suggesting that medical intervention may be needed for long-duration space travel, and point to several directions for therapeutic development.”

Fruit flies are surprisingly good models for studying the human heart. The insects share nearly 75% of disease-causing genes found in humans, and their tube-shaped hearts mirror an early version of ours–which begins as a tube when we’re in the womb and later folds into the four chambers with which we’re familiar. Fortunately, fruit flies are also largely self-sustaining. All the food the flies needed for the duration of the trip were contained in special boxes designed for this study–allowing busy astronauts to focus on other tasks.

Journey to space

In the study, the scientists sent the special “vented fly boxes” containing vials filled with a few female and male fruit flies to the ISS for a one-month-long orbit. While in space, these flies produced hundreds of babies that experienced three weeks of microgravity–the human equivalent of three decades. The fruit flies that were born in space returned to Earth via a splashdown off the coast of Baja California. A member of the scientific team retrieved the flies from the Port of Long Beach and–very carefully–drove the specimens to Sanford Burnham Prebys’ campus in La Jolla, California.

Once the flies arrived at the lab, the scientists sprang into action. Tests of heart function had to be taken within 24 hours of the return to Earth so gravity wouldn’t interfere with the results. The researchers worked around the clock to measure the flies’

ability to climb up a test tube; to capture videos of the beating hearts to measure contractility and heart rate; and to preserve tissue for future genetic and biochemical assays, including mapping gene expression changes that occurred in the heart.

Extensive tissue remodeling

This work revealed that the space flies had smaller hearts that were less contractile–reducing their ability to pump blood and mirroring symptoms seen in astronauts. The heart tissue also underwent extensive remodeling. For example, the normally parallel muscle fibers became misaligned and lost contact with the surrounding fibrous structures that permit the heart to generate force–resulting in impaired pumping.

“In the normal fly heart, the muscle fibers work like your fingers when they squeeze a tube of toothpaste. In the space flies, the contraction was like trying to get toothpaste out by pressing down instead of squeezing,” explains Ocorr. “For humans, this could become a big problem.”

To the scientists’ surprise, the fibrous extracellular matrix (ECM) surrounding the heart of the space flies was significantly reduced. After a heart injury such as a heart attack, this supportive tissue is often overproduced and interferes with heart function. For this reason, the interplay between the ECM and the heart is an active area of research for heart scientists.

“We were very excited to find several ECM-interacting proteins that were dysregulated in the space flies,” says Rolf Bodmer, Ph.D., director and professor in the Development, Aging and Regeneration Program at Sanford Burnham Prebys and co-senior author of the study. “These proteins weren’t previously on the radar of heart researchers, so this could accelerate the development of therapies that improve heart function by reducing fibrosis.”

The tip of the iceberg

Ocorr and Bodmer are still busy analyzing genetic and molecular data from this study and believe these insights are the “tip of the iceberg” for this type of research. Vision problems are common in astronauts, so the scientists are also analyzing eye tissue from the space flies. Another area of interest relates to the babies of the flies that were born in space, which would help reveal any inherited effects of space flight. While astronaut health is the primary goal, people on Earth may ultimately be the greatest beneficiaries of this pioneering work.

“I am confident that heart disease research is going to benefit from the insights we’re gaining from these flights,” says Ocorr. “Understanding how the heart functions in space is also going to teach us more about how the heart works and can break on Earth.”

References: Stanley Walls, Soda Diop et al., “Prolonged Exposure to Microgravity Reduces Cardiac Contractility and Initiates Remodeling in Drosophila”, Cell Reports, 2020. DOI:

Provided by Sanford Burnham Prebys Medical Discovery Institute

Space Worms Experiment Reveals Gravity Affects Genes (Planetary Science)

Living at low gravity affects cells at the genetic level, according to a study of worms in space.

Genetic analysis of Caenorhabditis elegans worms on the International Space Station showed “subtle changes” in about 1,000 genes.

©Willis et al.

Stronger effects were found in some genes, especially among neurons (nervous system cells).

The study, by the University of Exeter and the NASA GeneLab, aids our understanding of why living organisms – including humans – suffer physical decline in space.

“We looked at levels of every gene in the worms’ genome and identified a clear pattern of genetic change,” said Dr Timothy Etheridge, of the University of Exeter.

“These changes might help explain why the body reacts badly to space flight.

“It also gives us some therapy targets in terms of reducing these health effects, which are currently a major barrier to deep-space exploration.”

The study exposed worms to low gravity on the International Space Station, and to high gravity in centrifuges.

The high-gravity tests gave the researchers more data on gravity’s genetic impacts, and allowed them to look for possible treatments using high gravity in space.

“A crucial step towards overcoming any physiological condition is first understanding its underlying molecular mechanism,” said lead author Craig Willis, of the University of Exeter.

“We have identified genes with roles in neuronal function and cellular metabolism that are affected by gravitational changes.

“These worms display molecular signatures and physiological features that closely mirror those observed in humans, so our findings should provide foundations for a better understanding of spaceflight-induced health decline in mammals and, eventually, humans.”

Dr Etheridge added: “This study highlights the ongoing role of scientists from Europe and the UK in space flight life sciences research.”

References: Craig Willis et al., “Comparative Transcriptomics Identifies Neuronal and Metabolic Adaptations to Hypergravity and Microgravity in Caenorhabditis elegans”, IScience, 2020. DOI:

Provided by University of Exeter

Water-to-land Transition in Early Tetrapods (Paleontology)

The water-to-land transition is one of the most important and inspiring major transitions in vertebrate evolution. And the question of how and when tetrapods transitioned from water to land has long been a source of wonder and scientific debate.

The aerial scene depicts two Late Devonian early tetrapods – Ichthyostega and Acanthostega – coming out of the water to move on land. Footprints trail behind the animals to show a sense of movement. ©Original artwork created by scientific illustrator Davide Bonadonna. Copyrighted, request permission to use,

Early ideas posited that drying-up-pools of water stranded fish on land and that being out of water provided the selective pressure to evolve more limb-like appendages to walk back to water. In the 1990s newly discovered specimens suggested that the first tetrapods retained many aquatic features, like gills and a tail fin, and that limbs may have evolved in the water before tetrapods adapted to life on land. There is, however, still uncertainty about when the water-to-land transition took place and how terrestrial early tetrapods really were.

A paper published November 25 in Nature addresses these questions using high-resolution fossil data and shows that although these early tetrapods were still tied to water and had aquatic features, they also had adaptations that indicate some ability to move on land. Although, they may not have been very good at doing it, at least by today’s standards.

Lead author Blake Dickson, PhD ’20 in the Department of Organismic and Evolutionary Biology at Harvard University, and senior author Stephanie Pierce, Thomas D. Cabot Associate Professor in the Department of Organismic and Evolutionary Biology and curator of vertebrate paleontology in the Museum of Comparative Zoology at Harvard University, examined 40 three-dimensional models of fossil humeri (upper arm bone) from extinct animals that bridge the water-to-land transition.

“Because the fossil record of the transition to land in tetrapods is so poor we went to a source of fossils that could better represent the entirety of the transition all the way from being a completely aquatic fish to a fully terrestrial tetrapod,” said Dickson.

Two thirds of the fossils came from the historical collections housed at Harvard’s Museum of Comparative Zoology, which are sourced from all over the world. To fill in the missing gaps, Pierce reached out to colleagues with key specimens from Canada, Scotland, and Australia. Of importance to the study were new fossils recently discovered by co-authors Dr. Tim Smithson and Professor Jennifer Clack, University of Cambridge, UK, as part of the TW:eed project, an initiative designed to understand the early evolution of land-going tetrapods.

Three major stages of humerus shape evolution: from the blocky humerus of aquatic fish, to the L-shape humerus of transitional tetrapods, and the twisted humerus of terrestrial tetrapods. Columns (left to right) = aquatic fish, transitional tetrapod, and terrestrial tetrapod. Rows = Top: extinct animal silhouettes; Middle: 3D humerus fossils; Bottom: landmarks used to quantified shape. Courtesy of Blake Dickson

The researchers chose the humerus bone because it is not only abundant and well preserved in the fossil record, but it is also present in all sarcopterygians – a group of animals which includes coelacanth fish, lungfish, and all tetrapods, including all of their fossil representatives. “We expected the humerus would carry a strong functional signal as the animals transitioned from being a fully functional fish to being fully terrestrial tetrapods, and that we could use that to predict when tetrapods started to move on land,” said Pierce. “We found that terrestrial ability appears to coincide with the origin of limbs, which is really exciting.”

The humerus anchors the front leg onto the body, hosts many muscles, and must resist a lot of stress during limb-based motion. Because of this, it holds a great deal of critical functional information related to an animal’s movement and ecology. Researchers have suggested that evolutionary changes in the shape of the humerus bone, from short and squat in fish to more elongate and featured in tetrapods, had important functional implications related to the transition to land locomotion. This idea has rarely been investigated from a quantitative perspective – that is, until now.

When Dickson was a second-year graduate student, he became fascinated with applying the theory of quantitative trait modeling to understanding functional evolution, a technique pioneered in a 2016 study led by a team of paleontologists and co-authored by Pierce. Central to quantitative trait modeling is paleontologist George Gaylord Simpson’s 1944 concept of the adaptive landscape, a rugged three-dimensional surface with peaks and valleys, like a mountain range. On this landscape, increasing height represents better functional performance and adaptive fitness, and over time it is expected that natural selection will drive populations uphill towards an adaptive peak.

Dickson and Pierce thought they could use this approach to model the tetrapod transition from water to land. They hypothesized that as the humerus changed shape, the adaptive landscape would change too. For instance, fish would have an adaptive peak where functional performance was maximized for swimming and terrestrial tetrapods would have an adaptive peak where functional performance was maximized for walking on land. “We could then use these landscapes to see if the humerus shape of earlier tetrapods was better adapted for performing in water or on land” said Pierce.

The evolutionary pathway and shape change from an aquatic fish humerus to a terrestrial tetrapod humerus. Courtesy of Blake Dickson.

“We started to think about what functional traits would be important to glean from the humerus,” said Dickson. “Which wasn’t an easy task as fish fins are very different from tetrapod limbs.” In the end, they narrowed their focus on six traits that could be reliably measured on all of the fossils including simple measurements like the relative length of the bone as a proxy for stride length and more sophisticated analyses that simulated mechanical stress under different weight bearing scenarios to estimate humerus strength.

“If you have an equal representation of all the functional traits you can map out how the performance changes as you go from one adaptive peak to another,” Dickson explained. Using computational optimization the team was able to reveal the exact combination of functional traits that maximized performance for aquatic fish, terrestrial tetrapods, and the earliest tetrapods. Their results showed that the earliest tetrapods had a unique combination of functional traits, but did not conform to their own adaptive peak.

“What we found was that the humeri of the earliest tetrapods clustered at the base of the terrestrial landscape,” said Pierce. “indicating increasing performance for moving on land. But these animals had only evolved a limited set of functional traits for effective terrestrial walking.”

The researchers suggest that the ability to move on land may have been limited due to selection on other traits, like feeding in water, that tied early tetrapods to their ancestral aquatic habitat. Once tetrapods broke free of this constraint, the humerus was free to evolve morphologies and functions that enhanced limb-based locomotion and the eventual invasion of terrestrial ecosystems

“Our study provides the first quantitative, high-resolution insight into the evolution of terrestrial locomotion across the water-land transition,” said Dickson. “It also provides a prediction of when and how [the transition] happened and what functions were important in the transition, at least in the humerus.”

“Moving forward, we are interested in extending our research to other parts of the tetrapod skeleton,” Pierce said. “For instance, it has been suggested that the forelimbs became terrestrially capable before the hindlimbs and our novel methodology can be used to help test that hypothesis.”

Dickson recently started as a Postdoctoral Researcher in the Animal Locomotion lab at Duke University, but continues to collaborate with Pierce and her lab members on further studies involving the use of these methods on other parts of the skeleton and fossil record.

References: BV Dickson, JA Clack, TR Smithson and SE Pierce. 2020. Functional Adaptive Landscapes Predict Terrestrial Capacity at the Origin of Limbs. Nature. DOI: 10.1038/s41586-020-2974-5.

Provided by University of Harvard

Basketball on the brain: Neuroscientists use sports to study surprise (Neuroscience)

A team of neuroscientists tracked the brains and pupils of self-described basketball fans as they watched March Madness games to study how people process surprise, an unexpected change of circumstances that shifts an anticipated outcome.

The gasp of surprise. Fans leap to their feet. Shouts ring out.

The most exciting moments in sports are often linked to surprise, an unexpected change of circumstances that abruptly shifts the anticipated outcome of the game.

A team of Princeton neuroscientists tracked the brains and pupils of self-described basketball fans as they watched March Madness games to study how people process surprise, an unexpected change of circumstances that shifts an anticipated outcome. ©Victoria Ritvo, Princeton University

Princeton neuroscientist James Antony decided to capitalize on these moments to study how human brains process surprise.

“We’re trying to figure out how people update their understanding of things that are occurring in the real world, based on how events unfold over time — how they set up these contextually-based predictions, and what happens when those are confirmed or contradicted,” said Antony, a CV Starr Fellow in Neuroscience and the first author on a paper published today in the journal Neuron.

The researchers observed 20 self-identified basketball fans as they watched the last five minutes of nine games from the 2012 men’s NCAA March Madness tournament. While they watched the games, a specialized camera tracked their eye movements and functional MRI scans measured their neural activity. The scientists chose basketball because the frequent scoring provided more opportunities to observe how the brain responded to changes.

“This study has both theoretical significance, in terms of testing and refining models of how surprise affects the brain and behavior, and also popular science appeal,” said Ken Norman, the senior author on the paper, who is the Huo Professor in Computational and Theoretical Neuroscience and the chair of the Department of Psychology. “Sporting events like the NCAA tournament are both incredibly compelling and also hyper-quantifiable — you can assess, moment-by-moment, exactly how probable an outcome will be, given what happened in previous games — making them an ideal domain for studying how cognitive processes like memory, event understanding and emotional responses work in the real world. James’ paper is the first to unlock the potential of this approach.”

At surprising moments in the March Madness games — key turnovers, last-minute three-pointers — a typical participant would register rapid pupil dilation and shifts in the pattern of activity in high-level areas of the brain areas like the prefrontal cortex.

“There’s a lot of nuance — it’s not like ‘Surprise is surprise is surprise is surprise,'” Antony said. “Different kinds of surprises have different effects that we observed in different brain systems.”

One interesting result was that shifts in the pattern of activity in high-level brain areas only happened at moments that contradicted the watchers’ current beliefs about which team was more likely to win. “This fits with the idea that patterns in these areas reflect the story of the game, and that the chapters of this story are defined by which team has momentum,” Norman said.

The researchers received help from legendary basketball statistician Ken Pomeroy to create a “win-probability graph,” a tracker for which team was most likely to win at any given moment. Sport websites and sports announcers have long used win-probability graphs to quantify the likely impact of any given turnover or basket.

What the scientists realized was that avid sports fans have an intuitive version of that graph in their heads, Antony said.

“You can tell this by the way people react to things,” he said. “We’re measuring it in this somewhat confined setting here, but if you imagine two friends watching a championship game, and there’s a huge moment, one might get so excited that they tackle their friend over the couch. That doesn’t happen at a moment that isn’t eventful or only has a minimal impact on the overall outcome.”

“People really do have win-probability graphs in their heads,” Norman said. “When the win-probability graph shifts in either direction, that leads to better memory for that part of the game, and it seems to affect pupillary response in addition to memory. There’s an interesting association between those things.”

Historically, neuroscientists studying surprise have created very stripped-down experiments to build a particular expectation, then violate it.

“As a field, we’ve been eager to see whether the principles that we’ve come up with — based on these very simplified scenarios — apply in real life,” Norman said. “The challenge is that in real life, it’s hard to pinpoint the moment when the surprise occurs, or how big the surprise was. Sports let us precisely quantify surprise in a real-world setting, giving us the perfect opportunity to see whether these ideas about surprise generalize outside of the lab.”

References: “Behavioral, physiological, and neural signatures of surprise during naturalistic sports viewing,” by James W. Antony, Thomas H. Hartshorne, Ken Pomeroy, Todd M. Gureckis, Uri Hasson, Samuel D. McDougle and Kenneth A. Norman appears in the Jan. 20, 2021 issue of Neuron, published online Nov. 25 (DOI: 10.1016/j.neuron.2020.10.029).

Provided by Princeton University

Understanding the Power Of Our Sun (Planetary Science)

The Borexino collaboration, in which also scientists from TU Dresden are involved, has succeeded after more than 80 years in experimentally confirming the Bethe-Weizsäcker cycle.

Stars produce their energy through nuclear fusion by converting hydrogen into helium – a process known to researchers as “hydrogen burning”. There are two ways of carrying out this fusion reaction: on the one hand, the so-called pp cycle (proton-proton reaction) and the Bethe Weizsäcker cycle (also known as the CNO cycle, derived from the elements carbon (C), nitrogen (N) and oxygen (O)) on the other hand.

The Borexino detector in combination with the Sun. Copyright: Borexino Collaboration/Maxim Gromov

The pp cycle is the predominant energy source in our Sun, only about 1.6 per mil of its energy comes from the CNO cycle. However, the Standard Solar Model (SSM) predicts that the CNO cycle is probably the predominant reaction in much larger stars. As early as the 1930s, the cycle was theoretically predicted by the physicists Hans Bethe and Carl Friedrich von Weizsäcker and subsequently named after these two gentlemen. While the pp cycle could already be experimentally proven in 1992 at the GALLEX experiment, also in the Gran Sasso massif, the experimental proof of the CNO cycle has so far not been successful.

Both the pp cycle and the CNO cycle produce countless neutrinos – very light and electrically neutral elementary particles. The fact that neutrinos hardly interact with other matter allows them to leave the interior of the sun at almost the speed of light and to transport the information about their origin to earth unhindered. Here the ghost particles have no more than to be captured. This is a rather complex undertaking, which is only possible in a few large-scale experiments worldwide, since neutrinos show up as small flashes of light in a huge tank full of a mixture of water, mineral oil and other substances, also called scintillator. The evaluation of the measured data is complex and resembles looking for a needle in a haystack.

Compared to all previous and ongoing solar neutrino experiments, Borexino is the first and only experiment worldwide that is able to measure these different components individually, in real time and with a high statistical power. This week, the Borexino research collaboration was able to announce a great success: In the renowned scientific journal Nature, they present their results on the first experimental detection of CNO neutrinos – a milestone in neutrino research.

Dresden physicist Professor Kai Zuber is a passionate neutrino hunter.

He is involved in many different experiments worldwide, such as the SNO collaboration in Canada, which was awarded the Nobel Prize for its discovery of a neutrino mass. The fact that with Borexino, he and his colleagues Dr Mikko Meyer and Jan Thurn have now succeeded in experimentally proving the CNO neutrinos for the first time is another major milestone in Zuber’s scientific career: “Actually, I have now achieved everything I had imagined and hoped for. I (almost) no longer believe in great new discoveries in solar neutrino research for the rest of my lifetime. However, I would like to continue working on the optimization of the experiments, in which the Felsenkeller accelerator here in Dresden plays an extremely important role. For sure, we will be able to have even more precise measurements of the Sun in the future.”

References: M. Agostini, K. Altenmüller […] K. Zuber, G. Zuzel: Experimental evidence of neutrinos produced in the CNO fusion cycle in the Sun. Nature.

Provided by Technische Universität Dresden