BioQuakes

AP Biology class blog for discussing current research in Biology

Tag: Ancient DNA

The Shell that has a lot to tell

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On October 22, 2023

In Student Post

Sea Turtles are one of the most fascinating creatures in the world. When snorkeling in the middle of the Caribbean you hope and pray that you get to swim along with one of these wonderful creatures. But little did you know, they have millions of years of history hidden within their shells. Currently, only 7 species of sea turtles are alive, among the seven are those in the genus Lepidochelys: the olive ridley and the Kemp’s ridley. These two species are some of the most popular in the Caribbean Sea yet we know so little about their history. Until…

A group of paleontologists found remains of a turtle shell in 2015 in the Chagres Formation on Panama’s Caribbean coast. This turtle shell happened to be 6 million years old and it represents the oldest known fossil evidence of Lepidochelys turtles.

Lepidochelys olivacea

When analyzing the fossil, the scientists discovered preserved bone cells called osteocytes. These bone cells are the most abundant in the vertebrates and have nucleus-like structures. To test for genetic material the group used DAPI, a blue-fluorescent DNA stain. The test was successful and they were amazed because this was the first time DNA remains have been found in a fossilized turtle that is millions of years old. Not only does this discovery bring understanding to the biodiversity present in Panama millions of years ago, but it also brings a whole new topic of molecular paleontology.

Ki67-Tubulin

Molecular paleontology is a study of ancient and prehistoric biomatter including proteins, carbohydrates, lipids, and DNA that can sometimes be extracted from fossils. The understanding of how these complex molecules such as DNA and proteins can be preserved in fossils will continue to help scientists now to understand how soft tissues can be preserved over time. In Unit 1 of AP Bio, we are introduced to DNA. DNA is a fascinating molecule that carries most of the genetic instructions used in the growth, development, functioning, and reproduction of all known living organisms and many viruses. It is composed of two long strands forming a double helix structure. Each strand is made up of nucleotides, which consist of three components: Deoxyribose Sugar which makes up the backbone, a Phosphate group that contributes to the backbone structure, and a Nitrogenous base whose sequence encodes genetic information. At this point you may be thinking, why is this turtle so special? Can’t they find DNA in every fossil? Well, you would be shocked; before the discovery of DNA in this 6 million-year-old turtle, scientists were simply amazed by discoveries of DNA over 1 million years old. This is because DNA consists of sequences of base pairs that are chemically linked along the sides of a double-helix structure, resembling a twisting ladder. Being an organic substance, the constituent parts of this helical structure can deteriorate naturally over time. In the absence of active cellular processes within a living organism to repair and replicate DNA, it can degrade relatively quickly, rendering its components meaningless. Although DNA is plentiful and easily obtainable from living organisms, the task of retrieving viable DNA becomes increasingly challenging with extinct organisms, especially the further back in time they lived. All of these reasons indicate why this singular turtle fossil has more to tell about our genetic code than the millions of other fossils we have found over millions of years. Before reading these articles I had never understood how we were able to learn so much about animals and their ways of life just by a single fossil. But this discovery begs the question of why the DNA was able to survive so long within the shell of a turtle and not in the million of other animals around the world?

 

 

Is De-Extinction Upon Us? The Woolly Mammoth is Planned to be Introduced Back on Earth by 2027

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On March 15, 2023

In Student Post

You may be familiar with the large Woolly Mammoth’s (Mammuthus primigenius) from the movie Ice Age. These animals had once roamed the Earth for thousands of years, only recently going extinct at the end of the Pleistocene Period. Scientists Ben Lamm and George Church are leading the research into the second ever human provoked de-extinction, planning to release the Mammoth’s in Siberia. With an initial $15 million dollars in private funding, the team has received an additional $60 million to help achieve the 2027 deadline.

The closest living relative to these Mammoths is the Asian Elephant. Having once shared an ancestor 6 million years ago, scientists are working on pinpointing the genetic differences that set the ancient species apart from their modern (living) cousins. Fragments of Mammoth DNA have been retrieved from their ancient fossils (One of my previous blogs I wrote about DNA in fossils!), making it possible for scientists to modify the genome of an elephant to produce something that would look and act like a mammoth. The team will try to create an elephant embryo with its genome modified to resemble an ancient mammoth. To do this, the scientists will need to remove DNA from an elephant egg and replace it with the mammoth-like DNA. Some traits the Mammoth’s will need is dense hair and thick fat to withstand the cold environment. Siegsdorfer Mammut

Some other challenges to this de-extinction process is the actual birth of a fetal Mammoth. Scientists have been able to create a sealed bag that can support a fetal lamb up to four weeks, but for the Mammoth to be successfully birthed, it will require an artificial uterus big enough to house a fetus for around two years, reaching a weight of 200 pounds (~22~ months). While this may seem like an impossible task to many, the researchers behind this operation have stated that they’re eager and confident that their expertise will prevail, showing the world that editing DNA can bring extinct species back to life.

This article connects to our most recent unit in AP Bio of genes, genetics, and DNA. As we know genes in DNA are what make each person different from the other. Physical traits are mostly represented through gene pools (genetics), such as the thicker fat needed for the mammoth to survive. DNA editing is a crucial step to bringing back this animal and the scientists are working carefully to create the closest representation of the extinct species. This goal cannot be succeeded without the things we learned in this unit!

The presence of Wooly Mammoths in todays world can help the Siberian tundra as it has been overruled by moss. The moss acts as an insulator for the permafrost soil from the cold temperatures, thus melting the permafrost and releasing harmful gasses such as methane and Co2 into the atmosphere. Mammoths are considered “ecosystem engineers” because they feed on the moss and provide a natural fertilizer with their waste. With the moss being broken up, it would allow the grasslands to come back which keep the soil from eroding and melting. Ecologists have imported bison into the tundra in an attempt to help the tundra return to grasslands, but they believe the Mammoth’s will be much more effective.

While the team is multiple steps away, facing many challenges not yet conquered, they are continuing to push on with their research, inching closer and closer to making this reality. If this mission is a success, it will open the door to numerous DNA editing opportunities, restoration of the Siberian Tundra, and will remain a great feat of human advancement.

Siberian tundra 05

Geneticist Svante Pääbo is the first person to extract DNA from extinct human species.

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On October 21, 2022

In Student Post

Various forms of the human species have been alive for hundreds of thousands of years before us. For the longest time, it was concluded that DNA breaks down over time and cannot be excreted from ancient fossils…until Svante Pääbo joined the research.

Pääbo, the leader of his research team, was able to extract fragments of DNA from the bones of Neanderthals and Denisovans. By extracting mitochondria outside the cell nuclei, Pääbo’s team was able to place the genetic information into the appropriate chromosome locations “by matching each fragment to similar sequences in human DNA” (Bower). As we learned in class, mitochondria contain circular chromosomes of DNA. Pääbo’s team was able to extract the mitochondria from the cell and then analyze the mtDNA in comparison to modern-day humans. With this process, he concluded that humans diverged from Neanderthals about 516,000 years ago.

Another way they were able to identify common genetic information in the present-day Homo sapiens was by putting DNA into a certain bacteria, which would then make copies of DNA fragments. With this effort, they were able to recover 29 out of the 35 genes that they were targeting.

These new techniques brought research teams to conclude that modern-day humans share similar genes to Denisovans such as ones that regulate brain size, help us adapt to altitude, or even make covid-19 more severe in some cases. The evidence around the commonalities of certain genes encourages the theory that at some point there was interbreeding between Homo lineage.

Pääbo’s findings have paved the way for groundbreaking research, identifying commonalities in evolution, and have helped us understand what makes humans so unique. This new state-of-the-art process can hopefully one day expand to multiple labs, research teams, and even countries. This would allow us to learn even more about our sophisticated past and maybe even some things about our future!

Mitochondrial DNA lgNeanderthalensis

 

 

Shocking Connection Between Ancient Neanderthals and COVID-19

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On October 27, 2020

In Student Post

As stated in an article that details the shocking discoveries of an investigation led by Professors Svante Pääbo and Hugo Zeberg, genetic material from our neanderthal ancestors can be linked to the development of severe COVID-19. COVID-19, as I am sure you are all aware, is the disease ravaging the world and is caused by the newly

discovered coronavirus. While most people only have mild reactions to the disease and recover relatively easily, some people with underlying conditions may have a severe reaction to the disease and require hospitalization. However, this new study indicates that certain people may be genetically predisposed to a severe COVID-19 reaction, and it all links back to our 60,000-year-old Neanderthal ancestors.

The study that discovered this connection analyzed the genetic material of 3,000 patients who had both severe and mild COVID-19. The study identified a section of the chromosome that contained the genetic material responsible for the severe COVID-19. Chromosomes are tiny structures located in the nucleus of cells and these structures hold the genetic material that determines virtually everything about the cell. This genetic material is made up of nucleic acids that — when combined into a double-strand helix by covalent bonds between the phosphate, sugar, and base groups– create DNA. The order of the bases in the chain determines the amino acid sequence. We inherit our genetic material from our parents, and chromosomes are present in pairs, with one part of the pair inherited from each parent. This means that you hold genetic information from your earliest ancestors, which could potentially include Neanderthals. Neanderthals were archaic humanoids that were eventually assimilated into the homo sapien species.  However, cross-breeding was required to absorb the Neanderthals into our species, which means that most of the people alive today have a percentage of Neanderthal DNA. If a person holds one of the thirteen variants that are present in Neanderthal DNA, they are far more likely to have severe COVID-19.

Professors Pääbo and Zeberg proved this to be true by discovering that the Neanderthal variants distinctly matched the variants associated with severe COVID-19. However, they discovered that the genetic material only originated from Neanderthals located in southern Europe. Therefore, they concluded that when the Neanderthals of southern Europe merged with present-day people 60,000 years ago, they introduced the DNA region responsible for severe cases of COVID-19. Additionally, the people who possess these Neanderthal variants today are three times more likely to have severe COVID-19. The fact that I found the most interesting is how dramatically the presence of the variants vary in different parts of the world. For example, in South Asia, 50% of the population holds the variants, but in East Asia, almost nobody has them. I also think that it is rather tragic how genetic material that has not had any effect on the world for 60,000 years is just now becoming active. What do you think about this discovery? Why do you believe Neanderthal DNA is causing these extreme cases?

 

How Old “Chewing Gum” Allows Us To See Into The Past

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On January 21, 2020

In Student Post

In a recent study conducted by the University of Copenhagen, scientists have discovered a complete human genome extracted from a sample of old birch pitch “chewing gum”.

 

While excavating in Lolland, and island in Denmark, archeologists found a sample of 5,700 thousand year old birch pitch sealed in mud. Since the sample was sealed in mud, it was preserved very well. The birch pitch was found in a place called Syltholm, a site where many past archaeological finds have been made.

 

Why is this Discovery Important?

This is the first time a complete ancient genome has been extracted from something other than a bone sample. Samples of oral DNA as well as other human pathogens were found which are very important finds due to the fact that there are no other human remains left from that time period. From the initial birch pitch sample, scientists could figure out that the person who chewed the birch pitch was a female who most likely had dark hair, dark skin, blue eyes, and was genetically related to hunter-gatherers.

Scientists also made bacterial discoveries. Bacteria that come from oral microbiomes were found which allows us to also study the diet and microbiomes of  the people living 5,700 years ago. Scientist Hannes Schroeder says that studying these DNA samples will help us understand ancient microbiomes as well as the evolution of human pathogens.

I think it is interesting that so much information could be uncovered from a sample of ancient tree bark tar. What do you think?

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