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Have You Been Diagnosed With An Autoimmune Disease? Medical medium If you or someone you love have been diagnosed with an autoimmune disease, chances are you’ve been told that your body is attacking itself. Hearing this probably stripped you of hope that you can heal and left you feeling betrayed by your own body. Today there are countless mysterious diseases that have been labeled as autoimmune conditions. But the problem is that the concept of autoimmunity is inherently flawed and this mistaken theory only hurts you and your loved ones in the end. Surprised? When we believe our own bodies are attacking themselves, we are unknowingly hindering our healing process. Our immune systems can weaken in the absence of this truth: Your body never attacks itself. It’s always working for you and loves you unconditionally. It’s never been more critical for you and your loved ones to know and feel this truth in your heart. It will greatly support you and those you care about to heal. Continue reading to learn more and check out the accompanying radio show to further immerse yourself in truth.When medical science and research do not know what is causing symptoms, such as mysterious rashes, mysterious dizziness, mysterious fatigue, mysterious aches and pains, or mysterious inflammation, it gets labeled as an autoimmune issue. This is a mere theory that was initiated in the 1950s and has since been grandfathered in to modern medicine and collectively agreed upon as law. There was a discovery of an antibody but no one had any idea of what it was or what it was for. There were theories and ideas of what it was, but they were just that: theories. One of those theories was that the antibody was there to destroy healthy cells. This theory came about because researchers didn’t have an answer as to what was causing chronic illnesses and symptoms or even an answer to what the antibody was for. Instead the blame was put on those with chronic illness and our bodies became the scapegoat. Better to blame it on our bodies than to blame it on the medical industry and research and science not having the answers. The theory of autoimmune conditions and diseases became a catch-all explanation for dozens of conditions and symptoms that medical communities don’t yet have answers for. When someone is diagnosed with Hashimoto’s, they are told their body is creating antibodies that are destroying their thyroid tissue. With eczema and psoriasis, you will likely be told your body is attacking your skin. If you have lupus, you will likely be told your body is attacking itself and that’s what creates all the inflammation. This same theory is used for countless other chronic illnesses. This is the best explanation that modern medicine has to offer about mysterious diseases today. It’s never been more important for you to know this isn’t accurate because it affects your ability to heal. Not only are you given incorrect information about your health problems, you’re also told your body has turned against you when nothing could be further from the truth. The information I am sharing with you here is meant to free you of the misguided notion that your body would ever attack itself and to reveal the true cause of mysterious diseases that have been labeled autoimmune disorders.The True Causes of Autoimmune DiseasesIf you have an illness that has been labeled as an autoimmune disease, your body truly is attacking something, but it is not attacking itself. As I said, your body is working for you every single day. It works tirelessly for you and is doing the very best it can. When you are sick and have mysterious symptoms, such as fatigue, butterfly rashes, dizziness, tremors, vertigo, aches and pains, digestive trouble, weight loss, insomnia, weight gain, memory loss, numbness, tingling, blood sugar issues, brain fog, mood swings, night sweats, loss of appetite, and many others, it means there is an invader in your body. The same is true if you have lupus, Hashimoto’s, Grave’s, Addison’s, Type 1 Diabetes, colitis, vitiligo, celiac, eczema, Graves’, chronic fatigue syndrome (CFS), myalgic encephalomyelitis (ME), rheumatoid arthritis, fibromyalgia, Lyme disease, multiple sclerosis, parkinson’s, alopecia, or any other disease that is considered to be in the autoimmune category. There is a pathogen invader in your body that it’s working hard to attack and get rid of.Modern medicine has yet to come to this conclusion about mysterious illnesses due to a few reasons. First of all, this theory about the body attacking itself has become law inside the minds of well-intentioned doctors and health professionals who are just doing their best to provide care for their patients. No one is willing to question it because they have come to believe it is the truth, even though there is no evidence backing it.Another reason is because there is no incentive to look into these mysterious diseases. When there is already an acceptable answer that seems to fit, there doesn’t appear to be a need to spend more money on research that they assume will get them nowhere. And finally, even if doctors were to seriously look for these pathogens in their patients coming into their offices with a long list of mysterious symptoms, they would come up dry. Most tests the blood lab offers cannot detect the viruses and bacteria that are invading so many people and causing so many conditions and symptoms. Many of the pathogens causing autoimmune labeled illnesses are yet to be discovered and classified; therefore, it would be quite impossible to detect. You can’t find something when you do not know what you are looking for. For example, medical communities believe there is only one Epstein-Barr virus (EBV)—the virus that causes mono—but in truth there are 61 strains of EBV that cause all kinds of different symptoms and illnesses. I revealed this truth in my book Medical Medium. You can read more about EBV and how it creates illnesses, including cancer, in my book Thyroid Healing.If the medical industry was willing to put more money into researching pathogens, it would be more likely that answers would be coming out in literature today. Viruses and bacteria would be called by name and accurate tests would be created and administered. However, the most popular answer medicine has at the moment is that the body is attacking itself and as I have shared, this is not the truth. The second most popular answer is that it’s your faulty genes causing disease, which is a theory that’s quickly on the rise and still not the answer. In fact, people are told their body is attacking itself and that their genes are the problem.The First Barrier to DestroyThe biggest barrier obstructing your path to true healing is this belief that the body is attacking itself. It may have been ingrained into you not only by your medical practitioners, but also by what you read on the Internet. You are told there is very little you can do to manage your symptom or condition, and nothing you can do to reverse it. This is a lie and something that should be discarded immediately not that you know the truth.Know this: Your body is not attacking itself. I have already said it multiple times in this article, but I must say it over and over until we all understand it deep within our beings. It’s that fundamentally important. Your body is not self-destructive. And your body is not searching out healthy blood cells to harm and kill off. In fact, your body is doing the opposite. Every day your body is working for you. It is on your side. Your immune system cannot do one thing to harm a single cell in your body. It has never been able to do that, and it never will do that. When we know this deep within our being and replace the lie with this truth, something begins to change. That barrier that was once in your way is obliterated, and your path to healing becomes clear and unhampered. It may seem like a small switch, but it is in fact very significant. When your mind is aware that it is a pathogen you are going after, a revelation clicks into place and your body begins to work even more efficiently to kill off that virus. Your immune system fires up and kicks into gear to work for you even harder. This is essential to understand. The power of knowing the truth cannot be underestimated, especially when it comes to healing from these diseases that have plagued so many people for so many years. If you know your body is working for you, it works for you even more. Recovery is finally possible when you are armed with real information that is not hiding behind funding agendas and the bureaucracy of the medical world. This simple understanding sends a message to your body to start breaking down the pathogen fast. And when you start robbing food from the pathogen, which I discuss in the section about healing foods, recovery is even faster. Triggers vs. CauseThere are many medical professionals these days that are offering advice on how to manage your autoimmune disease. Some of this advice discusses “triggers” related to your illness but ironically it’s not even the correct triggers. For example, some experts are just beginning to say that EBV is a trigger for thyroid disease. This is because the never before known information that I have released has forced experts to look at EBV as a possible concern, but this has only led these experts to say that EBV could be a trigger. But in fact, EBV is not a trigger, it is the direct cause. This is a critical distinction that must be understood.The reason we need to make a distinction between trigger and cause is because when we just manage our illness by avoiding triggers, we are not actively fighting the pathogen and addressing the root cause. And if today’s medical professionals and experts believe that EBV is possibly just a trigger but have no idea how to rid the EBV out of the body, then they’re not helping people to heal. We want to do everything we can to kill off the virus invading our body. When we simply just avoid triggers, for example gluten, the virus that’s really behind your suffering can cause further issues. And obviously, we want to do everything we can to ensure the pathogen does not proliferate and cause more symptoms again. Plus, not all triggers can be avoided. We all eventually lose a loved one for example, and the grief we experience can trigger illness if the cause hasn’t been addressed. Or we’re not choosing the right triggers we can avoid. When we recognize the true cause of our illness, we can start to move toward true and total recovery, which is something I’ve witnessed tens of thousands of people doing over the years with the information I’ve shared, and now many more.Let’s take a look at some of the illness labeled as autoimmune diseases and conditions.LupusMedical science and research are unaware that lupus is a viral condition, specifically it is the body reacting to Epstein-Barr’s byproducts and neurotoxins. Medical science and research are completely unaware of this true cause. In fact, lupus is not even diagnosable. It is only visibly diagnosed by inflammation markers. I share more about the undiscovered true cause of lupus in Thyroid Healing.Multiple Sclerosis (MS)With this autoimmune labeled condition, EBV is in the body feeding on high levels of toxic heavy metals. It is not always lesions on the brain that are causing MS symptoms. Many people have spots that show up on brain scans, and they do not have any of the symptoms related to MS. There is so much that is going on in people’s brains: calcifications, crystallizations, dark spots, white spots, heavy metal deposits, MSG deposits, and chemical solvent stains. This does not mean someone has MS. What is actually causing the MS is EBV in addition to the heavy metals—a truth that medical communities are unaware of.Hashimoto's ThyroiditisEBV is also the true cause of Hashimoto’s thyroiditis. The thyroid becomes inflamed because the virus has infected it. Your immune system is not going haywire or out to get you. It’s this virus that’s causing the damage and making you feel miserable. Your body just needs the proper support, which I describe in Thyroid Healing, to triumph over the virus.CeliacCeliac is not a genetic disease. It is inflammation in the intestinal lining from streptococcus bacteria. Medical communities believe that celiac is an autoimmune condition and that it’s limited to a sensitivity to gluten. Rather, wheat gluten is one trigger to this inflammation of the intestinal tract by feeding the strep bacteria in there.Type 1 DiabetesType 1 diabetes occurs when there is an injury to your pancreas. If you have type 1 diabetes, at one point some of your pancreatic tissue was injured from a viral condition or toxic bacteria. Your body is not attacking your pancreas.Grave's DiseaseIn Grave’s disease, a mutated variety of EBV is causing inflammation, which is scarring the thyroid. There are specific unknown varieties of EBV that prompt the thyroid gland to produce more tissue and, as a result, more thyroid hormones. Find out more about Grave’s in Thyroid Healing.Hepatitis A, B, C, DAll versions of hepatitis are viral conditions from the herpetic family, mainly the Epstein-Barr Virus. They are at different stages of what the virus is doing to the liver. Autoimmune hepatitis is a mistake all on its own because medical research doesn’t actually know the true cause of these conditions. They merely see inflammation and antibodies and make the conclusion that the antibodies are going after the liver. However, the immune system is creating these antibodies to help you go after the virus.Mysterious Skin RashingMany varieties of mysterious skin rashing is from the shingles virus. Specifically, eczema and psoriasis can be a combination of EBV and shingles, both in the liver, feeding off of high levels of copper and DDT. The reason mysterious skin rashing does not get diagnosed as shingles is because when something does not look like textbook shingles, they would never think to call it that. However, what modern medicine is unaware of is that there are over 31 varieties of the shingles virus that they have yet to discover. Therefore, it would be impossible to diagnose it as such without further research. Ehler's-Danlos SyndromeEhlers-Danlos syndrome is another example of an illness that has been labeled as autoimmune simply because medical professionals are unaware of the true cause. The truth is that this condition is caused by a virus that’s injuring connective tissue; it’s not genetic.FibromyalgiaThe aches, pains, tenderness, fatigue, and stiffness of fibromyalgia are a result of EBV’s neurotoxins creating chronic inflammation of both the central nervous system and nerves throughout the body. Knowing the true cause means that you can begin to implement the steps needed to allow for healing. You can find out more about fibromyalgia and many other autoimmune diseases and condition in Thyroid Healing.Viruses EatNow that you know that your body is not attacking itself, but rather that it is attacking a pathogen in your body, you can move onto the next step toward healing. The next thing that’s important for you to know is a truth about viruses that science has yet to discover: viruses eat. Modern medicine is still oblivious to the fact that viruses must eat in order to grow and proliferate. Without their favorite foods, viruses will die. Therefore, logically we must know which are their favorite foods and eliminate them from your diet so the virus can exit your system, leaving you free of your symptoms over time.As an example, eczema is due to a virus in the liver. And that virus feeds off certain foods, which then creates an internal dermatoxin that leaches out from the liver, goes into the bloodstream, and then surfaces through the skin. When you know this is the real cause, you can take away the foods the virus likes best.In my book Thyroid Healing I explain in depth how the Epstein-Barr virus feeds, what it feeds on, and how it excretes when it feeds. For example, EBV feeds on toxic heavy metals, as well as all pesticides, including old ones such as DDT stored in the liver, and certain foods we eat. In the book, I explain the entire process of this particular virus as it feeds, excretes, develops, and continues to feed.Viruses Love Heavy MetalsViruses love to feed off of heavy metals, such as mercury, arsenic, cadmium, lead, nickel, alloys, steel, aluminum, and copper, that are in our systems, including in our liver. Heavy metals are not the cause of your autoimmune labeled disease. They simply feed the viruses that are the cause. The good news is you can take active steps to eliminate these metals from your body by eating the five heavy metal detox foods I recommend every day within a 24-hour period. These foods are wild blueberries, Hawaiian spirulina, barley grass juice extract powder, cilantro, and Atlantic dulse. All five of these foods work together to slowly eliminate the heavy metals. Find out how you can incorporate these foods in Thyroid Healing.Many people believe chlorella is actually better for you than spirulina, but chlorella simply does not eliminate heavy metals the way spirulina does. Chlorella drops the metals instantly, while spirulina holds onto them and in tandem with the other key foods, effectively aids in the process of removing them from the body.Foods that Viruses LoveEggs may be considered the perfect food in some circles, but in reality, they are the perfect food for viruses. They essentially incubate viruses, making them stronger and more aggressive. Stay away from eggs if you have a disease that is labeled as autoimmune, especially lupus and PCOS. Unknown to medical communities, eggs are disastrous for those who have ovarian issues. Eggs feed every single virus and bacteria that create conditions that are thought to be autoimmune diseases.Even if you are eating cage-free, natural eggs, these still act as food for pathogens. Viruses look for egg material in the body to feed on. They feed on the natural hormones that are in eggs, which act as a steroid for the virus. It does not matter what kind of eggs you get because unfortunately all eggs feed viruses.In a very similar way, all dairy products feed viruses. Some doctors are knowledgeable about the allergy concern of eating dairy, but we have to recognize that simply eliminating dairy is not enough. We need to understand why we are eliminating it. It’s critical to stop eating foods like dairy and eggs if you have any symptoms or a chronic illness so that they do not continue to feed the pathogens that are causing your symptoms. It is also a good idea to stay away from all corn products and canola oil. These are in almost every packaged food out there, even organic ones, so be mindful of what is in the ingredients list. If it is intimidating to you to avoid these ingredients that seem minor, think of it this way. The more fresh fruits and vegetables you include in our diet, the more apples, sweet potatoes, salads, bananas, and squash, the less room you have in diet for processed foods that likely contain ingredients you are trying to avoid. Think of crowding out your plate with so much good stuff that the packaged foods simply do not have as much space. Also, the more fresh fruits and vegetables you eat, the more you crave them. Keeping this in mind will help you increase your whole foods intake because you know that the more you do it, the easier it will get. It’s also helpful to reduce animal protein while you’re healing because, again, we need room for the fruits, leafy greens, and vegetables, the secrets weapons, as I like to call them. If you like to eat animal protein, try not to eat it three times a day. Instead eat it once a day and find other filling options to enjoy. Instead of chicken on your salad, add black beans, avocado, sweet potato, or hummus. Instead of bacon with your toast, bake potato fries with lots of herbs of spices. And when you do eat animal proteins, choose the cleanest meats possible. Wild fish is one of the better choices. When healing from chronic illnesses and symptoms, it’s helpful to minimize added fats in the diet to allow the liver to cleanse and toxins and viruses to be most effectively purged from the body. One easy way to cut down fats is to stay away from or minimize oils, even olive oil and coconut oil. A small drizzle here or there is fine, but do not overdo the oils. The same goes for other fat sources like nuts for example. Eat just a few with lots of fresh veggies versus having a large portion of nuts.Foods that Fight PathogensThere are so many amazing powerhouse foods that you can eat in order to give your body an extra boost when fighting off pathogens. The first group we can focus on is cruciferous vegetables. There is a misconception circulating around that cruciferous vegetables, also called brassicas, are harmful because of the goitrogenic compounds in them. We are being told to stay away from kale, broccoli, cauliflower, and brussels sprouts, but this is a misguided and unproductive trend. These foods are actually incredible for anyone with an illness that has been labeled as an autoimmune disease, including thyroid conditions. Cruciferous vegetables cannot harm you. They contain phytochemicals that actually fight the bug you are trying to get rid of. These foods can be some of your greatest allies in your path to healing, and it would be wise to include them, both raw and cooked, on a daily basis.Straight cucumber juice is something that can be included daily in order to flush out toxins from the body. Straight celery juice is also important to include because its mineral salts clean up the liver, build up hydrochloric acid, and strengthen bile so you can break down bacteria and viruses in the intestinal tract that cause conditions like colitis, celiac, and crohn's disease. I share recipes for these foods and juices in my book Thyroid Healing.Include plenty of squash in your diet. There are so many delicious varieties to enjoy, such as butternut, kabocha, spaghetti, and acorn. Also, remember to eat lots of fresh herbs like cilantro, rosemary, and thyme. Eat plenty of salads with red leaf lettuce, butter lettuce, arugula, parsley, and radishes. Radishes are a miracle food when fighting off pathogens. Radish greens kill off viruses, and the radishes themselves push poisons out of the body and support the thyroid.Eating plenty of fruit is one of the best ways you can support your healing. If you are afraid of fruit, know that fruit cannot feed candida and fruit sugar isn’t bad for you. It’s the opposite—fruit is the most healing food on earth! So eat plenty of apples, bananas, oranges, and berries. Melons are wonderful for flushing out poisons that the virus creates. Bring in more tropical fruits like papaya, pineapple, and passionfruit if you are able to find them. Eat the fruits that are in season like pears and persimmons in the fall and peaches and plums in the summer. Fruit is an amazing antiviral food that is essential to include when you are fighting a pathogen such as Epstein-Barr virus that is causing your mystery illness. Bananas in particular are great for killing off pathogens in the intestinal tract. If you fear fruit, check out my chapter on Fruit Fear in my book Medical Medium.Another power food that is worth seeking out is dandelion greens. These are often sold at farmers markets and health food stores among other greens like kale and collard greens. Dandelion greens are particularly supportive for the liver because they work to push out poisons that are created from a virus or bacteria. There are so many wonderful herbal teas to include, as well. Nettle leaf and lemon balm are two particularly powerful ones that fight viruses. There is a phytochemical in lemon balm that helps you go after the virus you want to kill. Many people know that nettle leaf tea is anti-inflammatory, but they do not know why. The reason is because it’s killing the pathogens that are creating the inflammation in the first place. When you are drinking your herbal teas with this knowledge, the properties become that much more powerful.In the same way, people are aware that turmeric is anti-inflammatory, but they do not know why. Turmeric has phytochemicals that are poisonous to the bugs that are inflaming people’s joints and backs. This herb is attacking viruses and bacteria.SupplementsIncorporating supplements is critical to fighting off the viruses that are causing your autoimmune disease. As I always recommend, talk to your medical practitioner before you begin taking supplements so you can work together to find the right dosages. Bring your doctor this information and work together to fight the virus with these powerful herbs and supplements. Be sure to get the right supplements. I have a list of preferred supplements that you can find on my website. ZincZinc deficiencies are rampant and can trigger an autoimmune condition. Simply taking zinc can be a huge step toward healing and can be critical for anyone suffering from the symptoms associated with autoimmune diseases. When you take zinc sulfate, it goes directly to where the virus is and starts working on stopping it in its tracks. Additionally, zinc increases your immune system’s ability to fight. B12 with adenosylcobalamin & methylcobalaminMany people are recommending B12 today, which is good. However, there is still very little talk about the right kind of B12. When fighting a viral condition, it is essential to use a combination of both adenosylcobalamin and methylcobalamin. Including a methylfolate supplement along with this specific B12 is especially helpful. Vitamin CWhen fighting a viral condition, it’s important to include some vitamin c supplements, particularly the liposomal c. The Liposomal c I recommend on my preferred supplements page does not contain any corn, which feeds viruses, unlike other brands. Ester C is also very helpful.
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The ObserverWhy two brains are better than oneA radical technique that makes mature cells act like stem cells is growing a mini brain from tissue I donated. One day it could produce whole organs for transplantPhilip BallSat 31 Mar 2018 17.00 BST Last modified on Sun 1 Apr 2018 00.10 Might we soon be able to grow new brains? Last week, I was told my other brain is fully grown. It doesn’t look like much. A blob of pale flesh about the size of a small pea, it floats in a bath of blood-red nutrient. It would fit into the cranium of a foetus barely a month old.Still, it’s a “brain” after a fashion and it’s made from me. From a piece of my arm, to be precise.I’m not going to pretend this isn’t strange. But neither is it an exercise in gratuitously ghoulish biological engineering, a piece of Frankensteinian scientific hubris 200 years after Mary Shelley’s tale. The researchers who made my mini-brain are trying to understand how neurodegenerative diseases develop. With mini-brains grown from the tissues of people who have a genetic susceptibility to the early onset of conditions such as Alzheimer’s, they hope to unravel what goes awry in the mature adult brain.It’s this link to studies of dementia that led me to the little room in the Dementia Research Centre of University College London last July, where neuroscientist Ross Paterson anaesthetised my upper arm and then sliced a small plug of flesh from it. This biopsy was going to be the seed for growing brain cells – neurons – that would organise themselves into mini-brains.The Brains in a Dish project is one of many strands of Created Out of Mind, an initiative hosted at the Wellcome Collection in London and funded by the Wellcome Trust for two years to explore, challenge and shape perceptions and understanding of dementias through science and the creative arts. Neuroscientist Selina Wray at UCL is studying the genetics of Alzheimer’s and other neurodegenerative diseases and she and her PhD student Christopher Lovejoy gamely agreed to culture mini-brains from cells taken from four of the Created Out of Mind team: artist Charlie Murphy, who is leading Brains in a Dish, BBC journalist Fergus Walsh, neurologist Nick Fox and me.It was a no-brainer… well, you know what I mean. Who could resist the narcissistic flattery of having another brain grown for them? I was curious how it would feel. Would I see this piece of disembodied tissue as truly mine? Would I feel protective of, even concerned for, a tiny “organoid” floating in a petri dish? Most of all, I was attracted by the extraordinary scientific feat of turning a lump of arm into something like a brain.There’s a lot of baggage in that “something like”. Some researchers dislike the term “mini-brain” and with reason. This pea-size object is not a miniature version of the brain in my skull. It’s not even quite like the immature developing brain of an early-stage foetus. Without a body, neurons don’t quite know how to make a proper brain.But neither are mini-brains blobs of identical neurons, like, say, a small chunk of my cortex. One can fairly say that the neurons “want” to make a brain but, lacking proper guidance, don’t quite know how to go about it. So they make a reasonable but imperfect approximation.The mini-brain contains several types of brain cell, arranged somewhat as in a real brain – in layers such as those of the cortex, for example. The mini-brain even contains sketchy little versions of the folds and grooves on the surface of a true brain and appendages that, in a foetal brain, would become the brain stem and central nervous system, extending down the spine.What’s most astonishing about this project is that these neurons started out as a piece of my arm. Those skin-forming cells, fibroblasts, were turned into brain cells using a technique discovered barely 10 years ago and that has revolutionised tissue engineering and embryo research and won its creator, Shinya Yamanaka, a Nobel prize. It also overturned decades of conventional wisdom in cell biology. Induced stem cells labelled with fluorescent tags. Photograph: Chris Lovejoy and Selina Wray/UCLOur bodies grow from a single cell – a fertilised egg – by cell division accompanied by increasing cell specialisation. In the very earliest days of an embryo’s development, all its cells are capable of growing into any kind of tissue in the body. These are called embryonic stem cells and their complete versatility is called “pluripotency”.As the embryo grows, some cells become committed to particular fates – they become skin cells, liver, heart, brain or bone-forming cells and so on. This differentiation springs from a modification of the cells’ genetic programme: the switching on and off of genes. As they differentiate, cells may change their shapes as well as their functions. Neurons grow the long, thin appendages that wire them into networks, the ends equipped with synapses where one cell sends an electrical signal to others. That signalling is the stuff of thought.It was believed cell differentiation was one way – that once a cell was committed to a fate, there was no going back and that the silenced genes were switched off for ever. So it came as a surprise to many researchers when, in 2007, Yamanaka, a biologist at Kyoto University, reported that he could convert differentiated human cells directly back to a stem-cell-like state by adding to them the genetic material for making certain types of protein.Yamanaka and his colleagues used viruses to inject into the mature cells some of the genes that are highly active in embryonic stem cells and they found that just four of these were enough to switch the cells into a pluripotent state, becoming, to all intents and purposes, like stem cells. These became known as induced pluripotent stem cells (iPSCs). I do think of these brain organoids as 'mine', although not with any sense of ownership or pastoral dutyIn principle, iPSCs can be grown outside the body into any tissue type, perhaps even into entire organs such as a pancreas or kidney, to replace a malfunctioning one by transplantation. Organs could be grown from cells – taken, like mine, from an arm, say – of the recipient, thus avoiding problems of immune rejection.Creating organs involves knowing how to guide iPSCs towards the appropriate fate. This might involve giving them an extra dose of the genes that are highly active in that particular tissue type. But Chris turned my own iPSCs into neurons simply by changing the nutrient medium; such stem cells seem to have a preference for becoming neurons, so they only need a nudge to get them going.Organs aren’t just big masses of a single cell type, however. The heart, kidney, brain and so on all contain many types of cell, organised in particular ways and fed with a blood supply. Reproducing that complex architecture in organs grown outside the body remains a huge challenge.Yet cells can do a lot of it themselves. The biologist Madeline Lancaster discovered this when she was studying the growth of neurons from stem cells as a doctoral student in Vienna with the neuroscientist Jürgen Knoblich in 2010. She found that the neurons, left to their own devices, would start to specialise and organise into mini-brains. The author’s brain organoid.The plan, Lancaster (who now runs her own lab at the University of Cambridge) told me, was that she would make flat neural structures called rosettes, which had been done before. But the mouse stem cells she worked with wouldn’t stick well to the surface of the dishes. Instead, says Lancaster, “they formed these really beautiful 3D structures. It was a complete accident.”Once they realised what they had made, she and Knoblich started to grow the structures from human stem cells, too. “At first, it was totally surprising that these cells could make a structure rather like a brain all by themselves”, she says. But in retrospect, she says, it makes complete sense. That kind of self-organisation is “just what an embryo does.” And it’s what I can now see in my own mini-brain, the different cell types stained with fluorescent dye to become a beautiful, multicoloured constellation under the microscope.Lancaster and others are now seeking to find ways to supply mini-brains with more of the environmental cues they would get in a developing foetus, so that they can become even more brain-like. “You don’t need a completely well-formed human brain in a dish to study biological questions, ” she explains. But if you can improve the resemblance in the right respects, you’ll get a better picture of the process in real bodies.Lancaster uses brain organoids to investigate how the size of the human brain gets fixed. She has studied microcephaly, a growth defect that results in abnormally small brain size, and is also interested in what can make brains grow too big, which, contrary to what you might expect, is not a good thing and is linked to neurological disorders such as autism.Other researchers are using these mini-brains to study conditions such as schizophrenia and epilepsy. At UCL, Wray is making them to understand the neurodegenerative process in two types of dementia: Alzheimer’s and frontotemporal dementia. The atrophy of brain tissue may start when two proteins called tau and amyloid beta switch from normal to misshapen form. These forms stick together in clumps and tangles that accumulate in the brain and cause neurons to die. The author’s brain organoid in cross-section, with the cells stained different colours by type. The author’s brain organoid in cross-section, with the cells stained different colours by type. Photograph: Chris Lovejoy and Selina Wray/UCLBy culturing mini-brains from the cells of people with a genetic predisposition to these diseases (who account for about 1% to 5% of all cases), Wray hopes to find out what goes awry with the two proteins as neurons grow. “We are making mini-brains to try to follow the disease in real time, ” she says. “We hope to see the very earliest disease-associated changes – that’s important when we think about developing treatment.” She has found that the tau proteins for the disease samples are different from those in healthy samples. My cultures may eventually be anonymised and used as one of those control samples.How do I feel about these pieces of me growing in dishes in the centre of the city, six miles away from where I live? I was surprised to discover that they are no longer, officially, pieces of me at all. Cells that have divided outside the body are not classed as samples of tissue from an individual, but as “cell lines” – more nebulous entities that are distinct from their original donor.Nobel prize in physiology or medicine 2012: Yet I do think of these brain organoids as “mine”, although not with any sense of ownership or pastoral duty. That’s probably a common response in people whose cells are cultured in the lab. The cancer cells taken in 1951 from the patient Henrietta Lacks at Johns Hopkins University hospital in Baltimore just before she died, and used for research (without her consent, which was not then required), are still regarded by Lacks’s surviving family as in some sense “her”, as Rebecca Skloot described in her bestselling 2011 book The Immortal Life of Henrietta Lacks. These “HeLa” cells are now the standard cell line for studying cancer and millions of tonnes of them have been grown worldwide: a piece of a person turned into a mass-produced commodity.I’ll be very glad if my mini-brain can contribute in some small way to Wray’s research. I do not fear that it will have anything like anguished thoughts, any awareness at all, in its Matrix-like nutrient bath. But it does still seem like a piece of me, a wistful little attempt to remake the brain I take so much for granted. We have no frame of reference for thinking about such things. It is exciting and odd. But it’s also a glimpse of the future.
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Colour-enhanced image of the bacteriophage T4.Photo courtesy David Gregory & Debbie Marshall/Wellcome ImagesViral rescueWhen antibiotics fail, could phage therapy succeed? The germ’s-eye view of infection might open up revolutionary treatmentsEmily Monossonis a writer and toxicologist at the Ronin Institute. Her latest book is Natural Defense: Enlisting Bugs and Germs to Protect Our Food and Health (2017).Listen hereBrought to you by curio.io, an Aeon partnerSYNDICATE THIS ESSAY521TweetShe was only 22 years old, but her attending doctor in Texas was running out of options. The sticky substance coating the patient’s lungs was par for the course with cystic fibrosis (CF); mucus is a signature of this heritable, progressive and incurable disease. So, too, is infection. But this time, a particularly nasty and stubborn bug had taken hold. The persistent presence of bacteria was putting an additional burden on the young woman’s already overtaxed respiratory system, and chronic infection degrades lung function. The best antibiotics Western medicine had to offer had failed.The Scottish physician Alexander Fleming discovered the first modern antibiotic, penicillin, in 1928. In 1945, Fleming issued a warning: should we misuse or overuse antibiotics, bacteria can and will resist. Today, resistance has become a scourge of modern medicine. Not only did we deploy antibiotics to save lives, but for commercial gain – pumping them into industrial farm animals, from cows and pigs to chicken and fish. Under pressure from this assault, bacterial populations did what they’d done for aeons: evolve or die. Those strains that could survive antibiotics are now winning the evolutionary race, and we are progressively running out of cures.One solution, according to the late Joshua Lederberg, a Nobel Prize-winning molecular biologist, is to ‘drop the Manichean view of microbes: “We good; they evil”.’ In a 2000 essay in Science magazine, he argued that humans needed to work with nature rather than against it; we needed to take ‘the germs’-eye view of infection’. Modern medicine tends to adopt a somewhat mechanistic approach: fix the flaw, repair the malfunction, extricate and eradicate the invading entity. But the human body and illness do not follow such linear paths; they are influenced by ecological and evolutionary processes, which new treatments might try to manage in a more holistic way.In the case of the young woman, the bacteria that had colonised her respiratory system was called Pseudomonas aeruginosa. It’s one of a dozen or more bugs commonly acquired in hospitals, but can be found almost anywhere, from a door knob to the kitchen sink. Those with CF are particularly susceptible; by some estimates nearly 60 per cent of adults with CF are infected with the potentially lethal bacteria. In a petri dish, P aeruginosa grows into a shimmering blue-green colony of cells; in an infected lung, the microbes build a fortress of sticky slime. Within these so-called biofilms, the community of bacteria work together, share food, provide protection for one another, and swap DNA. Like most of us, bacteria work ‘better’ together. They can also hide from a body’s immune cells, and from antibiotics. When a biofilm forms, whether on the inner surface of the lungs, a catheter or a surgical patch, it’s tricky to eradicate. To add insult to infection, like many other pathogens, P aeuroginosa is becoming increasingly antibiotic-resistant.But the patient’s father had read about an experimental approach called ‘phage therapy’ that involved infecting infections with a virus. He suggested it to the physician. In October 2017, she contacted Benjamin Chan, a young microbiologist at Yale University. Alongside his colleague, the ecologist and evolutionary biologist Paul Turner, he’d been pioneering ways to make the therapy more reliable. Did Chan and Turner, she wondered, have a phage that might save her patient?Subscribe to our newsletterDaily/weekly updates on everything new at Aeon.DailyWeeklyPhage therapy is not so much a cutting-edge new treatment as a revival and updating of an old one. ‘Phage’ derives from the Ancient Greek phágos, for ‘glutton’, and phageîn, ‘to eat’. In a biological context, it’s short for ‘bacteriophage’: a category of viruses, each of which targets a specific species or strain of bacteria. You can find them anywhere and everywhere. Chan goes ‘bioprospecting’ for phages in sewage, ponds and drains – basically ‘wherever the bacteria are, ’ he told me. ‘It’s pretty gross.’Phages were discovered before modern antibiotics, more than a century ago, when physicians had few options for curing infectious diseases. At the time, the bacteria behind diseases such as anthrax, tuberculosis, syphilis and diphtheria had been revealed, but viruses remained something of an enigma. Here were disease-causing agents capable of passing through the finest bacteria-catching filters. What could be smaller than bacteria? The true nature of viruses would remain a mystery for decades: bits of DNA wrapped in protein, straddling the netherworld between living and inert, which commandeer the cell’s reproductive machinery to make dozens or hundreds of copies of themselves.By 1919, Félix d’Herelle, a French-Canadian microbiologist, had noticed that certain viruses had bacteria-busting powers. That summer at a hospital in Paris, three young brothers whose sister died from dysentery had come under the care of the paediatrician Victor Henri Hutinel. Having isolated a phage from the faeces of another dysentery patient, d’Herelle was ready to give the treatment a go. After taking a swig of the prepared phage solution (along with Hutinel and several interns) and showing no ill effect, the microbiologist was permitted to inject one sibling, and eventually the others. Within a day, their symptoms subsided. By the next decade, physicians around the globe were preparing phage ‘cocktails’, mixing multiple live viruses, to treat patients with typhoid, staph, strep and cholera.Antibiotics can attack a number of infections, but each phage responds only to a specific bacterial strainBut phages were soon eclipsed by other treatments. In 1910, the first synthetic antimicrobial, a molecule related to arsenic known as arsphenamine or Salvarsan, had been found to be an effective treatment for syphilis. Then came Fleming’s discovery of penicillin, a naturally occurring chemical compound originally extracted from mould. It worked by attacking the bacterial cell wall, a structure made of sugars and amino acids that is common to most bacteria. Like a chicken-wire frame, the wall is what prevents bacteria from exploding under their own internal pressure. Make a chink in the wall, and – bam! The cell bursts like an overfilled balloon, leaving our human cells, which have a different structure, relatively unscathed. By the 1940s, doctors were liberally dispensing the ‘miracle drug’ of penicillin; in the following decades, other antibiotics such as carbapenems, polymyxins and macrolides were developed, each capitalising on some distinctive feature that divided bacterial cells from our own.Throughout the first half of the 20th century, research into phage therapy continued. But it soon became obvious that antibiotics enjoyed several advantages. They could be meted out in much more precise and effective doses than phage viruses, which had to be grown within their bacterial host cells, and then collected and cleaned up. Antibiotics could also attack a number of different infections, but because each phage responded only to a specific bacterial strain, a doctor had to be sure that he (as most of them were back then) had the right phage for the relevant infection. Unscrupulous producers hawked products with little or no virus, or the wrong kind of phage. Sometimes the therapy worked brilliantly but other times it failed. A couple of negative reviews published in The Journal of the American Medical Association in the 1930s and ’40s didn’t help. By the middle of the century, phage therapy was essentially dead in the US and Western Europe – though it continued in parts of Eastern Europe, where antibiotics were expensive and doctors continued to refine treatments and build phage libraries, indexed by the strain of bacteria they preyed upon.In 2015, Thomas Patterson, a professor at the University of California, San Diego, was on holiday in Egypt. He became ill with a fever and stomach pain; he started vomiting, and his heart was racing. He was eventually diagnosed with an inflammation of the pancreas and, after being evacuated to Germany, an infection. The bug infecting Patterson, Acinetobacter baumannii, outmanoeuvred one antibiotic treatment after another. Physicians drained and drugged him, but the microbes continued to reproduce and cause havoc. Flown back home to California, Patterson lay in the intensive-care unit, in a coma and clinging to life after four months of hospitalisation and treatment.Patterson’s wife, Steffanie Strathdee, is an infectious disease epidemiologist. She began searching for alternative treatments and, at her request, the physician agreed to try phages. At the time, there were only a few known locations in the US that had been collecting and characterising such viruses. But as it turned out, A baumannii was also a problem for patients with combat injuries, and the US Army and Navy had already been experimenting with a relevant phage. Another option for a phage cocktail came from a university in Texas and a California-based biotech company.Because the therapy wasn’t yet approved in the US, Patterson’s medical team had to obtain permission from the Food and Drug Administration (FDA) to use an ‘emergency investigational new drug’. The first treatment was promising: within days, Patterson awoke after weeks in a coma. But then A baumannii began resisting the phages that had been administered. Just as bacteria can evolve resistance to antibiotics, they can develop resistance to bacteriophages. So the doctors sought a new combination of phages able to infect the resistant strain.In the end, Patterson recovered; because he remained on antibiotics throughout the ordeal and under a great deal of medical care, it’s difficult to attribute the success to any one treatment. But it’s very likely that phages helped to turn the situation to Patterson’s advantage. During the episode, while isolating and culturing the bug that the virus would attack, the team noticed something curious: A baumannii had apparently regained some sensitivity to antibiotics. It seemed that the phage exerted selective evolutionary pressure on the bacterium, so that it could survive the virus only by losing its antibiotic resistance. These sorts of effects had been observed decades ago, before phages slid out of Western medicine. If better understood, could this phenomenon be used to our advantage? Could evolution be used as a tool?Unlike traditional antibiotics, phages are both a self-sustaining and self-limiting treatmentThis is what Chan and Turner have been trying to do for the past five years. Their strategy is to find phages that can do more than simply kill offending bacteria, the way antibiotics do; they want phages that can push the right evolutionary buttons, rendering the patient’s bacteria more vulnerable to antibiotics, less virulent, or even harmless. Chan and Turner call this wizardry ‘evolutionary engineering’.Phages exploit what are known as receptors: a bit of protein or other biomolecule protruding from the bacterial cell’s surface. When a phage enters the bloodstream or slips into a layer of mucus, it tumbles about until it bumps into a strain of bacteria that possesses a receptor that matches its own particular needs, even if the bug is sheltering within a biofilm: unlike many antibiotics, phages can penetrate the sticky protective layer. Upon gaining access, the virus then hijacks the bacterial cell to make copies of itself, and these new phages go about infecting more bacterial cells, until there are no more left to infect. This makes phages, unlike traditional antibiotics, both a self-sustaining and self-limiting treatment.One way that phages can help is by targeting receptors known as virulence factors, which enhance bacteria’s capacity to survive and reproduce in the body. If a phage goes after a particular virulence factor, only those cells that are less virulent – and therefore less nasty for the patient – will likely survive.Another set of targets are the factors that act as defences against antibiotics. Some resistant bacteria use certain receptors as molecular pumps, which allow them to push out the drugs before they can enter and kill the bacterial cell. Certain phages use these very same pumps for their entrance into the bug. Should a random mutation to the right receptor occur, the virus might no longer be able to penetrate the bacterium. But the twist is that this same bacterium will no longer be able to pump out antibiotics. Only those without resistance will be likely to survive. This sort of evolutionary game is the dance of life, whether it’s happening in the ocean, a pond or inside a patient suffering from infection. Here, the phage is like a predator, forcing the bacteria to innovate to survive. The pressure that the virus exerts on the process of natural selection nudges the bacteria onto a pathway that enables them to withstand a viral attack – but thereby renders them vulnerable to antibiotics.By the fall of 2017, Chan had an assortment of promising phages stowed away in his laboratory. But phages that work in a Petri dish, lab animal or even a human patient might not behave the same way when administered to another person.The previous year, Chan had isolated a phage that saved Ali Khodadoust, an Iranian ophthalmologist in Connecticut, from a life-threatening infection. Years earlier, he had been diagnosed with a weak and bulging aorta. Doctors patched it up with mesh, but Khodadoust had been left with a nasty P aeruginosa chest infection. Antibiotic after antibiotic had failed; three years in, after multiple operations, the bug was so well-established that doctors feared that cutting it out and replacing the patch would only spread the infection. The doctor’s condition was an opportunity to provide proof of concept, and save a life.Chan had collected a sample phage known as ‘OMKO1’, which turned out to be a good match for Khodadoust’s bug; it infected the bacteria by way of the resistance pump. Here was a chance to not only bust apart the stubborn infection, but make it respond once again to antibiotics. Chan and Turner asked for the same allowance from the FDA as Patterson’s doctors had done, and it was granted.In January 2016, Chan stood nervously outside the operating room, watching through the window as computer-guided needles delivered a combination of OMK01 and antibiotics to Khodadoust. ‘This was the first application, as far as I know, with the understanding that this would be a forced trade-off and trying to capitalise on that, ’ Chan said. He was referring to the evolutionary give and take: the loss of a useful pump in exchange for resistance to a virus. It was a success in Khodadoust’s case – but success in one patient does not make a treatment. For that, the therapy must be effective again and again. (Despite winning out over the infection in 2016, Khodadoust passed away in March 2018 after a long battle with post-operative complications, at the age of 82.)A personalised cocktail of live viruses capable of reproducing and evolving is a new beast for regulationWhen the doctor in Texas asked Chan if there was a phage that might help her young CF patient, Chan asked for a sputum sample. This time, there were several promising candidates, including OMK01. After gaining FDA permission as before, on 12 December 2017 Chan flew to Texas carrying a cooler with 10 tubes of a phage-saline cocktail. ‘She took the first dose in the hospital with a nebuliser, ’ Chan recounted, ‘then she nebulised at home, in the bathroom, for an hour.’ By day two, she regained energy and her lungs were clearer. After 10 days of treatment, although the phage hadn’t cleared the infection (CF makes it very difficult to fully eradicate infections), it did force the P aeruginosa to become sensitive to all antibiotics save one, opening many more options for treatment.To date, no form of phage therapy has yet made its way through the long and expensive road to FDA approval, although a handful of groups, including Chan and Turner’s, are getting close. As a personalised cocktail of live viruses capable of reproducing and evolving, phages are a new beast for regulatory agencies. Chan and Turner’s long-term goal is to develop a library of phages that can push bacteria to evolve in the desired, even beneficial, directions. ‘Ben calls it Phage Therapy 2.0, ’ Turner told me. But despite the hype, Turner is not a phage evangelist – he is a researcher who sees promise, he says. But there are dangers: if a phage uses a protein independent of resistance or virulence to gain access, should the bacteria evolve resistance, it could lead to a strain that continues to cause infection but now resists the phage. Worse, there is a small possibility that a nonpathogenic bystander, should it become infected by a phage, might evolve to become pathogenic.Still, when such cases as Patterson’s and Khodadoust’s make the news, word gets out. Now Chan and Turner are fielding an increasing number of requests from desperate physicians or their patients. What might save more lives in the long run is the research they’re doing to better understand the evolution and ecology of phages, bacteria and antibiotics. Like current work on the extraordinary influence of the human microbiome, it represents a new model of infection control: less about one-hit interventions and more about the complexity of ecological systems and evolutionary processes. These approaches incorporate the notion that the human body is not a single entity, but an ecosystem teeming with bacteria, viruses, fungi and other microscopic inhabitants. Their efforts and those of others who adopt this ‘eco-evo’ model of medicine might someday lead us towards a different medical paradigm – one that recognises and works with, rather than against, the invisible world thriving within, upon and all around us
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In the future we won’t edit genomes—we’ll just print out new onesWhy redesigning the humble yeast could kick off the next industrial revolution.by Bryan Walsh February 16, 2018At least since thirsty Sumerians began brewing beer thousands of years ago, Homo sapiens has had a tight relationship with Saccharomyces cerevisiae, the unicellular fungus better known as brewer’s yeast. Through fermentation, humans were able to harness a microscopic species for our own ends. These days yeast cells produce ethanol and insulin and are the workhorse of science labs.That doesn’t mean S. cerevisiae can’t be further improved—at least not if Jef Boeke has his way. The director of the Institute for Systems Genetics at New York University’s Langone Health, Boeke is leading an international team of hundreds dedicated to synthesizing the 12.5 million genetic letters that make up a yeast’s cells genome.In practice, that means gradually replacing each yeast chromosome—there are 16 of them—with DNA fabricated on stove-size chemical synthesizers. As they go, Boeke and collaborators at nearly a dozen institutions are streamlining the yeast genome and putting in back doors to let researchers shuffle its genes at will. In the end, the synthetic yeast—called Sc2.0—will be fully customizable.“Over the next 10 years synthetic biology is going to be producing all kinds of compounds and materials with microorganisms, ” says Boeke. “We hope that our yeast is going to play a big role in that.”Think of the project as something like Henry Ford’s first automobile—hand built and, for now, one of a kind. One day, though, we may routinely design genomes on computer screens. Instead of engineering or even editing the DNA of an organism, it could become easier to just print out a fresh copy. Imagine designer algae that make fuel; disease-proof organs; even extinct species resurrected.Jef Boeke leads an effort to create yeast with a man-made genome.“I think this could be bigger than the space revolution or the computer revolution, ” says George Church, a genome scientist at Harvard Medical School.Researchers have previously synthesized the genetic instructions that operate viruses and bacteria. But yeast cells are eukaryotic—meaning they confine their genomes in a nucleus and bundle them in chromosomes, just as humans do. Their genomes are also much bigger.That’s a problem because synthesizing DNA is still nowhere near as cheap as reading it. A human genome can now be sequenced for $1, 000, with the cost still falling. By comparison, to replace every DNA letter in yeast, Boeke will have to buy $1.25 million worth of it. Add labor and computer power, and the total cost of the project, already under way for a decade, is considerably more.Along with Church, among others, Boeke is a leader of GP-write, an organization advocating for international research to reduce the cost of designing, engineering, and testing genomes by a factor of a thousand over the next decade. “We have all kinds of challenges facing ourselves as a species on this planet, and biology could have a huge impact on them, ” he says. “But only if we can drive down costs.”Bottom upA scientist named Ronald Davis at Stanford first suggested the possibility of synthesizing the yeast genome at a conference in 2004—though initially, Boeke didn’t see the point. “Why would anyone want to do this?” he recalls thinking.But Boeke came around to the idea that manufacturing a yeast genome might be the best way to comprehend the organism. By replacing each part, you might learn which genes are necessary and which the organism can live without. Some team members call the idea “build to understand.”“It’s a different take on trying to understand how living things work, ” says Leslie Mitchell, a postdoctoral fellow in the NYU lab and one of the main designers of the synthetic yeast. “We learn what gaps in our knowledge exist in a bottom-up genetic approach.”Joel Bader, a computer scientist at Johns Hopkins, signed on to develop software that let scientists see the yeast chromosomes on a screen and keep track of versions as they changed, like a Google Docs for biology. And in 2008, to make the DNA, Boeke launched an undergraduate course at Hopkins called “Build a Genome.” Students would learn basic molecular biology as each one assembled a continuous stretch of 10, 000 DNA letters that would go toward the synthetic-yeast project. Later, several institutions in China joined to share the workload, along with collaborators in Britain, Australia, and Japan.“We assign chromosomes to individual teams, like assigning a chapter of a book, and they have the freedom to decide how to do it, as long as it’s based 100 percent on what we design, ” says Patrick Cai, a synthetic biologist at the University of Manchester and the yeast project’s international coordinator.Next stepsIt took Boeke and his team eight years before they were able to publish their first fully artificial yeast chromosome. The project has since accelerated. Last March, the next five synthetic yeast chromosomes were described in a suite of papers in Science, and Boeke says that all 16 chromosomes are now at least 80 percent done. These efforts represent the largest amount of genetic material ever synthesized and then joined together.It helps that the yeast genome has proved remarkably resilient to the team’s visions and revisions. “Probably the biggest headline here is that you can torture the genome in a multitude of different ways, and the yeast just laughs, ” says Boeke.
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HUMAN DEVELOPMENTHow to build a human brainSome steps for growing mini versions of human organs are easier than othersBY INGFEI CHEN 3:30PM, FEBRUARY 20, 2018SHARE ARTICLEorganoid brainBRAIN-MAKING 101 As blobs of two types of brainlike tissue fuse, interneurons (green) migrate from the left clump to the right, linking with neurons (not stained) in the right blob. On both sides, neural support cells called glia appear in purple.PAŞCA LAB/STANFORD UNIV.Magazine issue: Vol. 193, No. 4, March 3, 2018, p. 22SPONSOR MESSAGEIn a white lab coat and blue latex gloves, Neda Vishlaghi peers through a light microscope at six milky-white blobs. Each is about the size of a couscous grain, bathed in the pale orange broth of a petri dish. With tweezers in one hand and surgical scissors in the other, she deftly snips one tiny clump in half.When growing human brains, sometimes you need to do some pruning.The blobs are 8-week-old bits of brainlike tissue. While they wouldn’t be mistaken for Lilliputian-sized brains, some of their fine-grained features bear a remarkable resemblance to the human cerebral cortex, home to our memories, decision making and other high-level cognitive powers.Vishlaghi created these “minibrains” at the Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research at UCLA, where she’s a research assistant. First she immersed batches of human pluripotent stem cells — which can morph into any cell type in the body — in a special mix of chemicals.The free-floating cells multiplied and coalesced into itty-bitty balls of neural tissue. Nurtured with meticulously timed doses of growth-supporting ingredients, the cell clumps were eventually transferred to petri dishes of broth laced with Matrigel, a gelatin-like matrix of proteins.On day 56, the blobs display shadowy clusters of neural “rosettes.” Under a laser scanning microscope, razor-thin slices of those rosettes reveal loose-knit layers of a variety of dividing neural stem cells and the nerve cells, or neurons, they give rise to. The layered structures look similar to the architecture of a human fetal brain at 14 weeks of gestation.By eight weeks, brainlike clumps (top) show neural clusters called rosettes. Within one cluster (red box, expanded at bottom), stem cells (blue and teal) churn out layers of neural precursor cells (pink) and neurons (not stained).BOTH: M. WATANABE ET AL/CELL REPORTS 2017Across the globe, labs such as this one, led by UCLA developmental biologist and neuroscientist Bennett Novitch, are cultivating thousands of these brainy clumps for research. Less than five years ago, a team of biologists in Austria and the United Kingdom and one in Japan wowed the world when they announced they had made rudimentary bits of 3-D human cerebral cortex in a dish. Since then, researchers have been eagerly tinkering with techniques for producing these miniature brain models, like chefs obsessively refining their favorite recipes.“It’s like making a cake: You have many different ways in which you can do it, ” says Novitch, who prefers using the Japanese method with a few tweaks. “There are all sorts of little tricks that people have come up with to overcome some of the common challenges.”For instance, because the brain blobs lack a built-in blood supply, they must absorb enough oxygen and nutrients from the tissue-culture broth to remain healthy. To help, some labs circulate the broth around the tissue clumps. The UCLA researchers choose instead to grow theirs at higher oxygen levels and chop the blobs at the 35-day mark, when they are as wide as three millimeters, and then about every two weeks after. Sounds radical, but the slicing gives cells on the inside — some of which start dying — exposure to much-needed oxygen and nutrients. Those divided bits then continue growing separately. But cutting can be done only so many times before the expanding rosette structures inside are damaged.With all the experimenting, researchers have cooked up a lot of innovations, including some nifty progress reported in just the last year. Scientists have concocted tiny versions of several brain regions ranging from the hypothalamus, which regulates body temperature, thirst and hunger, to the movement-controlling basal ganglia. Electrical chatter among neurons, reflecting active brain circuits, has been detected. And research groups have recently begun linking bits of specific regions like Legos. Scientists have even observed some early developmental processes as they happen within the human brain blobs.Stem cell payoffThe work is part of a broader scientific bonanza that comes from coaxing human stem cells to self-assemble into balls of organlike tissue, known as organoids, that are usually no bigger than a lentil. Although the organoids don’t grow enough to replicate entire human organs, these mini-versions can mimic the 3-D cellular infrastructure of everything from our guts to our lungs. That’s something you can’t get from studies of rodents, which have different biology than humans do.Mini-organ models promise enormous advantages for understanding basic human biology, teasing apart human disease processes, and offering an accurate testing ground for finding or vetting drug therapies. And by creating personalized organoids from the reprogrammed cells of patients, scientists could study disease in a very individualized way — or maybe even use organoid structures to replace certain damaged tissues, such as in the liver or spinal cord.“Organoids offer an unprecedented level of access into the inner workings of the human brain, ” Novitch says, noting that our brains are largely off-limits to poking and cutting into for research. If scientists can study accurate models of working neural circuits in these brain bits, he and others say, researchers might finally get a handle on uniquely human neurological conditions. Such disorders, which include epilepsy and, experts theorize, schizophrenia and autism (SN Online: 7/17/15), can arise when the brain’s communication networks develop off-kilter.
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Medical Medium Have you or someone you love been diagnosed with rheumatoid arthritis (RA) or psoriatic arthritis (PA)? Have you been told that the cause is a mystery or that it’s your body attacking itself? The truth is that there’s a real cause behind these illnesses that medical science and research are unaware of. Fortunately, this article and the accompanying radio show explore the information medical science has yet to fully understand or uncover. Once you know the real cause, you can begin to move forward with healing as you will be addressing the root issue. The Autoimmune TheoryMost people are told that their rheumatoid and psoriatic arthritis are caused by an antibody that has been created within the body that attacks the joints. This is a misguided theory that not only has never been proven, but has also sadly become law within the medical community. When this antibody was discovered, science and research did not even know what it did, and they still don’t. This means that all of the treatments and prognoses that have been delivered since this theory was put in place have been precariously balancing on an antibody whose function is still a complete mystery, which makes the true cause of RA and PA just as enigmatic as it was when research on these illnesses first began. Additionally, since the current treatments and medications prescribed for patients are based on this erroneous theory, there are so many people who are still suffering from swelling, stiffness, and pain in the joints, as well as the other symptoms that are associated with these diseases.When people first began suffering from mystery illnesses in the 1950s, research and science was compelled to blame hormones. This is because, like so many other times in medical research, all the money was in hormones. There was such a deluge of research being conducted on hormones at the time that pharmaceutical companies were primed and ready to sell their new hormone drugs they had been itching to promote.However, one doctor was not convinced hormones were to blame, so he got funding for more research and dug further. He eventually stumbled upon an antibody, which, he thought, was the ticket. He created a theory that the antibody was the body’s inexplicable weapon against itself, even though the actual reason for the antibody was still completely unknown. This research was so heavily funded that it would have been unacceptable to emerge and explain that they have no idea what the antibody does. Therefore, some sort of conclusion was necessary, some theory that would stick. The reason researchers eventually concluded the body was attacking itself was because it protected the institution of modern medicine. In this theory, the patient is blamed above all else, which in turn prevents any fingers being pointed at medicine. Currently, most funding is going toward gene research, which always concludes that the patient’s genes are to blame and there is nothing to be done. In this theory, the patient is blamed above all else, which in turn prevents any fingers being pointed at medicine.The Truth about the AntibodyThis antibody that has become the false poster child for autoimmune diseases is actually just one of many antibodies that have yet to be discovered by science and research. The most ironic part about the events of the last half century is that everything medical research claims to be true about this antibody is actually the exact opposite. Rather than attacking the body, this antibody has been created by the body to protect itself from an outside intruder. The antibody, while an indicator of something being attacked, is not the one doing the attacking. It is proof of your body doing everything it can to support and safeguard you. It doesn’t go after tissue; it goes after the pathogen.The True Cause of RA and PAWe are currently living in a virus culture. Our world is rampant with pathogens that are causing the diseases so many are mystified by and calling autoimmune. Medical science and research are unaware that Epstein-Barr Virus (EBV) is the cause of so many illnesses, including fibromyalgia, chronic fatigue syndrome, multiple sclerosis, thyroid disorders, lupus, Lyme disease, tinnitus, vertigo, rheumatoid arthritis, and psoriatic arthritis. There are over 60 varieties of EBV, which may come as a shock to anyone who is only nominally familiar with this virus as well as to those who work in the medical field.Psoriatic arthritis is created by EBV, which feeds on the heavy metal copper in the liver. Toxic varieties of copper are perfect food for the virus that creates PA. When there is an abundant amount of food that EBV likes, such as copper, the virus becomes stronger and more rampant in the body, attacking the joints and tissues. EBV then creates an internal dermatoxin, which is different to the known external dermatoxin, which then surfaces to the skin. This is when a rash, either of the psoriasis and/or eczema variety, occurs, as well as aches, pains, and inflammation, Thyroid Healing. Medical communities are not aware that this is the true cause of PA, or even that viruses feed on specific foods, metals, and toxins. This is one huge reason why people are not able to receive the answers and help they need to truly heal.Copper can be absorbed into the system in many ways. Someone could have lived in an old house with ancient pipes made of copper that turned everything green. Or they could have used copper pans that flaked the metal off into the food. Copper is rife in pesticides, which means living near farmland, even 50 miles away, can be conducive to toxic copper exposure. Copper is in all pesticides, rodenticides, herbicides, and fungicides, which means we should avoid spraying both inside and outside the house. Anytime you purchase new linens or fabrics, such as towels, sheets, clothing, underwear, or socks, it would be prudent to wash them twice before using. New linens and clothing are loaded with fungicides, which are full of copper that can seep into the skin, your largest organ. It’s important to note that this toxic heavy metal copper is different to the helpful trace mineral copper which is found in plants.Rheumatoid arthritis is also caused by Epstein-Barr Virus that’s in a late stage (read more about the stages of EBV in my book Thyroid Healing, ) except this variety of EBV either does not like to feed on copper as much, or there simply is not an excessive amount of toxic copper in the system. The particular variety of EBV that causes RA much prefers the heavy metal mercury as its food. This specific variety of EBV gets into connective tissue, joints, and ligaments in its fourth stage, causing inflammation that’s evidence of your body trying to hold the invader at bay. Swelling of the knuckles, cervical spine, and the like is an indication that the body is reacting to the virus burrowing deeper and causing permanent damage to nerves and tissue. In its milder forms, this may display itself as mystery aches and pains. In its advanced forms, people experience severe joint swelling and a diagnosis of RA. This information is unknown to medical science and research.The Very First StepThe most important step you can take today toward true healing is way beyond diet or avoiding sprays. You must first know in your heart the true cause of your disease. Your body is not attacking itself. It is the biggest mistake to believe your immune system is not supporting you. When you believe your disease is autoimmune, you are preventing true healing from taking place because you are not giving your body the support it needs as it continues the fight against the pathogen in your body. Knowing your body is not fighting itself but rather a pathogen such as a virus ignites your immune system to become stronger, more focused, and work even harder for you. Additionally, when you know you should be fighting a virus, you can learn the practical steps you can take to give your body as much support as you possibly can.How to HealUnknown to medical research and science, the antibody was created to fight Epstein-Barr Virus; however, your body still needs all the support it can get. The following are some steps to take that can help you to begin recovering from rheumatoid and psoriatic arthritis.Remove Heavy MetalsHeavy metals are one of EBV’s favorite foods. And almost all of us unknowingly have toxic heavy metals inside our bodies. These metals make it possible for the virus to continue growing and becoming more prolific. And the more it feeds on metals such as mercury and copper, the more toxic waste matter the virus excretes in the body, which leads to the symptoms of psoriatic and rheumatoid arthritis. To get rid of heavy metals, heavy metal detox foods to include in your diet daily: barley grass juice, cilantro, spirulina, wild blueberries. Foods to AvoidWhen healing from RA and PA, it is essential to avoid eating things that happen to be some of EBV’s favorite foods, such as eggs and dairy. Also, it’s best to avoid pork because it burdens the liver to such a degree that it gives viruses an opportunity to proliferate, grow, and inflame the joints and skin. It’s also important to stay away from gluten as well because unknown to all medical communities it also provides fuel for the virus. If you have taken out eggs, dairy, and gluten, and you are still experiencing symptoms after several months, consider removing all grains from your diet, including oats and rice, while you heal. Some people tolerate grains well but for some, grains have to be removed to allow for deeper healing. It’s also helpful to avoid corn, soy, and canola oil.The Healing Food: FruitWhile many have been told to avoid fruit because of its sugar content, this trend is actually another example of misinformation that is only preventing people from taking advantage of the powerful antiviral properties in bananas, dates, apples, melons, mangoes, and all other kinds of fruit. Fruit is the most antioxidant-rich food in the world. Antioxidant should really be synonymous with longevity, as fruit is the best food to prolong life and fight disease. Wild blueberries, blackberries, and cherries are among the most antioxidant-filled foods. You can focus on whichever fruits are most attractive to you. If you have the luxury of a farmers market near you, make it a weekly habit to do your shopping there and explore the numerous varieties of fruit that are available to you: apples, pears, peaches, persimmons, apricots, watermelons, and dates. Different kinds of citrus are also a wonderful addition to your fruit-filled diet. While some people may think oranges, lemon water, or grapefruit cause flare ups in their RA or PA, it only feels that way because the citrus is detoxifying the poisons and viral byproduct in your system. In addition to fruit, be sure to eat plenty of leafy greens, vegetables, and include celery juice daily.Helpful SupplementsFor healing supplements, consider including the following supplements:Zinc sulfate is one of the most important resources to fight EBV. The body uses up supplies and even deep reserves of zinc at a rapid rate—meaning that it’s very common to become zinc-deficient when you have EBV, if you weren’t already. This supplement gives a major boost to the immune system so that EBV cells can be destroyed and suppressed.L-Lysine inhibits and reduces an EBV viral load and acts as an anti-inflammatory to the entire body.Cat's claw is a powerful anti-inflammatory and anti-viral that can be very helpful for rheumatoid and psoriatic arthritis.Taking a methylfolate supplement that supports methylation issues is very important for those suffering with rheumatoid and psoriatic arthritis.Bringing in the right B-12 supplement that contains adenosylcobalamin and methylcobalamin can be a wonderful addition as well.Glutathione helps to detoxify the liver, which is where the virus and toxins that cause these conditions can be found.Alpha Lipoic Acid (ALA) repairs and fortifies areas of the body that have been damaged by the virus.Mullein leaf’s strong anti-viral abilities make it an important supplement to consider.Additional TherapiesMany people with RA go to an infrared sauna to help with the fatigue and stiffness. This can be a good option for you, just be sure not to have the heat set too high Be conscious about how long you stay in the sauna. Another extremely helpful treatment is gentle massage therapy, one of the oldest modalities since the beginning of time. Healing touch from one person to another can be incredible for RA.Moving ForwardRheumatoid arthritis and psoriatic arthritis are not autoimmune diseases, and this myth is one that needs to rectified immediately so that the millions of people who are suffering can begin to get true answers. When you are given wrong information about your illness, you are essentially given a stop sign. My hope is for you to walk away from this understanding of RA or PA with a renewed hope and green light. Realizing that your body is fighting a virus that is feeding on toxins and metals in your system is the first and most powerful thing you can do. You must let go of the idea that your body is working against you. It is impossible for the body to attack a single cell in our bodies.When you are considering your healing options, it can be overwhelming. Remember to take it slow and at your own pace. Everyone’s path is going to look a little different. Maybe the foods to avoid will take you some time to remove but the supplements will come more easily. Maybe eating fruit will be an easy step but including celery juice is too much for you up front. Do what you can today and keep building on it from here. Never forget that your body is working with you, not against you, and healing is possible.
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Decoding the chemistry of fearSalk team charts pathway for fear in worms to reveal more about human anxietyLA JOLLA—Ask a dozen people about their greatest fears, and you’ll likely get a dozen different responses. That, along with the complexity of the human brain, makes fear—and its close cousin, anxiety—difficult to study. For this reason, clinical anti-anxiety medicines have mixed results, even though they are broadly prescribed. In fact, one in six Americans takes a psychiatric drug.A team of investigators from the Salk Institute uncovered new clues about the mechanisms of fear and anxiety through an unlikely creature: the tiny nematode worm. By analyzing the responses of worms exposed to chemicals secreted by its natural predator and studying the underlying molecular pathways, the team uncovered a rudimentary fear-like response that has parallels to human anxiety. Such insights may eventually help refine prescriptions for current anti-anxiety drugs and enable the development of new drugs to treat conditions like PTSD and panic disorder.In this illustration, a C. elegans worm (lower right) exposed to sulfolipid chemicals from one of its natural predators, a worm called P. pacificus, quickly reverses direction in a response analogous to human fear.“For the past 30 or 40 years, scientists have used simpler animals to figure out how fear might work in humans, ” says Sreekanth Chalasani, associate professor in Salk’s Molecular Neurobiology Laboratory and senior author of the paper, published in Nature Communications on March 19, 2018. “The idea has been that if you could figure out which underlying signals in the brain are related to fear and anxiety, you could develop better drugs to block them.”The team at Salk started with a simple creature, the microscopic worm called Caenorhabditis elegans. C. elegans, which contains only 302 neurons, has a natural predator—another worm called Pristionchus pacificus, which bites and kills C. elegans. The researchers discovered that by exposing C. elegans to chemicals that are excreted by P. pacificus, they could elicit a fear-like response. When it encounters these predator-excreted chemicals, C. elegans rapidly reverses direction and crawls away.They found that this fear-inducing chemical, a new class of molecules called sulfolipids, could activate four redundant brain circuits that led to this behavior. Additionally, C. elegans continued to change its behavior even after the fear-chemical was removed. This is analogous to behavior in mice, who express fear when exposed to the scent of cat urine, even if a cat is nowhere nearby.“For years, we thought that only advanced brains like those of mammals would have this complex reaction, ” Chalasani says. “But our study is showing that a simple animal expresses something very much like fear.”In the experiment, coauthor and UC San Diego graduate student Amy Pribadi soaked C. elegans in a solution containing the sulfolipid for 30 minutes. The worms failed to lay eggs, even for an hour after they had been removed from the solution—an indicator of acute stress as well as a longer-term response akin to anxiety. Further research showed that the signaling pathways activated during the worms’ response are similar to the pathways activated when more complex animals experience fear.When the worms were soaked in a solution containing Zoloft (a human anti-anxiety drug), however, these fear- and anxiety-like responses were not observed. This suggested that at least some of the pathways that the drug acts on to eliminate anxiety in mammals have been preserved by evolution.Also intriguingly, the team found that Zoloft acted on the worms’ GABA signaling in a neuron that affects the animal’s sleep. Whether this is also the case in humans is not yet known, but points to a potential pathway to understand why Zoloft works in some people and not others. The research eventually could lead to a change in how these drugs are prescribed.“We hope the findings from this paper will contribute to the field by providing a broader picture of some of these signaling activities, ” Chalasani says. “Our findings suggest that fear and anxiety are ancient and evolved much earlier than we originally thought. The pathways, nerves, circuits and genes that we’ll now be able to study in the worm should inform us about this process in humans.”In addition, he says, understanding which chemicals may repel nematodes could have implications for developing new kinds of pesticides, potentially ones that are even nontoxic. “C. elegans is not a pathogen, but many other types of nematodes can do severe damage to crops, ” he explains. “Biology research can go in many different directions, and you never know what you’re going to uncover.”The paper’s other authors were Zheng Liu, Maro J. Kariya, Christopher D. Chute, Sarah G. Leinwand, Ada Tong, and Kevin P. Curran of Salk; Neelanjan Bose and Frank C. Schroeder of Cornell University; and Jagan Srinivasan of Worcester Polytechnic Institute.This work was funded by the W. M. Keck Foundation, the National Institutes of Health and a Salk Alumni Fellowship.PUBLICATION INFORMATION JOURNALNature CommunicationsTITLEPredator-secreted sulfolipids induce defensive responses in C. elegansAUTHORSZheng Liu, Maro J. Kariya, Christopher D. Chute, Amy K. Pribadi, Sarah G. Leinwand, Ada Tong, Kevin P. Curran, Neelanjan Bose, Frank C. Schroeder, Jagan Srinivasan and Sreekanth H. Chalasani
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A breakthrough in our understanding of how red blood cells developPosted on March 15, 2018 by Kat J. McAlpine Posted in People, Science, Therapeutics By taking a deep dive into the molecular underpinnings of Diamond-Blackfan anemia, scientists have made a new discovery about what drives the development of mature red blood cells from the earliest form of blood cells, called hematopoietic (blood-forming) stem cells.For the first time, cellular machines called ribosomes — which create proteins in every cell of the body — have been linked to blood stem cell differentiation. The findings, published today in Cell, have revealed a potential new therapeutic pathway to treat Diamond-Blackfan anemia. They also cap off a research effort at Boston Children’s Hospital spanning nearly 80 years and several generations of scientists.Diamond-Blackfan anemia — a severe, rare, congenital blood disorder — was first described in 1938 by Louis Diamond, MD, and Kenneth Blackfan, MD, of Boston Children’s. The disorder impairs red blood cell production, impacting delivery of oxygen throughout the body and causing anemia. Forty years ago, David Nathan, MD, of Boston Children’s determined that the disorder specifically affects the way blood stem cells become mature red blood cells.Then, nearly 30 years ago, Stuart Orkin, MD, also of Boston Children’s, identified a protein called GATA1 as being a key factor in the production of hemoglobin, the essential protein in red blood cells that is responsible for transporting oxygen. Interestingly, in more recent years, genetic analysis has revealed that some patients with Diamond-Blackfan have mutations that block normal GATA1 production.Now, the final pieces of the puzzle — what causes Diamond-Blackfan anemia on a molecular level and how exactly ribosomes and GATA1 are involved — have finally been solved by another member of the Boston Children’s scientific community, Vijay Sankaran, MD, PhD, senior author of the new Cell paper.“Much of the history of how this disorder works was written at Boston Children’s, ” says Sankaran, who is a hematologist/oncologist and a principal investigator at the Dana-Farber/Boston Children’s Cancer and Blood Disorders Center. “Now, we can move on to the next era of research — what we can do to treat it.”Learning from an error of naturePrevious studies have found that many patients with Diamond-Blackfan anemia have mutated ribosomal protein genes. But the question has remained: Do these mutations have something to do with GATA1 and why do they only impair the maturation of red blood cells? In Diamond-Blackfan, other mature blood cells — such as platelets, T cells and B cells — still fare well despite mutations of ribosomal protein or GATA1 genes.EPO molecule which is linked to production of red blood cellsLast year, Sankaran’s research on Diamond-Blackfan anemia led to a discovery that saved an infant’s life.“There has been controversy over whether a ribosomal protein mutation changes the composition of the ribosomes or the quantity of the ribosomes, ” Sankaran says. “We know now that it is the latter.”By closely examining human cell samples from patients with Diamond-Blackfan anemia, Sankaran and his team of collaborators found that the quantity of ribosomes within blood cell precursors directly influences their ability to produce effective levels of GATA1, which, if you remember, is needed for hemoglobin production and also for red blood cell production.Now, finally tying all the pieces together, Sankaran and his team have definitively found that a reduced number of ribosomes slashes the output of GATA1 proteins inside blood stem cells, therefore impairing their differentiation into mature red blood cells.An opportunity for gene therapyTheir finding supports the hypothesis that the presence of GATA1 proteins in early blood stem cells helps prime them for differentiation into red blood cells. Without enough ribosomes to produce enough GATA1 proteins, these early cells simply never receive the signal to become red blood cells.“This raises the question of whether we can design a gene therapy to overcome the GATA1 deficiency, ” Sankaran says. “We now have a tremendous interest in this approach and believe it can be done.”Although a bone marrow transplant from a matched donor can treat Diamond-Blackfan anemia, Sankaran says that a gene therapy would be advantageous since it would use a patient’s own engineered cells, avoiding dangerous risks associated with graft versus host disease.“I think what’s great is that we can learn about developmental biology just by looking at our own patients very carefully, ” says Sankaran. “Genetic errors can give us the chance to pick apart the complex pieces of health and discover how they relate to one another.”In addition to Sankaran, additional authors of the new paper are Rajiv K. Khajuria, Mathias Munschauer, Jacob C. Ulirsch, Claudia Fiorini, Leif S. Ludwig, Sean K. McFarland, Nour J. Abdulhay, Harrison Specht, Hasmik Keshishian, D.R. Mani, Marko Jovanovic, Steven R. Ellis, Charles P. Fulco, Jesse M. Engreitz, Sabina Schütz, John Lian, Karen W. Gripp, Olga K. Weinberg, Geraldine S. Pinkus, Lee Gehrke, Aviv Regev, Eric S. Lander, Hanna T. Gazda, Winston Y. Lee, Vikram G. Panse and Steven A. Carr.This research was supported by the National Institutes of Health (DK103794, R33 HL120791 and T32 HL007574), a Manton Center Endowed Scholar Award, a DBA Foundation and March of Dimes Basil O’Connor Scholar Award, a Boehringer Ingelheim MD Fellowship, the Swiss National Science Foundation, Novartis Foundation, Olga Maybenfisch Stiftung and the European Research Council (EURIBIO260676).
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How To Evaluate Forensic DNA Quality With Quantifiler Trio DNA Quantification KitBy Angie Lackey04.05.2018Wouldn’t it be wonderful if there was a tool that forensic scientists could use to assess the quality of an unknown DNA sample before attempting to generate an STR profile? DNA samples collected from crime scenes range from DNA-rich fluids, like blood and saliva, to a few skin cells left behind from a casual touch. For example, there is generally much more DNA in a bloodstain than on, say, a knife handle. Getting an accurate estimate of DNA concentration is crucial to generating a robust DNA profile. But what if the process of DNA quantification could provide even more information? What if it could provide information about the quality of a DNA sample?Well, luckily there is the Quantifiler Trio Quantification Kit. The Quant Trio kit provides DNA concentration, in addition to quality assessments for degradation and inhibition of the sample. And it can help you make workflow decisions based on quantity of autosomal vs male DNA present.DNA can be degraded by environmental influences like sunlight, extreme heat, and humidity; degradation may manifest as a ski-slope pattern in the STR electropherogram. You see this pattern with degraded DNA because small fragments remain intact and amplify well, but the large fragments are damaged and don’t amplify well.To evaluate degradation in forensic samples, a Degradation Index, or DI, has been added to the Quantifiler Trio Kit. The DI is the ratio of the smaller to larger DNA fragments in a sample. It is automatically calculated in the software.The DI for intact DNA will be ≤1, as the concentration of the small and large fragments are approximately equal. Any DI over 1 could indicate degradation. To overcome degradation, you could target more DNA during STR amplification in an effort to increase the signal of the large DNA fragments.Impurities in a DNA extract can also suppress amplification of DNA – we call this inhibition of the reaction. Inhibition can occur at the quantification or amplification stages and can affect the interpretability of your DNA profile. Inhibition could appear similar to degradation, because large DNA fragments don’t amplify as well as small DNA fragments in the presence of the inhibitor.Although the STR profiles from degraded and inhibited samples may appear similar, don’t be fooled. Unlike with degraded DNA, increasing your target adds even more inhibitor to the reaction, making the inhibition even worse.The Internal PCR Control (IPC) is synthetic DNA that is amplified along with each sample. It just confirms that the assay worked as expected. Inhibitors can affect the IPC amplification; an increase in the threshold cycle value for the IPC indicates that it took the synthetic DNA longer than expected to reach a defined threshold; therefore something was impeding the reaction.There is one tricky thing about interpreting elevated IPC CTvalues. High concentrations of DNA in an extract (above 5ng/uL) can elevate the IPC Ct slightly because the entire reaction becomes saturated. Because of this, it is very important to evaluate the IPC CTvalue in conjunction with the DNA concentration. For example, if you were to question whether a sample that is at a concentration of 50ng/ul is inhibited, you would have to compare it to other samples or standards with a similarly high concentration. The same is true for a sample with a low concentration – you should only compare like to like.Because degradation and inhibition both affect large DNA targets more than small, it is necessary to assess the quality flags for degradation and inhibition together. For example, if the DI is elevated, and the IPC is as expected then the sample is degraded and not inhibited. However, if the IPC and DI are both elevated, you may not be able to determine if the sample is simply inhibited, or both degraded and inhibited. In a severely inhibited sample, the inhibition should be addressed by dilution or clean up and if necessary, the treated sample can be re-quantified to assess whether degradation is present.You can learn more from forensic scientists, who work with bone, and use real-time PCR analysis to make decisions that deliver improved recovery of alleles.
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