BioQuakes

AP Biology class blog for discussing current research in Biology

Tag: gene research

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

 

 

What does the future hold for CRISPR-Cas9?

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On March 13, 2018

In Student Post

Genome editing, or the technologies in which scientists can change the DNA of an organism, is on the rise, especially with its latest development, CRISPR-Cas9, the most efficient method of all of the methods to edit DNA.

Like many other discoveries in science, CRISPR-Cas9 was discovered through nature. Scientists learned that certain bacteria capture snippets of DNA from invading viruses, making DNA segments called CRISPR arrays, helping them remember the virus to prepare for future invasions of that virus. When they are confronted with that virus again, RNA segments from the CRISPR arrays are created which target the DNA of the virus, causing the enzyme Cas9 to cut the virus’ DNA apart, which would destroy the virus.

 

We use the same method in genome editing with CRISPR-Cas9 by creating RNA that binds to a specific sequence in a DNA strand and the Cas9, causing the Cas9 to cut the DNA at that specific sequence. Once this is done, the scientists create a sequence to replace the one that was cut to get the desired genome.

This technology is most prominently used to attempt to treat diseases, where the somatic cells’ genomes are altered which affect tissues, as well as prevent genetic diseases where the sperm or egg’s genome is changed. However, the latter causes some serious ethical concerns of whether we should use this technology to enhance human traits. But this begs the question that if we start using it more and more to prevent genetic diseases, will this open the door for it to be used in new ways?

Does long-term endurance training impact muscle epigenetics?

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On March 8, 2015

In Student Post

800px-Nucleosome_1KX5_2

 

Epigenetics translates to “above” or “on top of” genetics. To be more specific, Epigenetics is the study of how modification of gene expression can cause changes in many organisms.

A new study from Karolinska Institutet in Sweden explores the theory that long-term endurance training alters the epigenetic pattern in the human skeletal muscle. The team that conducted the research also explored strong links between these altered epigenetic patterns and the activity in genes controlling improved metabolism and inflammation.

The study was conducted using 23 young and healthy men and women. The men and woman would perform one-legged cycling – where the untrained leg would be the control of the experiment. Four times a week and over the course of three months, the volunteers would participate in a 45 minute training session. Though skeletal muscle biopsies, supervisors would measure their markers for skeletal muscle metabolism, methylation status of 480,000 sites in the genome, and activity of over 20,000 genes.

At the end of the study, the researchers concluded that there was a strong relationship between epigenetic methylation and the change in activity of 4000 genes in total. Epigenetic methylation is defined as the “addition of a methyl group to a substrate or the substitution of an atom or group by a methyl group. ” Moreover, it was determined that methylation levels increased when involved in skeletal muscle adaptation and the metabolism of carbohydrates. However, methylation levels decreased in regions associated to inflammation.

Furthermore, Carl Johan Sundberg found that “endurance training in a coordinated fashion affects thousands of DNA methylation sites and genes associated to improvement in muscle function and health.” He believes that this determination could be vital to understanding the treatment of diabetes and cardiovascular disease as well as how to properly maintain good muscle function throughout life.

This article relates very much to our work in class as we learn the Molecular Genetics Unit. It connects because we are learning what happens when mutations occur in one’s genome and the impacts those mutations have on someone. For example, cancer is one of the most researched and explored topics in regard to how modification of gene expression alters organisms. Oncogenes and Tumor suppressor genes have vital impacts on cellular division, changes to cellular function, and the growth of tumors.

Could There be Good Gene Mutations?

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On January 16, 2015

In Student Post

Is there an epic battle occurring within our bodies right now? The classic battle royale between good and bad? I suppose in the body’s case the fight between good and bad genes.  There is a new field in medical research in which researchers are on the quest to find good gene mutations that fight against the disease causing mutations.  One individual, Doug Whitney, sparked the interest of a few doctors because he has fought his genetic odds to be health at 65 years old.  Whitney has a gene mutation, presenilin, that causes early onset Alzheimer’s disease in those who has inherited it. Whitney’s mother and 9 out of his 13 siblings were killed by this mutation and so Whitney’s fate seemed to be sealed.  However when Whitney reached his 40s and 50s having no symptoms he assumed he did not have the gene.  At 62 years old, Whitney, decided he would get a gene test.  He did have the gene.  This was an anomaly, He was doomed to have early onset Alzheimer’s Disease but had absolutely no symptoms. Although Whitney still have changes of getting Alzhiemers but the effects of his bad gene have been greatly delayed by another gene in Whitney’s DNA.  Whitney joined a study at Washington University in St. Louis led by Doctor Randall Bateman which recruited people with the early onset Alzheimer’s disease gene. This attracted the attention of Doctor Eric E. Schadt and Doctor Stephen H. Friend.  Doctor Schadt said that searching for good genes that protect against bad gene mutations is completely turning genetic research on its head.  Researchers have found gene mutations that partially protect diseases like osteoporosis, Type 2 diabetes, heart disease, and Alzheimer’s.  These good gene mutation’s partial protect have help to develop drugs to help fight certain diseases. Finding good gene mutations are substantially more difficult to find than bad genes, but the search has gotten a little easier with fast and inexpensive methods of sequencing DNA. Doctor Schadt and Doctor Friend decided to start the Resilience Project and search for good gene mutations that counteract bad gene mutations to help develop new break though treatments and drugs. They have contacted the researchers at Washington University, the research that Whitney is currently participating in.

For more information:

Article from NYT

Prokaryotic positive genetic influences

Genetics used for intrusion protection

About genetic testing

 

Incredible New Gene-Searching Software

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On February 10, 2013

In Student Post

MIKI Yoshihito
http://www.fotopedia.com/items/flickr-2559447601

Joseph T. Glessner, of the Center for Applied Genomics at the Children’s Hospital in Philadelphia recently invented a new software tool that will revolutionize accuracy in genetic disease studies. The software called ParseCNV is an algorithm that “detects copy number variation associations with higher levels of  accuracy than that available in existing software,” says Mr. Glessner. This incredible software automatically corrects for variations in the length of deleted or duplicated DNA sequences from one individual to another and produces high quality, replicable results for researchers studying genetic diseases.

CNV stands for copy number variations which are sequences of DNA, ranging from 1000 to millions of nucleotide bases, which may be deleted or duplicated. These CNV’s are very difficult to find because they are so rare but so important in the discovery of genetic diseases. Previous methods to find the link between CNV’s and disease involved individual case-control studies, in which diseased DNA is compared to healthy DNA. This method does not work accurately because different people have different CNV’s which can effect the outcome of the diagnosis.

ParseCNV is incredible in that it can account for and adjust to so many differences in genes and has so much versatility in that it is applicable to family studies and quantitative analyses of continuous traits. I am really looking forward to seeing the future of this amazing algorithm and its contributions to genetic research.

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