Making sense of scents: Deciphering our sense of smell

Breaking a longstanding impasse in our understanding of olfaction, scientists at UC San Francisco (UCSF) have created the first molecular-level, 3D picture of how an odor molecule activates a human odorant receptor, a crucial step in deciphering the sense of smell.

 The findings, appearing online March 15, 2023, in Nature, are poised to reignite interest in the science of smell with implications for fragrances, food science, and beyond. Odorant receptors -- proteins that bind odor molecules on the surface of olfactory cells -- make up half of the largest, most diverse family of receptors in our bodies; A deeper understanding of them paves the way for new insights about a range of biological processes.

"This has been a huge goal in the field for some time," said Aashish Manglik, MD, PhD, an associate professor of pharmaceutical chemistry and a senior author of the study. The dream, he said, is to map the interactions of thousands of scent molecules with hundreds of odorant receptors, so that a chemist could design a molecule and predict what it would smell like.

"But we haven't been able to make this map because, without a picture, we don't know how odor molecules react with their corresponding odor receptors," Manglik said.

A Picture Paints the Scent of Cheese

Smell involves about 400 unique receptors. Each of the hundreds of thousands of scents we can detect is made of a mixture of different odor molecules. Each type of molecule may be detected by an array of receptors, creating a puzzle for the brain to solve each time the nose catches a whiff of something new.

"It's like hitting keys on a piano to produce a chord," said Hiroaki Matsunami, PhD, professor of molecular genetics and microbiology at Duke University and a close collaborator of Manglik. Matsunami's work over the past two decades has focused on decoding the sense of smell. "Seeing how an odorant receptor binds an odorant explains how this works at a fundamental level."

To create that picture, Manglik's lab used a type of imaging called cryo-electron microscopy (cryo-EM), that allows researchers to see atomic structure and study the molecular shapes of proteins. But before Manglik's team could visualize the odorant receptor binding a scent molecule, they first needed to purify a sufficient quantity of the receptor protein.

Odorant receptors are notoriously challenging, some say impossible, to make in the lab for such purposes.

The Manglik and Matsunami teams looked for an odorant receptor that was abundant in both the body and the nose, thinking it might be easier to make artificially, and one that also could detect water-soluble odorants. They settled on a receptor called OR51E2, which is known to respond to propionate -- a molecule that contributes to the pungent smell of Swiss cheese.

But even OR51E2 proved hard to make in the lab. Typical cryo-EM experiments require a milligram of protein to produce atomic-level images, but co-first author Christian Billesbøelle, PhD, a senior scientist in the Manglik Lab, developed approaches to use only 1/100th of a milligram of OR51E2, putting the snapshot of receptor and odorant within reach.

"We made this happen by overcoming several technical impasses that have stifled the field for a long time," said Billesbøelle. "Doing that allowed us to catch the first glimpse of an odorant connecting with a human odorant receptor at the very moment a scent is detected."

This molecular snapshot showed that propionate sticks tightly to OR51E2 thanks to a very specific fit between odorant and receptor. The finding jibes with one of the duties of the olfactory system as a sentinel for danger.

While propionate contributes to the rich, nutty aroma of Swiss cheese, on its own, its scent is much less appetizing.

"This receptor is laser focused on trying to sense propionate and may have evolved to help detect when food has gone bad," said Manglik. Receptors for pleasing smells like menthol or caraway might instead interact more loosely with odorants, he speculated.

Just a Whiff

Along with employing a large number of receptors at a time, another interesting quality of the sense of smell is our ability to detect tiny amounts of odors that can come and go. To investigate how propionate activates this receptor, the collaboration enlisted quantitative biologist Nagarajan Vaidehi, PhD, at City of Hope, who used physics-based methods to simulate and make movies of how OR51E2 is turned on by propionate.

"We performed computer simulations to understand how propionate causes a shape change in the receptor at an atomic level," said Vaidehi. "These shape changes play a critical role in how the odorant receptor initiates the cell signaling process leading to our sense of smell."

The team is now developing more efficient techniques to study other odorant-receptor pairs, and to understand the non-olfactory biology associated with the receptors, which have been implicated in prostate cancer and serotonin release in the gut.

Manglik envisions a future where novel smells can be designed based on an understanding of how a chemical's shape leads to a perceptual experience, not unlike how pharmaceutical chemists today design drugs based on the atomic shapes of disease-causing proteins.

"We've dreamed of tackling this problem for years," he said. "We now have our first toehold, the first glimpse of how the molecules of smell bind to our odorant receptors. For us, this is just the beginning."

Bioengineering: Better photosynthesis increases yields in food crops

Soybean field 

.For the first time, RIPE researchers have proven that multigene bioengineering of photosynthesis increases the yield of a major food crop in field trials. After more than a decade of working toward this goal, a collaborative team led by the University of Illinois has transgenically altered soybean plants to increase the efficiency of photosynthesis, resulting in greater yields without loss of quality.

Results of this magnitude couldn't come at a more crucial time. The most recent UN report, The State of Food Security and Nutrition in the World 2022, found that in 2021 nearly 10% of the world population was hungry, a situation that has been steadily worsening over the last few years and eclipsing all other threats to global health in scale. According to UNICEF, by 2030, more than 660 million people are expected to face food scarcity and malnutrition. Two of the major causes of this are inefficient food supply chains (access to food) and harsher growing conditions for crops due to climate change. Improving access to food and improving the sustainability of food crops in impoverished areas are the key goals of this study and the RIPE project.

Realizing Increased Photosynthetic Efficiency, or RIPE, is an international research project that aims to increase global food production by improving photosynthetic efficiency in food crops for smallholder farmers in Sub-Saharan Africa with support from the Bill & Melinda Gates Foundation, Foundation for Food & Agriculture Research, and U.K. Foreign, Commonwealth & Development Office.

"The number of people affected by food insufficiency continues to grow, and projections clearly show that there needs to be a change at the food supply level to change the trajectory," said Amanda De Souza, RIPE project research scientist, and lead author. "Our research shows an effective way to contribute to food security for the people who need it most while avoiding more land being put into production. Improving photosynthesis is a major opportunity to gain the needed jump in yield potential."

Photosynthesis, the natural process all plants use to convert sunlight into energy and yield, is a surprisingly inefficient 100+ step process that RIPE researchers have been working to improve for more than a decade. In this first-of-its-kind work, recently published in Science, the group improved the VPZ construct within the soybean plant to improve photosynthesis and then conducted field trials to see if yield would be improved as a result.

The VPZ construct contains three genes that code for proteins of the xanthophyll cycle, which is a pigment cycle that helps in the photoprotection of the plants. Once in full sunlight, this cycle is activated in the leaves to protect them from damage, allowing leaves to dissipate the excess energy. However, when the leaves are shaded (by other leaves, clouds, or the sun moving in the sky) this photoprotection needs to switch off so the leaves can continue the photosynthesis process with a reserve of sunlight. It takes several minutes for the plant to switch off the protective mechanism, costing plants valuable time that could have been used for photosynthesis.

The overexpression of the three genes from the VPZ construct accelerates the process, so every time a leaf transitions from light to shade the photoprotection switches off faster. Leaves gain extra minutes of photosynthesis which, when added up throughout the entire growing season, increases the total photosynthetic rate. This research has shown that despite achieving a more than 20% increase in yield, seed quality was not impacted.

"Despite higher yield, seed protein content was unchanged. This suggests some of the extra energy gained from improved photosynthesis was likely diverted to the nitrogen-fixing bacteria in the plant's nodules," said RIPE Director Stephen Long, Ikenberry Endowed University Chair of Crop Sciences and Plant Biology at Illinois' Carl R. Woese Institute for Genomic Biology.

The researchers first tested their idea in tobacco plants because of the ease of transforming the crop's genetics and the amount of seeds that can be produced from a single plant. These factors allow researchers to go from genetic transformation to a field trial within months. Once the concept was proven in tobacco, they moved into the more complicated task of putting the genetics into a food crop, soybeans.

"Having now shown very substantial yield increases in both tobacco and soybean, two very different crops, suggests this has universal applicability," said Long. "Our study shows that realizing yield improvements is strongly affected by the environment. It is critical to determine the repeatability of this result across environments and further improvements to ensure the environmental stability of the gain."

Additional field tests of these transgenic soybean plants are being conducted this year, with results expected in early 2023.

"The major impact of this work is to open the roads for showing that we can bioengineer photosynthesis and improve yields to increase food production in major crops," said De Souza. "It is the beginning of the confirmation that the ideas ingrained by the RIPE project are a successful means to improve yield in major food crops."

The RIPE project and its sponsors are committed to ensuring Global Access and making the project's technologies available to the farmers who need them the most.

"This has been a road of more than a quarter century for me personally," said Long. "Starting first with a theoretical analysis of theoretical efficiency of crop photosynthesis, simulation of the complete process by high-performance computation, followed by application of optimization routines that indicated several bottlenecks in the process in our crops. Funding support over the past ten years has now allowed us to engineer alleviation of some of these indicated bottlenecks and test the products at field scale. After years of trial and tribulation, it is wonderfully rewarding to see such a spectacular result for the team."

 

Technology restores cell, organ function in pigs after death

 

Heart, concept illustration

Within minutes of the final heartbeat, a cascade of biochemical events triggered by a lack of blood flow, oxygen, and nutrients begins to destroy a body's cells and organs. But a team of Yale scientists has found that massive and permanent cellular failure doesn't have to happen so quickly.

Using a new technology they developed that delivers a specially designed cell-protective fluid to organs and tissues, the researchers restored blood circulation and other cellular functions in pigs a full hour after their deaths, they report in the Aug. 3 edition of the journal Nature.

The findings may help extend the health of human organs during surgery and expand availability of donor organs, the authors said.

"All cells do not die immediately, there is a more protracted series of events," said David Andrijevic, associate research scientist in neuroscience at Yale School of Medicine and co-lead author of the study. "It is a process in which you can intervene, stop, and restore some cellular function."

The research builds upon an earlier Yale-led project that restored circulation and certain cellular functions in the brain of a dead pig with technology dubbed BrainEx. Published in 2019, that study and the new one were led by the lab of Yale's Nenad Sestan, the Harvey and Kate Cushing Professor of Neuroscience and professor of comparative medicine, genetics, and psychiatry.

"If we were able to restore certain cellular functions in the dead brain, an organ known to be most susceptible to ischemia [inadequate blood supply], we hypothesized that something similar could also be achieved in other vital transplantable organs," Sestan said.

In the new study -- which involved senior author Sestan and colleagues Andrijevic, Zvonimir Vrselja, Taras Lysyy, and Shupei Zhang, all from Yale -- the researchers applied a modified version of BrainEx called OrganEx to the whole pig. The technology consists of a perfusion device similar to heart-lung machines -- which do the work of the heart and lungs during surgery -- and an experimental fluid containing compounds that can promote cellular health and suppress inflammation throughout the pig's body. Cardiac arrest was induced in anesthetized pigs, which were treated with OrganEx an hour after death.

Six hours after treatment with OrganEx, the scientists found that certain key cellular functions were active in many areas of the pigs' bodies -- including in the heart, liver, and kidneys -- and that some organ function had been restored. For instance, they found evidence of electrical activity in the heart, which retained the ability to contract.

"We were also able to restore circulation throughout the body, which amazed us," Sestan said.

Normally when the heart stops beating, organs begin to swell, collapsing blood vessels and blocking circulation, he said. Yet circulation was restored and organs in the deceased pigs that received OrganEx treatment appeared functional at the level of cells and tissue.

"Under the microscope, it was difficult to tell the difference between a healthy organ and one which had been treated with OrganEx technology after death," Vrselja said.

As in the 2019 experiment, the researchers also found that cellular activity in some areas of the brain had been restored, though no organized electrical activity that would indicate consciousness was detected during any part of the experiment.

The team was especially surprised to observe involuntary and spontaneous muscular movements in the head and neck areas when they evaluated the treated animals, which remained anesthetized through the entire six-hour experiment. These movements indicate the preservation of some motor functions, Sestan said.

The researchers stressed that additional studies are necessary to understand the apparently restored motor functions in the animals, and that rigorous ethical review from other scientists and bioethicists is required.

The experimental protocols for the latest study were approved by Yale's Institutional Animal Care and Use Committee and guided by an external advisory and ethics committee.

The OrganEx technology could eventually have several potential applications, the authors said. For instance, it could extend the life of organs in human patients and expand the availability of donor organs for transplant. It might also be able to help treat organs or tissue damaged by ischemia during heart attacks or strokes.

"There are numerous potential applications of this exciting new technology," said Stephen Latham, director of the Yale Interdisciplinary Center for Bioethics. "However, we need to maintain careful oversight of all future studies, particularly any that include perfusion of the brain."

Plesiosaur fossils found in the Sahara suggest they weren't just marine animals

Plesiosaur illustration

Fossils of small plesiosaurs, long-necked marine reptiles from the age of dinosaurs, have been found in a 100-million year old river system that is now Morocco's Sahara Desert. This discovery suggests some species of plesiosaur, traditionally thought to be sea creatures, may have lived in freshwater.

Plesiosaurs, first found in 1823 by fossil hunter Mary Anning, were prehistoric reptiles with small heads, long necks, and four long flippers. They inspired reconstructions of the Loch Ness Monster, but unlike the monster of Lake Loch Ness, plesiosaurs were marine animals -- or were widely thought to be.

Now, scientists from the University of Bath and University of Portsmouth in the UK, and Université Hassan II in Morocco, have reported small plesiosaurs from a Cretaceous-aged river in Africa.

The fossils include bones and teeth from three-metre long adults and an arm bone from a 1.5 metre long baby. They hint that these creatures routinely lived and fed in freshwater, alongside frogs, crocodiles, turtles, fish, and the huge aquatic dinosaur Spinosaurus.

These fossils suggest the plesiosaurs were adapted to tolerate freshwater, possibly even spending their lives there, like today's river dolphins.

The new paper was headed by University of Bath Student Georgina Bunker, along with Nick Longrich from the University of Bath's Milner Centre for Evolution, David Martill and Roy Smith from the University of Portsmouth, and Samir Zouhri from the Universite Hassan II.

The fossils include vertebrae from the neck, back, and tail, shed teeth, and an arm bone from a young juvenile.

"It's scrappy stuff, but isolated bones actually tell us a lot about ancient ecosystems and animals in them. They're so much more common than skeletons, they give you more information to work with" said Dr. Nick Longrich, corresponding author on the paper.

"The bones and teeth were found scattered and in different localities, not as a skeleton. So each bone and each tooth is a different animal. We have over a dozen animals in this collection."

Whilst bones provide information on where animals died, the teeth are interesting because they were lost while the animal was alive -- so they show where the animals lived.

What's more, the teeth show heavy wear, like those fish-eating dinosaur Spinosaurus found in the same beds.

The scientists say that implies the plesiosaurs were eating the same food- chipping their teeth on the armored fish that lived in the river. This hints they spent a lot of time in the river, rather than being occasional visitors.

While marine animals like whales and dolphins wander up rivers, either to feed or because they're lost, the number of plesiosaur fossils in the river suggest that's unlikely.

A more likely possibility is that the plesiosaurs were able to tolerate fresh and salt water, like some whales, such as the beluga whale.

It's even possible that the plesiosaurs were permanent residents of the river, like modern river dolphins. The plesiosaurs' small size would have let them hunt in shallow rivers, and the fossils show an incredibly rich fish fauna.

Dr Longrich said: "We don't really know why the plesiosaurs are in freshwater.

"It's a bit controversial, but who's to say that because we paleontologists have always called them 'marine reptiles', they had to live in the sea? Lots of marine lineages invaded freshwater."

Freshwater dolphins evolved at least four times -- in the Ganges River, the Yangtze River, and twice in the Amazon. A species of freshwater seal inhabits Lake Baikal, in Siberia, so it's possible plesiosaurs adapted to freshwater as well.

The plesiosaurs belong to the family Leptocleididae- a family of small plesiosaurs often found in brackish or freshwater elsewhere in England, Africa, and Australia. And other plesiosaurs, including the long-necked elasmosaurs, turn up in brackish or fresh waters in North America and China.

Plesiosaurs were a diverse and adaptable group, and were around for more than 100 million years. Based on what they've found in Africa -- and what other scientists have found elsewhere -- the authors suggest they might have repeatedly invaded freshwater to different degrees.

"We don't really know, honestly. That's how paleontology works. People ask, how can paleontologists know anything for certain about the lives of animals that went extinct millions of years ago? The reality is, we can't always. All we can do is make educated guesses based on the information we have. We'll find more fossils. Maybe they'll confirm those guesses. Maybe not."

"It's been really interesting to see the direction this project has gone in," said lead author Georgina Bunker. The study initially began as an undergraduate project involving a single bone, but over time, more plesiosaur fossils started turning up, slowly providing a clearer picture of the animal.

The new discovery also expands the diversity of Morocco's Cretaceous. Said Dr. Samir Zouhri, "This is another sensational discovery that adds to the many discoveries we have made in the Kem Kem over the past fifteen years of work in this region of Morocco. Kem Kem was truly an incredible biodiversity hotspot in the Cretaceous."

"What amazes me" said coauthor Dave Martill, "is that the ancient Moroccan river contained so many carnivores all living alongside each other. This was no place to go for a swim."

But what does this all mean for the plausibility of something like a Loch Ness Monster? On one level, it's plausible. Plesiosaurs weren't confined to the seas, they did inhabit freshwater. But the fossil record also suggests that after almost a hundred and fifty million years, the last plesiosaurs finally died out at the same time as the dinosaurs, 66 million years ago.

Story Source: Science Daily

Scientists reveal how Venus fly trap plants snap shut

 

Venus fly trap

Scientists at Scripps Research have revealed the three-dimensional structure of Flycatcher1, an aptly named protein channel that may enable Venus fly trap plants to snap shut in response to prey. The structure of Flycatcher1, published February 14 in Nature Communications, helps shed light on longstanding questions about the remarkably sensitive touch response of Venus fly traps. The structure also gives the researchers a better understanding of how similar proteins in organisms including plants and bacteria, as well as proteins in the human body with similar functions (called mechanosensitive ion channels), might operate.

"Despite how different Venus fly traps are from humans, studying the structure and function of these mechanosensitive channels gives us a broader framework for understanding the ways that cells and organisms respond to touch and pressure," says co-senior author and Scripps Research professor Andrew Ward, PhD.

"Every new mechanosensitive channel that we study helps us make progress in understanding how these proteins can sense force and translate that to action and ultimately reveal more about human biology and health," adds co-senior author Ardem Patapoutian, PhD, a Scripps Research professor who won the Nobel Prize in Physiology or Medicine for research on the mechanosensitive channels that allow the body to sense touch and temperature.

Mechanosensitive ion channels are like tunnels that span the membranes of cells. When jostled by movement, the channels open, letting charged molecules rush across. In response, cells then alter their behavior -- a neuron might signal its neighbor, for instance. The ability for cells to sense pressure and movement is important for people's senses of touch and hearing, but also for many internal body processes -- from the ability of the bladder to sense that it's full to the ability of lungs to sense how much air is being breathed.

Previously, scientists had homed in on three ion channels in Venus fly traps thought to be related to the ability of the carnivorous plant to snap its leaves shut when its sensitive trigger hairs get touched. One, Flycatcher1, caught researchers' attention because its genetic sequence looked similar to a family of mechanosensitive channels, MscS, found in bacteria.

"The fact that variants of this channel are found throughout evolution tells us that it must have some fundamental, important functions that have been maintained in different types of organisms," says co-first author Sebastian Jojoa-Cruz, a graduate student at Scripps Research.

In the new study, the researchers used cryo-electron microscopy -- a cutting-edge technique that reveals the locations of atoms within a frozen protein sample -- to analyze the precise arrangement of molecules that form the Flycatcher1 protein channel in Venus fly trap plants. They found that Flycatcher1 is, in many ways, similar to bacterial MscS proteins -- seven groups of identical helices surrounding a central channel. But, unlike other MscS channels, Flycatcher1 has an unusual linker region extending outward from each group of helices. Like a switch, each linker can be flipped up or down. When the team determined the structure of Flycatcher1, they found six linkers in the down position, and just one flipped up.

"The architecture of Flycatcher1's channel core was similar to other channels that have been studied for years, but these linker regions were surprising," says Kei Saotome, PhD, a former postdoctoral research associate at Scripps Research and co-first author of the new paper.

To help elucidate the function of these switches, the researchers altered the linker to disrupt the up position. Flycatcher1, they found, no longer functioned as usual in response to pressure; the channel remained open for a longer duration when it would normally close upon removal of pressure.

"The profound effect of this mutation tells us that the conformations of these seven linkers is likely relevant for how the channel works," says co-senior author Swetha Murthy, PhD, of Vollum Institute at Oregon Health and Science University, a former postdoctoral research associate at Scripps Research.

Now that they solved the molecular structure, the research team is planning future studies on the function of Flycatcher1 to understand how different conformations affect its function. More work is also needed to determine whether Flycatcher1 is solely responsible for the snapping shut of Venus fly trap leaves, or whether other suspected channels play complementary roles.