BioQuakes

AP Biology class blog for discussing current research in Biology

Tag: Rats

Could Christmas Island rats make a comeback? Thanks to CRISPR gene editing, they might!

From climate change to overhunting by humans, there are many factors which contribute to the extinction of species in the animal kingdom. The Christmas Island rat, also known as Maclear’s rat, went extinct a century ago in what is believed to be the first and only case of extinction of a species due to disease. It has always been believed that once a species goes extinct, it is gone for good. That is until recently when scientists began experimenting with “de-extinction” efforts to bring back the Christmas Island rat.

As published March 9 in the science journal, Current Biologya team of paleo geneticists from the University of Copenhagen recently conducted a study into gene sequencing the Christmas Island rat, in order to estimate the possibilities of future gene editing experiments which could bring the species “back to life”. The process of genetic editing for de-extinction efforts, as explained by the research team in their abstract, consists of first identifying the genome of the species and then editing the genes of similar species to make it more similar to that of that extinct one. The team used frozen somatic cells of the extinct rats, cells with a 2n number of chromosomes which are made during the process of mitosis. The team was able to sequence the rats’ genome, aside from some small portions which remain missing. They then had to identify the modern species which they could gene edit. Their findings established that the Christmas Island rat shares around 95% of DNA with the modern Norway brown rat. At this point, it

Now that the rat’s genome has been sequenced to the best of the team’s ability and a similar species has been identified, the gene editing possibilities are endless, especially with CRISPR technologies and techniques. “CRISPR” stands for Clustered Regularly Interspaced Short Palindromic Repeats in DNA sequencing. This system was discovered by a group of scientists, led by Dr. Emmanuelle Charpentier. CRISPR uses Cas9, an enzyme which cuts DNA at specified sections as guided by RNA. There are three different types of edits drone with CRISPR technology: disruption, deletion, or correction/insertion. Disruption editing is when the DNA is cut at one point and base pairs are either added or removed to inactivate a gene. Deletion editing is when the DNA is cut at two points and a larger sequence of pairs is removed. Correction/insertion editing is when a new gene is added into a sequence using homology directed repair.

Thomas Gilbert, the lead scientist on the team, says that he would like to conduct CRISPR gene editing experiments on living species of rats before attempting to replicate the DNA of an extinct species. For example, attempting to mutate the DNA of the Norway brown rat into that of the common black rat. Once this experiment is conducted, the possibilities of reviving the Christmas Island rat will be more clear. Until then, we can only hope! Do you think it’s possible to see the Christmas Island rat revived anytime soon?

How CRISPR Technology Can Potentially Reverse Extinction

Though Christmas Island rats went extinct over one hundred years ago, Anna Gibbs in sciencenews describes how genetically modifying the Norway brown rat would essentially reincarnate the Christmas Island rat. CRISPR is a relatively new technology that can be used to edit the genes of animals and has changed the science world of extinction. It works by editing “an existing animal’s genome so that it resembles that of the desired extinct animal… making that proxy as similar to the extinct species”.

Gibbs explains how using this technology, scientists compared fragments of the extinct rat’s genetic makeup, the Christmas Island rat, to that of their living relative, the Norway brown rat. By taking DNA from two preserved skin samples of the Christmas IslanRattus norvegicus - Brown rat 04d rat, the scientists were able to recover 95% of their genome. They compared the samples of the extinct species with the Norway brown rat and found that their genomes were very similar, 95% to be exact. Because of evolutionary divergence between the two species, the last 5% of the genetic information was lost forever. The missing genes were mostly located in the regions that controlled the rat’s immune responses and sense of smell. If they were to edit the Norway brown rat’s genome to resemble that of the Christmas Island rat, the differences in smell would be detrimental to their survival. This tiny difference in their genomes would prevent scientists from being able to recover the extinction of the Christmas Island rat. 

Though the scientists didn’t intend on actually reincarnating the rats, Gilbert says that what they discovered “could prove useful for people working on even more ambitious projects, like bringing back the wooly mammoth”. The hurdles of CRISPR technology lie in the tiny details of genetic engineering, even the smallest difference can prevent de-extinction. Ben Novak, a leading scientist at a nonprofit that uses genetic engineering for conservation projects, says that though there are MaclearsRatSkullways to capture some of the missing data, “the fact that some data will always be missing is a limitation that de-extinction scientists have already come to terms with”. The goal of de-extinction isn’t to completely recreate the extinct species but rather to formulate a new species out of the old that will fool its environment and live on. As we learned in AP biology this year, our bodies contain DNA polymerases that are constantly proofreading our DNA strands to make sure all of our nucleotides are correctly paired. If they are not, they are programmed to cut out the incorrect segment and replace it with the correct nucleotides. We even have a DNA ligase that acts as the glue in our DNA and keeps everything together. If the DNA polymerase were unable to detect the incorrect nucleotide matchup then it would stay and end up as a permanent mutation in the next cell division. Errors with the DNA polymerase, such a tiny part of our whole working body, are alike to the small error in CRISPR technology. The inability to recover all of the genomes due to the tiniest difference will cause scientists to miss out on the reincarnation of animals lost forever. 

Overall, though CRISPR findings are really “awesome”, it may not be the best use of money when we are struggling to keep our rhinos alive. In my opinion, CRISPR is not worth the funding until we are able to figure out how to recover 100% of the extinct genome. Comment your opinion on whether CRISPR should continue to receive additional funding, essentially is it worth it knowing we will never recover 100% of the extinct genome? 

Dr. Apryl Pooley: The Incredible Neuroscientist, Activist, and Survivor Illuminating Sex Differences in PTSD Symptoms

“Trauma#neuroscientist,#author, artist, social justice activist, mental health advocate, unionizer, survivor/recover-er/contender of rape/addiction/#PTSD” This is the Twitter bio of Dr. Apryl Pooley, a neuroscientist who is studying sex differences in traumatic stress response using sperm producing and egg producing Sprauge-Dawley rats. Through her work, she came to the discovery that “trauma has divergent sex-specific effects at the behavioral, physiological, and cellular levels,” an idea that hasn’t been explored in modern neurobiology. 

A visual of the release of ACTH in response to a stressor

Dr. Pooley and her research team utilized two known identifiers of PTSD-like response in rats to monitor these differences between the males and females. One was the acoustic startle response (ASR), an involuntary contraction in the facial and skeletal muscles “to a sudden and intense startling stimulus,” and the other was the dexamethasone suppression test (DST), a test used to examine adrenal gland function after the administration of dexamethasone, a steroid that “provides negative feedback to the pituitary gland to suppress the secretion of adrenocorticotropic hormone (ACTH),” which is released in copious amounts in the presence of a biological stressor. In PTSD patients, enhanced ACTH suppression is consistently found after this test is performed, since the patient responds to the negative feedback loop which quells the excessive release of ACTH. While the male rats demonstrated a high startle response and this expected negative feedback control in the pituitary and adrenal glands, the female rats showed symptoms more common to depression in response to the stressor. This contrast lead to Pooley’s conclusion that the “trauma response of male and female rats is fundamentally different,” and that it is important to understand these differences to pave “the way for improved diagnostics and therapeutics that effectively treat both men and women.”

Her interest in trauma and PTSD, especially her “goal of determining how a traumatic event affects people differently,” stems from her personal experiences and struggles. While she was researching Parkinson’s disease in her doctoral training at MSU, she came across studies of PTSD symptoms and realized that is what she had been coping with her entire life after being raped as a teenager. She “didn’t know that rape could cause PTSD,” and became dedicated to helping others learn about the devestating effects and causes of traumatic stress response. She also struggled with an alcohol addiction to cope with her trauma and eventually sought help from counselors and psychiatrists. During her journey of recovery from alcoholism, she wrote a book about her experiences titled Shadow Brain: A Neuroscientist’s Journey through PTSD and Womanhood and changed her Ph.D. research to looking at PTSD, with a concentration on how symptoms present in women. 

Dr. Pooley is an inspiring scientist, activist, and survivor that is making history with ground breaking research in behavioral science. She is “excited” to continue finding “biological evidence for why men with PTSD tend to show signs of aggression and anger and women with PTSD tend to show signs of anxiety and depression” and shedding light on how behavioral health disorders and trauma affect women, a topic underrepresented in current scientific research. She especially hopes that her work leads to the development of increasingly effective treatment resources for sexual assault survivors, women, and LGTBQ+ people who have experienced trauma or struggle with PTSD. How do you think we can amplify the voices of female scientists studying behavioral health and trauma like Dr. Pooley? How do you think her work is changing the portrayal of behavioral and mental health in the scientific community? 

Pythons to Blame for Increase in Dangerous Mosquitoes in Florida

The Invasion of Burmese Pythons in Southern Florida has been well documented over the last few years, and as they increase in number in the Everglades, numbers of many mammals have diminished. The addition of an extra top predator such as the Burmese Python, the second largest snake in the world, growing up to about 19 (19!!!) feet long, has dire implications for the ecosystem of the Everglades and of Florida, but they pose a danger to the humans in the area as well!

That’s right, the Burmese Pythons are causing problems for Floridians. No, Floridians are not soon-to-be victims of a Python takeover, but the disruption of the Everglade ecosystem has begun to become apparent. As Burmese Pythons have lowered numbers of countless different mammals across the Everglades, mosquitoes have less variety among the animals they drink the blood from, per ScienceDaily. As a result, Mosquitoes have been taking more blood from the mammals that remain, most notably the hispid cotton rat. Mosquitoes in the area are now taking more than 75 percent of their meals from this rat, which is a massive 422 percent increase since 1979. Burmese Pythons were first reported in the area in the 1980s. The hispid cotton rat, which so many mosquitoes feed on now, hosts the Everglades Virus, which is transferred to humans by mosquitoes. As if we didn’t have enough reasons to hate mosquitoes. The hispid cotton rat is one of the only hosts for the virus, which causes “fever, headache and even encephalitis” in humans, according to the same ScienceDaily Article.Sigmodon hispidus1.jpg

This new research is not only  relevant because of the increased hatred we all now have for mosquitoes, though. It also represents a landmark in research on invasive species. Nathan Burkett-Cadena informs ScienceDaily that “As far as I am aware, this is the first time that researchers have found that an invasive predator (such as the python) has caused an increase in contact between mosquitoes and hosts of a human pathogen.”

So, python invasions lead to more virus-carrying mosquitoes in the Everglades. Does this make you as uncomfortable as it makes me? Let me know what you think, leave a comment. I for one am glad to be far away from both the pythons and the Everglade mosquitoes.

 

Photos:

James Gathany for CDC https://commons.wikimedia.org/wiki/File:Sigmodon_hispidus1.jpg

Susan Jewell for USFWShttps://en.wikipedia.org/wiki/Burmese_pythons_in_Florida#/media/File:Burmese_python_(6887388927).jpg

 

Are Rats Ticklish?

Up until now, ticklishness has been a mysterious physical sensation.  Michael Brecht, professor at the Humboldt University of Berlin and Animal Physiologist, headed a research project along with Shimpei Ishiyama to help understand the sensation of tickling. Many questions have been asked about this mysterious physical sensation for many years without sparking answers. Even Aristotle and Charles Darwin were curious about tickling. Why are certain body part more ticklish than other? Why does the body react with smiles and laughter? Why can you not tickle yourself? Can other animals be ticklish as well?

Tickle Tickle

This image was originally posted to Flickr by Yogi at http://flickr.com/photos/34427468531@N01/113215143

Turns out, rats are ticklish too! (Click HERE for video!) In the Study, Brecht and Ishiyama, tickled the rats.  The subjects responded really well to the researchers tickling them, emitting “laughter-calls” and playfully chasing the the researcher’s hand.  The calls are ultrasonic and can not be heard by the naked human ear.  According to their laughter calls and the “unsolicited joy jumps” after being tickled, the rats are most ticklish on their bellies and on the bottom of their feet.  Brecht observes, “It’s remarkable the similarities between rats and humans – the fact they vocalise and clearly enjoy tickling so much.”  

images

British Pest Control Association

To further the research, Brecht and Ishiyama studied the brain to see what area of the brain reacts to tickling.  Cells are activated in the somatosensory cortex of the brain causing the rats to giggle.  The somatosensory cortex is part of the brain that registers touch and Brecht remarks that “we managed to pinpoint the ticklish spot in the brain.” During this study, they were able to discover that rats ticklishness is dependent on their mood.  Rats response to being tickled was far less measurable when the rats were stressed  This finding could lead to very important future research on the brain because there has been little research about how moods affects the brain.  

brain

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Trust Your Gut and Exercise

 

File:Wild garden of the gut bacteria 5.jpg

According to an article on GEN news, the level of Microbiomes contained within the Gut is influenced by exercise as a young child. Microbiota are the organisms that share our body space, and the gut has a particularly concentrated region of these organisms. Scientists estimate that gut microbiomes make up anywhere from 1-3% of total body mass. As it turns out the saying, “trust your gut” has some scientific merit. Microbiomes promote healthy brain function and promote anti-depressant effects, as well as adding up to 5 million genes to the human genome. Having a healthy gut is a key to overall biological health.

A recent study by Colorado University claims a connection between early life exercise and healthy microbiome activity. This study was conducted with rats, with one group young of rats exercising daily contrasted against a control of rats who behaved normally. The younger exercising rats experienced a growth of probiotic bacteria in their guts, more so then the stationary rats or even older rats who exercised. Researchers “emphasize the ability of exercise” to promote a healthy brain and metabolic function. In the future, Colorado University will look for ways to promote healthy microbiome activity in adults who have a much more stagnant microbiome structure.

 

Sources:

1.http://www.genengnews.com/gen-news-highlights/gut-microbiome-influenced-by-early-life-exercise/81252160/

2.http://learn.genetics.utah.edu/content/microbiome/

3.http://patient.info/health/the-gut

 

Fossils of Massive Rats Found

Attention fellow biology lovers: it appears our biggest fears have been realized. In East Timor, in Southeast Asia, researchers have found fossils of rats up to ten times larger than modern rats. Fear not, however, as these rats are long gone. Researcher Dr. Julien Louys said that the rats lived tens of thousands of years ago, and that there is evidence of humans actually using them as a source of food. Many of the fossils were found with cut and burn marks. The findings came as a part of a project called From Sunda to Sahul. The purpose of the project team that found the rat fossils was to find when humans started moving through Southeast Asia.

Dr. Louys believes that the rats actually lived in Southeast Asia until about one thousand years ago. He cited their extinction as being cause by the introduction of metal tools into society in Southeast Asia, enabling the inhabitants to destroy forests faster and more completely. The team is working to find the impact of humans on the Southeast Asian Ecosystem, which is directly correlated to the rats. Once they find the exact conditions that existed in the area before the rats extinction, they will have a more exact idea of what happened that left the rats extinct.

The rats themselves are characterized as mega-fauna. Mega-fauna is a term that refers to animals that are abnormally large, and these rats fall under this category. The rats are part of a movement that has seen a mass extinction of mega-fauna animals across the globe. Although the most common explanation for this unfortunate trend is human influence- which undoubtedly played a role- the reality is that hard evidence points to climate change as having a larger impact. As more research takes place, it will become clearer as to the exact reason for extinction of these massive rats in Southeast Asia. What do you think caused the extinction? Feel free to comment!

A sketch of a Deinotherium, a mega-fauna species that went extinct about 12,000 years ago. Image from Wikipedia Commons.

 

 

Can Stress Affect Pregnancies in Later Generations?

We all know stress isn’t always a good thing, but it could be important to especially avoid it at certain points in one’s life. Recently researchers from the University of Lethbridge in Canada investigated the effects of stress on pregnancies and how it can influence pre-term births. It is already known that pre-term births them selves lead to health issues later in life, but there were some new discoveries involving epigenetics.

 

Epigenetic_mechanisms

 

These researchers studied the length pregnancies of rats, due to the generally small amounts of variation between them, and found something intriguing. They carried out the experiment by first splitting the first generation of rats into “stressed” and “not stressed” groups. What they found was that the daughters of stressed rats had a shorter pregnancy than the daughters of not stressed rats.

This trend continued into the granddaughters of the rats. They also displayed high levels of glucose than the control group, and they weighed less. The stress also compounded, or increased, through generations.

This can all translate into human pregnancies. The researchers believe that the epigenetic changes in the rats is due to microRNA (miRNA) – non-coding RNA molecules that play a role in regulating gene expression. They bind to complementary mRNAs and prevent them from being translated. This is different than what is usual belief with epigenetics which is that epigenomes are affected by DNA methylation of the nucleotide base pairs. Metz, a scientist working on this research states that microRNAs “are important biomarkers of human disease, can be generated by experiences and inherited across generations. We have now shown that maternal stress can generate miRNA modifications with effects across several generations.”

It is very similar to the information found with the generational epigenetic effects of famine in the “Ghost in Our Genes” video that we watched in class.

This research can help determine pre-term births and the causalities that can come along with them. While the research is still not the whole picture, it is another step towards understanding our genetics.

 

Caffeine- helpful or harmful?

CC licensed photo by Manny Hernandez

As we all know, the highly addictive drug, caffeine, found in our coffee, tea, soda, etc… simulates us. Many people use caffeine to stay a wake which works really well. But it also causes a build up of fatty acid in the blood, raises blood pressure,  stimulates the heart, respiratory system, and central nervous system, causes stomach to produce more acid, harder to digest food because muscles surrounding the intestinal system relax, increased urination, and many other symptoms.

Is caffeine more helpful or more harmful? And where does caffeine really affect our body?

Recently, scientist have been testing caffeine on lab rats to figure out which part of the brain caffeine stimulates the most. In the first trial, they gave the rats more caffeine than what a human would normally ingest. They then decided to use  smaller amounts of caffeine which affected the hippocampus. The hippocampus is part of the brain which allows for long term memory and spacial navigation. In humans, the hippocampus is located inside the medial temporal lobe. Damage to the hippocampus may cause oxygen starvation and/or amnesia. The rats received caffeine equivalent to two human cups of coffee which is two milligrams per kilogram of body weight. The scientists measured the nerve cell’s electrical messages but examining different parts of brain tissue.

The region that had the most response to the caffeine was called CA2. CA2 showed a burst of electrical energy, while other brain regions in the hippocampus showed no sign of stimulation. The then tested the rats giving a greater dosage which caused an even greater stimulation to CA2. After that the scientists directly injected caffeine into nerve cells in a dish and the results were the same as before. About 5 minutes of caffeine intake allowed for the synapses to stay amped for three hours.

The scientists believe that when humans use caffeine the same area, CA2, will be stimulated and may strengthen a persons ability to learn and memorize, but this is just a hypothesis since they only tested on rats. So you decide… is it helpful or harmful?

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