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genomes

Scientists Create First Viruses Designed By AI, What Does This Mean For The Future Of Medicine?

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Scientists have created the first viruses that were designed using artificial intelligence. This feat is being highly debated within the scientific community as both a major milestone advancement for medicine, and a potential threat if this technology isn’t protected. 

Dr. Brian Hie is a chemical engineer at Stanford University in California, who utilized genome language models to design functioning genomes for bacteriophages. The models are the genetic equivalent to the language models used for AI chatbots, and bacteriophages are the specific viruses that only infect bacteria, so they’re used to treat patients with persistent infections. 

The viruses were then made in the laboratory and specifically put against E. coli in a dish, according to the research recently published in the journal Science. “The ability to rapidly design genomes and tune them for specific bugs while overcoming resistance could transform phage therapy and expand biotechnological toolkits,” the researchers wrote. 

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On the other hand, the scientists have also stated that the new work raised “important biosafety, biocontainment, and biosecurity consideration,” telling other people who are designing whole genomes to “consult both safety and security professionals throughout the project.”

Professor Tom Inglesby and Dr. Mori Hanke at the Center for Health Security at Johns Hopkins University wrote an accompanying article in which they emphasized the researchers safety warnings: 

“Although this is promising for life sciences applications, it also raises urgent biosafety and biosecurity questions. The ability to compose viral genomes using generative AI now exists; the governance to safely steer it does not.”

Dr. Hie and his colleagues mapped out in their article how they used AI models named Evo1 and Evo2 to design the new viral genomes. The models were specifically trained with genetic data from 2 million bacteriophages.

To keep the focus on the bacteriophages that can be utilized in medicine, the scientists made sure to carefully exclude any genetic codes for viruses that can infect living beings so the AI training doesn’t design any dangerous viruses. 

The AI worked to generate thousands of potential genomes, and the researchers chose about 300 to then make in a lab. Those genomes were then dropped into bacteria which read the genetic code and created the new bacteriophages. 

Only 16 bacteriophages were viable, however, the makeup of them were able to overcome resistance in two different strains of E. coli. 

Professor Inglesby and Dr. Hanke said that although only 16 out of the 300 were viable, the work proves that generative AI can create viral genomes, and there should be safeguards put into place to ensure that the technology can never be used to create pathogens that can infect plants, animals, and especially humans. 

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“Such genomes might encode new pathogens that … cannot be contained by existing countermeasures,” they wrote. 

Tom Ellis, a professor of synthetic genome engineering at Imperial College London, stated that this work was very impressive, but when it comes to creating more complex genomes, there’s a lot more work to actually be done. 

“This is literally the smallest and easiest genome to make,” he said. 

“An AI trained on the genetic code of dangerous bugs could be used to design more harmful viruses,” the Guardian reported that Ellis said. 

“But controlling access to genetic data and having restrictions on making genomes that look dangerous would help. Governments are working hard to do this already,” he added.

“But honestly, the threat from full AI design and writing of a genome of a virus or bacteria is very overblown when we consider that just taking existing pathogens and making gain-of-function changes to their genomes is so much easier and much more likely to be a real pathogenic threat.”

Dr. Filippa Lentzos, a reader in science and international security at King’s College London, stated that one of the biggest things to now look out for with this type of work is making sure no scientific groups try to manufacture anything involving DNA. 

“It’s important to see the bigger governance picture and not focus regulation solely on the AI model,” she said. 

“A layered approach makes more sense: safeguards around model development and access, responsible research review, synthesis screening, and established laboratory biosafety and biosecurity.”

Colon Cancer Rates Have Doubled In Younger People, And It Could Be Because Of Gut Bacteria 

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Healthcare professionals have been uncertain as to why colon cancer cases have doubled in people under 55 within the past two decades. Now, a new study is giving some answers, and the answer has to do with damage caused by gut bacteria.

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Showerheads And Toothbrush Heads Are A Breeding Ground For Viruses, But They’re Actually Beneficial To Our Health 

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The warm and damp environments that exist in our bathrooms create an ideal breeding ground for microbes, specifically around our showerheads and toothbrushes. However, these specific microbes and viruses aren’t necessarily a bad thing, as they have evolved to hunt, attack, and absorb specific bacterial species that may be bad for us.

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Scientists Develop New Antibiotic to Kill Drug-Resistant Bacteria

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Scientists have developed a novel antibiotic to combat bacteria resistant to existing antibiotics. The bacteria, Acinetobacter baumannii, causes infections in the lungs, urinary tract and blood and has a high mortality rate.

The US Centers for Disease Control and Prevention (CDC) report that it is resistant to a class of broad-spectrum antibiotics known as carbapenems, and it kills a significant number of people via invasive infection.

In 2017, the World Health Organization released a list of antibiotic-resistant “priority pathogens,” listing Carbapenem-resistant Acinetobacter baumannii (CRAB) in its critical category. The organization describes pathogens of this designation as “ multidrug-resistant bacteria that pose a particular threat in hospitals, nursing homes, and among patients whose care requires devices such as ventilators and blood catheters.”

Data from the CDC shows that the bacteria caused 700 fatalities and 8,500 infections in hospitalized patients in the US that year. Being a Gram-negative bacteria, protected by inner and outer membranes, makes CRAB incredibly difficult to treat. The US Food and Drug Administration has not authorized a new class of antibiotics to treat it in over 50 years.

However, Acinetobacter baumannii can be effectively killed with the new antibiotic Zosurabalpin, according to researchers from Harvard University and the Swiss healthcare company Hoffmann-La Roche.

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Dr. Kenneth Bradley, one of the researchers and global head of infectious disease discovery with Roche Pharma Research and Early Development, stated that the drug is in its own chemical class and has a unique method of action.

The study’s primary objective was to discover and optimize a molecule capable of penetrating bacterial double membranes and killing them. “These two membranes create a very formidable barrier for entry of molecules like antibiotics,” he said.

“This is a novel approach, both in terms of the compound itself but as well as the mechanism by which it kills bacteria.”

The research found that Zosurabalpin was effective against over 100 CRAB clinical samples. To develop the drug, the scientists researched 45,000 small antibiotic molecules known as tethered macrocyclic peptides to find those that could inhibit bacterial growth. Researchers spent years honing the effectiveness and safety of a select few compounds before settling on a single modified molecule.

By blocking the transport of lipopolysaccharides, which are big molecules essential for maintaining the integrity of the outer membrane and ultimately leading to cell death, Zolofalacpin inhibits the growth of Acinetobacter baumannii.

According to the study, the antibiotic significantly decreased bacterial levels in mice with CRAB-induced pneumonia. Additionally, it prevented the death of mice infected with bacterial sepsis.

“Drug discovery that targets harmful Gram-negative bacteria is a long-standing challenge owing to difficulties in getting molecules to cross the bacterial membranes to reach targets in the cytoplasm. Compounds typically must possess a certain combination of chemical characteristics.”

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Dr. Michael Lobritz, the global head of infectious diseases at Roche Pharma Research and Early Development and an associate participant in the study, stated that the continued absence of effective treatments for antibiotic resistance means that the public health risk of this phenomenon is still a major one on a global scale, regardless of the new finding.

According to CNN, an analysis published in the Lancet in 2022 estimated that antimicrobial resistance was directly responsible for the deaths of about 1.3 million people worldwide in 2019. When put side by side, that year, 860,000 people died from HIV/AIDS and 640,000 from malaria.

The CDC stated in its 2019 Antibiotic Resistance Threats Report that more than 2.8 million cases of infections resistant to antibiotics are reported annually in the United States. Over 35,000 of those individuals lose their lives.

More antibiotics have been developed to treat Gram-positive infections in the last few decades, according to Lobritz. Gram-negative bacteria are more resistant to antibiotics and generally more dangerous. “These  Gram-negative bacteria, they’ve been accumulating resistance to many of our preferred first-line antibiotics for a long time.”

“Innovations are hard to come by. It’s taken us ten years of effort on this project to get it to where it is now, and there’s still more clinical trials to go before it can be determined whether or not it’s a medicine.”

According to the researchers, the method that was used to limit the growth of Acinetobacter, blocking the creation or formation of the outer membrane, could be useful for other difficult-to-treat bacteria such as E. coli. The drug is now in phase 1 clinical trials to assess for safety in humans.

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Mysterious Dog Respiratory Illness: What We Know And How To Protect Your Canine Companions

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Dog owners throughout the US are worried about their furry friend’s health after a new mysterious respiratory illness has begun making dogs sick. Here’s what we know about this new bacterial infection.

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Scientists Name Fungus-Killing Compound After Keanu Reeves

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Researchers from Germany’s Leibniz Institute have found a naturally occurring compound so effective at busting human and plant pathogenic fungi that they named it after actor Keanu Reeves.

The three nonribosomal lipopeptides scientists isolated—Keanumycins A, B, and C—are byproducts of Pseudomonas bacteria typically found in soil and water. Scientists observed the compounds while studying Pseudomonas for their effectiveness against predatory amoebas.

“We have been working with pseudomonads for some time and know that many of these bacterial species are very toxic to amoebae, which feed on bacteria,” said study leader and head of the department of Paleobiotechnology at Leibniz-HKI Pierre Stallforth.

The researchers wanted to know if the same bacteria would be effective against fungi, which have a cell structure similar to amoebas. Testing showed that the bacteria’s byproducts were lethal to a fungus infecting a hydrangea.

The scientists’ findings were published in the Journal of the American Chemical Society in January. The study’s first author, Sebastian Götze, said in a press release that they named the lipopeptides after Keanu Reeves because of his iconic roles in action films.

“The lipopeptides kill so efficiently that we named them after Keanu Reeves because he, too, is extremely deadly in his roles.”

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Notably, the Keanumycins were effective against Botrytis cinerea—the fungus responsible for gray mold rot that destroys various crops, such as strawberries and wine grapes, and causes significant harvest losses. Farmers frequently use chemical fungicides to combat its aggressive spread.

Having seen the potential of the Keanumycins, the study’s authors are conducting experiments to determine whether or not a fungicide containing Keanumycins can effectively eradicate crop-damaging fungi without leaving any harmful residues behind in soil or on produce.

If the results are promising, the compounds could provide a biodegradable alternative to chemical pesticides.

Götze said that the compounds may also help treat human fungal infections that are becoming resistant to conventional antifungals. For instance, Keanumycins are non-toxic to humans and were found to “strongly inhibit” the pathogenic fungus Candida albicans, which is responsible for yeast infections.

“We have a crisis in anti-infectives. Many human-pathogenic fungi are now resistant to antimycotics — partly because they are used in large quantities in agricultural fields.”

Dr. Matt Nelsen, a researcher from Chicago’s Field Museum, told CNN in an email that the study “documents another exciting means by which microbes have evolved to compete with and fight other organisms.”

“Previous efforts have sought to exploit such natural products for human use to combat animal and plant pathogens. However, over time, many pathogenic organisms — including fungi — have evolved resistance to the chemicals we use to battle them. Consequently, we need to find a new way to ‘outsmart’ or ‘one-up’ them.”

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This is not the first time a scientific discovery has been named after a famous face. In February, researchers Juan C. Sánchez-Nivicela, José M. Falcón-Reibán and Diego F. Cisneros-Heredia discovered a mystical steam frog in Ecuador and named it after fantasy author J.R.R. Tolkien.

The frog, Hyloscirtus tolkieni, was found in a habitat that reminded Sánchez-Nivicela of the Fangorn Forest from Tolkien’s “Lord of the Rings” series.

The paper on their findings started with an homage to the opening lines of Tolkien’s “The Hobbit.”

“In a stream in the forest, there lived a Hyloscirtus. Not a nasty, dirty stream, with spoor of contamination and a muddy smell, nor yet a dry, bare, sandy stream with nothing in it to perch on or to eat: it was a Hyloscirtus-stream, and that means environmental quality.”

There are also several beetles named after celebrities, including the Agaporomorphus colberti named after late-night talk show host Stephen Colbert, Agra catbellae named after actress Catherine Bell, Agra katewinsletae named after actress Kate Winslet, and Agra liv, named after actress Liv Tyler. 

Sir David Attenborough, famous broadcaster, biologist and natural historian, has over 40 species named after him, including a prehistoric marine reptile and a native British flower.

On Saturday, Keanu Reeves participated in a reddit AMA (ask me anything) where he was asked about his thoughts on having the killer compounds named after him.

“Hi, thank you…they should’ve called it John Wick…but that’s pretty cool…and surreal for me. But thanks, scientist people! Good luck, and thank you for helping us.”

Disinfect Cellphone

How To Properly Disinfect Your Smart Phone

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With the way things currently are, it’s important to be disinfecting the surfaces we touch everyday as much as we’re maintaining good hygiene for our own bodies. One of the surfaces we touch the most every day includes our cell phones. Whatever we touch, ends up on our phones, which we bring to our faces and touch with our hands daily. So here are some of the best ways to make sure your personal devices stay clean and germ-free. 

First thing you need to do is take off your phone case and change it periodically. Your phone case is what you touch arguably more than the actual back of your phone, so you need to be disinfecting it as often as you are your phone itself, which should be at least once a day. Be very careful and delicate when removing certain cases, such as an Otterbox, as they are designed to adhere and protect your phone for long periods of time. Improperly removing them could cause your phone to break, so if you need, look up your specific cases removal process to be safe. ‘

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The same concept goes with any kind of screen protector. While taking a disinfectant wipe to your phone’s screen protector daily will ensure that it’s clean, after a while certain dirt and bacteria can build up underneath the surface and get stuck. So frequently removing and replacing your screen protector will make sure that those particles are also removed. 

Before you disinfect your phone, it’s important to wipe down the surface with some sort of microfiber cloth. This will lift off any larger dust particles before you take a more wet disinfectant wipe to the surface, once you do so there’s less of a chance of these bigger particles being left behind after you’re done cleaning. 

Make sure you’re actually using a microfiber cloth of some sort, as traditional paper towels can be really abrasive to the glass on your phone’s screen and cause little scratches on the surface. It’s also important to note that during this entire cleaning process, your phone should be unplugged. If a charger is present, dirt and debris will only build up around the charging port of your phone and likely slip into the crevices and remain there indefinitely. 

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Anytime you’re cleaning around the charging port, speaker, or headphone jacks on your device, make sure you’re being very careful and mainly using dry cloths to clean those areas. Even if your device is waterproof, wet substances seeping into the phone itself will cause particles of dirt to build up and stay there. 

One thing you should make sure you’re not using is a compressed air can. Compressed air is typically used to clean keyboards and desktop computers, but when they’re used on smaller personal devices, they just push particles deeper into the crevices of your phone. These dust, dirt, and bacterial remains can cause germs to build up rapidly and therefore adhere to something you’re touching with your hands constantly. 

When it comes to choosing an actual disinfectant to use on your phone, steer clear of any Lysol aerosol-based cleaners, as they can be too harsh and abrasive. Simple disinfecting wipes will do, in fact, it’s what’s recommended. 

Apple officially recommends a “pack of 70% isopropyl alcohol wipes or Clorox Disinfecting Wipes (if you can find either). Use that to wipe down your iPhone and its case (but only if it’s hard plastic). Try not to let your device get too wet and definitely don’t scrub around openings where you could introduce lint or moisture buildup.”

Finally, make sure you’re repeating this process often, especially during times of a worldwide pandemic, keeping surfaces clean and germless is of the utmost importance right now, and will give you a greater peace of mind while playing Candy Crush during times of self-quarantine.      

Holding Stomach

Auto-Brewery Syndrome Turns Carbs Into Alcohol, Causing Patients To Appear Extremely Drunk

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“Officer I didn’t have anything to drink my stomach just turns carbs into alcohol!” Sounds like the funniest excuse one could give to an officer when pulled over for drunk driving, however, the actual medical implications behind this are no laughing matter. Auto-Brewery Syndrome just recently began making headlines in 2014 but has been publicized more throughout the past couple of years. The rare syndrome is caused by a fermenting fungi found in the digestive system. This fungi or gut bacteria produce ethanol through the fermentation process as your body digests carbs. The syndrome is most common in individuals with Crohn’s disease or diabetes, but can rarely affect individuals without any preexisting health conditions, according to Boston Magazine, who recently covered an auto-brewery syndrome case. 

Recently the syndrome made headlines when police pulled over a Boston man whose blood alcohol level was at .2, twice the legal amount for operating a vehicle. Police took the man to the hospital where he kept insisting that he hadn’t had anything to drink that night, but doctors weren’t so easily convinced. After rigorous testing they discovered that the man did in fact have this illness. The disease itself has rarely been diagnosed due to the fact that it’s rarely studied, however, with more and more cases appearing of this truly horrible illness doctors are studying and developing more ways to help treat it.

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According to CNN, “The condition made news in 2014, when the driver of a truck that spilled 11,000 salmon onto a highway claimed to have auto-brewery syndrome. The next year, a New York woman was charged with driving under the influence after she registered a blood alcohol level that was more than four times the legal limit.”

As previously stated the treatment for this really depends on the individual and their specific case of ABS. Regular blood alcohol level checks are a must, and anti-fungal/bacterial medications are also used which can sometimes work well enough to allow the person to continue their life with a fairly regular diet. Unfortunately there still is so little research and knowledge about this illness that treating it really is a game of trial and error. 

ABS should be taken just as seriously as any other major illness, as it can cause major accidents to occur without the individual even being fully aware of what they’re doing and why. The diagnosis just sounds so incredibly unbelievable that often doctors don’t treat patients because they just seem like they’re drunk. 

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According to Barbara Cordell, a researcher of auto-brewery syndrome and the author of ‘My Gut Makes Alcohol,’ “Auto-brewery syndrome seems to be caused by antibiotic use altering a person’s fungal growth, but researchers don’t know why few people who take antibiotics contract the condition. Other drugs, environmental toxins or preservatives in foods also could cause auto-brewery by disrupting the body’s normal balance of bacteria.”

While the cause is still not totally known for ABS, luckily Cordell also provided a lot of warning signs to look out for if you or someone you know is acting intoxicated but you know for a fact that they’re not a heavy drinker, they haven’t had anything to drink, or is on antibiotics of any kind. Symptoms of ABS include brain fogginess, mood swings, or delirium. Cordell mentioned that these symptoms normally appear before the person will seem truly intoxicated, but other symptoms can also mimic that of a stroke, so it’s of extreme importance to go to a hospital and test your blood alcohol levels whenever any symptoms begin arising. Additionally, individuals with ABS can reach a blood alcohol level five times that of the legal limit, so it’s important to treat patients for alcohol poisoning first and foremost in any situation.