CRISPR - Gene Editing Tool

CRISPR, it sounds like an app, but it really stands for "clusters of regularly interspaced short palindromic repeats." It is the worlds most advanced gene editing tool, which means it can alter DNA sequences and change DNA function in any cell. As we have discussed this semester a lot of the different diseases and disorders that occur when a DNA sequence is changed via a mutation I have been curious to better understand what possibilities we as humans have at either fixing these mutations or creating one of our own that would be beneficial. 

CRISPR acts as a pair of "molecular scissors" and was first tested by Rodolphe Barrangou and other researchers at Danisco, the food company, in 2007. They tested Streptococcus Thermophilus, a bacteria usually found in yogurt to see if the CRISPR segments of DNA were able to have an effect on the immunity of the bacteria against certain viruses. What they found is that once the CRIPSR region was genetically modified, the bacteria in the yogurt was able to fight off the viral strain much better than it previously had. This gave them the first clue of the potential that the CRISPR region might hold. CRISPR is used with Cas9, which is a protein that acts as an enzyme that allows DNA to be cut and new DNA replaced. When the CRIPSR was used, the bacteria was able to remember the DNA of the virus that had attacked it, which enabled them to fight off future attacks easier. 

CRISPR further works as a gene editing tool by cutting a part of the DNA, and tricking the DNA repair mechanisms to replace the DNA in a different order. In 2012 Robert Winthrop, a Professor at Harvard Medical School, discovered that this ability to cut DNA could be directed to any piece of DNA using a guide RNA. Similar to transcription, a corresponding RNA sequence could be sent in to match the DNA sequence desired to cut. Once that material was cut by the Cas9, scientists can introduce a new DNA sequence that will allow the section that was cut to be reorganized into whatever sequence is desired. 

Obviously the implications of this process are huge, and also ethically challenging. In 2013 the first attempts to apply this process to human cells were tested, and they found the technology could be effective at preventing certain diseases such as cystic fibrosis, cataracts, and fanconi anemia. It has also been applied to increase crop yield, make farming plants more resistant to disease, etc. At this time however, all reports have come back that CRISPR is only 50% effective at replacing the desired DNA. Before it could be applied to much larger and bigger respects such as an adult human cell, it must be much more accurate. Another possible side effect is if a negative mutation occurred in an adult human cell that was undesirable, the trait or defect could potentially be transferred onto offspring. 

Ultimately there are many different possibilities and issues, but the implications are huge and could effect potentially millions of lives for the better. 

Vidyasagar, Aparna. “What is CRIPSR?” Live Science, Apr. 2017. https://www.livescience.com/58790-crispr-explained.html. Accessed 16 November 2017

    Ebola has always been a disease that I have found scary and intimidating.  The lack of a cure or a way to stop the tremendous death that this disease causes is a high priority in the research world. The largest outbreak of Ebola happened in 2014-2015 in Western Africa.  This outbreak caused more than 11,000 deaths and infected nearly 29,000 people.   In an article published in Science magazine tells us how a team of scientists from Albert Einstein College of Medicine, U. S. Army Medical Research Institute of Infections Diseases(USAMRID), and the Scripps Research Institute, were able to target a hidden Achilles heel shared by all known types of the Ebola virus. 

      Monoclonal antibodies which bind to and neutralize specific pathogens and toxins,  have emerged through research as the most promising treatments for Ebola patients.  In the past there is usually only one specific virus that the antibodies are able to fight against.  The most successful of the experimental therapies, ZMapp-TM,  a cocktail of three monoclonal antibodies for example is specific for Ebola virus Zaire but does not work for Ebola Sudan and Bundibugyo.  

   As researchers discovered the problem with the monoclonal antibodies could potentially cause issues because the Ebola virus hides deep inside the cell in the lysosomes which make them invisible to the immune system and they are shielded from the conventional way that antibodies work.  A couple of the lead scientists came up with the Trojan Horse plan in order to beat the "invisibility cloak", that Ebola has.  The scientists tricked the Ebola virus into carrying the way that they can be destroyed into the host cells.  

    Once inside the cell the scientists had developed two monoclonal antibodies into one molecule.  One of the molecules was designed to neutralize NPC1 protein in and the other was made to target NPC1 protein and destroy it.  After the antibodies went into the lysosome specific antibodies were released into the cell and in studies the dual antibiotic approach showed tremendous promise in that they were able to neutralize all five forms of the virus.  The Trojan Horse approach was then tested in mice, the results were not as good, but the protein structure in mice is different than that of human and the scientists will next test the antibodies in primates and hope that the results will lead to an antibiotic to save thousands of people from the deadly Ebola virus.  

    I am very grateful for the progress that is happening on the Ebola virus front.  I am anxious to find out how the further studies for this project have turned out and when the next outbreak of Ebola occurs that this will be ready and will surprise Ebola.  It is due to have a time out.  

Nanoparticles Can Limit Inflammation By Distracting the Immune System

      Researchers at the University of Michigan have recently found that nanoparticles may be able to significantly reduce inflammation by cutting off the process at its source. The researchers originally intended to use plastic nanoparticles to deliver drugs to blood vessel walls. However, they found that neutrophils were removing the nanoparticles and taking them to the liver instead of allowing them to adhere to blood vessel walls. Neutrophils are first-responder white blood cells that induce acute inflammation at the site of an injury. Low neutrophil counts are dangerous due to lowering of the immune response. However, overreaction of neutrophils can be incredibly dangerous as well; inflammation is a key cause or symptom of a multitude of diseases and lethal reactions. The neutrophils were effectively diverted from causing inflammation at the site of injury by prioritizing removal of the plastic nanoparticles. While this is an important discovery, the researchers are continuing to study nanoparticles as drug carriers. The interaction with neutrophils may be evaded by using nonfouling (protein-resistant) materials in tandem with targeting chemicals as a coating for the nanoparticles.

     This finding has potential ramifications for the fates of many diseases that are caused or exacerbated by inflammation, such as depression, Alzheimer’s, asthma, sepsis, and immune overreactions to injuries. If inflammation is caught early enough, a curative injection of nanoparticles could disrupt the progression of the disease. This treatment could be particularly useful in reducing the lethality of sepsis. Sepsis is caused by heavy, body-wide inflammation in response to infection. This treatment could be particularly useful in reducing the lethality of sepsis; it is a common cause of death among hospitalized patients. Hospitals could maintain a supply of these nanoparticles and start an IV at the first sign of sepsis. Not only would this reduce the death rate, it would also reduce malpractice lawsuits. I find this useful on a personal level due to a propensity toward major depressive episodes. SSRIs and SNRIs have a long adjustment period that does not diminish symptoms of depression while producing uncomfortable side effects. This leads to prolonged reduced function in multiple areas of life. The resulting effects on productivity, social life, sleep, and diet tend to deepen depression before it can be affected by antidepressants. I would be willing to try an injection of nanoparticles at the onset of a depressive episode in hopes that it could circumvent the disruption of my life by depression.

Source: http://ns.umich.edu/new/multimedia/videos/25244-nanoparticles-can-limit-inflammation-by-distracting-the-immune-system

More tomatoes and faster. You might think, "hey that is awesome I love BLT's!" Or maybe you thought "Oh great... The world does not need more tomatoes." Well if you were excited don't worry there are still plenty of tomatoes to go around, but this discovery is not for eating. And for you doubters and tomato unlovers, you are in luck this is a study that helps scientists research and not have to wait for a long time while their tomatoes grow. They can produce them faster and in a larger quantity all because of a recent study.

Scientists have found a way to cut the growth time of tomatoes plants and make it six weeks faster to modify their genes. This means scientists can use the ideal tomato plant and make it even more efficient in doing research. The process involves injecting DNA into the tomato genome and grows a new plant. It may seem like a small feet, but really it is a breakthrough in making it possible to perform experiments on mass amounts of plants. If this experiment can transfer to other plants that have specific characteristics that make them ideal for experiments with specific gene questions.

Tomatoes are currently being used as models of how to perform and repeat these experiments. Then the experiments will move to other plants and then the studies will grow and spread to varied tests to see the results with all plants.

Its time to get excited about tomatoes! The future is bright as science continues to Progress and expand.

EG

You Can Live Longer and Healthier with Intermittent Fasting

Everybody would like to be healthy and live a longer. Some people would also want to lose weight and experience powerful body vigor and brain development. Intermittent fasting offers eating patterns that efficiently helps a person to achieve the earlier mentioned goals. Intermittent fasting includes the aspects of regular multiday fasts, skipping meals for a particular decided time of the day to promote health benefits through calorie restriction. However, this does not mean that a person is denied a chance to feast, but periodically sets an eating plan that objectively helps attain the desired intermittent fasting goal. Skipping a meal, a day for another; like rodents’ experiment for the ones that took less food, helps your body to consume fewer calories and therefore, it might help you live a longer and healthier life (Stipp, n.p).

The First Fasts

The implication for fasting in religion is attributed to the health of the soul whereas; the bodily benefits are lesser recognized until doctors recognized it in the early 20th century. However, the fasting of this level is beneficial to both the soul and the body as it helps fight diet or eating related diseases like obesity and epilepsy.

According to the colonel University Nutritionist’s’ researchers of the 1930s, exposure to stringent daily dieting from an early age are in a position to live longer and prevent some diseases such as diabetes, obesity, and cancer. In contrast, research on periodic fasting and restriction of calories, by the University of Chicago in the year 1945 showed that alternating feeding for a day helped in extending the span of human life, although the research was carried on the rodents; rats (Stipp, n.p).

Intermittent fasting has also been seen to slow the aging process through the control of antiaging diets. These diets have been proved to produce antibiotics and develop coronary artery bypass surgery that makes one look young always. Intermittent fasting counters the risks of degenerative brain diseases, stroke damage, and stress. Since the study used rodents as the specimen, Matson and colleagues prove that intermittent fasting suppressed motor deficits in the model of Parkinson’s disease in a mouse and that it slows the cognitive decline and affirms the observation with a personal experience after skipping meals and being more productive.

Another thing that a researcher; Matson, talks about is that intermittent fasting acts to trifle stress that accelerates defense of cellular elements against molecular damage.  The defense is as a result of leveled “chaperone proteins,” which hinders the assembly of other molecules in the body, thus resulting to the prevention of neurological disorders and increasing the responsiveness to the insulin that helps in regulating the blood sugars hence preventing diabetes and the heart illness or failure.

On Thin Ground

Intermittent fasting is beneficial to human health, to some levels it is discouraged as it can lead to some undesirable conditions such as an increase in blood glucose and sometimes, increasing the tissue levels of oxidizing compounds that can lead to damage of the cells and result to more complications.

Sometimes, intermittent fasting can result in undesirable weight loss. There is attributed dangers of compensatory gorging that can lead to a reduced lifespan of the primates. The damage of the cells calls for caution when altering the way people get their meals. However, Intermittent fasting is a smartening way to live if it is handled with caution. Fasting should be identified from starvation and malnutrition for it to be effective.

Stipp. D. How Intermittent Fasting Might Help You Live a Longer and Healthier Life, 2013, (n.p). Article, Retrieved from: https://www.scientificamerican.com/article/how-intermittent-fasting-might-help-you-live-longer-healthier-life/

To understand the origins of pain, ask a flatworm

It's always interesting to remember that, scientifically-speaking, we all came from a single celled organism, which eventually evolved into all life as we know it. Along the way, we picked up some interesting characteristics from our different ancestors of life. We got meiosis from eukaryotic organisms, bones from fish, and--per the title of this post--pain detectors from flatworms. Pain, while it isn't most amazing feeling, is very important for survival.

Now, it may not seem particularly vital to know where these biological processes have derived from, but according to biologist Paul Garrity of Brandeis University in Walton, Massachusetts, it’s actually really helpful. Getting a big picture view of how the systems are built gives us a clue on how pain detection might have originated millions of years ago [Sanders].

The study results feature a protein, TRPA1, a pain detector located on the outside of human cells and the cells of many other animal species. It helps many different animal species detect and escape anything that might harm them, including dangerous chemicals, bodily injuries, and harsh temperatures. What’s interesting about TRPA1 is that its triggers vary among different animals. In some animals, the protein is activated by cold, but in others, it’s activated by heat.

The experiment conducted used heat as a trigger for the flatworms. There were two groups, one group with the TRPA1 protein and the other without. The flat worms with the protein avoided the heat, but the ones without the protein didn’t care. The study concluded that TRPA1 is involved in flatworms responses to danger—at least by heat.

Although pain may be unpleasant in the moment, it signals to our bodies that danger is imminent and ultimately protects us from harm. Without pain, we wouldn't know when to stop or when we were pushing our bodies to their limits. For example, if we didn't feel pain, there would be nothing to stop us from sticking our hands in boiling water, damaging our cells and hindering our usage of those nerves and muscles.

While the development of sexual reproduction in eukaryotic cells is just a tad more exciting than the development of pain receptors in flatworms, all of these evolutionary processes make it possible for us to experience the life the way we do today. Without them, we would be nothing more than a single cell.


Reference article:

To understand the origins of pain, ask a flatworm. Laura Sanders. https://www.sciencenews.org/article/understand-origins-pain-ask-flatworm.

Circadian Rhythm Disruptions Before Contraception May Have Transgenerational Impacts

Circadian Rhythm Disruptions Before Contraception May Have Transgenerational Impacts

On a trip to Capitol Reef National Park, I noticed, for one of the only times in my life, I could clearly see the Milky Way. The night was so dark I couldn’t see anything around me. Capitol Reef National Park received an International Dark Sky Designation from the International Dark Sky Association, the leading organization advocating action light pollution worldwide. Capitol Reef is one of the rare remaining places in the continental United States with natural darkness. To maintain a dark sky the National Park enforces strict policy on lights. The Park requires a cover for any light at night to keep the light waves going down toward the ground for their intended purpose and not toward the sky. I only slept for a few hours, but I woke up feeling more rested than I had in months. After digging into the differences unnatural night time light causes, I concluded that light pollution is a highly underrated issue.

Modern society adopted artificial light without regard to environment or human health. Nighttime illumination has spread globally and touches nearly every ecosystem on the planet, through countless items used by people every night. Even dim light at night is associated with a variety of psychological and physiological issues that disrupt circadian rhythms in mammals. The circadian rhythm has been shown to affect mate selectivity, immune system, and alter hormonal function. The benefits of using technology during the night, without restrictions, currently seem to outweigh the risks. Many people produce nighttime illumination through cell phones, televisions, night-lights, and even the light emanating from an alarm clock. This common assumption may be wrong. This study shows the potential implication that through light pollution and nighttime light, future generations may continuously become less ffective at fighting infections.

Ohio State Neuroscience graduate student, Yasmine Cisse, published Parental Exposure to Dim Light at Night Prior to Mating Alters Offspring Adaptive Immunity. The study used Siberian hamsters to test the hypothesis that “dLAN (dim light at night) has transgenerational influences on immune function,” (Cisse). The F1 generation of adult hamsters were only exposed to dark night and light days. Their parental generation was also only exposed to dark nights and light days. The F1 generation was selectively mated with only the female exposed to dLAN, only the male exposed to dLAN, both or neither exposed. All dLAN exposed rodents were subject to dLAN conditions, for nine week, before mating. Gestation (when the embryo or fetus is carried in the uterus in viviparous females) and offspring rearing were in dark night and light day environments.

Figure 1: visual representation of the mating method researchers used.
From: Parental Exposure to Dim Light at Night Prior to Mating Alters Offspring Adaptive Immunity

Researches evaluated immune function in several ways to determine how the exposure affected the offspring. They evaluated splenic methylation. Methylation is the process by which methyl groups are added to a DNA molecule. The addition of a methyl group can alter the activity of a DNA segment without changing the actual sequence of the DNA, which is called an epigenetic change. This can change the organism’s phenotype without changing the actual DNA sequence and can be passed to daughter cells. Methylation helps the body’s enzymes work more efficiency. An increase or decrease in methylation can be bad or good. This study aims to support or refute the hypothesis that certain epigenetic impacts related to methylation can also be passed onto daughter cells in sexual reproduction; and ultimately be passed onto the hamster’s children.

The first way the study tests transgenerational impact is Delayed Type Hypersensitivity (DTH). DTH is an “antigen specific T-cell mediated immune response.” (Cisse). It is considered an index of effector T cell function. The hamsters are subjected to the antigen that causes inflammation, from monocytes and lymphocytes, penetrating the skin to fight the agent. The amount of swelling serves as an indicator on how intense the immune system response was. All test groups displayed swelling. In maternal F1 dLAN exposure, male F2 offspring displayed less swelling (p<.05), and in F1 paternal and maternal dLAN exposure, female offspring displayed significantly less swelling (p<.05) too. This data supports reduced immune system response.

Figure 2 shows most swelling in offspring where both parents had dark nights and least swelling for offspring of two dLAN exposed parents. 

From: Parental Exposure to Dim Light at Night Prior to Mating Alters Offspring Adaptive Immunity

Researchers used Splenic Melatonin (MT1) to evaluate endocrine function. Melatonin is a hormone produced by various tissues in the body. It is released continuously at different levels to regulate sleep. “Melatonin is immediately diminished by exposure to light at night in both humans and rodents... The majority of immune cells and organs express melatonin receptors.” (Cisse). In the absence of light, melatonin is secreted. Peak melatonin levels should be secreted during the night and low levels during the day. Clear circadian rhythms regulate melatonin levels. “Melatonin is a potent immunomodulator and enhances immune responses by stimulating bone marrow proliferation, antigen presentation, and release of certain cytokines” (Cisse). Cytokines are small proteins that have an important cell signaling function and impact the behavior of cells around them. Their presence signals cells like white blood cells to come and help the body during times of infection. “Melatonin increases MT1 activity in the thymus and the spleen and enhances DTH response in Syrian hamsters.” (Cisse) Circadian rhythm plays a major role in both the immune system and endocrine system. The study found that paternal F1 dLAN produced F2 offspring with decreased melatonin in the spleen. When both parents were exposed there was also a decreased splenic methylation. MT1 was decreased significantly more in male offspring than in female offspring.  Researchers hypothesized that histone modification may play a role in offspring’s phenotype. They also suggesting sex played a role on the phenotypic inheritance. Offspring produced less than usual MT1 expressions when only the mothers were exposed to dLAN, in comparison to those who only had a father parent exposed. This might be because females have two copies of the X chromosome where many X-linked immune genes are while male offspring only have one copy allowing the females to express the altered phenotype in a less severe way than males.

The difference in effects between male and female offspring may be because of the X-chromosome contains more immune system-related genes than the Y chromosome (Bianchi). While a female mammal contains two copies of the X chromosome their male counterpart only contains one. A female receives twice the dosage of these immune system-related genes. After fertilization the cells undergoes a process where one of the two X chromosome genes is turned off, in a female called X-inactivation. The one inactivated chromosome is silenced. Every daughter cell produced from mitosis replicates the same one active and one inactivated gene as the parent cell. This occurs in the embryo’s early stages of development, and the few cells present don’t have to turn off the same gene. X-inactivation is random for each cell. While some female cells will have certain immune system genes silenced, those same genes may be expressed in other cells. Males who only have one copy of the X-chromosome are limited to that one X-chromosome’s immune genes in all of their cells. This unequal effect may also have a negative impact on a fitness and mating selection, in a species, in addition to a reduced immune system.

The data from this study supports that exposure to light at night; prior to conception does alter the offspring’s inherited immune system expression epigenetically. The effects of a completely normal part of modern life are very shocking. While some effects are only seen in the exposed generation such as increased body mass, others can be passed on. If light pollution or nighttime artificial light use can continue without any regard, generations will potentially become increasingly vulnerable to diseases and prone to conditions. Like with other, more publicized forms of pollution, light pollution should be considered serious. Simple lifestyle changes at home like turning off cell phones, televisions, and blacking out windows during night hours should be encouraged. Those changes in homes and in cities is for future generations as well as the present one.

Reference Study:

Cissé, Y. M. et al. Parental Exposure to Dim Light at Night Prior to Mating Alters Offspring Adaptive Immunity. Sci. Rep. 7, 45497; doi: 10.1038/srep45497 (2017).

Other references:

Brianchi, I, et al. The X chromosome and immune associated genes. Journal of Immunity, May 201, doi:10.1016/j.jaut.2011.11.012.

Morris, J., Hartl, D. L., & Knoll, A. H. (2016). Biology: how life works. New York, NY: Macmillian Education.