fbpx
Connect with us

The Conversation

AI plus gene editing promises to shift biotech into high gear

Published

on

theconversation.com – Marc Zimmer, Professor of Chemistry, Connecticut College – 2024-06-06 07:47:02
AI knowledge combined with gene-editing precision opens the way to dial-a-protein.
KTSFotos/Moment via Getty Images

Marc Zimmer, Connecticut College

During her chemistry Nobel Prize lecture in 2018, Frances Arnold said, “Today we can for all practical purposes read, write and edit any sequence of DNA, but we cannot compose it.” That isn't true anymore.

Since then, science and technology have progressed so much that artificial intelligence has learned to compose DNA, and with genetically modified bacteria, scientists are on their way to designing and making bespoke proteins.

The goal is that with AI's designing talents and gene editing's engineering abilities, scientists can modify bacteria to act as mini factories producing new proteins that can reduce greenhouse gases, digest plastics or act as species-specific pesticides.

As a chemistry professor and computational chemist who studies molecular science and environmental chemistry, I believe that advances in AI and gene editing make this a realistic possibility.

Advertisement

Gene sequencing – reading life's recipes

All living things contain genetic materials – DNA and RNA – that provide the hereditary information needed to replicate themselves and make proteins. Proteins constitute 75% of human dry weight. They make up muscles, enzymes, hormones, blood, hair and cartilage. Understanding proteins means understanding much of biology. The order of nucleotide bases in DNA, or RNA in some viruses, encodes this information, and genomic sequencing technologies identify the order of these bases.

The Human Genome Project was an international effort that sequenced the entire human genome from 1990 to 2003. Thanks to rapidly improving technologies, it took seven years to sequence the first 1% of the genome and another seven years for the remaining 99%. By 2003, scientists had the complete sequence of the 3 billion nucleotide base pairs coding for 20,000 to 25,000 genes in the human genome.

However, understanding the functions of most proteins and correcting their malfunctions remained a challenge.

AI learns proteins

Each protein's shape is critical to its function and is determined by the sequence of its amino acids, which is in turn determined by the gene's nucleotide sequence. Misfolded proteins have the wrong shape and can cause illnesses such as neurodegenerative diseases, cystic fibrosis and Type 2 diabetes. Understanding these diseases and developing treatments requires knowledge of protein shapes.

Before 2016, the only way to determine the shape of a protein was through X-ray crystallography, a laboratory technique that uses the diffraction of X-rays by single crystals to determine the precise arrangement of atoms and molecules in three dimensions in a molecule. At that time, the structure of about 200,000 proteins had been determined by crystallography, costing billions of dollars.

Advertisement

AlphaFold, a machine learning program, used these crystal structures as a training set to determine the shape of the proteins from their nucleotide sequences. And in less than a year, the program calculated the protein structures of all 214 million genes that have been sequenced and published. The protein structures AlphaFold determined have all been released in a freely available database.

To effectively address noninfectious diseases and design new drugs, scientists need more detailed knowledge of how proteins, especially enzymes, bind small molecules. Enzymes are protein catalysts that enable and regulate biochemical reactions.

AI system AlphaFold3 allows scientists to make intricately detailed models of life's molecular machinery.

AlphaFold3, released May 8, 2024, can predict protein shapes and the locations where small molecules can bind to these proteins. In rational drug design, drugs are designed to bind proteins involved in a pathway related to the disease being treated. The small molecule drugs bind to the protein binding site and modulate its activity, thereby influencing the disease path. By being able to predict protein binding sites, AlphaFold3 will enhance researchers' drug development capabilities.

AI + CRISPR = composing new proteins

Around 2015, the development of CRISPR technology revolutionized gene editing. CRISPR can be used to find a specific part of a gene, change or delete it, make the cell express more or less of its gene product, or even add an utterly foreign gene in its place.

In 2020, Jennifer Doudna and Emmanuelle Charpentier received the Nobel Prize in chemistry “for the development of a method (CRISPR) for genome editing.” With CRISPR, gene editing, which once took years and was species specific, costly and laborious, can now be done in days and for a fraction of the cost.

Advertisement

AI and genetic engineering are advancing rapidly. What was once complicated and expensive is now routine. Looking ahead, the dream is of bespoke proteins designed and produced by a combination of machine learning and CRISPR-modified bacteria. AI would design the proteins, and bacteria altered using CRISPR would produce the proteins. Enzymes produced this way could potentially breathe in carbon dioxide and methane while exhaling organic feedstocks, or break down plastics into substitutes for concrete.

I believe that these ambitions are not unrealistic, given that genetically modified organisms already account for 2% of the U.S. economy in agriculture and pharmaceuticals.

Two groups have made functioning enzymes from scratch that were designed by differing AI systems. David Baker's Institute for Protein Design at the University of Washington devised a new deep-learning-based protein design strategy it named “family-wide hallucination,” which they used to make a unique light-emitting enzyme. Meanwhile, biotech startup Profluent, has used an AI trained from the sum of all CRISPR-Cas knowledge to design new functioning genome editors.

If AI can learn to make new CRISPR systems as well as bioluminescent enzymes that work and have never been seen on Earth, there is hope that pairing CRISPR with AI can be used to design other new bespoke enzymes. Although the CRISPR-AI combination is still in its infancy, once it matures it is likely to be highly beneficial and could even help the world tackle climate change.

It's important to remember, however, that the more powerful a technology is, the greater the risks it poses. Also, humans have not been very successful at engineering nature due to the complexity and interconnectedness of natural systems, which often leads to unintended consequences.The Conversation

Marc Zimmer, Professor of Chemistry, Connecticut College

Advertisement

This article is republished from The Conversation under a Creative Commons license. Read the original article.

The Conversation

Making art is a uniquely human act, and one that provides a wellspring of health benefits

Published

on

theconversation.com – Girija Kaimal, Professor of Art Therapy Research, Drexel University – 2024-06-20 07:24:22
The act of creating art serves as exercise for the brain and is integral to physical and mental .
hzechphotography/Moment via Getty Images

Girija Kaimal, Drexel University

When you think about the word “art,” what comes to mind? A child's artwork pinned to the fridge? A favorite artist whose work always inspires? Abstract art that is hard to understand?

Each of these assumes that making art is something that other people do, such as children or “those with talent.”

However, as I explain in my book “The Expressive Instinct,” art is intrinsic to human evolution and history. Just as sports or workouts exercise the body, creating art exercises the imagination and is essential to mental as well as physical well-being.

I am a professor of art therapy who studies how creative self-expression affects physical and emotional health. In our clinical research studies, my colleagues and I are finding that any form of creative self-expression – including drawing, painting, fiber arts, woodworking or photography – can reduce stress, improve mood and increase self-confidence.

Advertisement

As a sickly child who needed to stay home from school a lot, I found that making art helped me cope. Today, creating art is my sanctuary. I use it as a sounding board to better understand myself and a way to recharge and learn from the challenges of life.

A bookmark covered in purple, white and yellow flowers sits on an open book.
Bookmark made with wildflowers and ink drawing, created by Girija Kaimal. ‘My aim here was to capture the beauty of nature and the work of the human hand.'
Girija Kaimal

The uniquely human attribute of creativity

Although everyone has their own concept of what defines art, one thing is universally true: Creativity is a defining feature of the human species.

How so? Well, human brains are not computers processing data. They are biological prediction machines that perceive the environment through memories and the senses, with the capacity to use that information to imagine plausible future scenarios.

These inherent predictive and imaginative capacities are the wellspring of humanity's abilities to survive and thrive – because self-expression is a safety valve that helps us cope with uncertainty. No one truly knows the future; they must live each day not sure of what will happen tomorrow. Art can help us all practice this imaginative muscle in a useful way.

In our study examining brain activity while using virtual reality tools to create 3-D digital artwork, my team demonstrated that creative expression is a natural state of being. The brain naturally uses fewer cognitive resources to be expressive and creative, compared with the brain power needed to do a rote task that requires conscious effort.

Seemingly ordinary everyday activities can provide opportunities to tap into one's natural creativity and imagination: whipping up a meal from leftovers, figuring out an alternate route to work, dancing a little jig in response to hearing a song, or planting and tending a garden.

Advertisement

We have repeatedly found in our studies that even a single session of real and honest self-expression can improve self-confidence and reduce feelings of stress, anxiety and burnout.

This is partly because creativity activates reward pathways in the brain. Using our hands and bodies to express ourselves activates dopamine pathways and helps us feel good. Dopamine is a neural messenger that is associated with feeling a sense of hope, accomplishment or reward. Our brains are wired to secrete feel-good hormones whenever we move, create something or engage in any type of expressive activity.

Tapping into the creative resources within is one of the most underrated seeds of well-being in the world.

By comparison, bottling up or denying these feelings can cause distress, anxiety and fear because we have not processed and expressed them. This is probably one of the reasons why every community around the world has its own creative and expressive practices. Even our ancestors in Indigenous communities all around the world intuitively knew that self-expression was essential to emotional health and social connection.

Being unable to share our lives, keeping secrets and feeling isolated and lonely tend to worsen our health. To our brains, social isolation feels like a chronic disease because it interprets this loneliness and inability to express as a threat to survival.

Advertisement

Since creative expression can engage the senses, it can also be a body workout: a sensual as well as emotional and cognitive experience. Being active in expression – be it art, music, dance, drama, writing, culinary arts or working with nature – imparts a sense of confidence and hope that challenges can be navigated and overcome.

A hand-drawn color portrait
Portrait artwork by Laila Ahuja, in progress.
Laila Ahuja

The role of art therapy

Given the integral role of art in our lives, it makes sense that making art can help people manage transitions, adversity and trauma, such as the stresses of puberty, the death of a loved one or experiencing a serious illness.

According to a global study, 1 in 2 people will experience a mental-health-related challenge in their lifetime, whether from life's challenges, genetic predispositions or a combination of the two.

This is where art therapy can come in. Art therapy is a regulated mental health profession in which clinical psychotherapists with extensive clinical training offer psychotherapy to patients with diagnosed mental health needs.

The origins of art therapy go back to attempts to treat soldiers struggling with post-traumatic stress during the 20th century's two world wars. Today there is evidence that traumatic experiences tend to be stored as sounds, images and physical sensations in the brain. When someone lacks the words to process these experiences through traditional talk therapy, art therapy can provide an indirect way to express and externalize those feelings and memories.

The process of making art can help people process feelings that they aren't able to put into words.

One of art therapy's unique strengths is that it provides nonverbal ways of communicating, processing and eventually managing the symptoms of post-traumatic stress disorder, or PTSD. In fact, in a recent study, my team has found that a personal history of trauma is related to how people react to evocative images. Images of distress and pain resonate with us when we have known similar kinds of distress ourselves. This implies that our life stories make us sensitized to distress in others and even personalize it more.

Advertisement

Creative self-expression is especially relevant in coping with trauma because it provides an outlet through which a person can regain a sense of agency and control.

A brightly colored stem of orange and yellow flowers with green leaves sits on a notebook page with handwritten description behind it.
Botanical notes artwork made by 12-year-old self-taught artist Laila Ahuja as part of a summer exercise to practice drawing and learn about different flowers around the world.
Laila Ahuja

How to bring creativity into daily life

For those new to exploring art as a creative pursuit or for well-being reasons, engaging in creative activities begins with letting go of unrealistic expectations. Being creative isn't about becoming a famous artist or even a mediocre one. It is about allowing ourselves to flex the creative muscle that we all have and enjoying all the sensory and emotional aspects of imagining.

Next, think about activities that made you feel free to explore when you were a child. Did you like singing, playing in the outdoors, dancing, making up pretend plays, or writing little tales? Allow yourself to indulge in any and all of these creative pursuits that made you feel relaxed and joyful.

A cultural tradition, tinkering with electronics, making a gift for someone or simply paying attention to everyday beauty – any of these can be a creative activity. And just like any muscle, the more you exercise it, the stronger it becomes. Over time, you will notice yourself getting more confident and adventurous in your creative practices.

Whatever it is, make time for this creative pursuit every week – which is possibly the hardest step of them all. If it seems “unimportant” compared with the demands of daily life, such as work or family, try thinking of it as another form of sustenance.

Remember that creativity is just as critical to human health as eating nutritious meals or getting exercise and good rest. So as the Latin saying goes: “Plene vivere.” Live fully.

Advertisement

A square box with the words 'Art & Science Collide' and a drawing of a lightbulb with its wire filament in the shape of a brain, surrounded by a circle.
Art & Science Collide series.

This article is part of Art & Science Collide, a series examining the intersections between art and science.
You may be interested in:

Literature inspired my medical career: Why the humanities are needed in health care

I wrote a play for children about integrating the arts into STEM fields – here's what I learned about interdisciplinary thinking

Art and science entwined: This course explores the long, interrelated history of two ways of seeing the world The Conversation

Girija Kaimal, Professor of Art Therapy Research, Drexel University

This article is republished from The Conversation under a Creative Commons license. Read the original article.

Advertisement

Read More

The post Making art is a uniquely human act, and one that provides a wellspring of health benefits appeared first on theconversation.com

Continue Reading

The Conversation

Boost your immune system with this centuries-old health hack: Vaccines

Published

on

theconversation.com – Aimee Pugh Bernard, Assistant Professor of Immunology and Microbiology, University of Colorado Anschutz Medical Campus – 2024-06-20 07:24:38

When it comes to vaccines and immune , the results aren't too good to be true.

Jena Ardell/Moment via Getty Images

Aimee Pugh Bernard, University of Colorado Anschutz Medical Campus and David Higgins, University of Colorado Anschutz Medical Campus

There are a dizzying number of tips, hacks and recommendations on how to stay healthy, from dietary supplements to what color of clothes promotes optimal wellness. Some of these tips are helpful and based on good evidence, while others are not.

However, one of the easiest, most effective and safest ways to stay healthy is rarely mentioned: vaccination.

Advertisement

We are a preventive medicine physician and an immunologist who want people to live the healthiest lives possible. Among the many research-backed ways to live healthier, we encourage people to eat well, exercise regularly, get good sleep and care for their mental health.

And when it comes to your immune system, nothing can replace the essential role vaccines play in promoting whole health. The protection that vaccines provide is an irreplaceable part of living the healthiest lifestyle possible.

Vaccines are essential to health

Some healthy people think they don't need a vaccine. But your immune system needs more than just a healthy lifestyle to protect your body when vaccine-preventable diseases come knocking on the door.

Imagine the cells of your immune system as athletes preparing for the Olympics. Just as athletes undergo rigorous and specialized training to meet every possible challenge they might face in their event, immune cells need to be primed and ready to fight off every pathogenic challenge you encounter.

Vaccines expose your immune cells to inactivated versions of a pathogen, providing them with practice sessions to recognize and combat the real threat with speed and precision. Vaccines ensure that your immune cells are at their peak performance when faced with the actual infection. Just as well-trained athletes can tackle their competition with skill and confidence, vaccinated immune cells can swiftly and effectively protect your body from diseases.

Advertisement

If a person is unvaccinated and exposed to a disease they haven't encountered before, their immune cells are unprepared and must play catch-up to fight the pathogen. This leaves your body vulnerable to severe disease.

Without vaccination, even young, healthy people are vulnerable to diseases like the flu.

Even people at the pinnacle of health can unnecessarily suffer from vaccine-preventable diseases because their immune systems might not have been well-trained. Take the story of Austin Booth, a healthy and athletic 17-year-old who was not vaccinated for influenza. Just days after he started to feel ill, he died of the disease.

For healthy people, vaccination can reduce the risk of death from influenza by two-thirds. When people choose to skip vaccines recommended as an essential part of their overall health, there is a greater chance of serious complications or death from a vaccine-preventable disease, regardless of how healthy they may be. These people are playing a potentially life-altering and deadly game of chance.

Vaccine-preventable diseases are still common. In the U.S., hundreds of thousands of adults are hospitalized and thousands die every year from vaccine-preventable diseases such as influenza, pneumococcal pneumonia, respiratory syncytial virus (RSV) and COVID-19. And tens of thousands of adults develop cancer every year from vaccine-preventable diseases such as HPV.

Vaccines are the safest immune health hack

Many of the trendiest health hacks have little to no evidence of improving health. Some are even dangerous. But vaccines are one of the most tested and proven ways to stay healthy.

Advertisement

Vaccines have been used for centuries. In the past 50 years, they have saved an estimated 154 million lives worldwide. Mathematical models estimate that a 25-year-old now has a 35% greater chance of living to their next birthday thanks to vaccines alone.

Smiling person rolling up sleeve to show bandaid on upper arm that reads 'fight flu'

Vaccines are a tried and true way to improve your health.

CDC/Robin Spratling

Not only are vaccines effective, but they are also safe. Yes, vaccines can come with mild and limited side effects – who hasn't felt a little sluggish or bumped their sore arm after getting vaccinated? More severe vaccine side effects are extremely rare. If you have concerns, talk to your doctor. As opposed to dietary supplements, trendy health hacks and even many over-the-counter medications, there are robust systems in place to test and monitor the safety and effectiveness of vaccines.

Of all the tips available to improve your health, one recommendation is clear: Even healthy, fit people need recommended vaccines to stay healthy and live well.The Conversation

Aimee Pugh Bernard, Assistant Professor of Immunology and Microbiology, University of Colorado Anschutz Medical Campus and David Higgins, Research fellow, Instructor of Pediatrics, University of Colorado Anschutz Medical Campus

This article is republished from The Conversation under a Creative Commons license. Read the original article.

Advertisement

Read More

The post Boost your immune system with this centuries-old health hack: Vaccines appeared first on theconversation.com

Continue Reading

The Conversation

Raw milk health risks significantly outweigh any potential benefits − food scientists and nutritionists explain why

Published

on

theconversation.com – Juan Silva, Professor of Food Science, Nutrition and Promotion, Mississippi State University – 2024-06-19 07:45:26
Influencers extoll the benefits of drinking raw milk over pasteurized milk, but there isn't substantive evidence to support these claims.
AP Photo/Charlie Neibergall

Juan Silva, Mississippi State University; Joel Komakech, Mississippi State University, and Mandy Conrad, Mississippi State University

Despite an ongoing outbreak of bird flu in dairy cows, the popularity of raw milk has only risen. Advocates claim raw milk has superior health benefits over pasteurized milk. There is little evidence to support these claims, however, and the risk of serious illness is much greater.

Mississippi State University food scientists Juan Silva and Joel Komakech and nutritionist Mandy Conrad explain the difference between pasteurized and raw milk, addressing common misconceptions about the health risks and purported benefits of consuming unpasteurized milk. These questions are more important than ever, since cattle can shed viral material into their milk. Not only can pathogens end up in milk, but at least three farmworkers reportedly have contracted H5N1, the virus that causes avian influenza, in 2024. Farmworkers can get sick by handling infected animals or their byproducts, such as raw milk.

What is pasteurization? Does it destroy nutrients?

Pasteurization is a process that involves heating beverages and foods at high temperatures – over 145 degrees Fahrenheit (62.78 degrees Celsius) – to kill harmful microorganisms, such as bacteria, viruses and parasites. This reduces the total number of microorganisms in the product and also inactivates enzymes that could contribute to spoilage.

The taste, nutritional value and quality of pasteurized products aren't significantly affected by the process.

Advertisement

While pasteurization can lead to some nutrient losses, the changes are generally minimal and outweighed by the benefits. Pasteurization typically causes minor denaturation of proteins and has little effect on fats and carbohydrates. While water-soluble vitamins such as vitamin C and some B vitamins, usually not abundant in milk except vitamin B2, can be partially degraded during pasteurization, fat-soluble vitamins (A, D, E and K, found in significant amounts in milk) are more heat stable and suffer minimal loss.

Thus, nutritional losses in milk due to pasteurization are generally small compared with the significant benefits of reducing foodborne illnesses and spoilage.

Is raw milk healthier than pasteurized milk?

Studies have compared the benefits of raw milk with pasteurized milk and have found little evidence that raw milk is superior to pasteurized milk. The perceived advantages of raw milk are outweighed by its health risks.

First, raw milk does not improve lactose intolerance.

Raw milk also does not have more vitamins than pasteurized milk. Milk is not a good source of vitamin C or other heat-sensitive vitamins, and pasteurization does little to reduce vitamin B2 or riboflavin, which is not as sensitive to heat. Moreover, Vitamin D is added to pasteurized milk to enhance your body's ability to absorb the calcium in milk.

Advertisement
Assortment of milk products in grocery store aisle
Pasteurized milk is fortified with vitamin D and other nutrients.
Burke/Triolo Productions/The Image Bank via Getty Images

Fortified milk replaces nutrients that may be lost in the pasteurization process. Vitamin D is added to milk to enhance uptake of the calcium found in the milk. No single food is perfect, so it is OK for milk to lack some nutrients, as these can be obtained from other foods.

Some people believe that probiotics – foods or supplements that contain live bacteria beneficial to health – are more prevalent in unpasteurized milk and products made from raw milk. However, raw milk is generally lacking in probiotics and has significantly more harmful bacteria. Probiotics are added to many dairy foods such as yogurt after pasteurization.

Furthermore, a 2011 review of the available research on the health benefits of raw milk found that many of these studies were conducted with poor methods, meaning their results should be interpreted with caution.

What are the health risks of consuming raw milk?

The health risks of consuming raw, unpasteurized milk come from the harmful microorganisms that may be present.

Raw milk has been associated with hundreds of foodborne disease outbreaks. Between 1998 and 2018, 202 outbreaks resulted in 2,645 illnesses and 228 hospitalizations. More recently, from 2022 to 2023, there were 18 outbreaks and recalls associated with raw milk. A number of outbreaks and recalls associated with pathogens in raw milk have already occurred in 2024. In all cases, pathogens in the raw milk that cause human diseases were directly responsible for these illnesses.

Hind legs of cows standing in a stall
Pathogens from infected cattle can be found in their raw milk.
Tunvarat Pruksachat/Moment via Getty Images

Some illnesses from the pathogens in raw milk can have serious long-term effects, including paralysis, kidney failure and death.

Researchers found that areas where raw milk was legally sold in the U.S. from 1998 to 2018 had over three times more outbreaks than areas where selling raw milk was illegal. Areas where raw milk was allowed to be sold in retail stores had nearly four times more outbreaks than areas where sales were allowed only on farms.

Advertisement

Is it safe to eat foods made from raw milk?

Many, if not all, dairy products made from unpasteurized milk are not safe to eat. A number of products can be made from raw milk, including soft cheeses, such as brie and Camembert; Mexican-style soft cheeses, such as queso fresco, panela, asadero and queso blanco; yogurt and puddings; and ice cream or frozen yogurt. Pathogens in raw milk can survive the processes involved in making these types of dairy products and thus be unsafe for consumption.

Only products that undergo a process to inhibit or kill harmful microorganisms may be safe enough to be made from unpasteurized milk. However, the potential for cross contamination of raw and cooked food as well as the survival of pathogens from inadequate processing is high when products are made with raw milk.

Can pasteurized milk still get you sick?

The few reported outbreaks associated with pasteurized milk can be traced to contamination after pasteurization. When handled properly, pasteurized milk is a very safe product.

The U.S. government requires farmers to destroy milk from herds infected with avian influenza. As of June 2024, 12 states have reported herds positive with H1N5, the virus that causes bird flu.

There is currently no evidence that consuming pasteurized milk from infected cows causes illness in people. Based on the evidence available, the Food and Drug Administration currently states that pasteurization is able to destroy or inactivate heat-sensitive viruses such as H5N1 in milk.

Advertisement

Consuming raw milk, however, may pose a risk of disease transmission to people.

Can you gain immunity from H5N1 from drinking raw milk?

Some people believe that drinking raw milk can strengthen their immune system. However, there is no scientific evidence to support that drinking raw milk can improve immunity against disease.

Vaccines train your body to protect itself from future infections without actually getting sick from that infection. They do this by exposing your immune system to very small amounts of dead or significantly weakened pathogen.

Bird flu is spreading among dairy cows in the U.S.

Raw milk contains live H5N1 virus, meaning it could still infect you and make you sick. Rather than contributing to your immunity, raw milk exposes you to the virus at its full strength and can result in severe illness. Any protective antibodies that may be present in raw milk are likely degraded in stomach acid.

Moreover, people who contract bird flu from raw milk run the risk of transmitting it to other people or animals by giving the virus a chance to adapt and improve its ability to spread between people. This increases the risk of more widespread disease outbreaks.The Conversation

Juan Silva, Professor of Food Science, Nutrition and Health Promotion, Mississippi State University; Joel Komakech, Assisstant Professor of Food Science, Nutrition and Health Promotion, Mississippi State University, and Mandy Conrad, Assistant Clinical Professor in Nutrition and Dietetics, Mississippi State University

Advertisement

This article is republished from The Conversation under a Creative Commons license. Read the original article.

Read More

The post Raw milk health risks significantly outweigh any potential benefits − food scientists and nutritionists explain why appeared first on theconversation.com

Continue Reading

News from the South

Trending