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Back in May of 2018 researchers at the University of Oregon developed a computer program that brings us one step closer to understanding the links between genetic mutations and disease. The new software is called bpRNA and has the capability to interpret secondary structures in RNA. This allows for more precise and complete study of structure and sequencing. RNA is responsible for delivering DNA codes. Viewing noncoding RNA caring diseases caused by gene mutation are now more accessible through the invention of this tool. Ribonucleic acids are a fundamental part of life and this new invention unlocks massive potential in unlocking the key to curing or preventing gene related diseases.


https://www.sciencedaily.com/releases/2018/05/180520090916.htm

Vaping is a form of e-cigarette that has become very popular in todays world. It is better than smoking cigarettes because it does not contain tobacco which coats the mouth, throat, and lungs in tar.  Vaping however can increase the risk of mouth cancers, according to a new study, which suggests e-cigarettes lead to the buildup of chemicals known to cause harmful DNA mutations. A research study showed, after a 15 minute vaping session, they found three chemicals known to be carcinogens increased measurably in the saliva. Most of the participants showed signs of DNA damage which was caused by the chemical Acrolein that is found in vape. For this research study, they found five volunteers and looked at the cancer-causing chemicals that built up after vaping, as well as looking into the type of DNA damage they caused They found three chemicals build up in the mouth after vaping: formaldehyde, acrolein, and methylglyoxal,  all of which are known to cause DNA mutations, but there is little information on their effect in combination, Dr Balbo, a researcher said. If the cells are unable to repair the damage or if mutations build up over time, then it can cause cancer. Vaping may be better than smoking a cigarette but it still is not a healthy decision. 

https://www.independent.co.uk/news/health/vaping-ecigarette-cancer-smoking-dna-mutation-tobacco-study-a8499246.html

A Father's Mitochondria

In a recent study by Proceedings of the National Academy of Sciences of the United States of America (PNAS), recent research has concluded that the mitochondria (the powerhouse of our cells) can come from both our parents and not simply our mothers. PNAS concluded that, in multiple families, mitochondria from the father’s sperm was able to pass through children over various generations. This new information could lead to better treatment of mitochondrial disorders and even expand our knowledge over the “mitochondrial Eve”.

The mitochondria are able to power our bodies through converting sugars, fats, and proteins that we eat into molecules our cells can use to function. Knowing this, when something goes wrong the result is often grave, generating lifelong problems or even death of babies that have been affected in the womb. Every person with a mitochondrial disease is affected differently, MELAS syndrome begins in early childhood and causes seizures and dementia. Another, Kearns-Sayre syndrome, can result in problems with sight and hearing which can leave a person blind and deaf.

Mitochondria sit separately inside of cells and have their own DNA, different from the cell’s main DNA in its nucleus. They reproduce themselves and move from each generation by accompanying the egg. During fertilization, the father’s sperm transfers his DNA into an egg, however, only a few or none of the sperm’s mitochondria get in. Even if they did, the egg still has special mechanisms designed to destroy them. This new research that PNAS conducted has concluded that, in a few families, the mitochondria from the father was able to enter the egg without getting destroyed. Sometimes the DNA from the father would be more apparent as the fertilized egg grew into an embryo, even more than that of the mothers. Unfortunately, they are not sure how some father’s mitochondria were permissible in the egg yet.


Since even tiny changes can be fatal when a human’s mitochondrial DNA is altered, this can help us study distant ancestors and other people from our ethnic group (we learned this in class too!). However, all of this work has been based on the fact that the mitochondria were passed down from the female line only, and we now know it could be from either parent.


Considered the most significant implications of these findings, we could now produce better treatments because of this new understanding of how the mitochondria are passed on. It could possibly encourage properly functioning mitochondria to multiply inside a fertilized egg at the expense of broken ones as well. The downfall of all of this is how controversial it is to do any of these treatments. Since these treatments would involve influencing someone’s DNA in a way that would be inherited by further generations. However, a Chinese researcher recently gene edited two babies successfully, so maybe, depending on the outcome, this could allow testing treatment on a person’s mitochondria.


The website used - https://theconversation.com/study-shows-mitochondrial-dna-can-be-passed-through-fathers-what-does-this-mean-for-genetics-107641


LCA in People & Animals

Since she was born, Misty Lovelace struggled with progressively going blind throughout her life. When she was 12, doctors concluded that Misty’s blindness had a genetic cause called Leber Congenital Amaurosis (LCA). For those of you who didn't know, LCA is an eye disorder that mainly afflicts the retina. The retina is the specialized tissue at the back of the eye that recognizes light and color. People with this disorder typically experience severe visual impairment. Although the visual impairment tends to be stable, it could worsen very slowly over time. Fortunately, Jean Bennett and Albert Maguire, a team at the University of Pennsylvania, were testing a potential cure for LCA. The very next day after the surgery, Misty was able to see for the first time in years. After they were home, Misty was in the backyard pool, when she looked up and started to scream. Being a caring mother, she rushed out, with the thought of fear that something was hurting her daughter. Misty was finally able to see the stars.The treatment that Misty was able to undergo, first was performed on a dog named Mercery as well as mice. In Mercery's case, he was born with defective copies of RPE65, the gene affected by LCA, which is crucial for the visual cycle in mammals. This is due to the fact, that when the light hits sensitive pigments in the retina, it launches a series of reactions that make sight possible. For people who have two defective copies of RPE65 aren't able to react to light properly. As time passes, the light-sensing cells, causing the rods and cones die off. Thus creating their vision to disappear. While working with the dogs, scientists altered a small virus that’s harmless to mammals (adeno-associated virus). This virus carries the DNA with normal RPE65. Which they then inject into one eye of each blind dog. Within days, the frightened dogs who once bumped into objects around the house had turned into active, sighted animals.

Source: 

https://www.smithsonianmag.com/science-nature/new-treatment-blindness-ingenuity-180970719/

In July of 2018, 23andMe announced that GlaxoSmithKline- a large pharmaceutical corporation- purchased a $300 million stake in the genetic testing company. The pharmaceutical company hopes to collaborate with 23andMe and use their genetic data to develop new drugs. Privacy is one of the biggest concerns for consumers. Peter Pitts, president of the Center for Medicine in the Public Interest, was quoted in a TIME article stating, “This information is never 100% safe. The risk is magnified when one organization shares it with a second organization. When information moves from one place to another, there’s always a chance for it to be intercepted by unintended third parties.” Not only should the people who completed the DNA test be concerned, but blood relatives could also be identified with the right information. 23andMe commented in the article assuring consumers that data privacy is a top priority for the company and data from customers is never used for research without consent. However, some critics believe that users who allow their data to be used in research should be compensated in some way or be able to take the test for free since the company will be profiting off their data. In my opinion, customers should be told who will have access to their data and what it will be used for before they take the test. I also think it is a good idea to offer free tests for customers who are willing to allow their sample to be used in research since they will essentially be profiting off of it.

 

Source 

Ducharme, Jamie. “23andMe's GlaxoSmithKline Partership Raises Privacy Concerns.” Time, Time, 26 July 2018, time.com/5349896/23andme-glaxo-smith-kline/.

On Monday, the FDA approved a drug that targets cancer through genetics and DNA rather than the tumor. This drug is called Vitrakvi and was developed by a company named Loxo Oncology. This company's approach is to develop drugs that act on cancerous genetic mutations rather than the type of cancer/tumor the person has and Vitrakvi was the first one that the company has gotten approved. Although, this treatment does come with a big price tag. This drug costs $393,000 a year for adults. For pediatric patients the drug costs around $132,000. This whole topic interests me because this company is targeting the specific genetic mutation rather than the type of cancer. It is more specific and is a new way to approach a cancer treatment. This whole idea of research targeted on the genetic mutation started after the attention in 2013 when it was discovered that endometrial cancer was genetically similar to forms of ovarian and breast cancer. This company has said to have promising results with a 81% response rate, meaning their tumor shrank. This is only the second time the FDA approved a drug for cancer that is based on a specific mutation rather than the cancer's tumor type. 

Recently a Chinese scientist, Dr. He, allegedly created genetically altered human twins that are resistant to HIV. Dr. He managed to do this by using a CRSPR Cas-9 protein, which essentially cut out the CCR5 gene. The CCR5 gene is responsible for creating a protein that allows HIV to enter cells, so by cutting out this gene Dr. He seemingly made the twins HIV resistant.

When Dr.He and his team shared their experiment at a conference in Hong Kong, where it received a lot of criticism and backlash for a couple of reasons. The first reason being that in most places in the world using humans as test subjects in experiments is illegal, and can lead to time in prison. Another reason for the backlash is that using humans as test subjects goes against an agreed upon code of ethics in the field. A third reason for the extreme backlash is that the technology used to edit genes is nowhere near perfect, and when used can lead to a multitude of life threatening problems from birth defects to never before seen diseases. These diseases may be caused, because the protein CRSPR used could have possibly cut the wrong part of the gene sequence. The opinion of many scientists at the conference was that Dr.He recklessly endangered the lives of babies for a reason that was nowhere near good enough. 

To try and ease some of the tension Dr. He told fellow scientists that after testing cells of the newborn babies nothing harmful was found, which provides evidence that his gene editing worked correctly. Even though Dr. He is though to be ethically in the wrong, his experiment may have opened a whole new realm of possibilities in the future of gene editing. 


Source: 

“Chinese Scientist Creates Genetically Edited HIV Resistant Babies.” IAfrica.com, 27 Nov. 2018, www.iafrica.com/chinese-scientist-creates-genetically-edited-hiv-resistant-babies/.

Cancer Risk and Height

Leonard Nunney is an evolutionary biologist at the University of California, Riverside. He recently decided to start exploring the idea that cancer risk may be correlated to a person's height. He conducted four large studies that included hundreds of thousands of cancer patients. “He found that every additional 10 centimeters in height was associated with a 10% increase in cancer risk” (Pultarova). This study was published October 24, in the Proceedings of the Royal Society Journal. His research did not necessarily prove that being tall increases your risk of cancer, but rather, the two factors might be associated. In an interview with LiveScience, Nunny stated that these findings could have a very simple explanation- “Taller people have more cells in their bodies” (Pultarova). Cancer is often a result of mutations in a single cell’s DNA that occurs when the cell divides. Ultimately, Nunney concluded that “The more cells, the higher rates of mutations and the higher odds that one of these mutations will lead to cancer” (Pultarova). The study focused on 23 different types of cancer and found that 14 of the illnesses can be traced back to a person’s height. There are many other influences and genetic factors that are correlated with cancer, however, it is interesting to think that height might be one of them. 


Source: 
Pultarova, Tereza. “Cancer Risk May Increase with Height for a Simple Reason.” LiveScience, Purch, 1 Nov. 2018, www.livescience.com/63990-cancer-risk-height.html.

According to a study done at NASA's national jet propulsion laboratory, bacteria found on the International Space Station (ISS) have been found to be resistant to multiple antibiotics tested against them. Inevitably, where there are humans, there are bacteria, even up in space. Continuing research done prior, scientists at the NASA lab identified a strain of Enterobacter bugandensis, that was resistant to all nine antibiotics tested against them. The scientists compared the genetics of the ISS strains to three strains of E. bugandensis collected back on Earth that were found to be pathogenic. The ISS strains were similar in many ways to strains found on Earth, including genes associated with antimicrobial resistance and potential virulence . Based on the genetic findings, it is estimated that the ISS strains were around 79 percent likely to be pathogenic and cause disease. Although the astronauts have not been sickened because of the bacteria, the news will certainly impact the planning of future missions. E. Bugandensis is a common bacteria that can cause disease on people with weakened immune systems and can even cause sepsis. Given the limited medical support on the ISS, this is something else to take into consideration.

I find the genetic connections to this case very interesting. How exactly do the strains differ genetically? How does space play a factor in the genetics? How will this effect future planning? Bacteria in space have been know to exist, especially coming from humans on the ISS. Even with no known diseases caused as of yet, the emergence of antibiotic resistance would make the treatment of any bacterial infections caught much more difficult. If an astronaut would get sepsis, they would need to be sent back to Earth, but that would be a very dangerous option. More investigation is definitely needed to look into the danger posed. But another interesting though posed earlier is how these strains compare to those on Earth. I wonder which astronauts brought the specific strains up, and what their history of antibiotic use is. Additionally, what is the capability to treat an infection in house on the ISS, and has antibiotic use their contributed to the problem. Certainly isolation from Earth for some time would limit the amount of antibiotic exposure they had, but there has been interesting research in the last few years on evolutionary pressures creating resistance in bacteria. Would space have an effect on this?



Source: https://gizmodo.com/nasa-scientists-find-possibly-infectious-superbugs-on-b-1830664400

In the 1970's scientists discovered that certain cells can shuffle and edit DNA which is known as somatic recombination. Some of these cells include immune cells and B cells. Scientists have also seen hints that it could also be occuring in our brains in neurons. Neurons can differ dramatically from one another with some having more DNA than neighboring cells. Neuroscientist Jerold Chun and his colleagues aim to find definite evidence of somatic recombination in the brain. They conducted research on donated brains of healthy elderly people and patients who had non-inherited Alzheimer's disease. They tested to see if the cells had different versions of the gene for the amyloid precursor protein (APP), the source of the plaques in brains of those with Alzheimer's. They wanted to do it on APP because other studies have shown that neurons of patients with Alzheimer's can have extra copies of the gene which could possibly come from somatic recombination. The researchers were able to identify that neurons seem to carry thousands of APP gene variants. From the study they also discovered that neurons from the Alzheimer patients had about six times as many varieties of the APP gene as did the cells from the healthy people. His team thinks that reshuffling depends on an enzyme called reverse transcriptase that makes DNA copies from RNA molecules. They believe that a new variant could arise when the enzyme duplicates the APP gene and slips it back into the genome. This can create a sloppy copy that may not match the original and code for a different variant of APP. If more studies occur that confirm what they think then we can block the enzyme like treatment for HIV and work against Alzheimer's disease. 

http://www.sciencemag.org/news/2018/11/landmark-study-shows-brain-cells-revamp-their-dna-make-new-proteins-perhaps-sparking

The first human genome sequence was published in 2001. The reference genome has since had constant additions to it so that it can better represent the range of variations between us humans. The current version is called GRCh38. A group of researchers, led by Rachel Sherman, set out to create a pan-genome for Africa. Of the tested DNA they discovered some sections, longer than 1,000 base pairs, did not match the reference, GRCh38. They found nearly 300 million base pairs or about 10% of the reference genome. The big problem with this new information is that it can have medical consequences. Since the reference genome doesn't adequately represent certain populations, when looking for genome variations linked to conditions you are going to want a reference that's more representative of the tested DNA. By creating a pan-African genome they plan to help with this problem. 

https://arstechnica.com/science/2018/11/our-human-reference-genome-is-missing-a-lot-of-material/

Long life spans tend to run in families, its believed to be attributed through genes. But now, a large new study of data from the genealogy website Ancestry reveals that genetics may play less of a role in life span than previously thought. Previous studies failed to take into account a pattern of human relationships: that people tend select romantic partners with similar traits to their own. The findings mean that previous studies may have overestimated the heritability of life span, the researchers said.researchers analyzed information from more than 400 million people using publicly available family trees from Ancestry. Because the researchers needed to know the life span of these individuals, the study looked at only those who were born in the 1800s or early 1900s and were deceased. With the data they found that it doesn't have to do with family history or similar living environments, they looked at assortative mating. The large data set allowed researchers to examine the effect of what's called assortative mating, the phenomenon in which people tend to select spouses who are similar to themselves. If assortative mating was what they did, it would mean that factors that are important for life span tend to be similar among spouses. So, spouses tend to have the same life span because they picked a spouse that was like them. 

Recently, California has been plagued with intense wildfires that have taken more than forty lives. Officials are now using advanced DNA technology in order to identify victims of the wildfires. The new technology medical examiners are using is called Rapid DNA which “is a term for portable devices that can identify someone's genetic material in hours, rather than days or weeks and more extensive equipment it can take to test samples in labs.” This technology makes it easier to identify the deceased, and takes significantly less time. In order to use the machine DNA from when the person was alive is needed as well as viable remains, which are sometimes not found in cases of burning. Due to the rarity of having DNA tests, sometimes it is often easier for officials to use medical records such as dental x-rays or history of bone fractures to identify the deceased.


https://www.14news.com/2018/11/14/identifying-wildfire-dead-dna-likely-older-methods-too/


Scientists are using DNA from a 9,000 year old mummy found in Alaska along with the DNA of ancient Brazilians in order to theorize how humans migrated from Asia down to South America. Researchers have found that migration occurred from North America to South America in three major waves. By using DNA analysis, researchers have been able to find similarities in human remains found in North and South America. After finding similarities, scientists are able to see which groups from North America populated South America due to their similar genetics. This study is important because it shows that there were many levels of genetic diversity in the Americas, due to the different waves of migration. Analyzing ancient DNA discovered in  10,000 year old remains that Amazonians and indigenous Australians share DNA. Finding Australian DNA has raised many questions about how people crossed from Australia over the Pacific to reach the Americas. It is theorized that the ancestors of the two groups once lived in Asia and migrated to Australia and North America separately.


https://www.sciencenews.org/article/ancient-dna-fossils-south-america-populated

Many people have a great fear of loosing hair, for some this fear becomes a reality a soon as childhood.  This is called hypotrichinosis complex.  Those who have hyporichinosis complex will have hair as in infant, but their hair will begin to thin out early into childhood.  Researchers have known that this is a hereditary trait, but they have now discovered the gene responsible for this type of hair loss.  Those at the University Hospital of Bonn in Germany discovered that mutations is the LSS gene drive this defect.  Lanosterol Synthase (LSS) is a gene that impacts the metabolic pathway to the health of hair follicles.   

Image result for hair genetics

Researchers evaluated the DNA of three different families with no relation, of all the members eight of them experienced hair loss.  All eight of those members had mutations in the LSS gene.  Researchers continued their study from there.  They collected and analyzed tissue samples from those with and without the mutation in the LSS gene in attempt to find out exactly where the lanosterol sythase is located in the hair follicle.  They found that in the normal LSS gene enzymes of LSS where found in the endoplasmic reticulum.  Those with the mutation in the LSS gene where found to have the enzyme spread outside of the endoplasmic reticulum and into the cytosol.  This still doesn't fully explain why the hair falls out, but researchers have a theory.  

They believe that the leakage of the LSS into the cytosol confuses the follicle and cause it to get rid of the hair.  Although they don't fully understand the hair loss, this discovery broadens the picture behind the cause of this disease.  There is still a while until they find a cure for this hair loss, but thankfully there is no other effect besides hair loss. 




Cohut, Maria. “New Genetic Culprit Found for Early Progressive Hair Loss.” Medical News Today, MediLexicon International, 10 Nov. 2018, www.medicalnewstoday.com/articles/323635.php.