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Institutional Innovations - DNA sequencing issues

Nov

18

A November 15, 2019 report published by Nature.com calls for a multiplatform approach for researching structural variation (SV) in genome interpretation. "Identifying structural variation (SV) is essential for genome interpretation but has been historically difficult due to limitations inherent to available genome technologies," says the report. Detection methods have helped scientists discover thousands of SVs, showing their relationship to disease and possible effects on our biology. (see https://www.nature.com/articles/s41576-019-0180-9 ). By multiplatform, the article recommends testing on a variety of platforms and approaches, not relying on a single one, comparing results from different research labs and institutions around the world.

So much focus particularly in tech media has been about disruptive innovators and startups in the healthcare field. What about innovations by these more traditional institutions such as research institutions and hospitals?

Highly customizable and personalized healthcare solutions are at the cutting edge of disruptive innovation. You do not need to be an established entity to drive these disruptions, but you can be. The innovative applications of a person’s DNA sequence such as the tool for synthesizing DNA invented by biologist Leroy Hood’s Institute for Systems Biology, offer customizable health care at a genetic level, called genotyping. Seattle area’s Swedish Health Services has been recognized nationally for providing personalized health care using Dr. Hood’s DNA sequencing.

Another example, the creator of the CRISPR Cas9 technology, CRISPR Caribou Biosciences CEO, Dr. Jennifer Doudna invented the ability to edit our genetic code. Doudna showed how CRISPR, or "clustered regularly-interspaced short palindromic repeats", "bacteria’s natural defense system could be turned into a 'gene editing' tool to cut DNA strands", according to the Genetic Literacy Project. In addition to founding CRISPR, she teaches chemistry and molecular biology at University of California Berkeley. Both Hood and Doudna are said by peers to be viable candidates for the Nobel Prize.

Dr. Hood helped his associates at Swedish Health Services (Swedish Hospital and Providence Health Systems) play a leadership role in innovation, according to former Swedish CEO Anthony Armada in my interview with him for the Northwest Asian Weekly. “On the clinical side, for example, Swedish is the first to apply truly ‘personalized medicine’ using genotyping. Genotyping is a fingerprint of who you are genetically,” he adds. “For example, there can be five potential cures for a particular cancer. Genotyping can test and determine which of the five offers the best results, the least risk, and the best course of action for that particular patient” (source: NW Asian Weekly, Chris Beer). Thanks to help from Dr. Hood, the founding father of genomics, the hospital is lead the country in the medical and scientific applications of genomics.

#DNAsequencing #ai #artificialintelligence #bacteria #datascience #genomics #gutmicrobiome #healthinnovation #healthtech #machinelearning #mindbody #structuralvariance

Impact of Cooked vs. Raw Food on Gut Microbiota

Nov

7

An October 10, 2019 study reported by Andrew Padros of Gut Microbiota for Health demonstrated that raw and cooked diets have a distinct effect on the structure and metabolic activities of the gut microbiome in mice and humans. Dr. Rachel Carmody at Harvard University (USA), Dr. Peter Turnbaugh at University of California San Francisco (USA) and colleagues found that raw and cooked versions of the same foods affected the gut microbiome differently in mice.

Their research came up with that varied results between food types. It suggests that cooking sweet and white potatoes is a good idea, while consuming raw or cooked beef, carrots and beets is nearly the same. For example, consuming raw sweet potatoes led to lower microbiome diversity, a higher expression of genes and enzymes for metabolizing starch, sugar and xenobiotics. It also altered metabolic byproducts when compared with cooked-fed mice. However, raw and cooked lean beef had similar impacts on the gut microbiome; there was not much difference.

By feeding the mice controlled diets with different raw and cooked low- and high-starch foods—including sweet potato, white potato, corn, peas, carrots, and beets—the authors confirmed that gut microorganisms were sensitive to starch digestibility.

The study found that low-digestibility starch when raw (sweet potato and white potato) led to the most profound changes in gut microbial community structure. However, low-starch foods (carrot and beet) or foods with a high amount of high-digestibility starch when raw (corn and peas) led to almost undetectable changes in gut microbes.

Cooked foods were mainly digested and absorbed in the small intestine (thus, processed by host enzymes), whereas raw foods reached the colon, where they had detrimental effects on microbes, attributable to antimicrobial compounds.

By quantifying microbial cell damage in gut samples, Carmody and colleagues found that the mice fed raw tubers had the same extent of microbial cell damage as the mice group treated with the oral antibiotic ampicillin.

A metabolomic analysis of the six plant foods used in the experiments revealed multiple compounds that were both sensitive to cooking and showed antimicrobial activity, thus supporting the high xenobiotic gene expression found in mice that were fed raw food.
See report from Gut Microbiota for Health, https://www.gutmicrobiotaforhealth.com/en/beyond-nutrients-and-bioactive-compounds-in-food-cooking-also-matters-for-the-gut-microbiome/

#ai #artificialintelligence #bacteria #datascience #diet #food #gutmicrobiome #health #healthinnovation #healthtech #herbalmedicine #herbs #machinelearning #mindbody #plantnutrition #spices

Chinese herbal remedy & "bugs in the belly" aid weight loss / diabetes

Oct

31

It is becoming more accepted that Chinese herbs such as ginseng, berberine, and curcumin, have wide ranging biological impacts on our gut microbiome. On April 15, 2019, Chinese scientists published test results of the microbial effects of a popular Chinese herb called Coptis chinensis. Berberine, the main active ingredient of Coptis chinensis, is known as an antidiabetes drug and can regulate blood glucose. Berberine is beneficial for HFD-induced (high fat diet) insulin resistance, as it improves insulin sensitivity and reduces the homeostasis caused by insulin. They found that administration of berberine reduced the ratio of F/B (Firmicutes/Bacteroidetes) and partly recovered the composition of gut microbiota changed by HFD feeding. The report was published by China's State Key Laboratory of Natural Medicines, Jiangsu Key Laboratory of Carcinogenesis and Intervention, Department of Basic Medicine, School of Basic Medicine and Clinical Pharmacy (China Pharmaceutical University, 24 Tongjiaxiang, Nanjing 210009, China; see https://www.hindawi.com/journals/ecam/2019/2682748/ ).

A July 2019 paper published in the journal Nature, demonstrated ways to apply specific strains of microbiota to positively influence weight and diabetes. They found that a molecule produced by certain bacteria can interact with protein receptors in mice and improve the rodent's glucose regulation. These same receptors are also found in humans. It was a key step toward understanding how bacteria keeps us healthy, and what changes in bacteria occur when we fall prey to disease, empowering us to harness naturally occurring microbes to treat illness. Scientists found that microbiome differences can relate to our weight and diabetes. For example, studies of the microbe Akkermansia muciniphila has shown influence in obesity among humans. The July 2019 study by Nature Medicine showed "evidence for a negative correlation between Akkermansia muciniphila abundance and overweight, obesity, untreated type 2 diabetes mellitus or hypertension". 40 volunteers were enrolled and 32 completed the three month trial resulting in improved insulin sensitivity, reduced cholesterol, and slightly decreased body weight. A. muciniphila reduced the levels of liver dysfunction and inflammation. (See article, https://www.nature.com/articles/s41591-019-0495-2 ).

Other microbial species may also impact diabetes. Researchers at Rockefeller University were able to isolate N-acil amides with GPR119, which helps control blood sugar in mice. “Mice that received N-acil amides had significantly better glucose metabolism that those that didn’t. Over the past couple of years, Rockefeller biologist's Sean Brady and his team analyzed stool samples for microbial DNA. In essence, they found that N-acil amides help the body regulate itself.

A person with diabetes is more likely to have this certain suite of microbes than a person without diabetes, for example. But the mechanisms of this bacterial influence are still pretty mysterious.” (Source: “Scientists want to Turn our Gut Bacteria into Medicine,” Popular Science, Claire Maldarelli, Aug. 31, 2017; http://www.popsci.com/gut-bacteria-medicine?zLzbIvdKfbdGTwyp.03 ).

#ai #artificialintelligence #bacteria #chinesemedicine #datascience #diet #gutmicrobiome #health #healthinnovation #healthtech #herbalmedicine #herbs #machinelearning #mindbody #plantnutrition #spices

Using Classic models (Lotka-Volterra) to do microbiome research

Oct

24

What is Lotka-Volterra modeling? It is the simple model of the population dynamics of species competing for common resource, according to Wikipedia. Because there are trillions of microbes in our bodies, it becomes a huge challenge collecting, breaking down, processing, packaging, then accurately making sense of the data in presentable formats. Thanks to computing, high throughput DNA sequencing enables the exploration of dynamics in microbial populations. Mathematical modeling and simulation of such microbiome time series data can help in getting better understanding of bacterial communities.

Researchers today are able to use an "interactive platform for generalized Lotka-Volterra (gLV) based modeling and simulation of microbial populations. The tool can be used to generate the mathematical models with automatic estimation of parameters and use them to predict future trajectories using numerical simulations", according to a February 22, 2019 Frontierso India report (see https://www.frontiersin.org/articles/10.3389/fmicb.2019.00288/full).

"We have developed “Web-gLV” to bridge data delivery gaps to enable biologists to take advantage of the multispecies modeling and simulation without any programming expertise," adds the report. This way, scientists can focus on the Science and rely on the "Web-glv" for the computing and delivery.

#ai #artificialintelligence #bacteria #datascience #gutmicrobiome #health #healthinnovation #healthtech #machinelearning #mindbody

Prebiotic fiber, short chain fatty acids drive gut and immune health

Oct

22

Downline immune health grid.

Chicory root pictured here is a leading source of Inulin fiber.

Certain foods and herbs support the growth of short chain fatty acids (SCFA). These fiber-rich foods - such as fruit, vegetables, and legumes - contain large amounts of Inulin.

Inulin is a type of soluble fiber found in many plants which gut bacteria convert into SCFA. SCFAs such as butyrate, nourish colon cells, break down glucose and cholesterol, and provide other health benefits. SCFA inhibit histone deacetylases (HDACs) and activate G-protein-coupled receptors (GPCRs). Since HDACs regulate gene expression, inhibition of HDACs has a vast array of downstream consequences. GPCRs, particularly GPR43, GPR41, and GPR109A, have been identified as receptors for SCFAs, but little is known beyond that. Studies have implicated a major role for these GPCRs in the regulation of metabolism, inflammation, and disease. In effect, SCFAs have anti-inflammatory, antitumorigenic, and antimicrobial effects. Butyrate, a four-carbon SCFA, is produced through microbial fermentation of dietary fibers in the lower intestinal tract, enhancing intestinal health and mucosal immunity. They alter and maintain gut and immune system integrity.

Plants naturally produce inulin and use it as an energy source. Today, it’s being added to more and more food products because of its benefits and adaptability. With its creamy consistency, inulin functions as a fat substitute in margarine, salad dressings, and baked goods.

Inulin can be found naturally in foods, such as:

- chicory root
- artichokes
- agave
- asparagus
- bananas
- garlic
- leeks
- wheat
- onions
- wild yams

Again, remember that no body is the same, so get to know your body and it's particular health needs. The key is to maintain a balanced diet, including but not limited to consumption of Inulin intensive food and herbs.

#ai #artificialintelligence #bacteria #datascience #diet #gutmicrobiome #health #healthinnovation #healthtech #herbalmedicine #herbs #machinelearning #mindbody #plantnutrition #spices

"Keystone Species" - Like the Wolves of Yellowstone Park

Oct

17

Isolating Key Bacterial Strains

Thanks in large part to innovative entrepreneurs, microbial influences on our health is reaching new heights. What this means scientifically is that research is showing more than just propensities and patterns. It is able to isolate strains using Ai, specific strains of bacteria that directly affect the neuro-degeneration of MS (multiple sclerosis) patients as one example of many.

Scientists refer to Bacteroides fragilis and Bacteroides stercosis as “keystone species” of the human gut microbiome. Though not abundant, they heavily influence the structure of microbial communities. It may be premature to say, but research points toward these gut microbiome as contributing to one's individuality.

Faecalibacterium prausnitzii might be another keystone species as a gut anti-inflammatory. Rather than “bad” microbes prompting Crohn's disease, for example, a single “good” microbe plays a key role in preventing the disease. Harry Sokol, a gastroenterologist at Saint Antoine Hospital in Paris, found that if he transferred F. prausnitzii in mice, it protected them against experimentally induced intestinal inflammation. "And when he subsequently mixed F. prausnitzii with human immune cells in a test tube, he noted a strong anti-inflammatory response," according to the Scientific American report (see https://www.scientificamerican.com/article/among-trillions-of-microbes-in-the-gut-a-few-are-special/ ).

Another “keystone species” microbe worth mentioning that resides in the human gut is the ruminococcus bromii. It is a dominant member of the suite of human gut microbiome that triggers energy and digestion of resistant starches by breaking down and releasing enzymes from these starches that we consume. The ruminococcus bromii primarily reside in the colon.

The function of these "keystone" species enable the proper functioning of other downline microbial activity, much in the same way that the presence of wolves in Yellowstone Park is a keystone species to maintain a balance in the park’s ecosystem.

#ai #artificialintelligence #bacteria #datascience #gutmicrobiome #health #healthinnovation #healthtech #machinelearning #mindbody

Japanese Health Care Offers Private Sector Options & Coverage for Herbal Remedies.

Oct

10

Japanese private insurance companies cover eastern medicine.

Author: Chris Kenji Beer

Japanese traditional medicine (Kampo medicine) has a long historical development in Japan that dates back more than 1500 years, and even further back in China. Kampo is similar to India's Ayurveda in its integrative approach that a balance of the human body and mind, mental and physical, are critical to our health. Today, Kampo medicine has been revived accompanied by a scientific reevaluation relevant to modern health care. Kampo medical treatments include chiropractic, aromatherapy, homeopathy, health spa therapy, Ayurveda, hypnosis, flower therapy, thalassotherapy, herb therapy, qigong, yoga, dietary therapy, imagery, meditation, art therapy and prayer (See NIH article, https://www.ncbi.nlm.nih.gov/pmc/articles/PMC516460/). This article references a survey of 1,000 Japanese residents and their percentage use of CAM (alternative medicine), such as Kampo: nutritional and tonic drinks, 43.1%; dietary supplements, 43.1%; health-related appliances, 21.5%; herbs or over-the-counter Kampo, 17.2%; massage or acupressure, 14.8%; ethical Kampo (Kampo prescribed by medical doctors), 10.0%; aromatherapy, 9.3%; chiropractic or osteopathy, 7.1%; acupuncture and moxibustion, 6.7%; homeopathy, 0.3%; other therapies, 6.5%.

HERBAL REMEDIES IN JAPAN.

In Japan, Agaricus blazei Murill is the most popular product. Many cancer patients take this mushroom. This medicinal mushroom contains special types of polysaccharides known as beta glucans which stimulate the activity of natural killer cells that are vital to the immune system. These polysaccharides are believed to be among the most potent polysaccharides for immune health. Beer yeast, Propolis, cereals, banaba, Japanese plum, Chlorella, barley verdure, vegetable juice, collagen, royal jelly and mulberry are also taken. Dong quai is an ingredient covered by Kampo. The ingredients of dong quai are coumarins, essential oils, ferulic acids, psoralens, and vitamin B12 and folinic acid, the active form of folic acid. Shakuyakukanzoto was the most frequently prescribed Kampo drug, known to relieve muscle pain and maintain healthy blood flow. It consists of peony root and licorice extract.

USA dietary supplements which are not covered by American health insurance include Gingko Biloba, Echinacea, Garlic, Ginseng, Soybean, Saw Palmetto, St John's Wort, Valerian, Black Cohosh, Milk Thistle, Evening Primrose, Grape Seed Extract, Bilberry, Green Tea, Pycnogenol, Ginger, Feverfew and Dong quai, amongst others.

JAPANESE HEALTH CARE FOR THE ELDERLY.

Though published so along ago, I was cleaning out the basement storage the other day, and came upon my only printed copy "Japanese Health Care for Elderly" which was published by US-Japan Foundation and National Conference of State Legislatures. I couldn’t find it anywhere. It has been referenced on a number of library websites, but no copy. I realized my co-author Dr. Bill Steslicke and I may have the only copies, along with a few die hard former legislators around the country, so here is a Word doc version. Noteworthy- 1) certain Japanese companies may form their own in-house HMO-style coverage and provisioning. 2) Japanese insurance covers eastern medicine, Kampo medicine described above, including but not limited to herbal remedies and acupuncture.

Here is a downloadable word doc copy of the original publication: https://kotojazz.files.wordpress.com/2016/07/ncsl_japanesehealthcare_forelderly.doc

#acupuncture #ai #artificialintelligence #bacteria #datascience #diet #elderlycare #gutmicrobiome #health #healthinnovation #healthtech #herbs #japanesehealthcare #machinelearning #mindbody #plantnutrition #seniorhealthcare #spices

Herbs that support "the happy chemical", microbiome health

Oct

4

Scientists have found that differences in a person’s gut can be a clue to our specific health propensities, to cancers, but also something as immediate as our daily mood, behaviors, even happiness. For example, 90% of the well-known serotonin neurotransmitter is made in the body’s digestive tract, according to a 2015 report by CalTech (“Microbes Help Produce Serotonin in Gut”, April 09, 2015). Serotonin is the chemical often referred to as the “happy chemical” and the balance of serotonin in our body influences our mood. A deficiency of serotonin can lead to depression.

Before getting into the research, what herbs support "healthy happy chemicals"? Herbs that help boost serotonin levels include oatstraw, which is loaded with B vitamins, and the roots of angelica, burdock, dandelion, ginseng, wild yam and black cohosh. There are lots of natural supplements containing these herbs and foods that you can buy online. You can also find supplements that contain L-tryptophan that supports serotonin synthesis, and vitamin B3 (magnesium glycenate) which helps metabolize fats, proteins, and carbohydrates. Basil contains serotonin boosting eugenol and rosmarinic acid.

As mentioned, there is growing evidence that the microbiome in our gut contribute not only to various body and brain diseases, but also to our mood and behavior relevant to many psychiatric and neurological disorders (Microbiome Journal, August 25, 2017). In particular, it has been repeatedly demonstrated that manipulation of the gut microbiome modulates anxiety-like behaviours, and our response to fear. The neural circuits that underlie anxiety- and fear-related behaviours are complex and heavily depend on functional communication between the amygdala and prefrontal cortex (PFC). Research at the University of California Los Angeles (UCLA) found a link between our stomach and a region of our brain that regulates mood and behavior, according IFLScience.com’s Robin Andrews (Source: “Our Gut Microbes Strongly Influence Our Emotional Behaviors,” IFL Science, July 4, 2017). The UCLA study was the first to link this connection within humans, based on the study of 40 healthy woman showing “brain-gut-microbial interactions in healthy humans”, according to the American Psychosomatic Society, affecting their mood and behaviors. Likewise, the Microbiome Journal reports that “transcriptional networks within the amygdala and PFC of Germ-Free mice are altered. MicroRNAs (miRNAs) act through translational repression to control gene translation and have been implicated in anxiety-like behaviours.” (See Microbiome Journal, August 25, 2017).

These results suggest that the microbiome is necessary for appropriate regulation of miRNA expression in brain regions implicated in anxiety-like behaviours.

"Serotonin is an important neurotransmitter and hormone that is involved in a variety of biological processes. The finding that gut microbes modulate serotonin levels raises the interesting prospect of using them to drive changes in biology," says Hsiao in the Caltech Journal. Hsao is quoted here from the CalTech journal Cell, April 09, 2015 issue.

#ai #artificialintelligence #bacteria #datascience #diet #gutmicrobiome #health #healthinnovation #healthtech #herbalmedicine #herbs #machinelearning #mindbody #neurotransmitters #plantnutrition #sertonin #spices #thehappychemical

A “Tsunami” of Ai is Coming to Health Care

Oct

1

1. Describe - handcrafted, rule based, symbolic knowledge.
2. Categorize - deep neural network, statistical learning.
3. Explain - contextual adaption, perceived learning and reasoning.

Serial entrepreneur and Viome CEO Naveen Jain believes there is a big wave of Ai coming to the health sector. “There is a tsunami that's coming," he told CNBC in a TV interview from the Slush technology conference in Helsinki, Finland (December 01, 2017). Jain partly attributes this tsunami to the huge demand for sensors that are driving down the prices, making Ai technology more available to the masses. "The sensors are becoming so cheap. For the first time in our lifetime, we can look deep inside our body (using sensors) to know exactly what is going on," he told CNBC. Jain believes food could become the "next drug," eliminating the need for traditional medicine.

On October 01, 2019, his company Viome was given a highly coveted endorsement in the form of research published about "A Robust Metatranscriptomic Technology for Population-Scale Studies of Diet, Gut Microbiome, and Human Health" in the International Journal of Genomics (Volume 2019, Article ID 171874 about Viome Inc., Los Alamos, NM 87544, USA). The report states that "Humans have co-evolved with the microbiome and have become dependent on its biochemical output, such as certain vitamins and short-chain fatty acids". (see full report, https://doi.org/10.1155/2019/1718741 ).

16S rRNA VS. METATRANSCRIPTOMIC SEQUENCING:

The report explains in detail the chasm of difference between the 16S r RNA and metatranscriptomic sequencing.

16S rRNA gene sequencing tracks a small portion of the prokaryotic 16S ribosomal RNA gen, but does not measure the biochemical functions of the microorganisms or distinguish living from dead organisms. It also excludes some bacteria, most archaea, and all eukaryotic organisms and viruses, resulting in a limited view of the gut microbiome ecosystem, according to the October 1 report.

Metatranscriptomic analysis (metatranscriptomics, RNA sequencing, and RNAseq) offers insights into what the gut microbiome are actually doing and why and how they are doing it. Viomega can make classifications based on a database of 110,000 microbial genomes, and quantitative microbial gene expression analysis using a database of 100 million microbial genes. "The biochemical activities of the gut microbiome by quantifying expression levels of active microbial genes, allowing for the assessment of pathway activities, while also providing strain-level taxonomic resolution for all metabolically active organisms and viruses," says the report. Viome's Viomega now makes this process affordable as well for the first time.

Naveen Jain founded Viome in 2016, a leading personalized microbiome gut sequencing technology company that uses deep machine learning and data science to offer optimal health care solutions for its customers. One of Jain’s “Moonshot” goals is to “truly make illness optional.” To do so, we must “think like the future has already arrived.”

Health care is one of those key global challenges facing this generation. The wholistic approach to wellness that has prevailed for centuries in Asia is being explored in a much broader scale with advanced Ai (artificial intelligence), data science, and other technology by the scientific communities in the U.S. and elsewhere that were not available to previous generations.

What Jain and his team at Viome are using Ai to discover a deeper and more detailed understanding of the mind and body. "Ai is going to play the biggest role because there is so much more data that no humans can ever process," he said.

#ai #artificialintelligence #bacteria #datascience #gutmicrobiome #healthinnovation #healthtech #machinelearning #mindbody

Ayurveda's "person-centric", non-standardized approach to health

Sep

30

Ayurvedic health is a 3,000 hear old holistic approach to an individual's personal health from India based on the three

Doshas: Vata (air, ether), Pitta (fire), and Kapha (water, earth).

How is Ayurvedic health different from the other approaches to health care? The modern scientific approach has been focused on standardization and applying solutions that work for the majority of people, such as if you get sick, you take this particular medicine and you will be healed of the ailment.

Ayurveda on the other hand, is person-centered vs. pathology-centered. It takes the approach that respects and considers the uniqueness of each individual in applying health care solutions. Ayurveda works with all levels of the person, the physical, mental, and spiritual, and both internal (microcosm) and external factors (macrocosm).

It believes each individual must take responsibility for their own health with a preventive, natural approach to addressing our symptoms and health issues.

#ai #artificialintelligence #ayurveda #bacteria #datascience #diet #doshas #gutmicrobiome #health #healthinnovation #healthtech #herbalmedicine #herbs #machinelearning #mindbody #plantnutrition #spices

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Institutional Innovations - DNA sequencing issues

Impact of Cooked vs. Raw Food on Gut Microbiota

Chinese herbal remedy & "bugs in the belly" aid weight loss / diabetes

Using Classic models (Lotka-Volterra) to do microbiome research

Prebiotic fiber, short chain fatty acids drive gut and immune health

"Keystone Species" - Like the Wolves of Yellowstone Park

Japanese Health Care Offers Private Sector Options & Coverage for Herbal Remedies.

Herbs that support "the happy chemical", microbiome health

A “Tsunami” of Ai is Coming to Health Care

Ayurveda's "person-centric", non-standardized approach to health

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