How alcohol damages DNA and increases cancer risk


https://speciality.medicaldialogues.in/how-alcohol-damages-dna-and-increases-cancer-risk/

Physicists Confirm There’s a Second Layer of Information Hidden in Our DNA


IN BRIEF

Theoretical physicists have confirmed that it’s not just the information coded in our DNA that shapes who we are—it’s also the way DNA folds itself that controls which genes are expressed inside our bodies.

We all learned in high school how Watson and Crick pieced together the findings of many scientists to come up with a model of deoxyribonucleic acid (DNA). Information in DNA is stored as code sequences made up of nitrogenous bases. Each cell has the same sequence of codes but executes a different function. Code sequences determine the type of protein to be produced in a certain cell, but it is hypothesized that the mechanical properties of the DNA acts as a second layer of information.

Each cell in our body contains around 2 meters of DNA. But since our cells are so tiny, DNA strands have to be tightly wrapped into bundles called nucleosomes in order to fit.

Learn more about DNA and nucleosomes in the video below:

URL”https://youtu.be/4Z4KwuUfh0A

The folding mechanism of DNA is believed to play a large role in how genes are read by the rest of the cell. Biologists have started to isolate mechanical cues that determine how DNA is folded. Now, theoretical physicists from Leiden University in the Netherlands confirmed through computer simulations that these cues are actually coded into our DNA.

Physicist Helmut Schiessel and his group simulated the folding of DNA strands with randomly assigned cues. The team used genomes of baker’s yeast and fission yeast to find correlations between the mechanics and the actual folding structure of DNA in the two organisms.

The results confirm that this second layer of information exists. This led them to conclude that genetic mutations are not just caused by a change in the sequence of codes but also by a change in the way the strands are folded. This simulation may be helpful in hiding unwanted sequences like those that cause diseases.

 Source:PLOS ONE.

Physicists Discover A Second Layer Of Information Hidden In Our DNA 


  DNA is fascinating, and we stand to learn so much about who we are, where we came from, and what we are capable of (biologically speaking) from its study. Our capabilities in particular have yet to be studied in-depth by the mainstream scientific community. Yet the study of phenomena like the placebo effect, distant healing, telepathy, and the physical impacts of human intention, not to mention the Mind-Body connection, has yielded statistically significant results which have been available in ‘reputable peer reviewed journals’ for decades.
How does this relate to DNA? Well, there are many codes in our DNA that scientists have yet to crack. Parts of our DNA, for example have no known biological function, or at least we have yet to discover them. Maybe they have spiritual applications, or are connected to the non-physical realm in some way. These seemingly useless DNA are referred to as ‘Junk DNA,’ or ‘non-coding DNA.’ But we are learning more about them each day, as Scientific American reports, so the label isn’t entirely accurate.

We may think we know a lot, but the things we think we know and hold to be true are always changing. Science was no less valid to us 50 years ago than it is today, but theories have changed because we have learned more. And our knowledge of DNA has just changed again, as physicists have confirmed that there is a second layer of information hidden in our DNA, meaning that there is more than one way that DNA mutations can affect us.

The way DNA folds plays a role in controlling which genes are expressed inside of our bodies. When it comes to biology, we’re taught that DNA ‘makes us who we are’ through a sequence of letters. These codes would then determine which proteins to make in order to produce the necessary result. For example, there is a code for a protein that will make your skin brown, or your eyes dark, etc. All of this is determined by the way DNA is folded. Since the DNA in our body is extremely long, spanning a length of up to two metres, it has to be wrapped and folded in a certain way to fit inside of our bodies.

Scientists have known for a long time that the way it is wrapped and folded determines what proteins are expressed. Right now, biologists are currently working on isolating mechanical cues that determine how DNA is folded, which is influenced by a number of environmental factors, and other concepts like epigenetics. Even the way we think and perceive the environment, how feel, and what we believe can shape our DNA.

Some of these mechanical cues have been identified by a group of scientists at Leiden University in the Netherlands. Led by Helmut Schiessel, they were, as Science Alert explains, “able to show that these cues affected how the DNA was folded and which proteins are expressed – further evidence that the mechanics of DNA are written into our DNA, and they’re just as important in our evolution as the code itself.”

 The discovery suggests that one day, we may be able to manipulate the mechanisms that determine the way DNA is folded in order to hide certain genes that produce deadly disease.

Is The Genetic ‘Tweaking’ Of Humans  On Its Way/Already Here?

Genetic manipulation is already occurring, and in fact we recently published an article about the first human being to have their DNA manipulated to make their white blood cells 20 years younger (you can read more about that here). And all my research into black budget programs suggests that human genetic engineering is already happening to further militaristic agendas. The evidence for the existence of multiple super soldier programs and other, equally frightening projects is compelling, but that’s a discussion for another article, as is the black budget topic that’s linked above.

Today, it’s hard to know what’s real and what’s not, and it’s unfortunate that it takes a mainstream media outlet to acknowledge something before the masses consider it to be real. That’s a tremendous amount of power to hold, and we know the media has been corrupted by financial, corporate and other elitist agendas. (This is a much broader topic than I wish to address in this article, however; you can learn more about it in this article we published on the it.)

It really is fascinating to imagine what we may be capable of. Perhaps one day we will eradicate all disease by learning how to manipulate our genetics, turning certain genes on and others off, even discovering new ones. What if there is already an intelligent extraterrestrial civilization out there somewhere in the universe which has learned to tweak their DNA so they can live for hundreds of years?

The future of genetic manipulation holds endless possibilities, and while many people worry about the consequences of us playing God, I argue that perhaps these types of discoveries were just waiting there for us to stumble upon, and our natural progression toward these discoveries was all part of ‘the plan,’ if there is one. Perhaps we create it ourselves.

One thing is for certain though — as with any new discovery, it does not matter what we find or what technology we develop, it’s the consciousness and intention behind how we use this knowledge that matters. Our history of innovation has been consistently marred by violence and the misuse of power, so I can only hope we are approaching a more peaceful era at this stage of our development.

Source:http://www.collective-evolution.com

Study Shows Why We Are Made of DNA and Not RNA


In Brief

The most important distinction between DNA and RNA is DNA’s ability to morph when its bases experience chemical damage. DNA can dynamically accommodate base pairs in either Watson-Crick or Hoogsteen configurations, RNA stiffens and falls apart.

Milestones in DNA

In 1869, Friedrich Miescher discovered DNA. About seventy years thereafter, Oswald Avery and his colleagues proved that DNA carries genetic information. A decade later, James Watson and Francis Crick described the structure of the DNA and published their model of the DNA double helix.

Although it has been more than a century since DNA was first identified, scientists continue to learn more about this complex molecule and why we regard it as “the source code of life itself.”

Now, research led by Hashim Al-Hashimi from Duke University provides the most recent milestone in DNA history, showing why DNA, and not RNA, forms the blueprint for life. But first, let us review the basic properties and differences between DNA and RNA.

Source: DifferenceBetween.net

Understanding DNA and RNA

DNA and RNA are both nucleic acids (long biological macromolecules consisting of smaller molecules called nucleotides).

DNA is a double-stranded molecule, with two nucleotide strands consisting of a phosphate backbone, deoxyribose sugar, and has adenine, guanine, cytosine, and thymine as bases; whereas RNA is a single-stranded helix consisting of shorter chains of nucleotides, a phosphate backbone, ribose sugar, and has adenine, guanine, cytosine, and uracil bases.

But perhaps the most important difference between the two, as is shown in Al-Hashimi’s study, is that DNA is capable of shapeshifting in a way that RNA can’t, making DNA a more resilient and a better repository of our genetic code. Specifically, it has to do with Hoogsteen base pairs, which is when one of the nucleic acids is flipped 180 degrees. Ultimately, this causes the whole double helix structure to bend or “kink,” meaning that DNA can accommodate damage by turning in this manner. RNA molecules are incapable of forming Hoogsteen pairs, and so they fall apart—completely unraveling when they encountered the methyl group that the team introduced.

Al-Hashimi tells The Washington Post, “if our genomes were made up of RNA, there’s a very good chance that they wouldn’t be able to sustain chemical damage that’s inflicted on them all the time. It seems like DNA’s ability to absorb damage is one reason why we evolved DNA-based genomes.”

There is still a lot left to discover about our DNA, but we are coming closer to understanding why it is so effective and resilient.

Physicists Confirm There’s a Second Layer of Information Hidden in Our DNA


IN BRIEF

Theoretical physicists have confirmed that it’s not just the information coded in our DNA that shapes who we are—it’s also the way DNA folds itself that controls which genes are expressed inside our bodies.

We all learned in high school how Watson and Crick pieced together the findings of many scientists to come up with a model of deoxyribonucleic acid (DNA). Information in DNA is stored as code sequences made up of nitrogenous bases. Each cell has the same sequence of codes but executes a different function. Code sequences determine the type of protein to be produced in a certain cell, but it is hypothesized that the mechanical properties of the DNA acts as a second layer of information.

Each cell in our body contains around 2 meters of DNA. But since our cells are so tiny, DNA strands have to be tightly wrapped into bundles called nucleosomes in order to fit.

Learn more about DNA and nucleosomes in the video below:

The folding mechanism of DNA is believed to play a large role in how genes are read by the rest of the cell. Biologists have started to isolate mechanical cues that determine how DNA is folded. Now, theoretical physicists from Leiden University in the Netherlands confirmed through computer simulations that these cues are actually coded into our DNA.

Physicist Helmut Schiessel and his group simulated the folding of DNA strands with randomly assigned cues. The team used genomes of baker’s yeast and fission yeast to find correlations between the mechanics and the actual folding structure of DNA in the two organisms.

The results confirm that this second layer of information exists. This led them to conclude that genetic mutations are not just caused by a change in the sequence of codes but also by a change in the way the strands are folded. This simulation may be helpful in hiding unwanted sequences like those that cause diseases.

Some Pacific Islanders Have DNA Not Linked To Any Known Human Ancestor.


Papua New Guinea

Children from the village of Hanuabada play cricket in the streets on February 24, 2012 in Port Moresby, Papua New Guinea.

Most everyone knows that the islands of the South Pacific are some of the most remote and unique places on Earth, but a new study reveals just how unique they really are.

According to a report from the University of Texas MD Anderson Cancer Center in Houston, researchers have found traces of a previously unknown extinct hominid species in the DNA of the Melanesians, a group living in an area northeast of Australia that encompasses Papua New Guinea and the surrounding islands.

A computer analysis suggests that the unidentified ancestral hominid species found in Melanesian DNA is unlikely to be either Neanderthal or Denisovan, the two known predecessors of humankind to this point.

Archaeologists have found many Neanderthal fossils in Europe and Asia, and although the only Denisovan DNA comes from a finger bone and a couple of teeth discovered in a Siberian cave, both species are well represented in the fossil record.

But now genetic modeling of the Melanesians has revealed a third, different human ancestor that may be an extinct, distinct cousin of the Neanderthals.

“We’re missing a population, or we’re misunderstanding something about the relationships,” researcher Ryan Bohlender told Science News. “Human history is a lot more complicated than we thought it was.”

New Theory on Origin of Life on Earth Questions ‘RNA World’ Hypothesis


DNA com GGN

A new study from The Scripps Research Institute (TSRI) has offered a surprising twist of how life began on earth, questioning the likeability of the “RNA World” Hypothesis and proposing that DNA may have also existed when life began.
A new study from The Scripps Research Institute (TSRI) has offered a surprising twist of how life began on earth, questioning the likeability of the “RNA World” Hypothesis and proposing that DNA may have also existed when life began.

According to the study published in the journal Angewandte Chemie International Edition, scientists from TSRI said that the RNA World Hypothesis, which states that proteins and DNA originated from RNA molecules, could not be entirely true. They suggested that something could have existed along RNA to help it evolve.

“Why not think of RNA and DNA rising together, rather than trying to convert RNA to DNA by means of some fantastic chemistry at a prebiotic stage?” said Ramanarayanan Krishnamurthy, associate professor of chemistry at TSRI and senior author of the new study, via Science Daily.

To recall, scientists have been studying the RNA World Hypothesis for years. The hypothesis claims that self-replicating RNA, which came from multiple chemical reactions, led to the evolution of proteins and enzymes. These byproducts of RNA mark the birth of life on Earth.

At first, scientists thought that DNA and RNA could have merged together to create “heterogeneous” strands that would result to blended “chimeras.” However, upon testing, the scientists found that the mixed-up RNA and DNA strands are unstable, especially when the two share the same backbone.

Thus, the researchers came up with an alternate theory, saying that instead of creating “chimeras,” RNA and DNA could have evolved at the same time.

This means that apart from RNA, DNA could have also evolved separately in its own homogeneous system. The theory of RNA producing DNA, according to the researchers, could still be possible but it could have occurred after RNA met DNA.

Watch the vido discussion. URL:https://youtu.be/K1xnYFCZ9Yg

Physicists Confirm There’s a Second Layer of Information Hidden in Our DNA


Theoretical physicists have confirmed that it’s not just the information coded in our DNA that shapes who we are—it’s also the way DNA folds itself that controls which genes are expressed inside our bodies.

We all learned in high school how Watson and Crick pieced together the findings of many scientists to come up with a model of deoxyribonucleic acid (DNA). Information in DNA is stored as code sequences made up of nitrogenous bases. Each cell has the same sequence of codes but executes a different function. Code sequences determine the type of protein to be produced in a certain cell, but it is hypothesized that the mechanical properties of the DNA acts as a second layer of information.

Each cell in our body contains around 2 meters of DNA. But since our cells are so tiny, DNA strands have to be tightly wrapped into bundles called nucleosomes in order to fit.

Learn more about DNA and nucleosomes in the video below:

The folding mechanism of DNA is believed to play a large role in how genes are read by the rest of the cell. Biologists have started to isolate mechanical cues that determine how DNA is folded. Now, theoretical physicists from Leiden University in the Netherlands confirmed through computer simulations that these cues are actually coded into our DNA.

Physicist Helmut Schiessel and his group simulated the folding of DNA strands with randomly assigned cues. The team used genomes of baker’s yeast and fission yeast to find correlations between the mechanics and the actual folding structure of DNA in the two organisms.

The results confirm that this second layer of information exists. This led them to conclude that genetic mutations are not just caused by a change in the sequence of codes but also by a change in the way the strands are folded. This simulation may be helpful in hiding unwanted sequences like those that cause diseases.

Scientists came to a fascinating conclusion after looking at the DNA of thousands of people with depression


A team of scientists pinpointed 17 genetic tweaks, or SNPs (pronounced “snips”), that appear to be tied to MDD.

It’s the leading disability worldwide and it can kill.

Yet for decades, scientists have known surprisingly little about what genes are linked with the development of Major Depressive Disorder (MDD).

A new study aims to change that. In their paper, published Monday in the journal Nature Genetics, a team of scientists pinpointed 17 genetic tweaks, or SNPs (pronounced “snips”), that appear to be tied to MDD.

The researchers combed through a trove of genetic data from thousands of people who submitted their information to the personal genomics company 23andMe.

Scientists have been looking for such genetic hallmarks of depression for years. And while some, including a 2013 study in the journal The Lancet and a 2015 paper in the journal Nature, have yielded some promising clues, none have been able to spot any precise, reliable genetic hallmarks of the disease.

And least not until now.

“My group has been chasing depression genes for more than a decade without success, so as you can imagine we were really thrilled with the outcome,” Harvard psychiatry professor Roy Perlis, one of the leading authors of the paper and the Associate Director of the Psychiatric Genetics Program at Massachusetts General Hospital, told Business Insider.

The hope is that identifying these watermarks in our DNA — tiny areas on genes where high amounts of variation tend to occur among individuals — will help usher in a series of new, more precise treatments for people suffering from the disease.

“But this is really just the beginning. Now the hard work is understanding what these findings tell us about how we might better treat depression,” said Perlis.

Using 23andMe data to uncover clues about depression

23andMe is a personal genomics company that lets you spit in a tube and get your DNA analyzed for $199. Most of the attention they’ve attracted recently has been focused on its tiffs with federal regulatory agencies like the FDA, who threatened to pull its tests because they were giving unauthorized “medical advice.”

But other research that the company is involved with has attracted less fanfare.

In a recent StarTalk interview with host Neil de Grasse Tyson, 23andMe CEO Anne Wojcicki said, “We are about individuals accessing, understanding, and benefiting from the human genome. The genome has a massive potential to transform healthcare. And we got a million people genotyped, so now we have a million people running around going to their doctors and talking about genetics, and that has the potential to be disruptive.”

This study — which drew from 23andMe data — could be one example of this disruptive potential.

Psychiatric diseases, since they are the result of a complex mix of genetics, environment, and behavioral factors, require large numbers of people, or what’s known as a large sample size. In the past, recruiting these large numbers of people, not to mention screening and interviewing each potential participant, has been extremely expensive and labor-intensive. In contrast, the current study drew from research that had already been done.

“We thought, what can we do with this huge set of data that’s already been collected by 23andMe?” said Perlis.

Quite a lot, it turns out.

Using data from more than 75,600 people who said they’d been clinically diagnosed with depression and from more than 231,700 people who reported no history of depression, Perlis and his team were able to identify 15 areas on our DNA that appear to be linked with Major Depressive Disorder. They also found some ties between these areas and those which have been previously identified as possibly playing a role in other psychiatric disorders, such as schizophrenia.

Still, the data has some limitations. For one thing, it’s based on self-reports, meaning that only people who were experiencing problematic symptoms and went to a doctor to seek help were included.  As a result, the data could exclude the many people who experience major depressive disorders, but have not yet been diagnosed. On the other hand, it could also include people who have been wrongfully diagnosed.

“What we might be identifying here is something much more to do with help-seeking behavior than anything to do with a psychiatric illness,” University of California, Los Angeles professor of psychiatry Jonathan Flint told The Guardian.

Regardless of its limitations, however, the research hits home the message that diseases of the brain, such as depression or Alzheimer’s are no less real — and no less serious — than diseases of the body, like cancer.

“Beyond giving us this so much data to explore,” said Perlis, “being able to show that depression is a brain disease, that there is biology associated with it, I think that’s really critical for people to understand that these are brain diseases. They’re not someone’s fault. They are diseases, like any other.”

First-of-their-kind images could aid in use of DNA to build nanoscale devices


Revealing the fluctuations of flexible DNA in 3-D
In a Berkeley Lab-led study, flexible double-helix DNA segments connected to gold nanoparticles are revealed from the 3-D density maps (purple and yellow) reconstructed from individual samples using a Berkeley Lab-developed technique called individual-particle electron tomography or IPET. Projections of the structures are shown in the background grid. Credit: Berkeley Lab

An international team working at the Department of Energy’s Lawrence Berkeley National Laboratory (Berkeley Lab) has captured the first high-resolution 3-D images from individual double-helix DNA segments attached at either end to gold nanoparticles. The images detail the flexible structure of the DNA segments, which appear as nanoscale jump ropes.

This unique imaging capability, pioneered by Berkeley Lab scientists, could aid in the use of DNA segments as building blocks for that function as nanoscale drug-delivery systems, markers for biological research, and components for computer memory and electronic devices. It could also lead to images of important disease-relevant proteins that have proven elusive for other imaging techniques, and of the assembly process that forms DNA from separate, individual strands.

The shapes of the coiled DNA strands, which were sandwiched between polygon-shaped gold nanoparticles, were reconstructed in 3-D using a cutting-edge electron microscope technique coupled with a protein-staining process and sophisticated software that provided structural details to the scale of about 2 nanometers, or two billionths of a meter.

“We had no idea about what the double-strand DNA would look like between the nanogold particles,” said Gang “Gary” Ren, a Berkeley Lab scientist who led the research. “This is the first time for directly visualizing an individual double-strand DNA segment in 3-D,” he said. The results were published in the March 30 edition of Nature Communications.

Revealing the fluctuations of flexible DNA in 3-D
Gang Ren (standing) and Lei Zhang participated in a study at Berkeley Lab’s Molecular Foundry that produced 3-D reproductions of individual samples of double-helix DNA segments attached to gold nanoparticles. Credit: Roy Kaltschmidt/Berkeley Lab

The method developed by this team, called individual-particle electron tomography (IPET), had earlier captured the 3-D structure of a single protein that plays a key role in human cholesterol metabolism. By grabbing 2-D images of the same object from different angles, the technique allows researchers to assemble a 3-D image of that object. The team has also used the technique to uncover the fluctuation of another well-known flexible protein, human immunoglobulin 1, which plays a role in our immune system.

For this latest study of DNA nanostructures, Ren used an electron-beam study technique called cryo-electron microscopy (cryo-EM) to examine frozen DNA-nanogold samples, and used IPET to reconstruct 3-D images from samples stained with heavy metal salts. The team also used molecular simulation tools to test the natural shape variations, called “conformations,” in the samples, and compared these simulated shapes with observations.

Ren explained that the naturally flexible dynamics of samples, like a man waving his arms, cannot be fully detailed by any method that uses an average of many observations.

A popular way to view the nanoscale structural details of delicate biological samples is to form them into crystals and zap them with X-rays, though this does not preserve their natural shape and the DNA-nanogold samples in this study are incredibly challenging to crystallize. Other common research techniques may require a collection of thousands near-identical objects, viewed with an electron microscope, to compile a single, averaged 3-D structure. But this 3-D image may not adequately show the natural shape fluctuations of a given object.

The samples in the latest experiment were formed from individual polygon gold nanostructures, measuring about 5 nanometers across, connected to single DNA-segment strands with 84 base pairs. Base pairs are basic chemical building blocks that give DNA its structure. Each individual DNA segment and gold nanoparticle naturally zipped together with a partner to form the double-stranded DNA segment with a gold particle at either end.

The samples were flash-frozen to preserve their structure for study with cryo-EM imaging, and the distance between the two gold particles in individual samples varied from 20-30 nanometers based on different shapes observed in the DNA segments. Researchers used a cryo-electron microscope at Berkeley Lab’s Molecular Foundry for this study.

They collected a series of tilted images of the stained objects, and reconstructed 14 electron-density maps that detailed the structure of individual samples using the IPET technique. They gathered a dozen conformations for the samples and found the DNA shape variations were consistent with those measured in the flash-frozen cryo-EM samples. The shapes were also consistent with samples studied using other electron-based imaging and X-ray scattering methods, and with computer simulations.

While the 3-D reconstructions show the basic nanoscale structure of the samples, Ren said that the next step will be to work to improve the resolution to the sub-nanometer scale.

“Even in this current state we begin to see 3-D structures at 1- to 2-nanometer resolution,” he said. “Through better instrumentation and improved computational algorithms, it would be promising to push the resolution to that visualizing a single DNA helix within an individual protein.”

The technique, he said, has already excited interest among some prominent pharmaceutical companies and nanotechnology researchers, and his science team already has dozens of related research projects in the pipeline.

In future studies, researchers could attempt to improve the imaging resolution for complex structures that incorporate more DNA segments as a sort of “DNA origami,” Ren said. Researchers hope to build and better characterize nanoscale molecular devices using DNA segments that can, for example, store and deliver drugs to targeted areas in the body.

“DNA is easy to program, synthesize and replicate, so it can be used as a special material to quickly self-assemble into nanostructures and to guide the operation of molecular-scale devices,” he said. “Our current study is just a proof of concept for imaging these kinds of molecular devices’ structures.”