After two decades the human genome is finally finished

GMO Babies

Subject: Human Gene Editing 

Article: ¨Strict new guidelines lay out a path to heritable human gene editing¨

    Scientists have already made gene editing possible, but then in 2018 Chinese scientist Jiankui He had announced he had created two genetically edited babies. Opening the doors to the possibility that the human genome could be edited. However scientists face the issue of having law preventing clinical trials as it's not something that is currently desired by society. If it were, countries would have to meet guidelines and would have to agree to being overseen internationally. Gene editing allows a DNA letter or base to be changed. Genome editing has allowed scientists to investigate inheritable human diseases and could even change physical traits but generally its useful in gene therapy. It is currently undergoing trials to possibly gene edit sickle cell anemia which is a mutation of the blood cell.  

    How gene editing works is by using tools like CRISPR/Cas9 and engineered proteins called TALENs to locate the precise base or area where the change or edit will occur. So far gene editing has been successful in trials with animals such as mice, but when it comes to a human embryo there is still uncertainty. Changing the DNA during the embryonic state or prior to that would allow for such changes to be inheritably passed down. Commissions are arguing that to prevent the craze for a fashionable baby otherwise known as the ¨designer baby¨ which would have desirable tightening of intellect, athleticism etc, it should be considered to help couples produce an offspring without disease causing variants. Things that are being considered is how serious are the illnesses, and what are the chances of producing offspring with the genetically inherited mutation. Until then more research is needed to determine if stem cells could produce egg and sperm dishes in labs that would result in embryos with non carrying diseases. As well as international commissions overseeing clinical tests and technological engineering that could make this possible.

Article Link: https://www.sciencenews.org/article/human-germline-gene-editing-crispr-strict-new-guidelines 

Supporting Link(s): https://www.genome.gov/about-genomics/policy-issues/what-is-Genome-Editing 

https://www.jax.org/personalized-medicine/precision-medicine-and-you/what-is-crispr 

Main Source: https://www.sciencenews.org/topic/genetics

The First Confirmed Hominin Hybrid Has Been Discovered

Denisova 11, as she is called, was an approximately 13-year-old girl who lived around 90,000 years ago in the Altai Mountains of Siberia. What is so fascinating about this girl is that she is clear evidence for interbreeding between species in the genus Homo (humans). She is indeed about half Denisovan and half Neandertal, two early members of the genus that are related to Homo sapiens.

Viviane Slon, a researcher at the Max Planck Institute in Leipzig, Germany, performed DNA analysis six times on Denisova 11's piece of limb bone that had been found. She simply could not believe the results of the analysis the first time and had thought she made a mistake. However, each successive test came to the same conclusion. This young girl had a Neandertal mother and a Denisovan father. Moreover, they discovered that her father in fact had a Neandertal ancestor of his own. This was further confirmation of how common hybridization must have been in early hominins.

So far, only Denisova 11 and four other individuals belonging to the species Homo denisova have been uncovered by the bone fragments that they left behind in a single cave in the Altai Mountain range. As I have previously reported, the species was first identified in 2010, when DNA sequencing of the toe bone of an individual called Denisova 3 led scientists to confirm the existence of an entirely new group of humans.

Svante Pääbo, the director of the Max Planck Institute of Evolutionary Anthropology, has stated that due to the fact that Neandertals originated in western Eurasia and that Denisovans originated in the east, they likely did not meet very often. But based on these latest findings, Pääbo and many other scientists now believe that when the two species did come face to face, mating between them was far more common than was ever previously thought.

The idea that Denisovans, Neandertals, and Homo sapiens were producing hybrids for possibly hundreds of thousands of years is supported by genetic studies of modern populations. The DNA of people living in Europe and Asia today is on average 2% Neandertal. The DNA of people living in Melanesia today is on average 5% Denisovan, with other varying amounts found in the rest of southeast Asia and Oceania.

The genomes of all these humans studied, ancient and modern, reveal that hybrids were not uncommon throughout our shared history on this planet.

Scientists Find the First Confirmed Denisovan Skull Fragment

Denisova Cave, Altai Mtns., Siberia

Within a cave in the Altai Mountains of Siberia, a piece of a skull that made up the back of a parietal bone was discovered. Using DNA analysis techniques, researchers have confirmed that this bone fragment is in fact part of an individual who belong to the species Homo denisova. These archaic humans are more casually called Denisovans, and they are closely related to Neandertals (Homo neanderthalensis) - the both which are somewhat less closely related to our species, Homo sapiens. This bone fragment belongs to only one of five separate Denisovan individuals that have been discovered yet, all within the same cave in Siberia.

While its DNA has been confidently identified, the true age is unknown because it is too old to radiocarbon date. Additionally, this fragment is quite small and too incomplete, and so it cannot be used to determine whether other hominin skeleton fragments found are Denisovan or not. The only way these can also be identified is through DNA analysis, which is often difficult to do on samples so ancient.

With the sequencing of both the Neandertal and the Denisovan genomes, in 2010 paleogeneticist Svante Pääbo and his team were about to make an astounding discovery about modern people across the globe when they compared their DNA to these archaic humans. They found that 2.5% of the DNA of modern Europeans and Asians has been inherited from Neandertals, and that around an additional 5% of the DNA of modern Melanesians has been inherited from Denisovans. This was clear evidence that our ancestors had socialized and interbred with other species of humans living at the same time in prehistory.

Today, anthropologists and geneticists are still waiting to find a more complete portion of a Denisovan skeleton. The hominin’s genome has much to say about who it was but seeing a complete skeleton will allow the world to visualize them. This can provide many other clues to how they lived and acclimated to their world. For now, they will have to continue to rely on the few Denisovan skeletal fragments unearthed in Siberia.

Three Distinct Denisovan Lineages Have Been Revealed

Map of four different species of the genus Homo, "Humans"

A new study has proven that the hominins discovered in 2010 that we have been referring to as Denisovans have much greater genetic diversity than scientists previously thought, constituting three separate lineages. One of these groups is so different from the other two, it could be considered a new species entirely.

An international team of researchers has analyzed the genomes of 161 modern humans from islands across Southeast Asia and New Guinea and have concluded that they have DNA that has been inherited from independent and diverse populations of Denisovans. It was in 2018 that it was first uncovered that more than one lineage existed. Now we know that the family tree of Homo denisova is increasingly complex.

Drawing on modern people’s DNA, the scientists realized that these hominins interbred with their Homo sapiens cousins in two different waves. The two interbreeding events have created distinct genetic patterns that can still be identified in the people of Oceania and East Asia today.

The specimens that were found in a cave in Siberia’s Altai Mountains are the only Denisovan skeletal fragments known to science. The lineage of these individuals is being called D0, while the other two are D1 and D2. The group that is closely related to the Altai line has DNA that is found in modern East Asians. The other group – more recently discovered – is very divergent from the Altai line and its DNA is found across modern Oceania and much of Asia. In fact, it is as genetically dissimilar to the Altai Denisovans as it is to Neandertals.

Thus, many scientists are calling for this group to be given their own name, as they may truly comprise a separate species from Homo denisova. Moreover, based on their analysis, the researchers propose that interbreeding between Homo sapiens and Homo denisova took place as recently as 15,000 years ago. If this date is accurate, the implications are shocking. This would mean that Denisovans are the last hominin species related to modern humans known to have died out.

Why Your DNA is Still Uncharted Territory

Researchers at Northwestern University, a data scientist, Luís A. Nunes Amaral in particular, have recently reported that in all of the 20,000 genes in the human genome, about 5,400 of those have yet to be studied in a scientific paper. There are about 2,000 genes that have been the bulk of the research done in the last few decades. Scientists do not want to undertake those genes that no one has began to study because it is far too risky. The astronomical amount of time needed to study these unknown genes is simply too long.
A gene may be discovered in multiple ways: the protein it encodes for is discovered or a strand of DNA with "distinctive sequences shared by all genes" is found in that particular gene. The field of genetics has drastically changed over the past decade, including a "detailed map of the human genome" and technology with power to sequence DNA. Dr. Amaral and his team decided to examine the scientific papers published up to 2015 and recognized the "wildly lopsided" knowledge of human genes. It was thought that particularly important genes, such as those for cancer and other diseases would be more readily studied but that not in fact the case. Dr. Amaral recalled: "There are lots of genes that are important for cancer, but only a small subset of them are being studied." The reason for such variation in the research on certain genes versus others has to availability and access to proteins secreted by the gene (if applicable), if that same gene is studied in animals as well, and if that gene has been studied for an extended period of time. For example, 16 percent of the genes found before 1991 are the genes used for research in the scientific papers analyzed by Dr. Amaral and his team. Researchers believed that the Human Genome Project would be much more advanced today than it is and at this rate, the genes of the human genome will take over a century for each one to have at least one scientific paper published.
I find this seemingly accessible (as of today's time) topic very disappointing to hear. Granted, I have no idea how much time and effort it would be to individually analyze 1 of the 20,000 human genes to determine its function and effectively communicate that purpose in a scientific paper. The amount of technology used in studying genetics is fascinating and the leaps and bounds made in just the past few years is a true sign of how effective studying the human genome can be in advancing cures for cancers and diseases in the future.
https://www.nytimes.com/2018/09/18/science/why-your-dna-is-still-uncharted-territory.html
https://www.genome.gov/12011238/an-overview-of-the-human-genome-project/
https://www.nature.com/scitable/topicpage/dna-sequencing-technologies-690

Scientists attempting to create "Virus-Proof" cells

In May 2018, a group of scientists called the Genome Project-write, announced a community wide project to develop cells resistant to viruses, radiation, freezing, aging and cancer. These cells have been termed, "ultra safe cells". The group believes that it can trick viruses into DNA illiteracy by "re coding" the DNA. Once the virus is unable to read the target's DNA it loses its capacity to manipulate human genes into viral reproduction.

Re coding the DNA refers to the process of recreating the human genome without redundancy. So essentially there would only be one codon coding for one amino acid, vs. multiple codons signaling for one amino acid. This logic seems to have been effective when executed with E.Coli. after making 321 changes to E. Coli's genome, the bacteria had become resistant to certain viruses.

The Genome Project-write has teamed up with Cellectis bio pharmaceuticals, who have provided the scientists with a genome editing tool called TALEN. It should come as no shock that pharmaceutical companies are helping finance this project because drug companies lose a tremendous deal of product to viral contamination in manufacturing. Researchers hope that these "ultra safe cells" can help preserve medicines and lower their cost.

This is ground breaking science that seems to be fairly attainable. The only fear researchers should mind is the evolutionary capacity of viruses. It would be a real shame to put an incredible amount of time and money into a project that viruses adapt to and learn in a few years.

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We are more genetically similar to our dogs than we thought

A study done by Dr Luis Pedro Coelho suggests that the genes of the gut micro biomes in dogs is genetically similar to the gut micro biome in humans. In fact more genetically similar than the micro biomes found in mice and pigs. The results of this study has revealed that dogs are a better model for nutrition studies than mice and pigs. The experiment showed that changes in carbohydrates and proteins has nearly the same effect on humans and dogs. The micro biomes in obese dogs were more receptive to high protein diets than in lean dogs. This same pattern can be seen in humans too. Dogs are becoming more and more obese and this is most likely because humans feed their pets food from the dinner table all the time. They are not getting fat because they can not eat human food, they are getting fat because they are eating more than they should for their size. If dogs were fed human food in a balanced diet they would not become obese because they have very similar gut micro biomes. I find this study very interesting because as a pet owner, I look at my dogs are being apart of my family. I have never been one to feed my dog food from the table because I do not want him begging every time I eat, but I may start feeding him more carbohydrates and proteins that humans would eat. There are also many different diets out there made for dogs using only "human food", the link is attached below to one of these diets.

Article: https://www.sciencedaily.com/releases/2018/04/180419131136.htm
Additional Information: https://www.whole-dog-journal.com/issues/15_7/features/Home-Prepared-Dog-Food-Nutritional-Information_20568-1.html

What We Can Learn from the Cockroach Genome

     The second largest genome in the world belongs to the Periplaneta americana, more commonly known as the cockroach. With a genome larger than that of the human's, there is a lot of data that can be collected from the cockroach. Within its genetic code holds the insect's  secrets to survive in the harshest environments and on such a variety of food in its diet. The cockroach's genome was actually sequenced outside of the United States. At the South China Normal University in Guangzhou, researchers found that the groups of genes related to the immune system, sensory perception, detoxification, and growth and reproduction were all enlarged. This enlargement helped to explain how the cockroach is able to survive in a variety of conditions. Such as freezing cold and blistering heat. Some cockroaches have been observed living for as long as days without their head and showed regeneration of lost limbs. 

     Researchers have taken the data collected from the cockroach genome and are attempting to apply it to humans in hopes to prolong the live span of humans. Some of the genes the researchers are 
attempting to use in humans include genes coded for safety. Nearly 300 genes in the cockroach are able to sense bitter tastes. Which assist the cockroach in which foods are safe to eat and which foods to avoid. Researchers also observed what genes were responsible in limb regeneration. I believe that this is of vital importance in the scientific community. As information in this research can be applied to the human genome. The cockroach's superb ability to survive and adapt to drastic changes in their environment could be taken and, hopefully, be put to use in the genes of humans to enhance the live and livelihood of the human race in the future.

Article Link: http://fortune.com/2018/03/27/american-cockroach-genome-roaches/

Genome of Cockroach from Chinese research: https://www.nature.com/articles/s41467-018-03281-1

Neanderthal DNA contributes to Human Genome

https://www.sciencedaily.com/releases/2017/02/170223124316.htm

https://phys.org/news/2016-02-neanderthal-dna-subtle-significant-impact.html

      Although the Neanderthals haven't been around for over 40,000 years a part of them still lives on today and it can be found in modern humans. Small bits and pieces of their genome is said to be observed.Recent research as been able to to show evidence of Neanderthal DNA sequence in today's humans and that it influences how our genes are expressed. The influence helps regulate what genes turn off and which ones turn on effecting such traits as height, schizophrenia, and even lupus among others.
      Previous studies have been done to find correlation between Neanderthal genes and traits and those of modern humans but they were not as successful. There was some evidence however that their traits could have effected depression and fat metabolism but not as supported as the recent studies. The Neanderthal gene ADAMTSL3 was uncovered in modern humans that helps to decrease the risk of schizophrenia while also influencing height, Researchers are pleased with these discoveries but say further investigation and studies need to be done. 

Drosophila effectively models human genes responsible for genetic kidney diseases

Genes associated with Nephrotic Syndrome (NS) in humans also plays a role in the Drosophila renal function, thus making Drosophila a ideal model to understand human disease. NS signals kidney damage symptoms include excess protein in urine, elevated cholesterol, swelling, and low protein in the blood. Researchers have found more than 40 different genes that can cause this specific genetic kidney disease, but gaps still remain in understanding the roles these genes play. Zhe Han a associate professor in the Center for Cancer and Immunology Research at Childrens National has begun studying the NS associated genes in Drosophila. Eighty-five percent of the genes required for kidney function in humans play a big role in flies. They can now be used to identify treatments for kidney disease and learn the function these genes play in the body. There is a need for more model organisms to study renal function. The renal system not only filters and eliminates waste but also indicates immune damage.  Using Drosophila as a model organism is quick, inexpensive , and relevant for this system of study.

https://www.sciencedaily.com/releases/2017/03/170317180606.htm

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3006309/

Karina Vetrano: Wider Police Use of DNA Database

Wider Police Use of the DNA Database 

As we have been discussing in class lately, DNA database examination has been in the news in wake of the Karina Vetrano case. Familial searching is using the DNA database to find relatives of people who have been charged with a crime. The argument is that if there is no exact match in the database, that a search should be conducted to find close relatives of the suspect. The state of New York does not authorize this method. Both officials involved in the case and Vetrano’s parents have advocated for the implementation of familial searching. The other side of the argument defends the idea of this being an invasion of privacy of innocent people, or even more seriously, someone being wrongfully acquitted based on the results of familial searching.

This article mentions other cases, such as that of the “Grim-Sleeper” in Los Angeles, CA, that led to an arrest because of the information familial searching had come up with. I believe that this technique should be authorized nation wide. Too often murder cases go unsolved even though we have the tools and technology to solve them right in the palm of our hands. Even when I put myself in the shoes of someone related to a possible suspect, I would feel as though I am facilitating the justice system… I would not be angry or frustrated with “having my privacy invaded”.

Check out this video of Vetrano's mother at the DNA hearing.

How Tall Will We BE?!!

      What dark Force makes people different sizes?

Why is Kevin Hart short and Shaq so tall?

As a 5 foot 8 inch man I stand rather short.  For many years I’ve wondered what evil gene could have caused this unfair discrepancy in height.  Turns out scientists just discovered about 83 evil genes that may be responsible for these transgressions against me.  They were identified by scientists who worked at the Broad Institute at MIT and Harvard.  These dedicated scientists examined genetic information from more than 700,000 people.  The data had been taken from the Genetic Investigation of Anthropometric Traits(GIANT).  However these 83 traits are rare markers only found in about 5.5% of the population.  The researchers had already found about 700 other traits responsible for height! I'm too far gone, for this information to help but maybe in the future through genetic information we could manipulate these genes to make the human race taller.  Obviously this would have "ethical implications," but through changing of the school curriculums we can have a generation of children raised without ethical concerns.

DNA The Culprit

This information was taken from the Huffington post
For more information on DNA search here

Studies on Human Genome Determine Why There is Little Neanderthal DNA in Modern Day Humans

Modern-day humans contain up to 4% of NeanderthalDNA in their genome. They shared a common ancestor with Neanderthals up until about half a million years ago. Humans and Neanderthals started to interbreed tens of thousands of years ago, producing human-Neanderthal hybrids. Over time, the prevalence of Neanderthal DNA has steadily decreased over human generations until it has reached its current amount.

The reasons as to why scientists believe this interbreeding occurred and why Neanderthals do not exist to this day is because of the small population sizes of Neanderthals. Because they originally tended to live in harsher climates than humans, population sizes were smaller to cope with the extreme conditions. This resulted in a higher amount of interbreeding in Neanderthal populations, leading to less gene variation and a lower chance of natural selection.

The scientists of this study used mathematical equations to predict how allele frequencies of Neanderthal DNA inthe human genome changed over time. They suspect that while the chosen alleles may be neutral in Neanderthals, they may pose a greater threat to hybrids, resulting in high mortality rates. Therefore, offspring of any surviving hybrids would have a greater chance of survival if the hybrid parent mated with a human, decreasing the amount of harmful Neanderthal DNA in the offspring. This repetition of surviving hybrids mating with humans, and the resulting offspring also mating with humans, lowered the frequency of Neanderthal alleles in generations over time. When the hybrids reproduced with humans, there was greater gene flow and any disadvantages from the Neanderthal DNA could be effectively bred out over time. The breeding habits and survival rates of different generations of hybrids and their offspring would result in the varying degrees of prevalence of Neanderthal DNA in modern day humans. This study is important in understanding the origins of modern-day humans and how we came to be.

http://www.nytimes.com/2016/11/09/science/neanderthal-dna-natural-selection.html?rref=collection%2Fsectioncollection%2Fscience&_r=0

http://www.nature.com/articles/srep37198

Ancestors of Modern Humans Interbred With Extinct Hominins, Study Finds

Neanderthals and Denisovans were found to of interbred with ancestors of modern humans at least four times. We still carry DNA from those meetings and these genes have specifically helped with our ability to resist pathogens. It wasn’t until a finger bone was discovered in the Siberian cave, called Denisova, that the new group of DNA was found. Some of this new DNA has been found in people in Melanesia. Joshua M. Akey, a geneticist at the University of Washington, ran a study that found that every non-African person in their study had Neanderthal DNA, while the Africans had little to none. Europeans, East Asians and Melanesians had their own mix of Neanderthal DNA. The best explanation they could come up with for this distinctive mix of DNA found in modern humans was that they acquired Neanderthal DNA on three occasions. “The first encounter happened when the common ancestor of all non-Africans interbred with Neanderthals. The second occurred among the ancestors of East Asians – but not Europeans – interbred a third time with Neanderthals.” The Melanesians were found to interbred with both Neanderthals and Denisovans. Dr. Akey noted that both their DNA was more common as generations passed because it provided some type of survival advantage with immune system genes. This Neanderthal and Denisovan mix of DNA was absent in four regions of the modern human genome and one of those regions includes a gene called FOXP2, which is involved in speech. In February, PingHsun Hsieh, a biologist at the University of Arizona, reported that the genomes of African pygmies contained DNA pieces that come from an unknown sources within the last 30,000 years.

Milestone for Breast Cancer

A Recent study published in Nature is said to be a milestone for breast cancer research. Cancer research UK found an important stepping stone to new drugs for treating cancer. Three billion letters of people’s genetic code were taken apart to look at, of which 560 were of breast cancer. Out of the 20,000 genes (approximately) in the human genome, if 93 of those could convert healthy breast tissue into the cancerous tissue if mutation takes place. The team of researchers identified 12 types of damages in the DNA that cause mutation in the breast tissue. Some are related to genetic factors but most are still unknown. The new findings have been released to pharmaceutical and biotech companies to develop new drugs.

I think this is a really important discovery because many suffer from cancer that are ‘unknown’ of their origin. As taught in genetics, not all cancers are hereditary so therefore people who have cancer have no way of tracing it. This study is nice because it is bringing us closer to knowing the genetic changes made in the DNA and we can understand things better.  

The Tomato Decoded

In a study, scientists from 14 countries spent nine years researching and trying to discover the tomato genome with the intention of breeding better ones. After successfully discovering the genome, they found the vegetable possesses 31,760 genes, more than the approximate 22,000 genes humans have. It was also found that the Potato shares about 92% of its DNA with that of the Tomato, which makes sense because they are part of the same family, the Solanaceae family. So how did the Tomato gain so many genes? Well it turns out about 70 million years, some lucky mishap in the process of cell division led to the triplication of the Solanum genome where then the two free copies of each gene were free to change through mutation. Some of these were useless so they were dropped but others developed new useful functions. Interestingly enough, burdening a plant with three times as much DNA as it needs would sometimes be considered a handicap but since this event occurred around the same time as dinosaurs became extinct it was actually a lifesaver. Jim Giovannoni, a plant geneticist says, “It’s easy to think that in that period, with a lot of volcanic activity and little sunlight, the reservoir of a lot of additional genes would be useful to a plant”. Because of this study, plant breeders have had more success breeding tomatoes that benefit everyone such as longer shelf life and better taste and quality.

I found this article interesting because it is surprising that something as simple as a tomato has more genes than a living human. Naturally, you would think that if something had as many genes as the tomato has, it would be more complex and advanced but as I am learning, that is not always the case.