BioQuakes

AP Biology class blog for discussing current research in Biology

Tag: Genes (Page 4 of 4)

Genome Project Helps Connect Ethnicity to Diseases

By

On November 19, 2012

In Student Post

Though people from all over the globe share over 99% of the same DNA, there are subtle differences that make us all individuals

Scientists at the Washington University School of Medicine in St. Louis have started the “1,000 Genomes Project” in which they will decode the genomes of 1,000 people from all over the world in hopes of finding genetic roots of both rare and common diseases worldwide. On October 31st, the results of DNA variations on people from 14 different ethnic groups were published, but the scientists hope for the project to expand to involve 2,500 people from 26 different world populations. According to Doctor Elaine Mardis, co-director of the Genome Institution at Washington University, “[scientists] estimate that each person carries up to several hundred rare DNA variants that could potentially contribute to disease. Now, scientists can investigate how detrimental particular rare variants are in different ethnic groups.”

 

We are One

Everyone on earth share 99% of the same DNA. That means you, your best friend, your mortal enemy, your boyfriend/girlfriend, next door neighbor, and The President of the United States all share 99% of your DNA. However, there are rare variants that occur with a frequency of less than 1% in a population that are thought to contribute to both rare diseases and common conditions (i.e cancer, diabetes). The rare variants explain why some medications do not effect certain people or cause nasty side effects (i.e insomnia, vomiting, and even death).

 

The goal of the “1,000 Genomes Project” is to identify rare variants across different populations. In the pilot phase of the program, researchers found that most rare variants different from one population to another, and the current study supports this theory.

 

The Study

Researches tested genomes from populations from the Han Chinese in Beijing (and the Southern Han Chinese in China) to Utah Residents with ancestry from Europe to the Toscani people of Italy to the Colombians in Columbia. Participants submitted an anonymous DNA sample and agreed to have their genetic material on an online database. Researchers than sequenced the entire genome of each individual in the study five times. However, decoding the entire genome only detects common DNA changes. In order to find the rare variants, researchers sequences small portions of the genomes about 80 times to look for single letter changes in the DNA called Single Nucleotide Polymorphisms, or SNPs.

 

The Results and Importance

The Study concluded that rare variants vary from one population to another. Researchers found a total of 38 million SNPs, including 99% of the rare variants in the participants’ DNA. In addition, researchers found 1.4 million small sections of insertions or deletions and 14,000 large sections of DNA deletion. The “1,000 Genomes Project” is incredibly important in medical science. It now allows researchers to study diseases, such as cancer, in specific ethnic groups. I personally think this project in incredibly important. As an Ashkenazi Jew from Eastern Europe, my family has a medical history of certain cancers and diseases. With the results of the “1,000 Genome Project,” researches could potentially find out why, and maybe even find a cure for some of these diseases.

Blondes Unite!

By

On May 6, 2012

In Student Post

Despite the ‘dumb blonde’ jokes, and Danish or Dutch teases, I have enjoyed being blonde haired. As far as hair colors go, I think being blonde is perfectly suitable. However, there are certain preconceptions about hair color and race that people have. One being that people of certain ethnicities and races cannot have naturally blonde hair. This new study proves that idea wrong.

Photo Cred: Aust Defence Force

An article in the New York Times describes the experiments done on a group of people from the Solomon Islands. For some inexplicable (but not any more!) reason, many of the dark- skinned inhabitants have naturally blonde hair. But why?

Scientists did experiments on a giant chunk of the islanders, taking saliva samples from over a thousand people. Then they looked specifically at 43 blonde, and 42 dark haired islanders. What the discovered was that the blonde haired islanders had a specific gene, now called TYRP1, that changes the pigmentation of their hair.

What is perhaps most surprising is that Europeans have no trace of the gene in their genome. This, as Carlos Bustamante says: “For me it breaks down any kind of simple notions you might have about race,”

Hopefully these scientists will continue to learn more about hair and skin pigments and the genes that cause them. Do you like your hair color? Ever wonder why certain people seem to have one type of hair color instead of another? Just remember, it can all be explained by the genes.

Sweet Genes Not So Sweet

By

On March 20, 2012

In Student Post

Do you enjoy eating foods that taste sweet? Do you also like to eat meat? Well, what would you do if you ate so much meat that your genes responsible for detecting the sweet taste suddenly stopped? Would you be upset? I certainly would be. Thankfully, humans do not have to worry about this problem yet, but a recent study shows that animals that are specialized carnivores have lost the power to taste sweetness.

Credit: Martin Heigan

The study analyzed twelve different mammals and their sweet detector gene Tas1r2. The researchers found that in seven out of the twelve animals, Tas1r2 experienced mutations. The gene carried disabling glitches in hyenas, otters, fossa, banded linsang, sea lions and two different kinds of seals. What these animals have in common is that they are all predators. The study’s coauthor Gary Beauchamp believes that this means that the mutations in Tas1r2 “could easily spread through populations.”

While these carnivores have lost their ability to taste sweetness, this loss is not universal among meat eaters. For example, animals like red wolves are fervent meat eaters, but have not lost their genetic sweet spot. Beauchamp believes that the carnivores that have not lost the function of this gene will soon lose it in the future due to evolution.

However, there are many arguments in opposition to Beauchamp’s proposal. Animals that do not specialize in meat may have also lost their ability to taste sweetness. Chickens eat both plant and animal foods, but do not seem to notice sweetness in their food and appear to lack a functional Tas1r2. Huabin Zhao of Wuhuan University in China believes that chickens are just one reason that Beauchamp’s conclusion is not convincing. Zhao suggests that “narrow diet specialization might be a better explanation” for the meat-eater sweet-loss scenario.

The only way to determine if Beauchamp’s conclusion is valid is

to see if there will be disabling genetic glitches in Tas1r2 in other types of carnivores in the future. If this does occur, then this genetic mutation has the potential to shape the evolution of carnivores. Similar to these carnivores, people have also had their “use-it-or-lose-it” sensory evolution. For example, humans are not great at detecting odors and even worse when it comes to noticing pheromones, the strong animal-to-animal chemical communications. Only time will tell if the mutations of Tas1r2 will spread to all carnivores, but let’s hope humans do not lose the functionality of their sweet detector gene because sweet food tastes too good!

Identical but Not the Same

By

On March 15, 2012

In Student Post

 

Some Rights Reserved. More Information: http://www.flickr.com/photos/timoni/3390886772/sizes/s/in/photostream/

After studying genetically inherited traits and diseases it could be easy to assume that genes determine everything about us. While it is true that colorblindness is a sex-linked trait – there is certainly more to the story.

Monozygotic “identical” twins are genetically identical, so they should be the same in all ways shouldn’t they?

Why, then, does one twin get early onset Alzheimer’s disease and the other “identical” twin doesn’t? The same is true for height, autism, and cancer. Although, when one twin has a disorder the other is more likely to get the disease also, that is not always the case.

In the January edition of National Geographic, author Peter Miller discusses the newest theories about how genes, environoment and epigenetics affect our life (and the end of it).

Twins offer scientists a unique opportunity to study how genetically identical people differ. Basically, that means scientists can study how things other than genes affect human development and lifespan. Already, scientists have found that a persons height is only 80% determined by genetics because the heights of “identical” twins differ by about .o8 on average. Using IQ tests, scientists have nearly disproved John Locke’s Tabula Rasa or blank slate theory (the idea that children are born with a blank mind that is either stimulated – (and made intelligent) – or not –  (kept unintelligent)). Specifically, scientists studied twins who had been separated at birth and adopted into different families. In this way, scientists have found that intelligence  is about 75% controlled by genetics.

So that leads to the question, what is it besides genes that affects us humans so drastically?

Environment has something to do with our differences. However, that cannot be the whole story. “The Jim Twins” as they are called in the twin science community, were studied in the 1870’s. They were adopted into different families where both boys were named Jim. Then went on to have the same jobs, marry wives of the same name (two Lynda’s first then two Betty’s), enjoy the same hobbies, enjoy the same brand of cigarette and beer, name their sons James Allan and James Alan… the list goes on. These two lived very similar lives, yet they grew up in very different environments. If environment isn’t the only factor in creating difference then what is?

Scientists have recently come to believe that epigenetics plays a significant role in our lives. Epigenetics (site 2) can be seen as the meshing of environment and DNA. In the words of author Peter Miller “If you think of our DNA as an immense piano keyboard and our genes as keys – each key seach key symbolizing a segment of DNA respinsible  for a particulare note or trait, and all the keys combining to make us who we are – then epigenetic prcesses determine when an how each key can be struck changing the tune.”  Environmental changes do have some impact.  When a pregnant mouse is put under stress during the pregnancy it can create changes in the fetus that lead to abnormal behavior as the rodent grows into adulthood.

However, scarily enough, many epigenetic changes appear to occur randomly (thus creating a probelm for the organized nature/nurture theory). Currently work is being done studying DNA methylation, which is known to make the expression of genes weaker or stronger. Specifically, Andrew Feinburg, director of the Center for Epigenetics at Johns Hopkins School of Medicine, is working to find how DNA methylation relates to autism. Currently, he is using scanners and computers to search samples of DNA from autistic twins who have the disease in varying degrees. He is looking to compare how and why

the genes are expressed differently.

In the end, all we know is that there is more to our future than our genes can tell us. Yes, our genes play a huge role in who we are as people – in terms of appearance, character, intelligence and more – but there are some variables that our environment and epigenetics control.

Main Article: Miller, Peter. “A Thing or Two About Twins.” National Geographic. Jan 2012: 38-65. Print.

Quarter Horse? More like Million Dollar Horse! But is it all worth it?

By

On February 27, 2012

In Student Post


According to the article, “How the Quarter Horse won the Rodeo” , quarter horses are known for their superior speed, agility, and tranquility.   Why are these horses so superior? According to BioMed Central’s open access journal, BMC Genomics, used sequencing to map variation in the genome of the quarter horse male. The sequencing revealed that the quarter horse’s genome was enriched for variants in genes involving sensory perception, signal transduction and the immune system.  Further research was done on the genetic variants of these horses by the researchers from Texas A&M University. The researchers evaluated genetic variants in quarter horses such as single nucleotide polymorphisms (SNP), copy number variants (CNV), and insertions and deletions (INDELs).

Not only do these variants help explain the uniqueness and superiority of these horses, but they have also been of use to equine breeders and veterinary medicine to improve the health and performance of these horses. For example, these variants can be used to fix HERDA, a disease in which the skin of the quarter horses is fragile and thus tears easily. So, in the spirit of the film GATTACA and the ethics of genetic engineering, what are your feelings on using these variants to enhance these quarter horses? And what about enhancing humans?

Secrets (almost) Revealed about the Evolution of Plants

By

On January 11, 2012

In Student Post

Now that we are studying plants in class, and learning about different adaptations and some of the evolution of plants I thought this study would be interesting to look at.

The sequencing of the genome of a plant known as spikemoss, may give scientists a better understanding of how all kinds of plants evolved over the past 500 million years! This is the first sequencing for a non-seed vascular plant. Selaginella has been on this earth for about 200 million years and is a lycophyte

I was surprised that the Selaginella genome has about 22,300 genes and that’s small according professor Jody Banks. Selaginella is the only known plan to not have experienced a polyploidy event and is also missing the genes known in other plants to control flowing and becoming and adult. These genes are unknown in the Selaginella, but the genome would help scientists understand how these plants genes give the plant some unique characteristics and also help understand how Selaginella and other plants are evolutionarily connected.

The genome sequence was compared with others, and researchers identified genes that are present only in vascular and flowering plants. These genes that were identified most likely played important roles in the early evolution of vascular and flowering plants. Many of these genes have unknown functions, but it is likely that those genes that were identified may function in the development of fruits and seeds. Banks said: “[having an idea of what the function of the genes is] gives us ideas. It’s an important piece of the puzzle in understanding how plants evolved.” Also there are metabolic genes that evolved independently in Selaginella and flowering plant, which means Selaginella, could be a huge resource for new pharmaceuticals. The Selaginella is defiantly an interesting and great plant to study.

Photo Credit:http://www.flickr.com/photos/ki/195802378/

Human Health in the Hands of a Naked Mole Rat?

By

On October 16, 2011

In Student Post

Our genome is similar to that?!

         What do you think of when you see a naked mole rat? Do you think it is hideous because it has no fur? Do you think you would want to pet it? Whatever you think about this animal, you would never expect that it could improve human health. Who knew they could be the key to increase the human life span? Yep, that’s right! Naked mole rats, as ugly as they may be, are now considered extremely helpful and important in designing treatments for fatal diseases.

            A recent study discovered that the newly deciphered genome of the naked mole rat could help researchers learn more about evolution and even help design better treatments for diseases like cancer and stroke. Scientists believe that this genome will help decipher the naked mole rat’s unique traits, behaviors and social characteristics.

            Scientists who deciphered the naked mole rat’s genome used shotgun sequencing to read it. The naked mole rat was raised in a lab and once it was an adult, the scientists studied its genome. They read long sequences of the nucleobases that make up the rat’s DNA and then lined them up to find where they overlapped. Once they read the complete genome, the researchers compared it to the genomes of humans and mice.

            The researchers found multiple mutations in the naked mole rat’s genes that correlate to its characteristics. They found that the rat had turned off several genes related to vision because they live in the dark. They also saw a mutation in the gene that functions in hairlessness, which explains why these rats are bald. Naked mole rats live in low-oxygen burrows and stroke and heart attack deprive parts of the body from oxygen. By comparing the genome of the naked mole rat to the human genome and discovering how they survive in this type of low-oxygen environment, scientists can design more effective treatments to improve diseases that deprive the body of oxygen. The researchers sequenced the whole genome and will make it available free online, so groups that study genes involved in cancer and longevity can compare those genes to the mole rat’s genome. You can even look it up online and determine for yourself which genes you think are similar to ours!

            This new information about the naked mole rat’s genome can be extremely helpful for treatments that could increase the human life span and improve human health. Who knows, maybe the deciphering of the genome could even lead to find the fountain of youth! What do you think? Do you think the rat’s genome is similar enough to ours that scientists can design more effective medication for diseases? How far do you think these researchers are able to go? If you are unsure, just be sure of one thing, the next time you see a naked mole rat, be sure you look at it with a different perspective because in twenty years that very rat’s genome may lead to the cure for cancer!

Always Sick? It may not be your fault

By

On September 29, 2011

In Student Post

I feel like I get sick more than most of my friends. I always come up with excuses as to why I am sick like: “I must have caught it from my sister”, “I’m just really stressed” or “my lack of sleep lowers my immune systems ability to fight off infection.” But now I have a new excuse: my genes.

A recent article immediately peaked my interest because it may not be my fault I am more susceptible to illnesses. An experimental study involved seventeen healthy individuals who were infected with a strain of seasonal flu (H3N2). Nine out of the seventeen got sick. The researchers drew blood before the individuals were infected and every eight hours for the next five days. Then examined the activity of 22,000 genes in each blood sample. Patterns in gene activity could predict how sick people would get.

Our immune systems respond to “foreign invaders.”  Surprisingly  the immune systems of the people who got sick and did not get sick acted similarly. Those who got sick activated “immune chemicals” that trigger inflammation and stress responses, and those who did not get sick still had an active immune response but “repressed the stress response [and] activated anti-inflammation and antioxidant genes.”

This study illustrates that gene activity analysis might be able to help doctors determine the patients who are in danger of getting seriously sick.

Despite these findings I think the researchers need to determine whether the different patterns of responses depend only on a persons genes. In this study in particular the properties of the specific virus that the individuals were infected with could have played a role in the findings, and maybe a different strain of flu would yield different results.

Still, the next time I get sick I might be blaming the genes I inherited. Thanks Mom and Dad.

 

 

 

Page 4 of 4

← Previous

Archives

Powered by WordPress & Theme by Anders Norén

Skip to toolbar