Tuesday, February 28, 2023

MAD SCIENTISTS INC.

Will future computers run on human brain cells?


Johns Hopkins researchers break ground on new field of ‘organoid intelligence’

Peer-Reviewed Publication

JOHNS HOPKINS UNIVERSITY

Thomas Hartung with brain organoids 

IMAGE: THOMAS HARTUNG WITH BRAIN ORGANOIDS IN HIS LAB AT THE JOHNS HOPKINS BLOOMBERG SCHOOL OF PUBLIC HEALTH view more 

CREDIT: WILL KIRK/JOHNS HOPKINS UNIVERSITY

A “biocomputer” powered by human brain cells could be developed within our lifetime, according to Johns Hopkins University researchers who expect such technology to exponentially expand the capabilities of modern computing and create novel fields of study.

The team outlines their plan for “organoid intelligence” today in the journal Frontiers in Science.

“Computing and artificial intelligence have been driving the technology revolution but they are reaching a ceiling,” said Thomas Hartung, a professor of environmental health sciences at the Johns Hopkins Bloomberg School of Public Health and Whiting School of Engineering who is spearheading the work. “Biocomputing is an enormous effort of compacting computational power and increasing its efficiency to push past our current technological limits.”

For nearly two decades scientists have used tiny organoids, lab-grown tissue resembling fully grown organs, to experiment on kidneys, lungs, and other organs without resorting to human or animal testing. More recently Hartung and colleagues at Johns Hopkins have been working with brain organoids, orbs the size of a pen dot with neurons and other features that promise to sustain basic functions like learning and remembering.

“This opens up research on how the human brain works,” Hartung said. “Because you can start manipulating the system, doing things you cannot ethically do with human brains.”

Hartung began to grow and assemble brain cells into functional organoids in 2012 using cells from human skin samples reprogrammed into an embryonic stem cell-like state. Each organoid contains about 50,000 cells, about the size of a fruit fly’s nervous system. He now envisions building a futuristic computer with such brain organoids.

Computers that run on this “biological hardware” could in the next decade begin to alleviate energy-consumption demands of supercomputing that are becoming increasingly unsustainable, Hartung said. Even though computers process calculations involving numbers and data faster than humans, brains are much smarter in making complex logical decisions, like telling a dog from a cat.

“The brain is still unmatched by modern computers,” Hartung said. “Frontier, the latest supercomputer in Kentucky, is a $600 million, 6,800-square-feet installation. Only in June of last year, it exceeded for the first time the computational capacity of a single human brain — but using a million times more energy.”

It might take decades before organoid intelligence can power a system as smart as a mouse, Hartung said. But by scaling up production of brain organoids and training them with artificial intelligence, he foresees a future where biocomputers support superior computing speed, processing power, data efficiency, and storage capabilities.

“It will take decades before we achieve the goal of something comparable to any type of computer,” Hartung said. “But if we don't start creating funding programs for this, it will be much more difficult.”

Organoid intelligence could also revolutionize drug testing research for neurodevelopmental disorders and neurodegeneration, said Lena Smirnova, a Johns Hopkins assistant professor of environmental health and engineering who co-leads the investigations.

“We want to compare brain organoids from typically developed donors versus brain organoids from donors with autism,” Smirnova said. “The tools we are developing towards biological computing are the same tools that will allow us to understand changes in neuronal networks specific for autism, without having to use animals or to access patients, so we can understand the underlying mechanisms of why patients have these cognition issues and impairments.”

To assess the ethical implications of working with organoid intelligence, a diverse consortium of scientists, bioethicists, and members of the public have been embedded within the team.

Johns Hopkins authors included: Brian S. Caffo, David H. Gracias, Qi Huang, Itzy E. Morales Pantoja, Bohao Tang, Donald J. Zack, Cynthia A. Berlinicke, J. Lomax Boyd, Timothy DHarris, Erik C. Johnson, Jeffrey Kahn, Barton L. Paulhamus, Jesse Plotkin, Alexander S. Szalay, Joshua T. Vogelstein, and Paul F. Worley.

Other authors included: Brett J. Kagan, of Cortical Labs; Alysson R. Muotri, of the University of California San Diego; and Jens C. Schwamborn of University of Luxembourg.

IMAGES: Top: Thomas Hartung with brain organoids in his lab at the Johns Hopkins Bloomberg School of Public Health. Credit: Will Kirk/Johns Hopkins University. Bottom: A close-up of a brain organoid. Credit: Jesse Plotkin/Johns Hopkins University. High resolution images available.

Magnified image of a brain organoid produced in Thomas Hartung’s lab, dyed to show neurons in magenta, cell nuclei in blue, and other supporting cells in red and green.

CREDIT

Jesse Plotkin/Johns Hopkins University

Johns Hopkins University news releases are available online, as is information for reporters. To arrange an interview with a Johns Hopkins expert, contact a media representative listed above. Find more Johns Hopkins experts on the Experts Hub, and more Johns Hopkins stories on the Hub.

THE NEGATION OF THE NEGATION

From anti-antibiotics to extinction therapy: how evolutionary thinking can transform medicine

An article published in Frontiers in Science demonstrates how applying an evolutionary perspective to medicine can inspire new ways of preventing and treating disease

Peer-Reviewed Publication

FRONTIERS

Evolutionary medicine can transform biomedicine and public health 

IMAGE: INFOGRAPHIC: EVOLUTIONARY MEDICINE CAN TRANSFORM BIOMEDICINE AND PUBLIC HEALTH view more 

CREDIT: NATTERSON-HOROWITZ ET AL.

The word ‘evolution’ may bring to mind dusty dinosaur bones, but it impacts our health every day. For example, even though antibiotics were invented only a century ago, the evolution of antibiotic resistance is already a major concern. The rise in modern health problems such as obesity can also be traced back to evolutionary principles.   

An article published in Frontiers in Science demonstrates how applying an evolutionary perspective to medicine can inspire new ways of preventing and treating disease.  

“Evolutionary medicine holds promise to transform our understanding of why we get sick and strengthen our ability to protect human health,” said Dr Barbara Natterson-Horowitz, a cardiologist and evolutionary biologist on the faculty of Harvard University and the University of California, Los Angeles. “We came together with experts across many fields to create an overarching research agenda for extending the field.” 

“Our aim is to drive new biomedical innovations and effective public health measures, for everything from infectious disease and pandemics to cancer, diabetes, and cardiovascular disease,” said Prof Daniel Blumstein of the University of California, Los Angeles.  

Overcoming chemotherapy and antibiotic resistance 

Drug resistance is a global health threat in urgent need of solutions. Since bacteria and cancer cells naturally adapt to survive medications, new drug-resistant variants emerge constantly. This problem is currently addressed by continuously producing new antibiotics and cancer chemotherapies – a temporary and costly solution.   

Evolutionary-inspired strategies could break this cycle. For example, ‘anti-evolution’ drugs could stop bacteria from sharing resistance genes with each other. ‘Anti-antibiotics’ are another innovative strategy that could stave off many hospital-acquired antibiotic-resistant infections. These infections often occur when antibiotics administered to the bloodstream reach harmless bacteria in the gut, causing antibiotic-resistant strains to evolve and spread. Oral anti-antibiotics that block these drugs in the gut could prevent this. 

In the case of cancer, a branch of evolution called extinction biology could help tackle chemotherapy resistance. “The idea is that an effective way to eradicate a population is to first critically reduce its size with an ecological catastrophe – like the meteor strike for the dinosaurs,” explained Blumstein. “And then kill remaining individuals with a second disaster – like the famine that followed the meteor.” 

Extinction therapy translates these principles into a clinical strategy. Patients would receive a high dose of one cancer drug to reduce the tumor size, as in current protocols. But before drug resistance has a chance to arise, the first treatment would be replaced by another to kill off the remaining cancer cells. 

Using biodiversity to drive biomedical innovation 

The authors highlight that many new therapeutic strategies may be hidden in plain sight, among the biodiversity of the natural world. 

“Giraffes have the highest blood pressure of any animal, and yet they don’t suffer from the organ damage that hypertension causes in people. And elephants and Tasmanian devils rarely get cancer,” said Natterson-Horowitz. “What is the biology that protects these animals from diseases that kill us? Extraordinarily powerful insights are out there that we haven’t tapped into yet.” 

The authors call for a systematic mapping of disease vulnerability and resistance mechanisms in nature: “Creating this database could, within a decade, help identify unique traits and ultimately lead to novel clinical treatments,” said Blumstein.  

Improving public health measures 

Evolutionary principles could also guide more effective public health policies. “Our bodies and minds evolved in one environment but are living in another – and that causes disease,” said Natterson-Horowitz. “Cardiovascular disease, low fertility, and other common ‘modern’ conditions all result from this evolutionary mismatch.”  

These conditions are often treated as ‘lifestyle’ diseases with interventions that place the responsibility fully on the individual, such as exercise and dietary changes. However, this approach of changing health behaviors doesn’t always work. The authors argue that evolutionary-based public health policies would focus on improving ecological conditions instead.  

“It’s not about treating diabetes when a person gets it at 40, but about making the investment during childhood. Policies that promote interventions early in life can have an immensely positive effect on future health and welfare,” Blumstein added. 

An evolutionary-inspired roadmap for better health 

Evolutionary perspectives are already making their way into the public and political agenda. Some countries have restricted antibiotics use and introduced taxes on sugar-sweetened beverages. However, the authors emphasize that realizing the full potential of evolutionary medicine requires greater investment and interdisciplinary collaboration.  

“Evolutionary insights have tremendous – and as yet unrealized – potential to better understand, prevent, and treat existing and emerging threats to human, animal, and planetary health. Our article provides a roadmap for basic biological and biomedical research as well as the development of innovative biomedicines and more effective public health measures,” the authors concluded.     

Infographic: Evolutionary diversity can inspire biomedical innovation

Infographic: Evolutionary medicine strategies can stem drug resistance


Researchers from the Institute of Botany discovered a new type of coexistence between algae and fungi


Peer-Reviewed Publication

BOTANICKY USTAV AKADEMIE VED CESKE REPUBLIKY

Alcobioses are common in urban areas, too. Lyomyces sambuci, pictured here, is abundant on elder bark. 

IMAGE: ALCOBIOSES ARE COMMON IN URBAN AREAS, TOO. LYOMYCES SAMBUCI, PICTURED HERE, IS ABUNDANT ON ELDER BARK. view more 

CREDIT: INSTITUTE OF BOTANY, CZECH ACADEMY OF SCIENCES

Researchers from the Institute of Botany, Czech Academy of Sciences, described the symbiotic relationship between fungi and algae which science has largely overlooked until now. The coexistence of algae and corticioid basidiomycetes, which are common in temperate forests, has been given a new name: alcobiosis.

Jan Vondrák of the Department of Taxonomy, Institute of Botany, and the first author of the study says “Years ago, during field trips, we were repeatedly puzzled to find a layer of green algae where some of the fungal coatings on wood or bark (so-called corticioid fungi) are disturbed. We discovered that this is a close symbiosis of fungi and algae, not a lichen, though, because the fungus does not depend on its alga for nourishment.“

Researchers introduced a new term for this type of coexistence: alcobiosis, formed by letters from the three key words: algae, corticioid fungi and symbiosis.

In the course of several years, the team of researchers gathered a large number of samples and performed DNA sequencing of the algal and fungal partners. They discovered that the symbiosis is very common and occurs in a great many corticioid fungi across the class of agaricomycetes. Individual fungal species are usualy faithful to a specific algal species from a range of algae described in various alcobises.

Ensuing physiological measurements of algal activity in alcobioses confirmed that the algae are alive, active and engage heavily in photosynthesis, which proves that they prosper inside fungal tissue. Alcobioses bear a striking resemblance to lichens, but differ from them in that the fungal partner does not depend on its alga for nourishment.

“And so the main unknown still is in what way this symbiosis is beneficial for each of the partners. However, our discovery also brings many questions related to geographic, ecological and taxonomic parameters of the symbiosis, such as whether alcobioses diversity increases from polar to tropical regions,“ Jan Vondrák comments on the team´s discovery and adds: “This coexistence has been mentioned in articles before. Most often, though, these were just fragmentary comments that such and such species of corticioid fungus is often found together with algae. We were the first to graps alcobioses as a widespread phenomenon which includes a large number of algae and fungi.“

During their research, the authors also discovered that the spread of alcobioses is aided by small gastropods who often feed on corticioid fungi. Their excrements contain viable cells of algae and fungi who give rise to new alcobiotic coating shortly after. This type of reproduction is similar to lichen isidia“ (i.e., specific lichen thallus structures used in vegetative reproduction).

Scientists at the Institute of Botany have described a symbiotic relationship that is very common in Europe, but which has so far escaped attention, despite the fact that many generations of naturalists have come and gone in Europe. In this way a new space has opened for the further study of alcobioses from various points of view by both professional biologists and biology enthusiasts. For alcobioses are clearly visible to the naked eye and it is easy to distinguish them from similar fungi which do not form this kind of relationship.

Cross-section of alcobiosis in a light microscope (where the algal chlorophyll is green) and a fluorescence microscope (where the chlorophyll is red due to autoflorescence).

CREDIT

Institute of Botany, Czech Academy of Sciences

More information is available at:

Jan Vondrák, Stanislav Svoboda, Lucie Zíbarová, Lenka Å tenclová, Jan MareÅ¡, Václav Pouska, Jiří KoÅ¡nar, Jiří Kubásek: „Alcobiosis, an algal-fungal association on the threshold of lichenisation,“ doi: 10.1038/s41598-023-29384-4 (Scientific Reports, 2023)

 

About the Institute of Botany of the Czech Academy of Sciences

The Institute of Botany is a public research institution that is part of the Czech Academy of Science. It is the largest centre of botanical research in the Czech Republic. It is involved in the research of vegetation at the level of organisms, populations, communities and ecosystems. It presently hosts over 150 scientists and doctoral students spanning the range of research fields from taxonomy through evolutionary biology, ecology through to biotechnology. The main seat of the institute is at the Chateau in Průhonice but it also incorporates separate scientific campuses in Brno and TÅ™eboň. The institute administers the park in Průhonice, which is listed as a National Cultural Heritage site and as a UNESCO World Heritage site, as well as the botanical gardens in Průhonice and in TÅ™eboň. More information at www.ibot.cas.cz/en.

Breathing is going to get tougher

Hotter temps = more air pollution from natural sources

Peer-Reviewed Publication

UNIVERSITY OF CALIFORNIA - RIVERSIDE

Increase in PM2.5 pollution 

IMAGE: CHANGE IN PM2.5 SURFACE CONCENTRATION AFTER 4 DEGREES C OF WARMING. BLACK DOTS SYMBOLIZE STATISTICALLY SIGNIFICANT CHANGES. view more 

CREDIT: JAMES GOMEZ/UCR

Not all pollution comes from people. When global temperatures increase by 4 degrees Celsius, harmful plant emissions and dust will also increase by as much as 14 percent, according to new UC Riverside research.

The research does not account for a simultaneous increase in human-made sources of air pollution, which has already been predicted by other studies. 

“We are not looking at human emissions of air pollution, because we can change what we emit,” said James Gomez, UCR doctoral student and lead author of the study. “We can switch to electric cars. But that may not change air pollution from plants or dust.”

Details of the degradation in future air quality from these natural sources have now been published in the journal Communications Earth & Environment. About two-thirds of the future pollution is predicted to come from plants.

All plants produce chemicals called biogenic volatile organic compounds, or BVOCs. “The smell of a just-mowed lawn, or the sweetness of a ripe strawberry, those are BVOCs. Plants are constantly emitting them,” Gomez said.

On their own, BVOCs are benign. However, once they react with oxygen, they produce organic aerosols. As they’re inhaled, these aerosols can cause infant mortality and childhood asthma, as well as heart disease and lung cancer in adults.

There are two reasons plants increase BVOC production: increases in atmospheric carbon dioxide and increases in temperatures. Both of these factors are projected to continue increasing.

To be clear, growing plants is a net positive for the environment. They reduce the amount of carbon dioxide in the atmosphere, which helps control global warming. BVOCs from small gardens will not harm people. 

“Your lawn, for example, won’t produce enough BVOCs to make you sick,” Gomez explained. “It’s the large-scale increase in carbon dioxide that contributes to the biosphere increasing BVOCs, and then organic aerosols.”

The second-largest contributor to future air pollution is likely to be dust from the Saharan desert. “In our models, an increase in winds is projected to loft more dust into the atmosphere,” said Robert Allen, associate professor of Earth and Planetary Sciences at UCR and co-author of the study. 

As the climate warms, increased Saharan dust is likely to get blown around the globe, with higher levels of dust in Africa, the eastern U.S., and the Caribbean. Dust over Northern Africa, including the Sahel and the Sahara, is likely to increase due to more intense West African monsoons.

Both organic aerosols and dust, as well as sea salt, black carbon, and sulfate, fall into a category of airborne pollutants known as PM2.5, because they have a diameter of 2.5 micrometers or less. The increase in naturally sourced PM2.5 pollution increased, in this study, in direct proportion to CO2 levels.

“The more we increase CO2, the more PM2.5 we see being put into the atmosphere, and the inverse is also true. The more we reduce, the better the air quality gets,” Gomez said. 

For example, if the climate warms only 2 degrees Celsius, the study found only a 7% increase in PM2.5. All of these results only apply to changes found in air quality over land, as the study is focused on human health impacts. 

The researchers hope the potential to improve air quality will inspire swift and decisive action to decrease CO2 emissions. Without it, temperatures may increase 4 degrees C by the end of this century, though it’s possible for the increase to happen sooner. 

Gomez warns that CO2 emissions will have to decrease sharply to have a positive effect on future air quality.

“The results of this experiment may even be a bit conservative because we did not include climate-dependent changes in wildfire emissions as a factor,” Gomez said. “In the future, make sure you get an air purifier.”
 

Coughing 

Japanese scientists with a novel research approach to study populations of deep-sea brittle stars

Peer-Reviewed Publication

PENSOFT PUBLISHERS

Brittle stars 

IMAGE: BRITTLE STARS COLLECTED FROM SAGAMI SEA, JAPAN view more 

CREDIT: HISANORI KOHTSUKA (THE UNIVERSITY OF TOKYO)

For the first time, researchers develop a metabarcoding technology for brittle stars. Japanese scientists, led by Dr Masanori Okanishi of the Hiroshima Shudo University and the University of Tokyo, analyzed environmental DNA (eDNA) released from marine invertebrates in the water, and successfully identified the species they were looking for. The study is published in the open-access journal Metabarcoding and Metagenomics.

Metabarcoding allows researchers to easily and quickly identify species and determine their number in a given location on the basis of environmental DNA (that is DNA released into, for example, the water in a particular lake). 

In Japan, this method has been used successfully to detect the number of species in specific locations in the sea by sampling as little as a bucket of water. Monitoring species is part of the effort for conservation of biological resources and maintenance of their economic value, and metabarcoding can be utilized as a less labor-intensive and more cost-effective tool for marine surveys of biodiversity.

The new study reports on the research team’s development of the first DNA primers for metabarcoding of brittle stars. Brittle stars are the most abundant species in the phylum Echinodermata (approximately 2,100 species), making them promising indicator organisms for environmental DNA metabarcoding. These marine invertebrates are thought to release abundant environmental DNA due to their size, large populations, and habitats in a variety of seafloor environments.

To determine the origin of DNA sequences obtained from samples and used for metabarcoding, Okanishi’s team constructed a database of reference DNA sequences based on specimens identified to 60 brittle star species from Sagami Bay. 

Up until now, metabarcoding had not been used for organisms with little mobility such as brittle stars, because many reference DNA sequences had been misidentified or unidentified. The new database will aid further research and application of the technology.

“If metabarcoding becomes possible through the development of additional primers and richer databases of reference DNA sequences, it will be possible to monitor the marine environment with a precision never before thought possible,” say the authors in conclusion.