Category Archives: Protein Folding

July 14, 2020

While the COVID-19 pandemic continues to impact the world, the research computing centers at Arizona State University, Northern Arizona Universityand University of Arizonahave united as a team to contribute to the Folding@homeproject. The project utilizes idle computing power to significantly contribute to vital scientific research and therapeutic drug discovery.

The Arizona Research Computing consortium is contributing to this collective effort by using advanced computing resources to perform complex protein modeling computations during brief idle periods on local supercomputers. By running these computations only during downtime, contributions to COVID-19 modeling and simulation efforts can be made through the Folding@home project without impacting everyday research. Artist rendition of the SARS-Cov-2 virus. The envelope protein is shown in cyan. (Figure from Klick health https://covid19.klick.com/) Download Full Image

The Folding@home project provides people around the world the opportunity to make active contributions to a variety of scientific research efforts including COVID-19. Volunteers, or citizen scientists, can download the Folding@home software to their personal computers, allowing simulations of complex scientific processes to run in the background while their personal computers are not in use. The Folding@home project is crowdsourcing at its best, using shared computing power at a massive scale to help solve grand challenges in biomedical research.

In addition to mobilizing citizen scientists across the globe, many institutions and corporations are contributing their own computational resources such as high performance workstations and servers. This distributed computational power is estimated to be 10 times faster than the worlds fastest individual supercomputer.

The onslaught of COVID-19 has raised the visibility of the Folding@home project, highlighting a unique opportunity to fight the virus. The project seeks to understand how proteins, which are large, complex molecules that play an important role in how our bodies function, fold to perform their biological functions. This helps researchers understand diseases that result from protein misfolding and identify novel ways to develop new drug therapies.

How proteins fold or misfold can help us understand what causes diseases like cancer, Alzheimer's disease and diabetes. It might also lend insight into viruses such as SARS-CoV-2,the cause of the recent COVID-19pandemic.

Imagine if I told 100 people to fold a pipe cleaner. They are going to fold it in 100 different ways because theres an infinite number of combinations of how to take something that is straight and fold it," said Blake Joyce, assistant director of research computing at the University of Arizona."Thats what viruses and living things do with proteins. They make copies of themselves and fold them up in their own particular way.

Using computational modeling, researchers can explore the mechanics of proteins of the virus and predict every possible way it might fold, or physically change shape.

In biology, shape is function. If you can disrupt that shape, the virus is inactive or cant do its thing. If you disrupt any of the mechanisms that can damage us, you have a cure, or at least something you can treat. And that is what were after. It just takes a lot of computing to come up with every possible way to bend a pipe cleaner, Joyce said.

By running computer simulations, researchers can take the virus and see how it interacts with various compounds or drugs and narrow down which ones might work to interrupt one of the critical mechanisms the virus needs to survive.

Folding@home assigns pieces of a protein simulation to each computer and the results are returned to create an overall simulation. Folding@home computations for COVID-19 research seem to be most productive on the kind of computers found in facilities like Arizonas research computing centers, making their contributions even more valuable.

Volunteers can track their contributions on the Folding@home website and combine their efforts as a team, receiving points for completing work assigned to them and even earning bonus points for work that is more computationally demanding or that might have a greater scientific priority.

The Arizona Research Computing team has risen quickly in the ranks, highlighting the powerful computing capabilities at Arizonas state universities and the effectiveness of regional collaborations. As of mid-June, the Arizona Research Computing team was ranked in the top 100 out of nearly a quarter of a million teams, surpassing Hewlett Packard, Cisco Systems, Apple Computer, Inc., Google, Ireland and Poland, as well as many other university, industry and national or international contributors.

The Folding@home project investigates many research questions that require an enormous amount of computing, but this specific use for COVID-19 provides a unique opportunity, spurring many computing centers to participate in Folding@home for the first time, said Gil Speyer, lead scientific software engineer for Arizona State Universitys research computing center.

Todays biomedical research requires vast amounts of time and computing power. While the Arizona Research Computing team may directly impact COVID-19 research in a small way, the overall impact of the Folding@home project is much broader and will continue to have applications beyond the COVID-19 pandemic.

ASU:

Sean Dudley, assistant vice president and chief research information officer, Research Technology Office

Douglas Jennewein, senior director, research computing, Research Technology Office

Gil Speyer, lead scientific software engineer, Research Technology Office

Marisa Brazil, associate director, research computing, Research Technology Office

Jason Yalim, postdoc,research computing, Research Technology Office

Lee Reynolds, systems analyst principal, research computing, Research Technology Office

Eric Tannenhill, senior software engineer,research computing, Research Technology Office

NAU:

Chris Coffey

UArizona:

Blake Joyce, assistant director, research computing

Todd Merritt, information technology manager, principal

Ric Anderson, systems administrator, principal

Chris Reidy, systems administrator, principal

Adam Michel, systems administrator, principal

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Arizona universities join forces to contribute to COVID-19 modeling and simulation efforts - ASU Now

Scrambled eggs are a breakfast staple and everyone seems to have their own particular method for cooking up the fluffiest eggs possible. But the quest for the perfect scrambled eggs may be over, thanks to this French-style recipe by private chef and YouTuber Bruno Albouze.

Unlike traditional scrambled eggs, which are fluffy and form more solid curds, the French style offers a silkier, creamier variation on the breakfast food, Albouze told TODAY.

If (the eggs are) cooked the right way, it changes the texture, the mouthfeel is just incredible, he said. If it's overcooked, you just don't get the same thing. You're pretty much eating chopped omelet.

According to Albouze, the French way of cooking scrambled eggs is the right way.

While Albouze may have mastered this classic technique, he didnt invent it. Chef Brendan Walsh, the dean of the School of Culinary Arts at The Culinary Institute of America, explained that while scrambled eggs have likely been around for thousands of years in places where chickens were first domesticated (like China and Egypt), the French style emerged in the early days of haute or "high cuisine." This term refers to the style of food preparation that blossomed in France during the 16th century, and is still served in many Michelin-starred eateries today.

Eggs are a staple in cooking school," Albouze said. "Cooking eggs is a big thing, because eggs are the trickiest thing to cook. It's composed mostly of water, because the egg white is watery, and the yolk is fat, but it's tricky because it can overcook very fast.

"Scrambled eggs are definitely the item not everyone knows how to cook it properly. And very very few restaurants know how to do it without them being overcooked.

Albouze, 50, has been cooking since he began an apprenticeship at the age of 14 in France, where he learned the art of cooking, baking and pastry making. Growing up, Albouze said he used to walk to nearby farms for fresh, pasture-raised eggs to make omelets and scrambled eggs.

During his career, the chef has worked at the Htel Plaza Athne in Paris under renowned chef Alain Ducasse and as an instructor at the Culinary Institute Lenotre in Houston.

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But the chef, who now lives in San Diego, really found his stride in 2009 when he started his own YouTube channel. Albouze now has over 760,000 subscribers and 70 million total video views. One of his most popular videos, a recipe for ratatouille, has garnered over 10 million views.

In one of his latest cooking demos, Albouze shared his favorite method for cooking scrambled eggs in the French style. In 2015, he showcased how to cook French-style eggs in water bath. Both methods require constant stirring and movement over low heat to achieve the desired creamy texture.

One method Albouze demonstrated uses a nonstick pan, while the other uses a water bath, which is known as a "bain marie in French and culinary terms.

Walsh added that the French way is a technique where "slow and low, patience and respect" result in the creamiest eggs possible. It is a preparation method that is taught at the CIA, although he said he rarely sees the technique used in America outside of fancier hotels and restaurants.

"It is important in egg cookery to create soft and supple textures," Walsh said via email. "Too high of heat will dry out the protein and take away the supple creaminess that the protein can provide.

Cooking is about ingredients, Albouze added. 80% (is) about the ingredients, 10% skills and 10% time. So, it tells us you don't have to be skilled, just if you understand that ingredients are the most important part of cooking.

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For this reason, he recommends using pasture-raised eggs, which means that the egg-laying hens are allowed to spend plenty of time outside, and feed on grass, bugs or worms instead of a corn- or soy-based diet.

These days, if the egg aisle at your supermarket seems a little empty, it might not be a bad idea to take a road trip out to a local farm, pick up some fresh eggs and try out this fun technique at home.

Said Walsh, Crispy toast and creamy French-style eggs are just the sexiest start to the chefs morning."

This recipes serves two people and takes about 15 minutes from start to finish.

Said Albouze, There's no question that the most important factor when cooking eggs is the cooking technique itself. In the case of scrambled eggs, that means using gentle heat and taking the eggs off the flame a little early to account for carryover cooking.

1. Crack eggs into a bowl and set aside. Do not whisk the eggs. Set flame to medium and allow heat to gently warm the pan prior to adding any fat.

2. Add the olive oil and butter to the pan. Let melt slightly before adding the unbeaten eggs. With a whisk or a rubber spatula, poke the egg yolks and cook slowly on medium heat while constantly stirring, folding and shaking the pan.

3. Continue to cook and move the eggs as they start to scramble. They should yield a soft, delicate and creamy texture in about 5 minutes. As the eggs start to come together, turn off the heat and continue to stir the eggs.

4. To stop the cooking process, whisk in a dash of milk or cream. Season the eggs with salt and a few grinds of pepper before youre ready to serve. Salting the eggs too early may make your eggs watery.

5. If desired, serve the scrambled eggs with some fresh herbs, such as dill or chives. Eggs also pair remarkably well with caviar, salmon roe, truffle, cured salmon or bacon. Either way, these eggs should be served immediately.

Bon apptit!

Read more:
Learn the 'right way' to make scrambled eggs with this French technique - TODAY

Scientists at Oak Ridge National Laboratory havetaken an important step in the race to understand SARS-CoV, the virus that causes COVID-19. Using sophisticated techniques, the scientists mapped out the structure of a critical protein of the coronavirus.

They'rehoping to answer this age-old scientific question that's more pressing than ever in this pandemic:How do you kill something that's not really alive?

The results of the groundbreaking work at Oak Ridge National Laboratory were published in Nature,a leading science journal.

Without this protein, the coronavirus cannot replicate. The scientists hope that by studying this structure, they will be able to find drugs that can stop it.

"The most important part is probably the fact that this protein is essential for the replication of this virus," said Dr.Daniel Kneller, a researcher at Oak Ridge National Lab andthe first author of the study. "If you inhibit this protein you're preventing the virus from assembling. Period."

While this study is focused on a very specific aspect of COVID-19, it opens a window onto the immense network of scientists and scientific organizations working on the pandemic. Tennessee is home to a state-spanning, drug development pipeline that is a microcosm of nationaland global research.

The COVID-19 protease protein is both shaped like a heart and functions as one. Without it the virus cannot grow and spread.(Photo: Andrey Kovalevsky, ORNL, U.S. Department of Energy)

Viruses are hard to treat because they arent like other things that cause diseases. Antibiotics, antifungals and antiparasitic drugs stop cells from replicating or kill them outright. But viruses arent made of cells. They are bundles of proteins and genetic material that hijack cells, forcing them to produce viral particles. Viruses cannot replicate on their own.

Theres debate among biologists as to whether viruses are actually alive because of this.

"How do you kill something that's not really alive?" said Dr. Martha S. Head, director of the Joint Institute for Biological Sciences at Oak Ridge National Lab. She oversees Oak Ridge's COVID-19 molecular design research projects. She explained that this study was part of a push to shut down viral replication at multiple stages, which is how HIV is treated.

"That combination (of drugs) shuts down so many parts of the (HIV) life cycle that you drive down viral loads to where they don't matter," Head explained.

COVID-19 Protease crystals, grown in Oak Ridge National Labs Protein Crystallization and Characterization laboratory and pictured in microscopic view.(Photo: Daniel Kneller: ORNL, U.S. Department of Energy)

To do this, the Oak Ridge team went right to the heart of the coronavirus itsproteins. When a virus infects a cell, it forces the cell to produce viral proteins. But host cells often cant create finished viral proteins, just long strands of unfinished, conjoined, protein.

Proteins are a bit like self-folding origami. Once theyre assembledthey fold into their final shape. Some proteins need to be cut by enzymes, like a protease, to get them into their final shape.Viral proteins cant do that when they're conjoined.

To make finished protein, each viral particle carries a protein enzyme called protease. The COVID-19 protease cuts unfinished viral protein, freeing it to fold itself into a final shape. If the protease cant do this, new virus cannot be made.

It is the heart of viral replication. Finding a chemical compound that can attach to and stop the heart of COVID-19 could be critical for developing a treatment. This is actually the therapeutic approach for anti-HIV drugs like Atazanavir.

But to quickly discover a drug,scientists it helps to have anaccurate map of the protease.

"If part of the protein is incorrectly modeled when you try to design drugs you may miss interactions that would otherwise form (between the drug and the protein)," explained Dr. Andrey Kovalesky, a researcher at Oak Ridge who worked on the study. He explained that without an accurate structure model, researchers might miss a potential drug or get bogged down in false positives.

To find the structure, the scientists grew large crystals made of viral protein in the lab. They took these crystals and exposed them to x-rays. When x-rays hit the protein crystal, they bend and scatter in different directions based on the shape of the protein. After they scatter they hit sensitive x-ray detectors. The scientists use the pattern of x-ray hits to ultimately figure out the shape of the protein.

This is called x-ray crystallography and was famously used to discover the structure of DNA.

The technique is like taking multiple photographs from different angles of the same object. By looking at all angles of the object you can figure out its 3-D structure.

Usually this kind of experiment is done at very cold temperatures. Thats because protein molecules tend to move more at warm temperatures. Its like photographing a moving object.

Unfortunately, getting a clearer picture can also mean missing theshape of the protein or how they move. Viruses often change shape but they cant when theyre frozen. Its like looking at frozen meat and expecting it to behave like a living muscle.

"You really have to appreciate that it's one single confirmation that you're looking at," said Dr. Paul McGonigle,director of the Drug Discovery and Development Program at Drexel University. "You hope that this is the confirmation the protein exists in most of the time, but you never know for sure."

The scientists at Oak Ridge did something special. They did this study at room temperature. Their equipment is more sensitive than the type typically used for this kind of experiment. Because of that, they could see the a fuller range of motion in the of COVID-19 protein that accuracy is very important for developing a drug.

"I think it's useful for them to have these different confirmations to target," said Dr. Ole Mortensen, associate professor of pharmacology at Drexel University. Mortensen explained that his own drug development work was made more challenging because he only had a single snapshot of his target protein.

"I'm worried that I could be missing some of the other ones. I think it makes sense what they're doing. They're opening up more possibilities." Mortensen said.

Oak Ridge might not immediately come to mind when you think medical research. But the national lab system has played a role in medical science since its inception. Sex chromosomes were discovered by pioneering geneticistLiane Russell at Oak Ridge, for example.

When Congress injected hundreds of millions of dollars into COVID-19 research through the CARES Act, The Department of Energy received $99.5 million for the national lab system. Compared to other agencies like the National Institutes of Health or Department of Defense, which got $945 million and $415 million respectively, that might not seem like a lot.

But the national lab system has unique resources that can be quickly marshaled against COVID-19. The Neutron Spallation Facility has the kind of sensitive x-ray detectors necessary to scan a protein at room temperature. The facility houses a lab capable of quickly growing large protein crystals.

"Oak Ridge is uniquely good at growing really big protein crystals," said Charles Sanders, a professor of biochemistry at Vanderbilt University. "Because they have that general expertise, it lets them do room temperature crystallography."

"They also have a network of people around the country, so if the big dogs at these agencies want stuff to happen then it can be, a wartime response, basically," Sanders said.

When the CARES act passed, it let the scientists clear their schedule and focus on COVID-19. Ordinarily, research like this takes months if not years of applying for grants and negotiating for time on equipment. This study mapped and published the protease structure in about a month.

"This is different than our usual projects," said Dr. Head. "Acrossthe Department of Energy as a whole, the speed (of organizing research) is astronomically fast."

Importantly, Oak Ridge houses the Summit supercomputer, one of the fastest supercomputers in the world. Once the structure was figured out by one team, the Summit team quickly screened it against a massive library of potential compounds, looking for potential matches.

"We broke a world record on the supercomputer," said Jeremy Smith,director of the Center for Molecular Biophysics at Oak Ridge. "We screened 1.2 billion compounds in less than a single day."

This is not the first time Dr. Smith has run a massive simulated drug test like this. Knox News covered his experiments back in March. The difference here is scale. Smiths team screened the COVID-19 protease against 1.2 billion possible drugs in a single day using Summit's whole processing system. Now the most promising candidates are being sorted out for eventual testing against live COVID-19 virus.

As impressive as Oak Ridges facilities are, they dont have the ability to do that kind of testing in house. For that, Smith turned to Dr. ColleenJonsson, a professorUniversity of Tennessee Health Sciences Center in Memphis.

Dr. Jonsson is an experienced virologist and virus hunter. She also happens to be the director of the Southeast Regional Biocontainment Laboratory, one of a small network of labs authorized by the federal government to do research on dangerous biological agents and emerging infectious diseases. She had the facility and staff to do what Oak Ridge could not:validate potential drug targets in the real world.

"A virtual screen (in a computer)is a theoretical screen." Dr. Jonsson said. "Once we find them we have to validate we're actually hitting the right thing."

Jonsson saidthat earlier in the year Smith reached out to her to test possible drugs targeting a different protein, the spike protein the coronavirus uses to attach to cells. Since then, her lab has expanded to validating other potential drugs targeting other proteins. While Dr. Jonsson hasnt yet begun to work on the COVID-19 protease, she expects to shortly.

This part of the process, where drugs are tested in live cells to see if they stop a virus from replicating, is arduous. Scientists working at the Biocontainment Lab don full biohazard suits to run their tests. Even after they validate that a potential drug works on a virus in a dish, they still need to run extensive dosage and safety testing, a process that can take months if not years.

Then they have to see if the drug actually works in a real infection. For this they need to test the drug in an infected animal that gets infected with COVID-19 like a human would. Getting an accurate animal model is a difficult process that requires its own experiments and validation.

Dr. Jonsson's team has been busy with this, and other COVID-19 work, since the start of the pandemic. They are among the very few people reporting to work at the University of Tennessee Health Sciences Center campus during the initial lockdowns. The Biocontainment team worked quickly to get everything ready for coronavirus research.

"They worked every day through the Safer at Home order with remarkable dedication," said Dr. Jonsson. "Everyone was working seven days a week to get everything ready."

In spite of its critical role in coronavirus research, the Biocontainment Lab is operating semi-independently. It has not received any funding yet through the CARES Act and is working solely on University of Tennessee funding.

None of thisscience is settled. The author of another structural study on the COVID-19 protease,Dr. Rolf Hilgenfeld of the German Center for Infection Research, was not convinced that the Oak Ridge study would amount to anything.

"I don't think this small difference, (between the shape of the proteins at different temperatures)whatever is its cause, matters for drug design," wrote Hilgenfeld in an email to Knox News.

The Oak Ridge team is planning to scan COVID-19 proteins using a higher resolution technique, neutron scattering,to get even better structures. Dr. Jonsson's team hopes to be running animal tests for possible COVID-19 drugs by the end of the year.

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Tennessee scientists have partnered on cutting-edge discoveries in a race against COVID-19 - Knoxville News Sentinel

Lets say youre a zombie. Youre lumbering around, doing your zombie-mumble, and just ten feet ahead you see a living human being. Your first impulse, of course, is to head over there and eat their brain. And youre about to do just that, when suddenly you feel a pang of something like shame. You remember, dimly, being a human yourself. You remember how you mightve felt, if an undead weirdogot to gnawing on your skull. Youre at an impasse: at once desperate for brain meat and reluctant to kill for it. So you head to your zombie psychologist and start explaining the situation, and your zombie psychologist starts grinning, which annoys you at first I mean, youre baring your soul to this guy until he explains whats on his mind. Turns out, hes been toying with an idea a pilot program for conscience-stricken zombies. Instead of human brains, theyll be fed stuff that looks and tastes justlikebrains, thereby sparing them the obligation to kill. The only thing they need to work out is: what would be an acceptable substitute for human brains? For this weeksGiz Asks, we reached out to a number of brain experts to find out.

Associate Professor, Neurobiology, Harvard Medical School

The brain is of course composed primarily of lipids, and so it is perfectly reasonable to assume that it is brain lipids that zombies really crave. But why human brains and not, say, mouse brains? Lipidomic analysis reveals that human brains are unusually enriched in a compound called sphingomyelin (relative to brains from rodents), and so it is further reasonable to assume that what zombies want is actually lots of sphingomyelin. So where to get it? Eggs. Eggs are packed with sphingomyelin. Furthermore, eggs also have the advantage of having a white outer cortex and a lipid-rich center, just like the human brain, so they seem a reasonable substitute all around.

Chair and Professor of Neurology at the David Geffen School of Medicine at UCLA and Co-Director UCLA Broad Stem Cell Center

A food-based substitute would require a fair amount of work, because youd have to get a sort of fatty, proteinaceous slop together as a mimic for the brain. A thick macaroni and cheese might work, with a larger noodle like ziti or rigatoni and no tang, meaning a thick white cheese, as opposed to cheddar.

The brain sandwich, made from cow brains, was an unusual delicacy in St. Louis for years. When I lived there, I saw what it looked like as they fried it, and its hard to imagine any other organ meat could substitute for the real thing. Kidney and liver are too firm and too structured; most foods we eat, or could think about eating, are also too firm, and not fatty enough.

A brain from another animal might work, though it would have to be an animal with an advanced brain that is, one with the folds we see when we look at the brains surface (which are called gyri and cilici). Those are what distinguish higher mammals from lower mammals. They also make the human brain this particularly characteristic thing in terms of substance and texture and appearance. So an animal brain, to sub for a human brain, would need to have those features. That would mean anything from, say, a dog or cat on up those both have gyri and cilici, whereas rodents and rabbits, for example, do not.

Assistant Professor of Brain Science, Psychiatry and Human Behaviourat Brown University

I think my Zombie would be a vegan. The thing that I have found to be the closest in texture to the brain is tofu (not the firm kind). People are often surprised by that fact, because its really soft you can put your finger through it easily.

Broadly, I study the kind of complex planning and decision making that is localised to the front of the brain, the prefrontal cortex. This area is also one of the most likely to be injured if you hit your head, because your very soft brain bounces around inside your skull. Our lab typically does a demo for Brain Week and other events that lets people feel tofu, and then shake it around in a container and see what happens to it. Shake it around in some water (mimicking some of the protections that our brain has in the cerebro-spinal fluid that it floats in) and the tofu does much better (which is why its packaged in water!).

Unfortunately tofu doesnt mimic all the wonderful folding that it has that lets us pack so many brain cells into a tight space. A sheet of paper crumpled up is best to show that capacity, but paper is probably much less tasty than tofu (to humans anyway, I dont know about zombies!).

Professor, Systems Biology, George Mason University

My proposal is: a literal pound of flesh. Many people have too much of it; its very similar to the brain in texture; it has a lot of cholesterol, which is important, because in my opinion at least zombies would crave exactly that. Also, adipose tissue is very rich with various kinds of growth hormones and other kinds of bioactive stuff. If you could develop some kind of device that would transfer the flesh to the zombies, people might even be grateful they wouldnt have to get liposuction.

Senior Lecturer, Medical Biotechnology, Deakin University

The best thing to do would be to make small versions of a brain from stem cells, called organoids. These are almost, but not quite, brains. You grow them in an artificial 3D environment that mimics the properties of the central nervous tissue, and allow them to develop networks of neural cells in a structured way. Theyre used for research into drugs and diseases and so on, but would probably be an acceptable meat-free snack for an ethically conscious zombie plague.

Professor in Neurology and Professor of Biomedical Engineering at Duke University

If I were a vegetarian zombie, I would try to make a brain substitute using the major components of the brain carbohydrates, proteins, and cells. The major carbohydrate component is hyaluronic acid (which is found in many beauty products, and can be purchased in bulk). Though by itself it does not form a solid, only a very viscous liquid, it can be combined with other materials that do form a solid. For example, sea weed has a carbohydrate named alginate that does form gels when combined with calcium. So, a blend of hyaluronic acid and alginate with calcium can yield a material that has the mechanics of the brain. For the protein component, eggs, beans, soy, and quinoa all can be good choices. To get the texture right, the calcium can be added while stirring to generate chunks. If it is ok to eat other animals, then I would buy pig brains, which are often discarded. Pig organs are close to the same size of humans and have even been used for transplantation due to similarities in physiology/biochemistry. That would be the simplest choice.

Associate Professor, Psychology and Neuroscience, George Mason University

Whenever I eat cauliflower, I think of the cerebellum or little brain. It is tucked away behind the cerebrum, or main part of the brain. The cerebellum is small, but it is where about 80 percent of the entire brains neurons are found! Most of the cerebellums neurons, or gray matter, are found on its outer surface. They are tightly packed together in little folds called folia. The neurons in the folia are connected to each other by nerve fibres, also known as white matter. When the cerebellum is cut in half, the white matter appears as this beautiful network of branches called the arbor vitae, or tree of life. It really does look just like a head of cauliflower!

Professor, Psychology and Neuroscience, Trinity College

The brain is actually quite soft and squishy. Fortunately for us it normally floats in a pool of cerebrospinal fluid that serves as a cushiony packing material protecting the delicate brain from the hard skull. But the brain is so soft it can easily become injured without the head striking any object. If there is enough rotational or acceleration/deceleration motion for the brain to hit the skull the tips of the brain can be bruised and individual cells can be stretched or sheared from their connections. This can happen, for example, in motor vehicle accidents or shaken baby syndrome where the head is thrown very quickly forwards and then backwards.

The consistency I think the brain comes closest to is a gelatin. But I would recommend that our zombie make the gelatin with milk rather than water. This will give it a closer consistency to a brain, the color will be more opaque like a real brain, and it will provide more of the much needed protein the zombie craves. There are even commercially made gelatin molds if the zombie is able to access stores or online shopping.

Another option would be a soft tofu. This might be a great option for a zombie who is a vegetarian or vegan. There is plenty of protein but it will be much harder to mold into the right shape. Sadly, most zombies are not portrayed to have the fine motor skills needed to create a brain shape from scratch, so the tofu would just have to be eaten as is.

On a side note, if our zombie truly finds that nothing satisfies like a real brain, they could certainly consider becoming a neurosurgeon that specializes in therapeutic surgeries, like temporal lobe resections. In this case, a small portion of the temporal lobe of the brain is removed to relieve a person of intractable epilepsy. This might allow for a chance to satisfy their craving while providing benefit to the person involved.

See the article here:
What's the Best Human Brain Alternative for Hungry Zombies? - Gizmodo UK

Lets say youre a zombie. Youre lumbering around, doing your zombie-mumble, and just ten feet ahead you see a living human being. Your first impulse, of course, is to head over there and eat their brain. And youre about to do just that, when suddenly you feel a pang of something like shame. You remember, dimly, being a human yourself. You remember how you mightve felt, if an undead weirdo got to gnawing on your skull. Youre at an impasse: at once desperate for brain meat and reluctant to kill for it. So you head to your zombie psychologist and start explaining the situation, and your zombie psychologist starts grinning, which annoys you at first I mean, youre baring your soul to this guy until he explains whats on his mind. Turns out, hes been toying with an idea a pilot program for conscience-stricken zombies. Instead of human brains, theyll be fed stuff that looks and tastes just like brains, thereby sparing them the obligation to kill. The only thing they need to work out is: what would be an acceptable substitute for human brains? For this weeks Giz Asks, we reached out to a number of brain experts to find out.

Associate Professor, Neurobiology, Harvard Medical School

The brain is of course composed primarily of lipids, and so it is perfectly reasonable to assume that it is brain lipids that zombies really crave. But why human brains and not, say, mouse brains? Lipidomic analysis reveals that human brains are unusually enriched in a compound called sphingomyelin (relative to brains from rodents), and so it is further reasonable to assume that what zombies want is actually lots of sphingomyelin. So where to get it? Eggs. Eggs are packed with sphingomyelin. Furthermore, eggs also have the advantage of having a white outer cortex and a lipid-rich centre, just like the human brain, so they seem a reasonable substitute all around.

Chair and Professor of Neurology at the David Geffen School of Medicine at UCLA and Co-Director UCLA Broad Stem Cell Centre

A food-based substitute would require a fair amount of work, because youd have to get a sort of fatty, proteinaceous slop together as a mimic for the brain. A thick macaroni and cheese might work, with a larger noodle like ziti or rigatoni and no tang, meaning a thick white cheese, as opposed to cheddar.

The brain sandwich, made from cow brains, was an unusual delicacy in St. Louis for years. When I lived there, I saw what it looked like as they fried it, and its hard to imagine any other organ meat could substitute for the real thing. Kidney and liver are too firm and too structured; most foods we eat, or could think about eating, are also too firm, and not fatty enough.

A brain from another animal might work, though it would have to be an animal with an advanced brain that is, one with the folds we see when we look at the brains surface (which are called gyri and cilici). Those are what distinguish higher mammals from lower mammals. They also make the human brain this particularly characteristic thing in terms of substance and texture and appearance. So an animal brain, to sub for a human brain, would need to have those features. That would mean anything from, say, a dog or cat on up those both have gyri and cilici, whereas rodents and rabbits, for example, do not.

Assistant Professor of Brain Science, Psychiatry and Human Behaviour at Brown University

I think my Zombie would be a vegan. The thing that I have found to be the closest in texture to the brain is tofu (not the firm kind). People are often surprised by that fact, because its really soft you can put your finger through it easily.

Broadly, I study the kind of complex planning and decision making that is localised to the front of the brain, the prefrontal cortex. This area is also one of the most likely to be injured if you hit your head, because your very soft brain bounces around inside your skull. Our lab typically does a demo for Brain Week and other events that lets people feel tofu, and then shake it around in a container and see what happens to it. Shake it around in some water (mimicking some of the protections that our brain has in the cerebro-spinal fluid that it floats in) and the tofu does much better (which is why its packaged in water!).

Unfortunately tofu doesnt mimic all the wonderful folding that it has that lets us pack so many brain cells into a tight space. A sheet of paper crumpled up is best to show that capacity, but paper is probably much less tasty than tofu (to humans anyway, I dont know about zombies!).

Professor, Systems Biology, George Mason University

My proposal is: a literal pound of flesh. Many people have too much of it; its very similar to the brain in texture; it has a lot of cholesterol, which is important, because in my opinion at least zombies would crave exactly that. Also, adipose tissue is very rich with various kinds of growth hormones and other kinds of bioactive stuff. If you could develop some kind of device that would transfer the flesh to the zombies, people might even be grateful they wouldnt have to get liposuction.

Senior Lecturer, Medical Biotechnology, Deakin University

The best thing to do would be to make small versions of a brain from stem cells, called organoids. These are almost, but not quite, brains. You grow them in an artificial 3D environment that mimics the properties of the central nervous tissue, and allow them to develop networks of neural cells in a structured way. Theyre used for research into drugs and diseases and so on, but would probably be an acceptable meat-free snack for an ethically conscious zombie plague.

Professor in Neurology and Professor of Biomedical Engineering at Duke University

If I were a vegetarian zombie, I would try to make a brain substitute using the major components of the brain carbohydrates, proteins, and cells. The major carbohydrate component is hyaluronic acid (which is found in many beauty products, and can be purchased in bulk). Though by itself it does not form a solid, only a very viscous liquid, it can be combined with other materials that do form a solid. For example, sea weed has a carbohydrate named alginate that does form gels when combined with calcium. So, a blend of hyaluronic acid and alginate with calcium can yield a material that has the mechanics of the brain. For the protein component, eggs, beans, soy, and quinoa all can be good choices. To get the texture right, the calcium can be added while stirring to generate chunks. If it is OK to eat other animals, then I would buy pig brains, which are often discarded. Pig organs are close to the same size of humans and have even been used for transplantation due to similarities in physiology/biochemistry. That would be the simplest choice.

Associate Professor, Psychology and Neuroscience, George Mason University

Whenever I eat cauliflower, I think of the cerebellum or little brain. It is tucked away behind the cerebrum, or main part of the brain. The cerebellum is small, but it is where about 80 per cent of the entire brains neurons are found! Most of the cerebellums neurons, or grey matter, are found on its outer surface. They are tightly packed together in little folds called folia. The neurons in the folia are connected to each other by nerve fibres, also known as white matter. When the cerebellum is cut in half, the white matter appears as this beautiful network of branches called the arbor vitae, or tree of life. It really does look just like a head of cauliflower!

Professor, Psychology and Neuroscience, Trinity College

The brain is actually quite soft and squishy. Fortunately for us it normally floats in a pool of cerebrospinal fluid that serves as a cushiony packing material protecting the delicate brain from the hard skull. But the brain is so soft it can easily become injured without the head striking any object. If there is enough rotational or acceleration/deceleration motion for the brain to hit the skull the tips of the brain can be bruised and individual cells can be stretched or sheared from their connections. This can happen, for example, in motor vehicle accidents or shaken baby syndrome where the head is thrown very quickly forwards and then backwards.

The consistency I think the brain comes closest to is a gelatin. But I would recommend that our zombie make the gelatin with milk rather than water. This will give it a closer consistency to a brain, the colour will be more opaque like a real brain, and it will provide more of the much needed protein the zombie craves. There are even commercially made gelatin molds if the zombie is able to access stores or online shopping.

Another option would be a soft tofu. This might be a great option for a zombie who is a vegetarian or vegan. There is plenty of protein but it will be much harder to mould into the right shape. Sadly, most zombies are not portrayed to have the fine motor skills needed to create a brain shape from scratch, so the tofu would just have to be eaten as is.

On a side note, if our zombie truly finds that nothing satisfies like a real brain, they could certainly consider becoming a neurosurgeon that specialises in therapeutic surgeries, like temporal lobe resections. In this case, a small portion of the temporal lobe of the brain is removed to relieve a person of intractable epilepsy. This might allow for a chance to satisfy their craving while providing benefit to the person involved.

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Whats the Best Human Brain Alternative for Hungry Zombies? - Gizmodo Australia

Story by Leann BurkePhotos by Marlena Sloss

Early afternoon sunlight shone through the stained glass windows of the new St. Mary Catholic Church building in Ireland as Pat Gress led his mother, the late Rita Gress, through the building she helped plan for and prayed about for decades.

As the pair entered the nave that late May day, Rita looked to the high altar a combination of the high altar and two side altars from the now closed St. Patrick Catholic Church in Corning and teared up.

Duane Gress takes his mother, Rita, on a tour led by his brother, Pat, not pictured, of the new St. Mary Catholic Church in Ireland on May 17. Rita was part of the original long-term planning committee for the new church and Pat was the construction manager. She had leukemia and was able to visit the new church weeks before she died.

Its just fantastic, she said of the whole church. I just cant believe it.

Im glad you like it, Pat said. You were instrumental in getting this thing going.

Pat managed construction on behalf of the church.

The congregation at St. Mary began discussing the possibility of building a new church about 40 years ago. The old building located at 2829 N. 500 W opened in 1905, and at that time, about 45 families attended the church. Today, the church is home to about 1,000 families, many of whom have been members for generations. The Gress family, for example, has been part of the congregation for about a century, and Rita was part of the early discussions about expanding.

When the first long-range planning committee formed in the 1970s, Rita joined and advocated for the construction of a new church building. Ultimately, the committee chose to expand the 1905 building and to begin saving for the construction of a new church down the line.

Then, in the early 2000s, discussion about building a new church picked up again. Rita eagerly took a role on that iteration of the long-range planning committee, as did her son-in-law, Steve Buechler. Steve attended Holy Family Catholic Church in Jasper before he married Ritas daughter, Margaret, and began attending St. Mary.

The 15-person committee spent hours talking to parishioners about what style they wanted the church to have traditional, country Catholic was the consensus and researching architects and designs. Part of their research included a structural study of the 1905 building, which revealed some issues that would have made the cost of remodeling that building about the same as building a new one. That, coupled with the knowledge that a remodel would mean losing that traditional, country look, led the committee to pursue building a new church.

We took a very serious approach, Steve said. We knew we were planning for the next 100 years of our parish.

The new church began to become a reality in 2017 when the parish launched the Building Our Future capital campaign to raise the $6 million needed for the project. As of March, the campaign had raised about $5.6 million.

Construction crews work on the pillars on the top of the new St. Mary Catholic Church in Ireland on Jan. 16. The new church was designed to look as similar as possible to the old church, seen in the background.

According to guidelines from the Catholic Diocese of Evansville, the campaign needed $4.8 million 80% of the total cost to break ground. That threshold was met by 2018, and construction crews broke ground that year. At last, the decades of research and planning were turning into something tangible.

St. Mary parishioners dedicated so many years to planning for their new church that when Evansvilles bishop, Joseph Siegel, dedicated the new building on June 28, he joked in his homily that the parishioners had been dreaming of their new church almost as long as the biblical Jews of Jesus time spent building the temple from which Jesus expelled merchants in the second chapter of The Gospel of John. According to the story which was the Gospel reading for the dedication Mass that biblical temple took 46 years to build.

The years of hard work and planning paid off, however. The final designs for the new church yielded a traditional country church that looks much like the old building, but will fit 700 per mass, with room for additional folding chairs if need be, rather than the 380 the 1905 building housed. It also includes several features the parishioners wanted, including an additional parking lot, a space inside the church building for offices, a cry/bridal room, a covered entrance and a narthex, a large open area before the nave where parishioners can gather before and after church services.

The builders did an amazing job of bringing our vision into reality, Steve said.

The wish list also included refurbishing the original nine stained-glass windows from the 1904 church for use in the new building, and the commissioning of 11 new windows. For that, the parish called on Mominee Studios of Evansville. The original windows were made according to the American Opalescent style following the technique developed by John La Farge, an artist at the forefront of the American Arts and Crafts Movement of the late 1800s, according to the Smithsonian American Art Museum.

When [St. Mary Church] was built in 1904, all the churches were using [that style], said Jules Mominee, owner of Mominee Studios.

To restore the nine old windows, Jules and members of his team spent most of a day carefully removing the century-old, intricately decorated windows some of which consisted of three glass panels and loading them into a truck for transport to the studio in Evansville. There, the team refurbished the windows to make them vibrant again.

Mominee Studios employee Nick Morgan assembles the St. Scholastica stained glass window in Evansville on Oct. 17. Mominee Studios worked on 26 windows for the new church, including designing and building 9 new windows. From the beginning of the design process to the installation of the final window, Mominee Studios spent two years on the project.

The artists also built the 11 new windows at the studio, following techniques almost identical to those used by La Farge in the late 1800s. If a single artist worked on one window from start to finish, Jules said, the process would take two months, but his team of six artists can complete a single window in two weeks, and they always work on groups of windows at the same time to make a project move along quickly.

Like the stained-glass windows, the high altar, too, took a long time to prepare for its place in the new church. Jim Buechlein, owner of Buechleins Kwik Strip & Custom Furniture & Design in Jasper, oversaw the removal of the three altars from St. Patrick in Corning three years ago and refurbished them into the ornate, gothic-style altar that is now the focal point in St. Marys nave.

It was no small task, but Jim who attends Precious Blood Catholic Church in Jasper and has built custom pieces for several local churches, including Precious Blood and St. Ferdinand was confident he could create a beautiful piece for the new church.

The process included sanding down and refinishing the altars before combining the three separate altars into a single high altar. The latter meant rebuilding some of the pieces before painting the entire structure white with milk paint, which is an architectural paint made from the milk protein casein mixed with lime, clay and earth pigments. Its a type of paint common to historic pieces.

All finished, Jim estimates the altar is worth about $1 million. He and his team installed the altar in late May.

It was like a sigh of relief, he said. It felt good to see it sitting in the church.

Jim Buechlein, left, of Buechlein's Kwik Strip & Custom Furniture & Design, hands a piece of the altar to Sam Wagner of Wagner Brothers Construction while they assemble the altar at the new St. Mary Catholic Church in Ireland on May 15. The altar was re-designed from three separate altars from a St. Patrick Parish Church in Corning that closed down.

Tom Wagner and a team of workers helped Jim install the altar. A lifelong member of St. Mary, Tom was excited to see the new church coming together and to be part of it.

It was time, Tom said of building a new church. Its going to be a lot better.

After about two years of construction, the new church building opened to parishioners on Sunday, June 28, with the Rite of Dedication led by Bishop Siegel. The pews filled with mask-clad parishioners who spread throughout the pews to socially distance and eagerly waited to anoint the halls of their new house of worship. Several local priests also attended to celebrate the event with St. Marys Father Joseph Effie Erbacher and the parish.

The dedication kicked off with the handing over of the building when representatives of the architect and general contractor presented plans for the building to Bishop Siegel. Then, Fr. Erbacher opened the doors to the nave, beginning the processional to the altar.

Enter the gates of the Lord with thanksgiving, his courts with songs of praise, Bishop Siegel said as Fr. Erbacher opened the doors.

In addition to the celebration of the eucharist, the dedication Mass also included several steps to consecrate the building and prepare it to house decades of worship. As soon as the bishop reached the altar, he performed the blessing and sprinkling of water where he blessed water before sprinkling it over the parishioners and the walls of the church. During the anointing of the altar and the walls of the church with sacred Chrism a consecrated oil used in certain sacraments the bishop spread Chrism over the Altar of Sacrifice before he and Fr. Erbacher anointed the walls of the church with the oil as well.

Pat participated in the anointing of the altar as one of two parishioners who wiped down the altar after it was anointed.

Im extremely happy to have been part of it. I almost teared up a few times, he said. Seeing people in there and knowing it is the first of hundreds of years of worshippers is an amazing feeling.

The bishop also blessed the altar with incense while deacons carried braziers with incense through the aisles to bless the parishioners and walls as well, and the candles surrounding the altar and throughout the church were lit ceremonially.

Bishop Joseph Siegel spreads holy water on The Altar of Sacrifice during the new St. Mary Catholic Church dedication in Ireland on June 28.

Toward the end of the dedication, Fr. Erbacher addressed his congregation.

It has been three years of faith, dedication and love, and I thank you all very much, he said.

Missing from the pews during the dedication was Rita. Despite the decades of prayer and intentional action she dedicated to making the new church a reality, she was not meant to attend Mass in the new building. She passed away a few weeks prior to the dedication. Her funeral Mass held June 29 was the first Mass Fr. Erbacher led in the new church.

Cindy Gress, Rita Gress' daughter-in-law, touches Rita's casket after speaking during her funeral Mass at the new St. Mary Catholic Church in Ireland on June 29.

The Gress family chose to wait to hold her funeral Mass until after the dedication because of how much the church meant to her and how active shed been in bringing the new building to fruition. In the last days of her life, the idea of having her funeral in the new building brought her peace, said her daughter, Carla Allbright of Mitchell.

Although Pat and the rest of his family had hoped Rita would live to see the new church building open, Rita didnt expect to herself, and she seemed at peace with that knowledge. As her tour of the nearly completed church came to an end that day in May, she looked around the nave with tears of joy in her eyes and a smile on her face.

When its all finished, she said, Ill see it from heaven.

Continued here:
Prayers Answered - The Herald