BioQuakes

AP Biology class blog for discussing current research in Biology

Tag: DNA (Page 1 of 3)

The journey to find a cure for cancer

What exactly does ‘epigenetic’ mean? Well epigenetic literally means “in addition to changes in genetic sequence.” The term now means any procedure to change genetic activity without changing the sequence of the actual DNA. So why is this important? Epigenetics can affect a lot of scientific research. For example DNA methylation is a hugely important epigenetic modification.

DNA methylation is where a methyl group would be added to a cytosine in a DNA sequence changing its function. This can be used in embryonic development, X-chromosome inactivation, genomic imprinting, gene suppression, carcinogenesis and chromosome stability. This means DNA methylation is very vital to growth and development- as it is a natural process- however can affect bad cells.

Examples of this are with cancer cells. DNA Methylation patterns- adding a group- are interrupted and changed when cancer is present. DNA methylation done on the promoters in tumor cells can turn off the expression of genes. In humans this can cause disruption of vital developmental pathways. This was then tested in an experiment (for now we will only observe human results because it was tested on mice as well) They tested human normal brain tissue vs. cancerous.

After testing the DNA methylation patterns on tumors, they found that 121 loci (loci is the central “hot spot” of genes) had strong methylation compared to the normal brain tissue which had 60% less. So what does all this mean??

Basically DNA methylation is a good thing in a normal environment. When cancer is present DNA methylation can change and be harmful in a negative environment such as a tumor because it causes hypermethylation.

While the take away is essentially the obvious- cancer is bad- scientists can use this data to find a correct cure for cancer and to create better medicine as some can harm even more by increasing DNA methylation in tumors. For more information on this click here.

 

 

 

How A Chemical From the Cypress Tree Could Advance Epigenetics Against Cancer

by Czechmate on Wikimedia Commons

Found in the essential oil extracted from the bark of a cypress tree, a chemical named hinokitiol shows potential to impact epigenetic tags on DNA and stop the activity of genes that assist the growth of tumors.

In order to develop an of understanding cancer, researches have had to comprehend the DNA methylation, an epigenetic function which controls gene expression. In regular DNA methylation, genes that work to fight against tumors are turned on, reducing the risk of cancer. However, if DNA methylation is negatively altered, then those cancer-fighting genes will be silenced, helping to progress cancer development. Scientists have tried to combat irregular DNA methylation and over-silencing of genes by creating epigenetic anti-cancer medications that reverse non-beneficial methylation effects. Like in most cases of medication usage, the users face unappealing side effects. Hinokitiol is attractive to scientists because it is a natural compound with many health benefits and way less side effects than modified drugs that can possibly cause mutagenesis and cytotoxicity.

 

Researchers from the Korea University College of Medicine tested the productivity of the hinokitiol chemical in a study by giving doses of it to colon cancer cells. It was found that this chemical helped to inhibit the colon cancer cells efficiency without affecting the colon cells without cancer. The scientists also found through careful inspection that the presence of hinokitiol decreases the expression of proteins DNMT1 and UHRF1; both of which are proteins that encourage carcinogenesis. In summary, the doses of hinokitiol appear to have allowed normal cells to remain healthy, while reducing the ability for the colon cancer cells to thrive and ceasing the production of proteins that promote cancer maturation.

Researchers are continuing their search for natural compounds, as opposed to artificial medications, that can prevent the flourishing of cancer in our bodies through playing a positive role in gene expression and DNA methylation.

http://www.whatisepigenetics.com/cypress-trees-epigenetically-protect-cancer/

 

 

https://commons.wikimedia.org/wiki/File:Raindrops_on_leyland_cypress.jpg

Sperm Epigenetics and the Next Generation

Jerome Jullien from the Welcome Trust CRUK Gurdon Institute in Cambridge experimented with frogs to see if more than just DNA is passed on to the second generation offspring.  Sperm contain something called epigenetic tags which are “chemical switches attached to the genomes of sperm.”  (It is important to understand that epigenetics does not alter an organism’s DNA.)  In order to test if these sperm epigenetics influence offspring Jullien used two types of sperm; regular frog sperm and spermatids which had different epigenetic tags.  They then injected the sperm and spermatid into genetically engineered eggs which took away some of the epigenetic tags (with specific enzymes) on the sperm.  This lead to abnormal gene expression causing problems for the offspring.

This basically shows that a male does not simply pass down his DNA to his offspring but other factors like epigenetic tags can also effect the life of their kids.  As Jullien says, “The obvious implication is that whatever experiences the father has in life that end up epigentically modifying sperm cells might also be transmitted to the offspring and affect their genetic development and characteristics.”  There is still disagreement over whether epigenetic tags on sperm influence offspring.  For example some feel the experiment tested was not realistic because the frogs were not exposed to different environments as a human would be in his lifetime.  What do you think; would epigenetic tags on male sperm have an effect on a mans offspring?

Disruption in Epigenetics Can Lead to Cancer

Epigenetics is the study of potentially inheritable gene expression that does not involve any changes to the underlying DNA sequence. Epigenetic change is natural and common, but can be brought on by changes in environment, age, lifestyle, etc. Epigenetic modifications are seen as cells terminally differentiate and end up as skin cells, brain cells, or even liver cells. Epigenetics is a constant battle between active and inactive genes. If one were to overtake the other, it would alter the equilibrium in a persons body, potentially causing cancer.

Scientists are now claiming that once they have a better understanding of epigenetics and the factors which cause the cancer, they will be able to design drugs to counter this loss of equilibrium. Recent data identified an epigenetic “writer” called methyltransferase EZH2. It’s been linked to several types of cancer including melanomas and lymphomas. They’ve also identified and epigenetic “eraser”, KDM3A, which takes on an oncogenetic role and activates tumor promoting genes in the body. Epigenomic changes also contribute to cancer’s ability to go undetected in the human immune system.

Using this information, researchers may have found the right pathway for drug targeting. Metabolites and epigenetics are tightly connected and rely on each other to stay in equilibrium. In addition, there is a strong cooperation of epigenetic factors with the transcriptional complex. Now, researchers are looking into finding a way to us this connection to suppress tumor causing epigentics, and amplify those that fight cancer.

Fabian V. Filipp, the author of the paper, states, “There is an intriguing crosstalk between metabolism and epigenetics… With both fields maturing, further synergy between epigenetic and metabolomics may deliver new therapeutic agents.”

This research is incredibly interesting because of its newness. Each day, new informatoin and research is being found in the field of epigenetics. What I would’ve liked to learn in this article is how they plan to use the metabolites to battle the cancerous cells, and in what way they would be administered. Each day we get closer to the answers. The new technology and knowledge of today may finally lead us to a cure or at least a way towards remission with certain types of cancer.

Image result for cancer epigenetics

Source article: https://www.sciencedaily.com/releases/2017/03/170324083018.htm

Playing God: New Technology Gives Scientists the Ability to Delete DNA

Since the relatively recent discovery of CRISPR-Cas9, scientists have explored multiple uses of this new technology, from eliminating a patient’s cancer to making super plants, furthering our understanding of DNA and how it works. CRISPR-Cas9 has become the most advanced and efficient gene-editing tool there is. However, thus far, its use has been largely limited to silencing protein-coding genes in the DNA. This leaves out what’s called the DNA “dark matter” — the non-coding DNA that covers about 99 percent of our genetic code. That’s about to change; this article from Futurism explains how a recent study from PLOS Computational Biology is creating a new technique, based on CRISPR, but delving deeper into this unexplored territory.

This brand-new software technology called CRISPETa evolved from a breakthrough tool (which uses CRISPR-Cas9) called DECKO. DECKO was designed for deleting pieces of non-coding DNA using two sgRNAs as molecular scissors. While the concept might seem simple, designing deletion experiments using DECKO was time-consuming due to the lack of software to create the required sgRNAs.

This is where the new tool, CRISPETa, comes in. According to the report, users can tell CRISPETa which region of DNA they wish to delete. The software then generates a pair of optimized sgRNAs that can be used directly for that experiment. Pulido, leader of the research team, stated that “We hope that this new software tool will allow the greatest possible number of researchers to harness the power of CRISPR deletion in their research.”

The software has already demonstrated its efficiency in deleting desired targets in human cells. The research team hopes that its use will go beyond a basic research tool, and be utilized as “a powerful therapeutic to reverse disease-causing mutations,” Johnson added. Herein lies the hidden value of CRISPR-Cas9 and all further developments from it: The more we understand DNA and genomics, the better we will be able to fight diseases and other aspects of human life that cause harm, ultimately leading to a higher quality of life for all.

 

Anti-CRISPR Proteins: What are they and can they be beneficial?

NIH Image Gallery Image Link

Understanding CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats)

For many bacteria, one line of defense against viral infection is the RNA guided “immune system” known as CRISPR-Cas. This particular complex is unique because of its ability to recognize viral DNA and trigger its destruction. Scientists have used CRISPR to degrade sections of viral RNA and use the CRISPR systems to remove unwanted genes from an organism. CRISPR proteins have also been studied with the hope of eliminating serious disease and illnesses. However, this CRISPR system does not always work do to anti-CRSPR proteins that inhibit the complex from working properly.

Research 

According to an article on ScienceDaily, researchers have finally discovered how these anti-CRISPR proteins work! Research done by biologist Gabriel C. Lander from the Scripps Research Institute, discovered that anti-CRISPR proteins work by inhibiting CRISPR’s ability to identify and attack viral genomes. Just like there are different CRISPR systems, there are multiple anti-CRISPR proteins as well. One in particular mimics DNA to throw the CRISPR-guided detection machine off its course. Scientists have been able to further discover certain aspects of CRISPR and anti-CRISPR systems by using a high-resolution imaging technique called cryo-electron microscopy. They have discovered that the CRISPR surveillance complex analyzes a virus’s genetic material to see where it should attack by having proteins within the complex wrap around the CRISPR RNA, exposing specific sections of bacterial RNA. These sections of RNA then scan viral DNA, looking for genetic sequences they recognize. Lander describes these proteins as being very clever because they “have evolved to target a crucial piece of the CRISPR machinery. If bacteria were to mutate this machinery to avoid viral attacks, the CRISPR system would cease to function.” Therefore, CRISPR systems cannot avoid anti-CRISPR proteins without completely chancing the mechanism used to recognize DNA. Another type anti-CRISPR protein works a bit differently. Based on its location and negative charge, this anti-CRISPR protein acts as a DNA mimic, fooling CRISPR into binding this immobilizing protein, rather than an invading viral DNA.

Can Anti-CRISPR Proteins be beneficial?

Researchers are saying that the understanding of how these anti-CRISPR proteins work are extremely important! According to an article on GEN, the discovery and understanding of anti-CRISPR proteins actually allows researchers to have greater control over gene-edits. In this article, Dr. Sontheimer, a professor in the RNA The RNA Therapeutics Institute at UMass Medical School, expressed how “CRISPR/Cas 9 is a good thing because it introduces specific chromosome breaks that can be exploited to create genome edits, but because chromosome breakage can be hazardous, it is possible to have too much of a good thing, or to have it go on for too long.” Anti-CRISPR proteins can be beneficial and work as an off switch for CRISPR, therefore advancing gene editing!

 

 

 

The Mystery of Epigenetics

Epigenetics, the process of altering what genes are activated in a certain DNA sequence, is in many ways, still a mystery to the scientific community. How it is done chemically, as well as what environmental factors cause it. New discoveries have been made, linking surprising regulation enzymes and cultural factors. Ultimately, no matter what causes this phenomenon, it is a key factor in the evolutionary development of many species, and the world as we know it.

Tryptase:

A new study has shown the role of the enzyme tryptase in epigenetic development. Tryptase works to cleave the tails of histones, which will stop some epigenetic changes, while cells that lack tryptase, begin to proliferate uncontrollably. Most importantly, this proliferation causes cells to lose their identity. With this discovery, we see that by introducing tryptase, we can influence epigenetic development in cells.

Culture:

Another recent study has shown that cultural and environmental factors can influence a genome rather than only genetic ancestry. By studying the genetic sequences of both Mexican and Puerto Rican children, researchers discovered that there were differences that couldn’t be accounted for by ancestry.   The rest may be an impact on genetic makeup by differences in experiences, practices, and culture distinct to the two ethnic subgroups.

Ultimately, epigenetics is a fascinating concept that is often influenced by factors we might not suspect.   As the scientific community continues to make discoveries, the epigenetic phenomenon continues to excite and inspire researchers.

Photo: https://www.sciencedaily.com/releases/2017/01/170110120638.htm

Preferential Gene Expression: Not As Random As We Thought

Our conventional knowledge of genetics dictates that the activation of genes in our DNA is random. It is equally likely that our body will express our mother’s alleles as it is that our body will express our father’s. In the case that one parent donates a defective copy, it will be silenced; the other parent’s healthy set of DNA takes precedence and becomes activated.

However, a new study indicates that gene expression and activation is not as random as we thought. In certain regions of the body, our genes demonstrate preferential expression.

A team of scientists at the University of Utah found that almost 85 percent of genes in juvenile mice brains displayed preferential treatment. The mice brains activated one parent’s set of DNA over the other’s. This phenomenon was observed in other areas of the body, as well as in primates.

Although the preferential expression came to a close within ten days, it could provide explanations for vulnerability to brain diseases such as schizophrenia, ADD, and Huntington’s. The temporary preferential treatment to one parent’s copy of DNA could trigger a host of problems specific to that cell site that lead to such disorders, if the parent had given a defective copy of genes.

The study has the potential to alter our basic understandings of genetics, and how we are more prone to certain specialized diseases.

Image: (Public Domain, https://pixabay.com/en/dna-biology-medicine-gene-163466/)

A Second Theory: Is the RNA World Hypothesis Wrong?

Introduction

Prior to recent research, scientists strongly supported the “RNA world” hypothesis, a theory that claims that DNA derived from RNA, and that RNA therefore provided the basis for life as we know it. The evidence of this new study under scientists at The Scripps Research Institute leads to an alternate theory that challenges this previous mode of thinking. This study is intriguing not only because it challenges what has mostly been accepted as factual truth by most scientists, but also because it attempts to solve the question of where and how first life developed.

Background: The “RNA world” hypothesis

The “RNA world” hypothesis dates back to over 30 years ago. Proposed independently by Carl Woese, Francis Crick, and Leslie Orgel, it essentially is a theory that states that RNA existed before modern cells, and stored genetic information and catalyzed chemical reactions within earlier cells. This theory further claims that DNA came later and only then contained the genetic material. It also infers that proteins served as a catalyst much later, only fulfilling this role once RNA evolved. The evidence that supports this theory lies with the chemical differences that distinguish RNA from DNA. RNA can be formed from formaldehyde (HCHO) which is chemically simple, especially in comparison to the much more complicated sugar deoxyribose. In a reaction catalyzed by a specific enzyme, deoxyribose is produced from ribose which also indicates the possibility that DNA comes directly after the structurally more simple and single helix RNA.

Recent Studies

Researchers believe that if this theory is correct, RNA nucleotides and DNA backbones would have mixed to create “heterogeneous” (or a product resulting from differing “parents” with unique charateristics) strands. The resulting “chimeras” (an organism composed of cells from different zygotes leading to subtle variations in form) would be an intermediate step in the transition to RNA if stable, however the study shows a decrease in stability (specifically in thermal stability or the ability to function at high temperatures) when the backbone is shared between the two nucleic acids. The researchers attribute this instability to a slight difference between the sugar in RNA and the sugar in DNA. As a result, if the RNA theory had been true, the chimeras would have died off. This proves that evolution has lead to a system where enzymes have developed to maintain the system of “homogenous” molecules, keeping RNA and DNA separate since they function much better separate from one another. Since these enzymes are fairly “new” in terms of the span of the existence of DNA and RNA, it is highly unlikely that RNA was able to transition to newly developed DNA. Without any mechanisms to keep DNA and RNA separate, it is logical to conclude that RNA does not predicate DNA. This concept is reminiscent of the endosymbiont theory that discusses the possible reason for the unique qualities of mitochondria and chloroplasts in that both theories rely on existing knowledge about these unique structures and how each component might contribute to a different function. Similar to the endosymbiont theory, there is no exact answer as to whether this theory is correct, however through challenging the theory and conducting experiments, we can further develop our understanding of certain biological phenomena.

Conclusion

This alternate theory, on the other hand, proposes a different view that RNA and DNA have coexisted and that one therefore did not develop from the other. While this theory is not completely new, these recent findings regarding instability for a backbone shared between the two nucleic acids provide more evidence for this secondary theory (to the RNA world theory). If this theory is accurate, DNA could have developed its homogenous system much earlier than scientists have predicted up until this point. According to this second theory, after RNA first interacted with DNA it still could have evolved to create DNA. Although scientists will never be able to discover life’s exact origin, these findings can provide insights for biology overall.

images

https://biologydirect.biomedcentral.com/articles/10.1186/1745-6150-7-23

http://www.sciencemag.org/news/2016/05/rna-world-inches-closer-explaining-origins-life

https://www.sciencedaily.com/releases/2016/09/160928153357.htm

http://www.medicinenet.com/script/main/art.asp?articlekey=8905

Is There a Limit to How Old Humans Will Get?

In the 1900s, the life expectancy for humans in the United States was approximately 50 years. Since then, the age to which humans can live has only grown. In 1997, a woman by the name of Jeanne Calment died at the age of 122- an astounding increase from the life expectancy less than a hundred years ago. A new study written about in the New York Times explains that Dr. Vijg, an expert on aging at the Albert Einstein College of Medicine, feels that we have now reached our “ceiling. From now on, this is it: Humans will never get older than 115.” Dr. Vijg and his graduate students published their pessimistic study in the journal Nature, presenting the evidence for their claim.

For their study, Dr. Vijg and his colleagues looked at how many people of varying ages were alive in a given year. Then they compared the figures from year to year, in order to calculate how fast the population grew at each age. For a while, it looked as though the fastest-growing group was constantly becoming older; “By the 1990s, the fastest growing group of Frenchwomen was the 102-year-olds. If that trend had continued, the fastest-growing group today might well be the 110-year-olds.” (NY Times Article). Instead, the increases slowed and eventually stopped, leading Dr. Vijg and his colleagues to conclude that humans have finally hit an upper limit to their longevity. Further research into the International Database of Longevity seemed to validate their findings; No one, except in rare cases like Ms. Calment, had lived beyond the age of 115. It appears as though human beings have hit the ceiling of longevity.

There was a varied mix of responses to the study. Some, like Leonard P. Guarente, a biology professor at MIT, praised it, saying “it confirms an intuition he has developed over decades of research on aging.” Others, like James W. Vaupel, the director of the Max-Planck Odense Center on the Biodemography of Aging, called the new study a travesty and said, “It is disheartening how many times the same mistake can be made in science and published in respectable journals.”

This study is by no means conclusive. It is simply one more piece of research in the ongoing debate over whether human beings will continue to live longer, and will continue to be debated by many experts in the field.

However, one must wonder whether living longer should be the goal. After all, as Dr. Vijg pointed out, “aging is the accumulation of damage to DNA and other molecules. Our bodies can slow the process by repairing some of this damage. But in the end, it’s too much to fix. At some point, everything goes wrong, and you collapse.” While morbid, he makes a valid observation: Humans can only go so long until necessary bodily functions begin to break down. Rather than worrying about whether we will live to an extraordinary age such as Ms. Calment, I concur with Dr. Vijg; the focus should be on living the most amount of healthy years and taking care of our bodies. While it may seem like a great idea to live to the age of 125, what good would that do if you aren’t able to continue with the activities you enjoy because your body is breaking down?

 

Other Relevant Articles:

In Depth Explanation of Longevity: https://en.wikipedia.org/wiki/Longevity

A brief summary of Dr. Vijg’s findings (a bit shorter than the NY Times article): http://www.newser.com/story/232121/human-lifespan-has-likely-maxed-out.html

An interesting article about an entrepreneur’s quest to make people live even longer: https://www.theguardian.com/science/2015/jan/11/-sp-live-forever-extend-life-calico-google-longevity

 

More CRISPR Improvements

Crispr-Cas9 is a genome editing tool that is creating a whole lot of buzz in the science world. It is the newest faster, cheaper and more accurate way of editing DNA.  Crispr- Cas9 also has a wide range of potential applications. It is a unique technology that enables geneticists and medical researchers to edit parts of the genome by cutting out, replacing or adding parts to the DNA sequence.  The CRISPR-Cas9 system consists of two key molecules that introduce a mutation into the DNA. The first Molecule is an enzyme called Cas9. Cas9 acts as a pair of scissors that can cut the two strands of DNA at a specific location in the genome so that bits of DNA can be added or removed.  The second is a piece of RNA called guide RNA or gRNA. This consists of a small piece of pre-designed RNA sequence located within a longer RNA scaffold. The scaffold part binds to DNA and the pre-designed sequence guides Cas9 to the right part of the genome. This makes sure that the Cas9 enzyme cuts at the right point in the genome.Screen Shot 2016-04-10 at 4.50.55 PM

CRISPR-Cas9 is efficient compared to previous gene-editing techniques, but there’s still plenty of room for improvement. CRISPR is less efficient when employing the cellular process of homology-directed DNA repair, or HDR, as opposed to nonhomologous end joining.  Jacob Corn, the scientific director of the Innovative Genomics Initiative at the University of California, Berkeley, and his colleagues have come up with a way to improve the success rate of homology-directed repair following CRISPR-Cas9. “We have found that Cas9-mediated HDR frequencies can be increased by rationally designing the orientation, polarity and length of the donor ssDNA to match the properties of the Cas9-DNA complex,” the researchers wrote in their paper, “We also found that these donor designs, when paired with tiled catalytically inactive dCas9 molecules, can stimulate HDR to approximately 1%, almost 50-fold greater than donor alone.”

“Our data indicate that Cas9 breaks could be different at a molecular level from breaks generated by other targeted nucleases, such as TALENS and zinc-finger nucleases, which suggests that strategies like the ones we are using can give you more efficient repair of Cas9 breaks,” coauthor Christopher Richardson, a postdoc in Corn’s lab, said in a statement.

Original Article:

http://www.the-scientist.com/?articles.view/articleNo/45159/title/More-CRISPR-Improvements/

Other Addtional Helpful Links:

http://www.yourgenome.org/facts/what-is-crispr-cas9

 

How CRISPR/Cas9 could one day prevent AIDS

CRISPR/Cas9 is a new gene editing tool that can target and modify DNA with great accuracy.  This new tool has many scientific uses, including treatment of many diseases.  Recently, several breakthroughs have been made in treating HIV with CRISPR Cas9.  However, a number of issues with the tool have come up at the same time.

To understand how CRISPR eliminates HIV, one must know how HIV replicates. HIV replicates by taking over a host cell and injecting its RNA into the cell.  This RNA becomes DNA and joins together with parts of the host cell’s DNA.  After entering the cells, the virus can lay dormant for several years, but will eventually start replicating and taking over other cells.  The standard form of treatment for HIV is an antiretroviral.  While antiretrovirals can be very effective at limiting the spread of the disease, it cannot fully remove it or stop it forever.

HIV virus

image source: http://bit.ly/1S4bcWY

The CRISPR Cas9 could potentially be used to inhibit the spread of HIV by editing the virus out of a cell’s DNA.  Researchers at The University of Massachusetts Medical School have been developing a technology to perform this impressive task.  While there have been several successful trials in preventing HIV from spreading, several trials have lead to increased resistance for the HIV.

“When we sequence the viral RNA of escaped HIV, the surprise is that the majority of the mutations that the virus has are nicely aligned at the site where Cas9 cleaves the DNA, which immediately indicates that these mutations, instead of resulting from the errors of viral reverse transcriptase, are rather introduced by the cellular non-homologous end joining machinery when repairing the broken DNA,” says Chen Liang, a senior investigator at the Lady Davis Institute at the Jewish General Hospital and the Associate Professor of Medicine at the McGill University AIDS Centre.

These mutations alter the strand of DNA, preventing the CRISPR Cas9 from recognizing it.  If the CRISPR Cas9 cannot recognize the virus, it cant remove the viral DNA, allowing the virus to create more copies of itself.  Despite these limitations, researchers like Liang are confident that they can succeed.

article: http://esciencenews.com/articles/2016/04/08/hiv.can.develop.resistance.crisprcas9

CRISPR/Cas9 Provides Promising Treatment for Duchenne Muscular Dystrophy

There are nine kinds of muscular dystrophy and of these, Duchenne MD is the most common severe form of childhood MD. It affects about 1 in 5000 newborn males, only in very rare cases has it affected females. DMD is a genetic disorder that causes progressive muscle degeneration and weakness. Patients usually die by age 30 to 40.

DMD is caused by the absence of a protein, dystrophin, that helps keep muscle cells intact. In 1986 it was discovered that there was a gene on the X chromosome that, when mutated, lead to DMD. Later, researchers discovered that the protein associated with this gene was dystrophin. From this information, we can tell that this disorder is sex-linked, which explains why women are mainly carriers.

No one has found an absolute cure for this genetic disorder until now. Even in recent years, people have discovered treatments that will make patients’ lives more bearable, but never reverse the disorder. As a result of these advances, mostly in cardiac and respiratory care, patients are able to live past teen year and as long as in to their fifties, though this is rare. Although there are still drugs being tested like Vamorolone (a “dissociative steroid,” is an anti-inflammatory compound), more treatments on the molecular level are now being considered. However, thanks to recent discoveries and research with the new genetic technology, CRISPR/ Cas9, scientists may have found a treatment for DMD.

This new approach to gene correction by genome editing has shown promise in studies recently. This particular correction can be achieved in a couple ways: one is by skipping exon 51 of the DMD gene using eterplirsen (a morpholino-based oligonucleotide). Studies over four years show prolonged movement abilities, and a change in the rate of decline compared to controls. The newest approach to gene correction using CRISPR/Cas9, which the article I’m writing about focuses on, was performed in this study as next described: the CRISPR/Cas9 system targets the point mutation in exon 23 of the mdx mouse that creates a premature stop codon and serves as a representative model of DMD. Multiple studies in three separate laboratories have provided a path and laid the groundwork for clinical translation addressing many of the critical questions that have been raised regarding this system. The labs also discovered by further demonstrations, that this is a feasible treatment for humans. Functional recovery was demonstrated in the mice, including grip strength, and improved force generation- all of which are very important and hopeful discoveries. It is estimated from these studies that this new method will pass clinical trials and go on to benefit as many as 80% of DMD sufferers. Even greater success rates are expected if this is performed in young and newborn DMD patients.

CRISPR-Cas9 Can Now Be Applied to Not Only DNA But RNA

Anyone who has seen the movie Gattaca knows that the plot is set in a futuristic society that is able to edit the human genome. Of course, there’s a reason that it’s set in the future. Scientists of today couldn’t possibly dream of being able to edit genes in our DNA…right?

Well, wrong. Say hello to CRISPR-Cas9. CRISPER-Cas9 is, in short, a highly effective and popular DNA-editing technique that scientists started to use to sequence and edit human genes.

However, thanks to scientists at University of California-San Diego, CRISPR-Cas9 is not only limited to editing DNA. By altering only a few key features, this mechanism can now also be used with RNA, another highly important and fundamental molecule in the human body. CRISPR-Cas9 as of now can be used to track RNA in its movement, such as its many essential roles in protein synthesis. Below is a picture that briefly shows the importance of mRNA and tRNA:

 

Screen Shot 2016-04-11 at 12.01.31 AM

(Source: http://www.proteinsynthesis.org/protein-synthesis-steps/)

It’s an exciting development in that certain diseases, such as cancer and autism, are linked to mutations in RNA. By using CRISPR-Cas9 to their advantage, scientists could study the movement of RNA in the cell—and how and when it gets there—to track any defective RNA that can potentially lead to such diseases and then hopefully develop treatments. Gene Yeo, PhD, an associate professor of cellular and molecular medicine at UC-San Diego, expresses hope that “future developments could enable researchers to measure other RNA features or advance therapeutic approaches to correct disease-causing RNA behaviors”.

Intrigued? Confused? Please leave any comments or questions below!

 

Original Article

How to Proofread the Genome

CRISPR-Cas9 is an emerging technology in the field of genetics that has opened an incredible number of  doors and revolutionized the field. It permanently changes the genome of cells while they are alive. CRISPR stands for Clustered Regularly Interspaced Short Palindromic Repeats. This sounds confusing but the actual technology is simple. Feng Zhang uses the analogy of proofreading a book to explain it.Let us say you are proofreading your novel and you find the phrase “twinkle twinkle big star”. Now you want to change it to “twinkle twinkle little star”. In this scenario, the words are base pairs and the change from “little” to “big” is a mutation. You can not just delete “big” or just “add” little you must do both. And that is what CRISPR does. It uses an enzyme to cut the DNA and silences that gene. It also can do the opposite and activate certain genes.

A diagram of how CRISPR works

This precise controls of genes have allow scientists to do research faster and cheaper. Its applications go beyond just research however. This technology can be used to treat certain genetic mutations by correcting the incorrect base pairs accurately.

Link to article:

https://www.broadinstitute.org/what-broad/areas-focus/project-spotlight/questions-and-answers-about-crispr

Other Links:

https://www.sciencedaily.com/releases/2015/12/151210125648.htm

https://www.addgene.org/crispr/guide/

The New and Improved CRISPR-Cas9

The CRISPR-Cas9 genome editing system has transformed into an even better version of itself. A new, elegant technique, coined by researches at the Broad Institute of MIT and Harvard and the McGovern Institute for Brain Research at MIT, has resolved one of the most reoccurring technical issues in genome editing.

https://commons.wikimedia.org/wiki/File:Crystal_Structure_of_Cas9_in_Complex_with_Guide_RNA_and_Target_DNA.jpg

Primarily, the CRISPR-Cas9 system works to specifically modify a cell’s DNA. CRISPR is dependent on protein Cas9, as it is specialized for cutting DNA. The DNA, at a location identified by a RNA’s sequence matching the target site, is altered by Cas9. Though it very efficient at cutting its target sites, there is a large complication in the process. Once the Cas9 is inside the cell, it can also bind and cut additional sites that are not targeted. Because of this, undesired edits are produced which can alter gene expression or kill off a gene completely. These setbacks can lead to cancer or other problems. Feng Zhang, along with his colleagues at MIT, reported that by just changing 3 out of the approximately 1,400 amino acids composing the Cas9 enzyme from S. pyogenes, a considerable reduction of “off-target editing” to undetectable levels are observed.

This newfound information was derived from studying the structure of the Cas9 protein. Since DNA is negatively charged, it binds to a positively charged groove in the Cas9 protein. The scientists predicted that by replacing some of the positively charged amino acids with a neutral charge, there would be a decrease in binding to “off target” sequences than to “on target” sequences. By mutating three amino acids, their technique proved to be successful.

The team is calling this newly-engineered enzyme “enhanced S. pyogenes Cas9” or “eSpCas9.” It’ll be particularly useful for genome editing that requires precise specificity and it is said to be available for researches worldwide.

I believe that this newfound resolution for the CRISPR-Cas9 genome editing hurtle is a huge game changer. This charge-changing approach might also be able to be used for other experiments involving RNA-guided DNA targeting enzymes. Ethical and societal concerns have also risen due to the idea of rapid and efficient genome editing. The eSpCas9 is highly beneficial in the scientific community, however there is a lot more research needed to be done in order to be used clinically.

 

Original article can be found here.

Forget DNA, Let’s Talk RNA!

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Photo of RNA (licensing information here)

The genetic code within DNA is responsible for determining who we are and what we are capable of. Because of this, scientists have been interested in cracking the genetic code and finding ways to alter it. There are many diseases linked to DNA, as well as RNA. However, scientists have not been as successful in targeting RNA in living cells as they have been in targeting DNA. Recently, using CRISPR-Cas9, researchers at University of California, San Diego School of Medicine have figured out how to do what has been troubling scientists.

Senior author Dr. Gene Yeo described how the researchers at UCSD have been tracking the movement of RNA throughout cells and plan to measure other RNA features and help to correct disease-causing RNA behaviors using CRISPR-Cas9. The location of RNA in a cell determines whether proteins are produced at the right time and in the right place. When defective RNA transport occurs, diseases ranging from autism to cancer can occur. In order to successfully treat these conditions, researchers must find a way to track and measure the movement of RNA. This process was first seen with DNA: scientists found they could use CRISPR-Cas9 to track and edit genes in mammalian systems. Now, however, Yeo and his colleagues at UC Berkeley have started to target RNA in live cells (RNA-targeted Cas9 or RCas9), as well as DNA in live cells.

When CRISPR-Cas9 is used for normal DNA-involved purposes, researchers design “guide” RNA to match the DNA sequence of the gene Cas9 is targeting. The “guide” RNA then directs the Cas9 enzyme to the target spot in the genome. The Cas9 enzyme then cuts the DNA, which causes the DNA to break in a manner that inactivates the gene. Researchers can also replace the section of the genome next to the cut DNA with a corrected version of the gene. In order to allow Cas9 to work for RNA as well as DNA, work originated by co-author Dr. Jennifer Doudna at UC Berkeley laid a base foundation for researchers to design the PAMmer: a short nucleic acid. The PAMmer works with the “guide” RNA to direct Cas9 to an RNA molecule, instead of DNA.

All in all, CRISPR-Cas9 is responsible for a revolution in genomics with it’s ability to target and modify human DNA. Although this breakthrough is crucial, scientists are now trying to use their lead to target and modify RNA. With an extension on already existing research, there is no doubt that scientists will soon be able to do more than just track RNA. So, let’s forget about DNA and shine a light on RNA for a little while!

Source

Harmless Mosquitoes…Yes Please

What are the most annoying things on Earth? Why, mosquitoes of course. They bite you and their bites are extremely irritating. Mosquitoes also carry life-threatening viruses, such as Malaria. However, scientists have come up with a way to get rid of mosquitoes carrying Malaria with the help of gene drives.

A gene drive is a self-generating “cut-and-paste system” that can sterilize mosquitoes. Well how do gene drives work? They operate using CRISPR/Cas9, precision molecular scissors that cut DNA. Scientists used CRISPR/Cas9 to disrupt the genes that are active in mosquito ovaries. If a female mosquito is missing one of these genes, they become sterile. Gene drives insert themselves into a target gene to assimilate every unaltered gene they pass. They break normal inheritance rules by being able to pass themselves into over 50% of an altered animal’s offspring.

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The first gene drive that was made stopped mosquitoes from transmitting Malaria. This new gene drive would eliminate Malaria-carrying mosquitoes in the future by making the females sterile, unable to reproduce. This gene drive is not 100% perfect yet, but scientists are hoping to perfect it soon to be able to release it. They hope that this gene drive will be able to control different insect populations, not only mosquitoes.

Source Article

“Selfish” DNA Defies Mendel’s Laws

R2D2 may be a heroic Star Wars character but in living animals it is a piece of DNA which violates laws of both genetic inheritance and Darwinian evolution. It has swept through mouse populations by mimicking helpful mutations when in fact it damages fertility. These new findings, described in this article by ScienceNews,  propose that even genes that are dangerous to an organism’s evolutionary chances can trick their way to the top. This is a warning for scientists looking for signs that natural selections has picked certain genes because they offer an evolutionary benefit. What looks like survival of the fittest may actually be a “cheater” prospering.

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Geneticist John Didion and colleagues examined DNA samples from wild mice from Europe and North America to determine how widespread R2d2 has become. The proportion of mice with the selfish gene more than tripled in one laboratory population from 18 percent to 62 percent within 13 generations. In another breeding population, R2d2 shot from being in 50 percent of the lab mice to 85 percent in 10 generations. By 15 generations, the selfish element reached “fixation” — all the mice in the population carried it. The rate of spread was much faster than researchers predicted—it was projected it would take 184 generations for the selfish DNA to spread to all of the mice.

R2d2 is a “selfish element,” a piece of DNA that causes itself to be inherited preferentially. It is a stretch of DNA on mouse chromosome 2 that contains multiple copies of the Cwc22 gene. When seven or more copies of that gene build up on the chromosome, R2d2 gets “selfish.” In female mice, it pushes aside the chromosome that doesn’t contain the selfish version of the gene and is preferentially placed into eggs. This violates Gregor Mendel’s laws of inheritance in which each gene or chromosome is supposed to have a fifty-fifty chance of being passed on to the next generation. But there is a cost to R2d2’s selfishness: Female mice that carry one copy of the selfish element have small litter sizes compared with mice that don’t carry the greedy DNA. The loss of fertility should cause natural selection to sift out out R2d2. But the selfish element’s greed is greater than the power of natural selection to combat it, as the lab experiments show.

But based on further lab experiments, researchers may have found that even this successful cheat can get caught. These other results revealed a relatively low proportion of wild mice carrying R2d2. Evolutionary geneticist, Matthew Dean says this could mean that some mice have developed ways to suppress the gene’s selfishness. There is still much more research to conduct on this topic.

Original Source

Additional Reading:

https://www.sciencedaily.com/releases/2016/02/160224133715.htm

 http://www.futurity.org/r2d2-gene-natural-selection-1110832/

New Research Sheds New Light on Cancer Preventing Proteins

Cells in the human body are constantly dividing. Whenever cells divide into two, the DNA within them must be copied as well. Most of the time this process works as planned, but some times the DNA can be copied incorrectly. Other factors such as UV rays and radiation can damage DNA and lead to problems like cancer. While these errors in DNA copying can cause significant mutations, they are usually corrected by certain proteins within the cell. New research at the University of Michigan is allowing scientists to get a better idea of how these proteins go about finding the damaged sites and repairing them.

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In this study, researchers at UM examined the MutS protein in bacteria. According to Lyle Simmons, associate professor of molecular, cellular, and developmental biology at UM, it has been known for a long time that the MutS protein could find and repair errors in DNA. “MutS is the first protein involved in DNA mismatch repair and is responsible for detecting rare errors that can predispose people to certain types of cancer, a hereditary condition called Lynch syndrome or cancer family syndrome. If a person’s mismatch repair system is hindered, the mutation rate increases 100-to-1,000 fold” says Simmons.  Despite knowing what these proteins do, it remained unclear as to how they perform these tasks.

To see how the protein works, researchers “fused the MutS protein to a fluorescent tag and activated fluorescence with a laser.” They then studied the protein’s actions inside of a bacterial cell. Tagging the proteins with fluorescence allowed researchers to track its movement through the cell. Scientists observed that MutS moved quickly through the nucleoid but slowed down at DNA replication sites. This indicates that the proteins look for sites of replication rather than individual mismatches. The protein then searched the new DNA being created for errors. Mismatches occur when the wrong nitrogenous bases are paired with each other. “The mismatched pair kinks the DNA at the replication fork where DNA is made. MutS positions itself at that fork so it’s ready to catch any mistakes. As an added bonus, this positioning likely tells MutS which side is correct and which side is the new, altered DNA.” says Julie Biteen, assistant professor of chemistry.

Despite the study being performed on bacteria, it is very likely that the same process occurs in human cells.  This discovery is very important because it provides information that will be essential to learning more about how the body responds to mutations.  Further advances in this area of study could possibly help researchers understand cancer better.

Original Article

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