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Category: genetics

Why hasn’t #MachineLearning conquered SARS-CoV-2 that causes COVID-19 (P.S., SARS-CoV-2 is the name of the #virus, while COVID-19 is the name of the disease)? One of the possible answers is that the virus “learns” faster than machines through “mutations”.

That causes us thinking: If mutation is such an efficient weapon (for virus), can we learn something from it and then apply our understanding to #DeepLearning to create “fast-mutating” #DeepLearning models capable of helping us to fight intractable crisis like a #pandemic?

https://bit.ly/3c9GE5s

Virus Mutation https://bit.ly/35xVvUQ

#COVID19 #AI #technology #innovation #NeuralNetworks

The remarkable capacity of some viruses to adapt to new hosts and environments is highly dependent on their ability to generate de novo diversity in a short period of time. Rates of spontaneous mutation vary amply among viruses. RNA viruses mutate faster than DNA viruses, single-stranded viruses mutate faster than double-strand virus, and genome size appears to correlate negatively with mutation rate. Viral mutation rates are modulated at different levels, including polymerase fidelity, sequence context, template secondary structure, cellular microenvironment, replication mechanisms, proofreading, and access to post-replicative repair. Additionally, massive numbers of mutations can be introduced by some virus-encoded diversity-generating elements, as well as by host-encoded cytidine/adenine deaminases. Our current knowledge of viral mutation rates indicates that viral genetic diversity is determined by multiple virus- and host-dependent processes, and that viral mutation rates can evolve in response to specific selective pressures.

The mutation rate of an organism is defined as the probability that a change in genetic information is passed to the next generation. In viruses, a generation is often defined as a cell infection cycle, which includes attachment to the cell surface, entry, gene expression, replication, encapsidation, and release of infectious particles. Mutations are not restricted to replication since they can also result from editing of the genetic material, or spontaneous nucleic acid damage. The mutation rate should not be confused with the frequency at which mutations are found in a given viral population. The latter is a measure of genetic variation that depends on a number of other processes such as natural selection, random genetic drift, recombination, and so on (Fig. 1 a). Higher mutation rates lead to higher genetic diversity but, except in special cases, it is not possible to infer mutation rates directly from observed population mutation frequencies [1].

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A study just released by Columbia University Mailman School of Public Health is reporting a blood-DNA-methylation measure that is sensitive to variation in the pace of biological aging among individuals born the same year. The tool—DunedinPoAm—offers a unique measurement for intervention trials and natural experiment studies investigating how the rate of aging may be changed by behavioral or drug therapy, or by changes to the environment. The study findings are published online in the journal eLife.

“The goal of our study was to distill a measurement of the rate of biological aging based on 12-years of follow-up on 18 different clinical tests into a blood test that can be administered at a single time point.” said lead author Daniel Belsky, Ph.D., assistant professor of epidemiology at Columbia Mailman School and a researcher at the Columbia Aging Center.

Midlife adults measured to be aging faster according to the new measurement showed faster declines in physical and cognitive functioning and looked older in facial photographs. Older adults measured to be aging faster by the tool were at increased risk for chronic disease and mortality. In other analyses, the researchers showed that DunedinPoAm captured new information not measured by proposed measures of biological aging known as epigenetic clocks, that 18-year-olds with histories of childhood poverty and victimization showed faster aging as measured by DunedinPoAm, and that DunedinPoAm predictions were disrupted by a caloric restriction intervention in a randomized trial.

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To trace the trail of the virus worldwide, Lim’s team is using a new technology called next-generation sequencing at ASU’s Genomics Facility, to rapidly read through all 30,000 chemical letters of the SARS-CoV-2 genetic code, called a genome.

Each sequence is deposited into a worldwide gene bank, run by a nonprofit scientific organization called GISAID. To date, over 16,000 SARS-CoV-2 sequences have been deposited GISAID’s EpiCoVTM Database. The sequence data shows that SARS-CoV-2 originated a single source from Wuhan, China, while many of the first Arizona cases analyzed showed travel from Europe as the most likely source.

Now, using a pool of 382 nasal swab samples obtained from possible COVID-19 cases in Arizona, Lim’s team has identified a SARS-CoV-2 mutation that had never been found before—where 81 of the letters have vanished, permanently deleted from the genome.

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The breakthrough, which identified the location and function of every human gene, offered the promise of medical care tailored specifically to individual patients, based on their personal genetic makeup.

When researchers identified a gene associated with a 44 per cent risk of breast cancer in women, for example, it seemed that protecting them might be as simple as deactivating that gene.

But the promise of such personalized medicine has not fully materialized, say two McMaster researchers, because the full sophistication of the genetic blueprint has a more complex and far-reaching influence on human health than scientists had first realized.

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Antibody found to block infection by the novel coronavirus SARS-CoV-2 in cells.

The ‘47D11’ antibody targets the ‘spike protein’ of the destructive coronavirus.

It could alter the ‘course of infection’ or protect an uninfected person exposed.

Here’s how to help people impacted by Covid-19.

Scientists say they’ve discovered an antibody that blocks infection by SARS-CoV-2, the coronavirus behind the current global health crisis.

The antibody, known as 47D11, targets the deadly virus’s infamous ‘spike protein’, which it uses to hook onto cells and insert its genetic material.

Tests in mice cells showed that 47D11 binds to this protein and prevents it from hooking on – effectively neutralising it.

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U.S. Secretary of State Michael Pompeo said “enormous evidence” shows the novel coronavirus outbreak began in a laboratory in Wuhan, China, but didn’t provide any proof for his claims.

“I can tell you that there is a significant amount of evidence that this came from that laboratory in Wuhan,” Pompeo said on ABC’s “This Week.” “These are not the first times that we’ve had a world exposed to viruses as a result of failures in a Chinese lab.”

Pompeo stopped short of saying the virus was man-made, noting that he agreed with a report by the Office of the Director of National Intelligence that ruled out genetic modification or it having been man-made.

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The tree helped build industrial America before disease wiped out an estimated three billion or more of them. To revive their lost glory, we may need to embrace tinkering with nature.

An American chestnut near Rockport, Maine. Credit… John Chiara for The New York Times.

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Maria became the very first COVID-19 patient to use Stem Cell Neurotherapy for COVID-19. In about 5 days, she will began to feel the healing effects of generating new lung cells which will eliminate her breathing problems.

We repurposed some tools from the Stem Cell Therapy for Cancer/Brain Tumor. Those tools are T-Cells, B-Cells, and Natural Killer Cells. Instead of programming those cancer killing cells to attack cancer cells, we have programmed them to seek out, identify, attack, and destroy all the Coronavirus cells in the entire body.

Stem Cell Neurotherapy sends therapeutic messages, e.g., “your stem cells are transforming into new cells for the lungs, liver, and kidneys” to the DNA inside the nucleus of stem cells. Inside the nucleus, the DNA receives the message and transmits it to the RNA, which translates the message into genetic code.

The genes inside the stem cells transmit the coded message to the proteins, which are converted by the mitochondria into ATP, which provides the energy for the coded message to transform the stem cells into a new set of lung cells, as well as new cells for the kidneys and liver.

These new cells in the lungs, kidneys, and liver will replace the cells that were infected by the COVID-19 virus. This results in the elimination of the coughing, fever, headaches, diarrhea, and breathing problems.

I’m reaching out with great humility, like a great many people are these days, to see if anyone has it within their means to help me directly or indirectly. As an artist, teaching in the New York City school system mostly working children in ESL and Special Needs, my work is seasonal and I am an independent contractor. This means no benefits even after close to 10 years in the same “job”, and from a complicated financial situation with my husband, neither of us has health insurance, everything is out of pocket for us. I’m not eligible for unemployment due to being a contractor. My gigs for this semester totaling almost $5000 for NYC schools just evaporated in the blink of an eye, but would have covered the cost my everyday healthcare/rent/etc until September. Things like medicines and supplements, healthy food that help control my Essential Tremor(neurological disease) and anxiety and vision care that allow me to function as an artist and make a meager living will be eliminated if we want to keep a roof over our heads. And now due to restrictions in NYC, my husband could be out of work by tomorrow(also contract work with no-unemployment benefits). If you can donate even the smallest token it would be of great help. Any amount would help me to weather the next several months of the NYC lockdown. If you feel strange donating cash, please take a look at the reproductions of my art, or maybe even buy a gift card for someone that might like my art here: opticvoid.com

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Jordan says Moderna is able to scale up quicker than traditional manufacturers, as its vaccines are created by manipulating mRNA, the molecule that carries genetic instructions from DNA to a cell’s protein-making ribosome. Moderna manipulates mRNA so that it instructs human cells to produce certain viral proteins; the proteins themselves don’t cause infection, but they do invoke an immune response. “The RNA uses the human body as its bioreactor,” says Jordan, so Moderna itself doesn’t have to manufacture the proteins. “To create a different vaccine candidate [for Moderna] is to trigger a different RNA sequence. We don’t need to build a different cell processing plant,” says Jordan.

The central dogma of molecular biology deals with the detailed residue-by-residue transfer of sequential information. It states that such information cannot be transferred back from protein to either protein or nucleic acid.— Francis Crick.

The dogma is a framework for understanding the transfer of sequence information between information-carrying biopolymers, in the most common or general case, in living organisms. There are 3 major classes of such biopolymers: DNA and RNA (both nucleic acids), and protein. There are 3×3=9 conceivable direct transfers of information that can occur between these. The dogma classes these into 3 groups of 3: three general transfers (believed to occur normally in most cells), three special transfers (known to occur, but only under specific conditions in case of some viruses or in a laboratory), and three unknown transfers (believed never to occur). The general transfers describe the normal flow of biological information: DNA can be copied to DNA (DNA replication), DNA information can be copied into mRNA (transcription), and proteins can be synthesized using the information in mRNA as a template (translation). The special transfers describe: RNA being copied from RNA (RNA replication), DNA being synthesised using an RNA template (reverse transcription), and proteins being synthesised directly from a DNA template without the use of mRNA. The unknown transfers describe: a protein being copied from a protein, synthesis of RNA using the primary structure of a protein as a template, and DNA synthesis using the primary structure of a protein as a template — these are not thought to naturally occur. [6].

The BARDA investments could go to waste, but ramping up Covid-19 vaccine production will help avoid delivery delays if a vaccine is approved.

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We can reprogram our DNA. The nucleus of a cell is not read only. It is actually read and write. Basically, the cell is a programmable device, in response to environmental information.

The templates for protein synthesis are RNA (ribonucleic acid) molecules. In particular, a class of RNA molecules called messenger RNA (mRNA) are the information-carrying intermediates in protein synthesis. Other RNA molecules, such as transfer RNA (tRNA) and ribosomal RNA (rRNA), are part of the protein-synthesizing machinery. All forms of cellular RNA are synthesized by RNA polymerases that take instructions from DNA templates. This process of transcription is followed by translation, the synthesis of proteins according to instructions given by mRNA templates.

The flow of information is dependent on the genetic code, which defines the relation between the sequence of bases in DNA (or its mRNA transcript) and the sequence of amino acids in a protein.

We can send therapeutic messages to the DNA inside the stem cells’ nucleus. DNA sends the information (in the form of nerve impulses) to the RNA molecules called messenger RNA. The transfer RNA synthesizes proteins to carry out the instructions given by messenger RNA templates for the stem cells to become new neurons and cells to replace the neurons and cells that were damaged or destroyed.

This 3D animation shows how proteins are made in the cell from the information in the DNA code.

To download the subtitles (.srt) for this site, please use the following link: https://goo.gl/Ew7l69 and for more information, please view the video and explore related resources on our site: http://www.yourgenome.org/video/from-dna-to-protein

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Animated by Polymime Animation Company Ltd.
http://www.polymime.com
http://www.instagram.com/polymimestudio

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