Rare Fossilized Algae, Discovered Unexpectedly, fill in Evolutionary Gaps (Paleontology)

When geobiology graduate student Katie Maloney trekked into the mountains of Canada’s remote Yukon territory, she was hoping to find microscopic fossils of early life. Even with detailed field plans, the odds of finding just the right rocks were low. Far from leaving empty-handed, though, she hiked back out with some of the most significant fossils for the time period.

Eukaryotic life (cells with a DNA-containing nucleus) evolved over two billion years ago, with photosynthetic algae dominating the playing field for hundreds of millions of years as oxygen accumulated in the Earth’s atmosphere. Geobiologists think that algae evolved first in freshwater environments on land, then moved to the oceans. But the timing of that evolutionary transition remains a mystery, in part because the fossil record from early Earth is sparse.

Maloney’s findings were published yesterday in Geology. She and her collaborators found macroscopic fossils of multiple species of algae that thrived together on the seafloor about 950 million years ago, nestled between bacterial mounds in a shallow ocean. The discovery partly fills in the evolutionary gap between algae and more complex life, providing critical time constraints for eukaryotic evolution.

Although the field site was carefully chosen by Maloney’s field team leader, sedimentologist Galen Halverson, who has worked in the region for years, the discovery was an unexpected stroke of luck.

“I was thinking, ‘maybe we’ll find some microfossils,’” Maloney said. The possibility of finding larger fossils didn’t cross her mind. “So as we started to find well-preserved specimens, we stopped everything and the whole team gathered to collect more fossils. Then we started to find these big, complex slabs with hundreds of specimens. That was really exciting!”

Determining if traces like the ones Maloney found are biogenic (formed by living organisms) is a necessary step in paleobiology. While that determination is ultimately made in the lab, a few things tipped her off in the field. The traces were very curvy, which can be a good indicator of life, and there were visible structures within them. The fact that there were hundreds of them twisted together sealed the deal for her.

Few people would likely have noticed the fossils that day.

On the right, a slab of gray shale sample. Two black boxes mark places where fossilized algae are present; those are shown on the left. The fossils are reddish-brown marks, curving and broken into segments, on a gray rock background. © Photo by K. Maloney.

“We were really lucky that Katie was there to find them because at first glance, they don’t really look like anything,” Maloney’s advisor, Marc Laflamme, said. “Katie is used to looking at very weird looking fossils, so she has a bit of an eye for saying, ‘This is something worth checking out.’”

Maloney and her colleagues in the field wrestled the heavy slabs into their helicopter for safe transport back to the lab at the University of Toronto–Mississauga. She, Laflamme, and their collaborators used microscopy and geochemical techniques to confirm that the fossils were indeed early eukaryotes. They then mapped out the specimens’ cellular features in detail, allowing them to identify multiple species in the community.

While Maloney and her coauthors were writing up their results, they were confident they had found the first macroscopic specimens from this critical time period. During the peer review process, though, they received word from a collaborator that another group in China had made a similar discovery at about the same time—macrofossils from a similar period. That did not dissuade them.

“What’s a few hundred million years between friends?” Laflamme laughed. “I think our fossils have more detail, which makes them easier to interpret… They’re beautiful. They’re huge, they’re well detailed, there’s anatomy. Your eyes are just drawn to them.”

Ultimately, having two sets of macrofossils from approximately the same time can only improve the timeline of eukaryotic evolution, serving as critical calibration points for DNA-based biologic dating techniques. The new fossils also push back the time when algae were living in marine environments, indicating that evolution had already occurred in lakes on land. But for Maloney, an expert in sedimentology, they also raise questions about what gets preserved in the rock record and why.

“Algae became really important early on because of their role in oxygenation and biogeochemical cycles,” Maloney said. “So why does it take them so long to show up reliably in the fossil record? It’s definitely making us think more about animal ecosystems and whether or not we’re seeing the whole picture, or if we’re missing quite a bit from a lack of preservation.”

The whole project has been engaging for Maloney, who pivoted to algae from more recent biota. “I never expected to be fascinated by algae,” she said. “But I was pleasantly surprised as I started investigating modern algae, finding what an important role they play in sustainability and climate change—all these big issues that we’re dealing with today. So it’s been amazing contributing to algae’s origin story.”

Featured image: The field team breaks for lunch after a morning of fossil-hunting in the Wernecke Mountains of the Yukon Territory in Canada. The ridge they’re sitting on is made of shales of the Dolores Creek Formation, where Maloney and her colleagues collected fossilized algae. (Photo: K. Maloney.)

Reference: Katie M. Maloney, Galen P. Halverson, James D. Schiffbauer, Shuhai Xiao, Timothy M. Gibson, Maxwell A. Lechte, Vivien M. Cumming, Alexie E.G. Millikin, Jack G. Murphy, Malcolm W. Wallace, David Selby, Marc Laflamme; New multicellular marine macroalgae from the early Tonian of northwestern Canada. Geology 2021; doi: https://doi.org/10.1130/G48508.1 URL: https://pubs.geoscienceworld.org/gsa/geology/article/doi/10.1130/G48508.1/595633/New-multicellular-marine-macroalgae-from-the-early

Provided by Geological Society of America

Introducing A Changing-look Blazar: B2 1420+32 (Planetary Science)

Hoda Mishra and colleagues presented multi-wavelength photometric and spectroscopic monitoring observations of the blazar, B2 1420+32, focusing on its outbursts in 2018-2020. They found that the object exhibits a large scale spectral variability and is the so-called “changing-look” blazar. Their study recently appeared on journal ArXiv.

Blazars are active galactic nuclei with their relativistic jets pointing toward the observer, with two major sub-classes, the flat spectrum radio quasars and BL Lac objects. 

AGNs are subdivided into several broad categories, including Type I (also called quasars, Seyfert I) that show a blue continuum from an accretion disk and broad emission lines created by photoionization and Type II (or Seyfert II), which show only narrow lines and no continuum variability. Some AGNs move from one class to another and therefore are dubbed “changing-look” sources. Studying changing look phenomena in blazars can provide useful insight into understanding the origin and particle acceleration processes of radio jets.

Now, Hora Mishra and colleagues reported the detection of a new changing-look blazar. Using mainly the Las Cumbres Observatory Global Telescope Network (LCOGT), they found that the blazar B2 1420+32, at a redshift of 0.682 and with a black hole mass of about 400 million solar masses, appears to shift back and forth between the optical spectrum of an FSRQ and that of a BL Lac several times, while also developing new spectral features.

They found that B2 1420+32 showcases large-scale spectral variability in both its continuum and line emission, together with dramatic gamma-ray and optical variability, on week to month timescales.

They also found that, between 2016–2019, the gamma-ray and optical fluxes increased by factors of 1500 (8 mags) and 40 (4 mags), respectively. The astronomers noted that observed optical variability amplitude is unprecedented, as the optical flux increases by a factor of 100 (5 mags) compared to the SDSS observations conducted in 1995.

For the first time, we detect components in the optical spectra consistent with single temperature blackbody emission, with 20% of the Eddington luminosity.

Wrote authors of the study.

This extreme variability we describe here has not been observed before. However, it may not be uncommon, because dedicated multi-band and spectroscopic monitoring of blazars are still rare. Dedicated searches for more changing-look blazars will extend the changing-look AGN studies to jetted AGNs and allow us to utilize the dramatic spectral changes to reveal AGN/jet physics.

— told Hora, lead author of the study.

Finally, researchers concluded that B2 1420+32 is a changing-look blazar transiting between FSRQ and BL Lac due to dramatic changes in the jet continuum flux diluting the line features. They emphasized that extreme variability, as in the case of B2 1420+32, has not been observed before in any blazar.

Featured image: Multi-band optical LCOGT, ASAS-SN, and Fermi light curves of B2 1420+32 © Mishra et al.

Reference: Hora D. Mishra, Xinyu Dai, Ping Chen, Jigui Cheng, T. Jayasinghe, Michael A. Tucker, Patrick J. Vallely, David Bersier, Subhash Bose, Aaron Do, Subo Dong, Thomas W. S. Holoien, Mark E. Huber, Christopher S. Kochanek, Enwei Liang, Anna V. Payne, Jose Prieto, Benjamin J. Shappee, K.Z. Stanek, Saloni Bhatiani, John Cox, Cora DeFrancesco, Zhiqiang Shen, Todd A. Thompson, Junfeng Wang, “The Changing Look Blazar B2 1420+32”, pp. 1-21, ArXiv, 2021. https://arxiv.org/abs/2103.08707

Copyright of this article totally belongs to our author S. Aman. One is allowed to reuse it only by giving proper credit either to him or to us

Astronomers Revealed Mass and True Nature Of TOI-263b (Planetary Science)

The TESS mission is dedicated to the search for transiting extrasolar planets around the brightest and closest stars in the sky. It was launched on April 18th 2018, and has recently completed its initial survey of (almost) the entire sky with 26 pointings over 2 years. Many of the new exciting planets discovered by TESS are excellent targets for precise radial velocity (RV) follow-up to determine accurate masses and bulk properties, and later explore the characterization of their atmospheres.

However, despite the thousands of planets discovered to date, many questions remain about their dominant formation mechanism(s) and the underlying statistical properties of the different exoplanet populations. Thus, new objects displaying extreme properties may deliver critical knowledge to understand the formation and evolution of planetary systems. One of those extreme systems is TOI-263 b (Gaia DR2 5119203027983398656).

TOI-263 b is a validated ultra-short period substellar object in a 0.56-day orbit around a faint (V = 18.97) M3.5 dwarf star. The substellar nature of TOI-263 b was explored using multi-color photometry, which determined a true radius of 0.87 ± 0.21RJ , establishing TOI-263 b’s nature ranging from an inflated Neptune to a brown dwarf. The orbital period-radius parameter space occupied by TOI-263 b is quite unique, which prompted a further characterization of its true nature.

We report radial velocity measurements of TOI-263 obtained with 3 VLT units and the ESPRESSO spectrograph to retrieve the mass of TOI-263b.

— told Palle, first author of the study.

Now, Palle and colleagues reported on the ESPRESSO 3-UT mode observations of the TOI263 system, and found that TOI-263 b is low-mass brown dwarf with a mass of 61.6 ± 4.0 MJup (61.6 times that of the mass of the Jupiter). With an ultra-short period of 0.56 days, TOI-263 b is the shortest period known brown dwarf around any stellar type, and a unique and extreme inhabitant of the so-called “brown dwarf desert”. It is also one of the lightest among transiting brown dwarfs found so far around stars of cold (Teff < 4000 K) stellar type.

They found that the orbital period of TOI-263 b is synchronized to the rotation period of the host star, indicative of interaction between the star and the brown dwarf than spun the stellar rotation, and that the star is relatively active. All these findings combined, suggested that the system formation history might be explained via disc fragmentation and later migration to close-in orbits.

These mechanisms have not yet been proven to occur for brown dwarfs, making TOI-263 an excellent system to study in detail.

Featured image credit: An artist impression of brown dwarf orbiting star © Mashable

Reference: E. Palle, R. Luque, M. R. Zapatero Osorio, H. Parviainen, M. Ikoma, H. M. Tabernero, M. Zechmeister, A.J. Mustill, V.S.J. Bejar, N. Narita, F. Murgas, “ESPRESSO Mass determination of TOI-263b: An extreme inhabitant of the brown dwarf desert”, ArXiv, pp. 1-9, 2021. https://arxiv.org/abs/2103.11150

Copyright of this article totally belongs to our author S. Aman. One is allowed to reuse it only by giving proper credit either to him or to us

More Than Words: Using AI to Map How the Brain Understands Sentences (Neuroscience)

Have you ever wondered why you are able to hear a sentence and understand its meaning – given that the same words in a different order would have an entirely different meaning? New research involving neuroimaging and A.I., describes the complex network within the brain that comprehends the meaning of a spoken sentence.

“It has been unclear whether the integration of this meaning is represented in a particular site in the brain, such as the anterior temporal lobes, or reflects a more network level operation that engages multiple brain regions,” said Andrew Anderson, Ph.D., research assistant professor in the University of Rochester Del Monte Institute for Neuroscience and lead author on of the study which was published in the Journal of Neuroscience. “The meaning of a sentence is more than the sum of its parts. Take a very simple example – ‘the car ran over the cat’ and ‘the cat ran over the car’ – each sentence has exactly the same words, but those words have a totally different meaning when reordered.”

The study is an example of how the application of artificial neural networks, or A.I., are enabling researchers to unlock the extremely complex signaling in the brain that underlies functions such as processing language. The researchers gather brain activity data from study participants who read sentences while undergoing fMRI. These scans showed activity in the brain spanning across a network of different regions – anterior and posterior temporal lobes, inferior parietal cortex, and inferior frontal cortex. Using the computational model InferSent – an A.I. model developed by Facebook trained to produce unified semantic representations of sentences – the researchers were able to predict patterns of fMRI activity reflecting the encoding of sentence meaning across those brain regions.

“It’s the first time that we’ve applied this model to predict brain activity within these regions, and that provides new evidence that contextualized semantic representations are encoded throughout a distributed language network, rather than at a single site in the brain.”

Anderson and his team believe the findings could be helpful in understanding clinical conditions. “We’re deploying similar methods to try to understand how language comprehension breaks down in early Alzheimer’s disease. We are also interested in moving the models forward to predict brain activity elicited as language is produced. The current study had people read sentences, in the future we’re interested in moving forward to predict brain activity as people might speak sentences.”

Additional co-authors include Edmund Lalor, Ph.D.Rajeev Raizada, Ph.D., and Scott Grimm, Ph.D., with the University of Rochester, Douwe Kiela with Facebook A.I. Research, and Jeffrey Binder, M.D., Leonardo Fernandino, Ph.D., Colin Humphries, Ph.D., and Lisa Conant, Ph.D. with the Medical College of Wisconsin. The research was supported with funding from the Del Monte Institute for Neuroscience’s Schimtt Program on Integrative Neuroscience and the Intelligence Advanced Research Projects Activity.

Featured image: Say what you see in this picture out loud – “The cat ran over the car.” A.I. is helping researchers unlock how your brain knows that sentence is different than – “The car ran over the cat.”

Reference: Andrew James Anderson, Douwe Kiela, Jeffrey R. Binder, Leonardo Fernandino, Colin J. Humphries, Lisa L. Conant, Rajeev D. S. Raizada, Scott Grimm and Edmund C. Lalor, “Deep artificial neural networks reveal a distributed cortical network encoding propositional sentence-level meaning”, Journal of Neuroscience 22 March 2021, JN-RM-1152-20; DOI: https://doi.org/10.1523/JNEUROSCI.1152-20.2021

Provided by University of Rochester Medical Center

Massey Researcher Finds New Strategy for Fighting Brain Cancer (Medicine)

Most people relate cholesterol to heart health, but it is also a critical component in the growth and spread of brain cancer. VCU Massey Cancer Center researcher Suyun Huang, Ph.D., recently discovered how cholesterol becomes dysregulated in brain cancer cells and showed that the gene responsible for it could be a target for future drugs. 

The mean survival of patients with the most common and aggressive type of brain cancer, glioblastoma multiforme (GBM), is 14 months. The need to find new, effective treatments is urgent and has driven Huang, a member of the Cancer Biology research program at Massey, to detail the workings of numerous genes, proteins, enzymes and other cellular components that contribute to brain cancer growth. Her studies are revealing a biological “roadmap” showing previously unknown functions of genes. 

Huang’s most recent study, published in the journal Nature Communications, pinpoints a gene called YTHDF2 as a crucial link in a chain leading to the development and growth of GBM. It works through a process set in motion by another gene with a well-established reputation for driving cancer progression, EGFR.

Suyun Hunag © Massey Cancer Center

“These findings are exciting because we can potentially target YTHDF2 expression by using YTHDF2 small molecule inhibitors to control glioblastoma tumor growth and spread,” says Huang, who is also a professor in the Department of Human and Molecular Genetics at VCU School of Medicine. “Our experiments also showed that we can stop the formation and growth of brain cancer cells by blocking YTHDF2 expression, so it could also be a powerful target for drug development.”

EGFR is frequently overactivated in many aggressive cancers, including GBM. Huang’s team found that EGFR drives the overexpression of TYHDF2, which then sustains increased cholesterol levels for the invasive growth and development of GBM cells through a process that degrades the LXRα and HIVEP2 genes. LXRα is known to regulate cholesterol levels within cells and HIVEP2 is involved in the development of brain tissue.

Huang’s study is the first to describe this cell signaling cascade, and it helps fill in important parts of the “roadmap” leading to GBM. It is also the first study to show that N6-methyladenosine (m6A), a DNA modification found in nearly all cell-based life forms, plays a role in brain tumor growth and cholesterol metabolism. Huang’s team found that the increase in YTHDF2 expression caused m6A modifications in the mRNA of LXRα and HIVEP2, which inhibited their functions.

Next, Huang and her collaborators plan to evaluate different YTHDF2 inhibitors and establish their effects in lab and animal models. 

“EGFR inhibition and cholesterol regulation are both promising strategies for GBM treatment,” says Huang. “Our study offers an exciting new approach that could potentially work hand-in-hand with these strategies to regulate and treat GBM.”

Additional researchers involved in this study include Runping Fang, Ph.D., and Peng Li, M.D., both from the Department of Human and Molecular Genetics at VCU School of Medicine; Xin Chen, Ph.D., Sicong Zhang, Ph.D., Qing Guo, Ph.D., and Li Ma, Ph.D., all from MD Anderson Cancer Center; Youqiong Ye, Ph.D., from the University of Texas Health Science Center; and Zhongyu Zou, Ph.D., Chuan He, Ph.D., and Hailing Shi, Ph.D., all from the University of Chicago.

This research was supported in part by National Institutes of Health grant R01CA182684, the Paul M. Corman, M.D., Chair in Cancer research endowment fund, and, in part, by VCU Massey Cancer Center’s National Cancer Institute Cancer Center Support Grant P30 CA016059.

Provided by Massey Cancer Center

New Structure That Mimics Blastocysts Could Aid Research into Early Human Development (Medicine)

 A UT Southwestern research team has generated biological structures that resemble blastocysts, the structures that form from the early development of fertilized eggs in mammals, using previously established human embryonic stem cells derived from embryos donated for research and human-induced pluripotent stem cells generated from adult cells – collectively known as human pluripotent stem cells.

The findings, published online today in Nature, could offer a new way to study early human development, pregnancy loss, and developmental defects. Despite their similar morphology to blastocysts, these structures cannot develop into fetuses, says study leader Jun Wu, Ph.D., an assistant professor of molecular biology at UTSW.

“Having an in vitro biological model for blastocyst development is critically important to fill the gap for understanding human development without relying extensively on human embryos,” Wu says.

Human pluripotent stem cells – cells at one of the earliest stages of development – have the potential to become nearly all of the body’s many tissue types. However, it was not known what molecular signals were important to get them to develop into blastocysts, hollow ball-shaped early embryos that form about five days after conception before implanting into the uterine wall. Studies of this stage of human development have largely relied on discarded/donated embryos from fertility treatments, a scarce resource that has ethical concerns, Wu says.  

Blastocysts contain three main cell types: epiblasts, hypoblasts, and trophoblasts. Epiblasts are the quintessential embryonic stem cell, explains Wu, forming various mature tissue types. Consequently, researchers have long maintained cell lines of epiblasts for research. Recent studies have shown that by exposing epiblasts to chemicals that activate the right combinations of genes, these cells can develop into hypoblast or trophoblast cells.

Building on these findings, Wu and his colleagues, including Gary Hon, Ph.D., assistant professor of obstetrics and gynecology and in the Lyda Hill Department of Bioinformatics at UTSW, used similar techniques to encourage epiblast cells to form entire blastocyst-like structures with all three blastocyst cell types present. The researchers treated human embryonic stem cells in cell culture dishes first with chemicals to activate the molecular pathways TGF-beta, FGF, and WNT that have been shown to steer development into hypoblasts, then with chemicals that shut these same pathways down, which guided development toward trophoblasts. In some experiments, they also switched the order in which these chemicals were administered. In both cases, the embryonic stem cells formed cavity-containing structures that looked much like human blastocysts. When Wu and his colleagues tried a similar method with induced pluripotent stem cells – adult cells that have been reprogrammed to regain embryonic stem cell-like qualities – they had similar results.

Analysis showed that these structures, which the researchers call human blastoids, matched the physical characteristics of human blastocysts – they had the same shape, size, and number of cells. A survey of lineage marker proteins showed that the trophoblasts, hypoblasts, and epiblasts were in the same places as found in natural blastocysts. Tests of global gene expression, performed by Hon’s laboratory, showed that genes activated or silenced in the blastoids roughly matched those in human embryos at the same stage of development.

Much like human blastocysts, the researchers could derive stem cells from each cell type in the blastoids. When Wu and his colleagues followed the blastoids into a slightly later stage of development, about 10 days old, they began forming amniotic cavity and yolk sacs and secreting human chorionic gonadotropin, characteristics that human embryos also display.

As proof of principle that these blastoids can be used for research related to human development, the researchers treated these structures with chemicals that inhibit different protein kinase C (PKC) isozymes, proteins thought to be important for the blastocyst cavity to develop. Sure enough, blastoids that received inhibitors for δ, ζ and η isozymes of PKC didn’t form their characteristic cavities.

Wu says this finding suggests that these structures could make good models for better understanding environmental or other chemicals that disrupt early human development. They could also be used to better understand gene activity in embryos or what factors affect successful implantation. Although the efficiency of generating structures of later stage of development from blastoids is low, he adds, further research can help refine this process to create these structures more robustly.

“Right now, much about this stage of human development is a black box,” Wu says. “Blastoids could eventually provide an unlimited resource for better understanding the workings of human blastocysts.”

Hon is a member of UTSW’s Cecil H. and Ida Green Center for Reproductive Biology Sciences.

Other researchers who contributed to this study include Leqian Yu, Yulei Wei, Jialei Duan, Daniel A. Schmitz, Masahiro Sakurai, and Lei Wang, all of UTSW; and Kunhua Wang and Shuhua Zhao of The First Affiliated Hospital of Kunming Medical University.

Wu is a Virginia Murchison Linthicum Scholar in Medical Research who is funded by the Cancer Research and Prevention Institute of Texas (CPRIT) (RR170076) and the Hamon Center for Regenerative Science and Medicine at UT Southwestern. Hon is supported by CPRIT (RP190451), the National Institutes of Health (DP2GM128203), The Welch Foundation (I-1926-20170325), the Burroughs Wellcome Fund (1019804), and the Green Center for Reproductive Biology Sciences.

Reference: Yu L, Wei Y, Duan J, Schmitz DA, Sakurai M, Wang L, Wang K, Zhao S, Hon GC, Wu J. Blastocyst-like structures generated from human pluripotent stem cells. Nature. 2021 Mar 17. doi: 10.1038/s41586-021-03356-y. Epub ahead of print. PMID: 33731924.

Provided by UT Southwestern Medical Center

Containing the Coronavirus Effects On The Nervous System (Biology)

INRS research could prevent infection of nervous system cells by coronaviruses, such as the one responsible for COVID-19

A number of studies have shown that human coronaviruses, including SARS-CoV-2 which causes COVID-19, appear to attack neurons and the nervous system in vulnerable populations. This neuroinvasion through the nasal cavity leads to the risk of neurological disorders in affected individuals. Research conducted at the Institut national de la recherche scientifique (INRS) has identified ways to prevent the spread of infection within the central nervous system (CNS). The study, led by Professor Pierre Talbot and his research associate Marc Desforges, now at CHU-Sainte-Justine, was published in the Journal of Virology.

Antiviral immunity to human coronaviruses

The research team is the first to make the demonstration of a direct link between neurovirulence, protein S cleavage by cellular proteases and innate immunity. This antiviral immunity arises from the production of interferons, frontline proteins that help to detect early the presence of the virus.

“Using a common cold coronavirus, similar to SARS-CoV-2, we were able to show that cleavage of the S protein and interferon could prevent its spread to the brain and spinal cord in mice,” says Talbot, who has been studying coronaviruses for nearly 40 years.

Two therapeutic approaches

According to Marc Desforges, currently a clinical specialist in medical biology at the CHU-Sainte-Justine virology laboratory, the cleavage of the S protein by various cellular proteases is essential for these viruses to effectively infect cells and spread to various organs and systems in the body, including the central nervous system (CNS).

“Our results demonstrate that interferon produced by different cells, including olfactory receptors and cerebrospinal fluid (CSF) producing cells in the brain, could modulate this cleavage. Thus, it could and does significantly limit the viral spread in the CNS and the severity of the associated disease,” says the specialist who worked for 16 years as a research associate at the Armand-Frappier Health Biotechnology Centre of the IRNS.

Taken together, these results point to two potential antiviral targets: protein S cleavage and effective interferon-related innate immunity. “Understanding the mechanisms of infection and viral propagation in neuronal cells is essential to better design therapeutic approaches,” says Talbot. This is especially important for vulnerable populations such as the elderly and immunocompromised.?” This discovery opens the door to new therapeutic strategies.

Featured image: INRS researcher Pierre Talbot surrounded by his team, including his previous research associate Marc Desforges (to his right), in the Laboratoire de neuroimmunovirologie of INRS © INRS

About the study

The article “Potential differences in cleavage of the S protein and type-1 interferon together control human coronavirus infection, propagation, and neuropathology within the central nervous system”, by Alain Le Coupanec, Marc Desforges, Benedikt Kaufer, Philippe Dubeau, Marceline Côté and Pierre J. Talbot, was published in the Journal of Virology. The study was supported by the Canadian Institutes of Health Research (CIHR).

Provided by INRS

Researchers Show Where And How Plants Detect the Nutrient Potassium (Botany)

Newly discovered group of cells in the root tip reacts to potassium deficiency and directs signalling pathways mediating plant adaptation

Potassium is an essential nutrient for all living things. Plants need it in large quantities, especially for growth and in order to withstand stress better. For this reason, they absorb large quantities of potassium from the soil. In agriculture, this leads to a lack of available potassium in the soil – which is why the mineral is an important component in fertilizers. A team of German and Chinese researchers has now shown, for the first time, where and how plants detect potassium deficiency in their roots, and which signalling pathways coordinate the adaptation of root growth and potassium absorption to to uphold the plants potassium supply.

The background: The absorption and transportation of potassium at the level of individual cells have been relatively well characterized, and many of the molecular structures and mechanisms which play a role in these processes are known. Also, researchers demonstrated decades ago that plants adapt very specifically to potassium deficiency. One puzzle that still remains, however, is how plants detect the availability of potassium in the soil and which mechanisms are behind the adaptational reactions in the plant’s organism. The new study sheds light on these questions. The results have been published in the journal “Developmental Cell”

Schematic representation of potassium and calcium concentration in root tip cells under potassium deficiency. The potassium concentration (green, K+) drops within seconds in the potassium-sensitive niche (KSN) above the meristematic zone (MZ) during potassium deficiency. At the same time, a calcium signal (yellow, Ca2+) is generated here, which initiates a signal chain to adapt the plant to potassium deficiency. DZ: differentiation zone; EZ: elongation zone; CS, Casparian stripe.© WWU – AG Kudla

Observations contradict the textbooks

The researchers examined thale cress plants (Arabidopsis thaliana) which were transformed with the newly developed potassium reporter protein GEPII. This reporter protein enables the microscopic detection of the concentration and distribution of potassium ions in cells and tissues. Even when there was no potassium deficiency, the research team made a very surprising discovery: the concentration of this nutrient in the cytoplasm of the cells increased with each cell layer within the root, from the outside to the inside.

“These observations were really surprising,” says Prof. Jörg Kudla from the Institute of Plant Biology and Biotechnology at the University of Münster. “They contradict the textbooks, which say that the nutrients are passed on evenly, from the outside to the inside, towards the root’s vascular tissue – not only from cell to cell but also through the intercellular spaces.”

“Potassium-sensitive niche” reacts to potassium deficiency

The team of researchers subsequently examined how roots react to potassium deficiency. In doing so, they demonstrated for the first time that if plants are subjected to potassium deficiency, the concentration of potassium is reduced only within certain cells in the root tip. These “postmeristematic cells” directly above the viable stem cells in the root tip react extremely rapidly to potassium deficiency; the concentration of potassium inside the cell (in the cytoplasm) decreases within seconds. It had not previously been known that a certain group of cells located centrally inside the root tip reacts to a potassium deficiency in its surroundings. The researchers named this group of cells “potassium-sensitive niche”.

“These observations, too, were very surprising,” says Kudla. “If plants are deprived of potassium, only the cells in the potassium-sensitive niche show a reaction; the concentration of potassium in the other root cells remains unchanged. Previously it was assumed that naturally the cells in the outermost cell layer, the epidermis, would react first to a reduction in the concentration of potassium in the soil.”

Visualizing the path of potassium

Simultaneously with the decrease in the potassium concentration in the potassium-sensitive niche, calcium signals occur in these cells and spread out in the root. As a messenger substance, calcium controls many processes in living organisms – just as it does here: the calcium signals start off a complex molecular signalling cascade. This chain of signals, which the researchers were the first to define in detail, ultimately causes not only an increased formation of potassium transport proteins, but also brings about changes in tissue differentiation in the root. This facilitates a more efficient absorption of potassium ions and maintains its distribution in the plant. “For the first time,” says Kudla, “using imaging methods, we have visualized the path of potassium in a living organism.”

The results provide fundamental insights into where plants detect the availability of the essential nutrient potassium and how they adapt to it. Understanding these processes could in future help to breed better plants for agricultural purposes and deploy fertilizers in a more tailor-made way.

Arabidopsis is an inconspicuous but particularly important plant for plant research.© WWU – AG Kudla

The methodology

To visualize the distribution of potassium in the plant’s roots, the researchers used special microscopic methods (for example, Förster resonance energy transfer, FRET), in combination with sensor proteins for potassium, calcium and hydrogen peroxide. In order to examine the molecular mechanisms, the researchers produced and compared transgenic Arabidopsis plants which, due to different genetic mutations, showed symptoms of potassium deficiency. They used a variety of genetic, molecular-biological and biochemical methods to identify and characterize the proteins and mechanisms involved in the transmission of the potassium and calcium signals.


The work received financial support from the National Natural Science Foundation of China, the German Research Foundation and the Beijing Outstanding University Discipline Program.

Original publication

Feng-Liu Wang, Ya-Lan Tan, Lukas Wallrad, Wei-Hua Wu, Jörg Kudla, Yi Wang (2021): A potassium-sensing niche in Arabidopsis roots orchestrates signaling and adaptation responses to maintain nutrient homeostasis. Developmental Cell 56, 6; 781-794; DOI: 10.1016/j.devcel.2021.02.027

Further information

Featured image: Potassium concentration in root cells (cytosol) immediately after the onset of potassium deficiency (time series, from left). Representation in false colors; red (highest concentration) > yellow > green > blue.© WWU – AG Kudla

Provided by University of Munster

‘Zombie’ Genes? Research Shows Some Genes Come to Life in the Brain After Death (Neuroscience)

In the hours after we die, certain cells in the human brain are still active. Some cells even increase their activity and grow to gargantuan proportions, according to new research from the University of Illinois Chicago.

In a newly published study in the journal Scientific Reports, the UIC researchers analyzed gene expression in fresh brain tissue — which was collected during routine brain surgery — at multiple times after removal to simulate the post-mortem interval and death. They found that gene expression in some cells actually increased after death.

These ‘zombie genes’ — those that increased expression after the post-mortem interval — were specific to one type of cell: inflammatory cells called glial cells. The researchers observed that glial cells grow and sprout long arm-like appendages for many hours after death.  

“That glial cells enlarge after death isn’t too surprising given that they are inflammatory and their job is to clean things up after brain injuries like oxygen deprivation or stroke,” said Dr. Jeffrey Loeb, the John S. Garvin Professor and head of neurology and rehabilitation at the UIC College of Medicine and corresponding author on the paper.

What’s significant, Loeb said, is the implications of this discovery — most research studies that use postmortem human brain tissues to find treatments and potential cures for disorders such as autism, schizophrenia and Alzheimer’s disease, do not account for the post-mortem gene expression or cell activity. 

“Most studies assume that everything in the brain stops when the heart stops beating, but this is not so,” Loeb said. “Our findings will be needed to interpret research on human brain tissues. We just haven’t quantified these changes until now.”

Loeb and his team noticed that the global pattern of gene expression in fresh human brain tissue didn’t match any of the published reports of postmortem brain gene expression from people without neurological disorders or from people with a wide variety of neurological disorders, ranging from autism to Alzheimer’s.

“We decided to run a simulated death experiment by looking at the expression of all human genes, at time points from 0 to 24 hours, from a large block of recently collected brain tissues, which were allowed to sit at room temperature to replicate the postmortem interval,” Loeb said. 

Jeffrey Loeb (Photo: Jenny Fontaine/UIC)

Loeb and colleagues are at a particular advantage when it comes to studying brain tissue. Loeb is director of the UI NeuroRepository, a bank of human brain tissues from patients with neurological disorders who have consented to having tissue collected and stored for research either after they die, or during standard of care surgery to treat disorders such as epilepsy. For example, during certain surgeries to treat epilepsy, epileptic brain tissue is removed to help eliminate seizures. Not all of the tissue is needed for pathological diagnosis, so some can be used for research. This is the tissue that Loeb and colleagues analyzed in their research.

They found that about 80% of the genes analyzed remained relatively stable for 24 hours — their expression didn’t change much. These included genes often referred to as housekeeping genes that provide basic cellular functions and are commonly used in research studies to show the quality of the tissue. Another group of genes, known to be present in neurons and shown to be intricately involved in human brain activity such as memory, thinking and seizure activity, rapidly degraded in the hours after death. These genes are important to researchers studying disorders like schizophrenia and Alzheimer’s disease, Loeb said.

A third group of genes — the ‘zombie genes’ — increased their activity at the same time the neuronal genes were ramping down. The pattern of post-mortem changes peaked at about 12 hours. 

“Our findings don’t mean that we should throw away human tissue research programs, it just means that researchers need to take into account these genetic and cellular changes, and reduce the post-mortem interval as much as possible to reduce the magnitude of these changes,” Loeb said. “The good news from our findings is that we now know which genes and cell types are stable, which degrade, and which increase over time so that results from postmortem brain studies can be better understood.”

Fabien Dachet, Tibor Valyi-Nagy, Kunwar Narayan, Anna Serafini and Gayatry Mohapatra of UIC; James Brown and Susan Celniker of Lawrence Berkeley National Laboratory; Nathan Boley of the University of California, Berkeley; and Thomas Gingeras of Cold Spring Harbor Laboratory are co-authors on the paper.

This research was funded by grants from the National Institutes of Health (R01NS109515, R56NS083527, and UL1TR002003).

Featured image: ‘Zombie’ cells come to life after the death of the human brain. (Image: Dr. Jeffrey Loeb/UIC).

Reference: Dachet, F., Brown, J.B., Valyi-Nagy, T. et al. Selective time-dependent changes in activity and cell-specific gene expression in human postmortem brain. Sci Rep 11, 6078 (2021). https://doi.org/10.1038/s41598-021-85801-6

Provided by UIC Today