In DNA, Clues to the Cheetah’s Speed and Hurdles

This article discussed the studies performed on cheetahs, determining their history and giving some hints as to “how the big cats became the world’s fastest land animals.” These studies were conducted by scientists at the Cheetah Conservation Fund in Namibia, on a cheetah rescued when it was a ten day old orphan, Chewbaaka. Later, more studies were done by scientists at the Theodosius Dobzhansky Center for Genome Bioinformatics at St. Petersburg State University in Russia, who collaborated with BGI-Shenzhen in China and the Cheetah Conservation Fund to analyze the entire genome of the species. After genetic analysis, scientists discovered that the cheetah has less than 5 percent of the genomic diversity (determined by variation in enzyme genes inherited by an animal’s two parents and is critical to its healthy reproduction and immunity to disease) of other wild cats, a level much lower than even inbred domestic dogs and cats and the lowest among the 30 mammals whose genomes have been sequenced. This therefore led to the scientists beginning to think that the cheetah was genetically monotonous several decades ago. These scientists in Russia then figured out the specific underpinnings of the cheetah’s genetic impoverishment and glimpsed the evolutionary chain of events that produced its unparalleled running speed. It was found that there were two specific points in history in which the genetic diversity of the cheetah was reduced. One of these instances was when the population bottlenecks were formed after cheetahs crossed the Bering strait into Asia. The other was late in the Pleistocene epoch when a global extinction event caused cheetah populations to crash. They examined how natural selection affected the cheetahs, firstly that the sequencing of the genome illuminated gene mutations that probably explain the sperm abnormalities seen in all cheetahs today, for they had the gene AKAP4, which likely block sperm development. The second effect natural selection had on the cheetahs, a positive effect, was their running ability. Eleven different genes showed evidence of mutations occurring over generations that boosted the animal’s muscle contraction, stress response and regulation of energy-releasing processes, which improved the cheetah’s running ability.

This article is important to society today because it discusses the possible extinction of yet another animal that played a large role in the world. The article shows the difficulty for the cheetahs to repopulate or enlarge their population because of the disadvantages they have in the field of reproducing, like having the sperm development blocking gene. This article is also relevant to us considering we previously studied genes and how a specific gene can result in traits or diseases passed down, which can also be seen in the cheetahs, which went through much interbreeding to keep the species from decreasing even more in population.

One strength of this article was how it went into depth explaining some of the genes and gene mutations that the cheetahs experienced, explaining some specific examples of traits in the cheetahs the scientists found. Although the article had many strengths, I still feel a few things could have been improved upon. For example, the article did not include much regarding the actual process undergone by the scientists performing the study, for it just gave a general overview of it. I would have liked if maybe it included more about this specific process undergone by the scientists, and not just the broad description of it.

Moffet, Barbara S. "In DNA, Clues to the Cheetah’s Speed and Hurdles." The New York Times. The New York Times, 29 Feb. 2016. Web. 01 Mar. 2016. <http://www.nytimes.com/2016/03/01/science/in-dna-clues-to-the-cheetahs-speed-and-hurdles.html?rref=collection%2Fsectioncollection%2Fscience&action=click&contentCollection=science®ion=rank&module=package&version=highlights&contentPlacement=8&pgtype=sectionfront>.

Gene Editing Tool Hailed As A Breakthrough, And It Really Is One

Ford Neild         March 1st, 2016

Current Event 13           Review

Palca, Joe. "Gene Editing Tool Hailed As A Breakthrough, And It Really Is One." NPR. NPR, 28                     Dec. 2015. Web. 01 Mar. 2016.

http://www.npr.org/sections/health-shots/2015/12/28/460705645/gene-editing-tool-hailed-as-a-breakthrough-and-it-really-is-one

This article, "Gene Editing Tool Hailed As A Breakthrough, And It Really Is One," by Joe Palca, summarizes the new and exciting scientific prospects made possible by CRISPR. CRISPR is a process that has simplified and advanced the way we edit genomes today. Palca acknowledges that despite all of the positive feedback CRISPR is getting, there is some ethical concern as to the potential uses of the powerful new ability. Concerned individuals fear that scientists may abuse the ability to cut out and replace unwanted genes in order to create the infamous “designer babies.” Despite these concerns, Palca’s own interactions with scientists has him convinced that creating designer babies is far from priority one for the curiosity-driven researchers. palca then proceeds to give several example of how CRISPR has positively impacted the work of scientist in several different fields. Christopher Allen, a researcher in the field of oncology and radiology claims that CRISPR allows him to create and compare cancer cells with specific genomic differences, providing previously unattainable insight into the genetics of cancerous mutations. Another scientist, Jan Leach, studies diseases in plants and spoke to Palca about the impact CRISPR has had on her work. By modifying the genes that allow plants to fight off fungus and other foreign bodies, she hopes to create new plants that can survive without the use of pesticides. "I've been working in this particular area for over 20 years, and in 20 years I've been able to do [modify] one or two genes," says Allen. "With CRISPR-Cas I'll be able to do [modify] 20 or 30." Palca comments on the immense range of fields that CRISPR has positively affected and expects to see even more changes as a result of this new process of genomic editing.

Clearly, as described by Palca, CRISPR has immense practical use in our society today. Technology is advanced enough today that we are able to detect genetic flaws before birth. Imagine if, using CRISPR, we were able to cure this conditions before the child was even born. Even genetic mutations in living humans today have the potential to be cured. HIV infected cells could have the infectious genetic code cut out and replaced with new clean code. Cancerous mutations could be cut out and replaced. Genetic conditions, such as sickle cell anemia could be fixed to produce normal blood cells. Beyond this however, being able to create specimens with genetic code to one's preference allows for scientist to create and then compare cell cultures with different genes. This allows new advances to be made into fields where genomic editing may not even have a direct effect, but rather indirectly cure the disease by facilitating efficient and fast observation of cell cultures.

Overall this article was very condensed and made a strong argument for the positive effects CRISPR will have in almost every field of relevance. To support his argument he interviewed a number of scientists from completely unrelated fields of science and showed of CRISPR has affected their studies. Palca used several quote to give his article the perspectives of several scientists, adding more credibility and substance to his article. While this article was successful in many areas, I felt that some level of explanation was required as to how CRISPR actually works. As a eager scientist  I would have wanted to see how scientists are able to select which genes to cut out and they then proceed to insert different DNA into that segment of code. To the author's credit, making the article more complex by explain the science would have make the article less appealing to minds that were less scientifically inclined. To improve this I would recommend that Palca out in a brief, digestible explanation of the process of CRISPR. All in all, this article was very interesting and made a great case as to how CRISPR will positively impact many scientific fields of study.

Mutant lice are probably coming! But first, the hype

Mutant lice are probably coming! But first, the hype

An itchy scalp, irritability, poor sleep -- even those of us like myself who were never a part of the 6-12 million United States children infected with lice every year are familiar with these symptoms. The following weeks are filled with permethrin and pyrethrin solutions, the active pesticide ingredients in almost all over the counter lice treatments across the country. However, since 1990, a growing population of lice has shown mutated genes resulting in a resistance to these compounds in the United States, Europe, and Australia. In fact, among samples of lice from 84 individuals across the country in 2014, 99.6% of the lice had gene mutations allowing them to survive permethrin and pyrethrin. A 2015 study further validated these findings: 95% of 109 lice populations, each created from the lice of several individuals across 30 states, were found to have these permethrin and pyrethrin resistant mutated genes. Further analysis of the study reveals that 25 of the 30 states had lice with these genes. Professor Kyong Sup Yoon of Southern Illinois University elaborated on the 2014 study, stating, “[the population is] almost saturated with [these genes], which means that people using permethrin and pyrethrin based products will probably have a very hard time controlling the lice.” Unfortunately, prescription products that serve as an alternative to these permethrin and pyrethrin products come with an additional cost of $100-$200, plus doctor visit fees. Consequently, others have looked elsewhere for answers. Many have found the “nit-picking” industry serves as an attractive alternative. For $150-250 an hour, dependent on hair volume, an individual can bathe your hair in oil and then hand pick the lice from it.

This article is extremely relevant because it applies some of the logic we used in the Hardy-Weinberg lab. For one round of the experiment, we eliminated all individuals with a homozygous recessive genotype, causing the population to mutate in favor of dominant genes. Insecticide has put a similar selective pressure on the population of lice: since permethrin and pyrethrin are used to treat nearly every single case of lice, lice resistant to these insecticides will be better able to live and pass their traits on, in turn further favoring insecticide resistant traits. This article is also relevant because we attend a K-12 school where there are dozens of lice cases annually. 

I thought that this article was very well written. As expected from a reputable source like CNN, spelling and grammar contained no visible errors while all data from studies was properly cited. Furthermore, I felt that the author did an excellent job addressing how individuals seek further treatment in the case of insecticide resistant lice. Lastly, I thought the author was thorough in explaining the economic impact of insecticide resistant lice. The only area in which I felt the article was lacking was in that of worldwide significance. I feel that comparing the data found in the US to that found abroad would add another layer of significance to the case of insecticide resistant lice.

Work Cited:

Storrs, Carrina. "Mutant Lice Are Probably Coming! But First, the Hype."CNN. Cable News Network, n.d. Web. 01 Mar. 2016. <http://www.cnn.com/2015/08/18/health/mutant-lice/index.html>.

Scott Kelly, American Astronaut, Is Returning to Earth After 340 Days in Space

Following a 340 day trip to space, American astronaut Scott Kelly is coming home. This voyage 249 miles above the earth was the longest of its kind ever taken by an American. Scott was sent into space for the purpose of identifying what happens to a human body that is exposed to the conditions of space for long periods of time. This so that we know how to prepare for a Mars landing. Scott and his brother Mark, who is also an astronaut, will be examined together in order to have a control and experimental group. In space, Scott witnessed an amazing 10,944 sunrises and sunsets. Scott can now say that he has spent a total of 540 days of his life in space. His 340 day trip easily bested the former American record of 215 days, but failed to compete with the overall record of 438 days, set by cosmonaut Valeri Polyakov. Scott enjoyed his experience and would do it again if offered the chance, and livened things up by dressing up as a gorilla, going on a spacewalk, and eating the first lettuce grown and harvested in space. He claimed that the lettuce was “Kind of like arugula,” and captioned this momentous occasion “It was one small bite for man, one giant leap for#NASAVEGGIE and our #JourneytoMars. #YearInSpace”.

This article greatly relates to our society. This is paving the way for truly interplanetary space travel, which is not only a hot topic for governments but also private companies such as Space X. The findings from this adventure will undoubtedly prove essential in our quest for adventure as time goes on. Additionally, because this is preparation for a Mars mission, it has the potential to indirectly inspire millions of people both in America and around the world to look up at the sky and make something more of themselves. A Mars landing would capture the world’s attention just as the moon landing did. Sending a man to another planet will have a profound impact on our society, and this is one of the first steps towards that noble goal.

I thought this article was excellent. It was very informative but also kept itself light and upbeat. If I had to add something I would add more about the future Mars mission, such as a rough timeline of the preparation and further depth as to how this research is helping to bring us closer to that goal. All in all, this article was a solid 8.5/10.

Victor, Daniel. "Scott Kelly, American Astronaut, Is Returning to Earth After 340 Days in Space." The New York Times. The New York Times, 01 Mar. 2016. Web. 01 Mar. 2016. <http://www.nytimes.com/2016/03/02/science/scott-kelly-astronaut-nasa-space-station-return.html?rref=collection%2Fsectioncollection%2Fscience&action=click&contentCollection=science®ion=rank&module=package&version=highlights&contentPlacement=1&pgtype=sectionfront>.

Invasive Species Aren't Always Unwanted

       For my current event, I read the article “Invasive Species Aren’t Always Unwanted” by Erica Goode. While traversing through our unit on evolution, we have often heard of invasive species causing a tremendous amount of damage to native populations, forcing them to adapt, wane, or ultimately falter completely. However, recent research suggests that not all invasive species have overwhelmingly negative affects on the area in which they reside. In the past, a certain fungus decimated the chestnut tree population across the continental United States. Currently, Asian carp are taking over the ecosystems in rivers throughout the Midwest. Because of this seemingly “unnatural” reduction in diversity, “the dominant paradigm in the field (of ecology) is still a ‘when in doubt, kill them’ sort of attitude,’” says Dov Sax, a reputable and honored evolutionary biology professor at Brown University referring to the invasive species. Nonetheless, recent studies are arguing for the counterpoint: that certain invasive species are indeed beneficial. In California, a study found that eucalyptus trees, the site of monarch butterfly socialization and feeding during the winter, hold an established, revered history beginning with their importation in the early 1880s. While they would be classified as “invasive,” they are critical and healthy to the ecosystem’s function. A separate sub-study supported the hypothesis that the tamarisk tree (a long-time invasive species in the southwest), once thought to hog water and other resources without providing much benefit to its neighboring organisms in the region, is actually a remarkable port for birds and does not take in significantly more water than other species of trees. Together, these studies are challenging the status quo in ecology.

This article and the studies it points to have widespread implications as the earth perpetually warms and becomes interconnected. As the article points out, “…as climate change pushes more species out of their home ranges and into new areas, the number of so-called invaders is likely to multiply exponentially.” Since the planet is warming, many species are migrating north to where it is slightly colder, thus residing in temperatures that resemble their ideal conditions. For example, the Zika virus is spreading north by mosquitoes migrating due to climate change. This leaves existing species open to new interactions with these alien ones, increasing our own: human beings. We need to study these species and find out their ultimate implications if we are to continue with our current way of life. On a parallel note, as the world becomes even more deeply connected economically, politically, and socially, our travel leads (often unintentionally) to the introduction of new species and diseases into previously unexposed populations. For example, a previous study found that the brown snake species was accidentally introduced to Guam, an area whose birds had had no previous experience with these predators. In the absence of proper defenses having arisen over time via natural selection, the bird population has been decimated. While the introduction of an alien species can come with both positive and negative consequences depending on the situation, one thing is clear: in this day and age, the study and understanding of ecology is very important.

Overall, this article was written extremely well and thus easy to understand. Each idea flowed to the next, and the author backed her claims up with relevant studies and quotes from established sources like the journal Nature. In addition, the article itself was published in the Science section of The New York Times, a newspaper widely considered to be one of the world’s trustiest. Personally, I particularly liked that the author included both sides of the debate over invasive species and was careful to point out any bias in the quotes or studies referred to. Also, the author used the NY Times database to utilize pictures and facilitate the reader’s understanding of the article. As a result, this article proved interesting, wholesome, and worthwhile. This article was practically flawless, and I would not change any aspect of it.

Link to Article: 

http://www.nytimes.com/2016/03/01/science/invasive-species.html?_r=0

MLA Citation: 

Goode, Erica. "Invasive Species Aren’t Always Unwanted." The New York Times. The New York Times, 29 Feb. 2016. Web. 01 Mar. 2016. <http://www.nytimes.com/2016/03/01/science/invasive-species.html?_r=0>.

Freddie Reichel AP Biology

2/28/16 Current Event #13

“In DNA, Clues to the Cheetah’s Speed and Hurdles”

Through a cheetah named Chewbaaka, scientists have uncovered the species’ long complex history, including how the cheetah became the world’s fastest land animal.  Chewbaaka was rescued as a 10-day-old orphan in Namibia and died in 2010 at the age of sixteen, twice the average lifespan of the cheetah in the wild.  However, geneticists were able to draw his blood and six other cheetahs from Namibia and East Africa.  This blood sample has been used to sequence the species’ complete genome; its full set of chromosomes.  The cheetah are characterized by their spotted coats and black “teardrop” facial markings.”  The animals race across the African savanna at speeds reaching 70 miles per hour, due to their unique physiology: elongated legs, aerodynamic skull, enlarged adrenal glands and heart muscles, and claws that grip the earth.  The cheetah is critically endangered, only 10,000 today, the majority living in southern and eastern Africa.  The genomic analysis is not encouraging; the cheetah has less than 5 percent of the genomic diversity of other wild cats, a level significantly lower than even inbred domestic dogs and cats and the lowest among the thirty mammals whose genomes have been sequenced.  Furthermore, genetic diversity is defined by the variation in enzyme genes inherited by an animal’s two parents.  It is vital to the species healthy reproduction and immunity to disease.  This genomic analysis confirmed scientists suspicions that the cheetah is “genetically monotonous.”  Several decades ago, surgical skins grafts were obtained experimentally among unrelated cheetahs and were tolerated without the normal rate of tissue rejection, as if all the animals were identical twins.  Cheetahs in captivity were difficult to breed and had unusually high mortality rates among the cubs, in addition to high vulnerability to the outbreak of disease.  This research was conducted by scientists at the Theodosius Dobzhansky Center for Genome Bioinformatics at St. Petersburg State University in Russia collaborated with BGI-Shenzhen in China and the Cheetah Conservation Fund to analyze the entire genome of the species.  These scientists figured out the specific underpinnings of the cheetah’s genetic impoverishment and the evolutionary sequence of events that created the cheetah’s unparalleled running speed.  The 3,000,000 year old tale of the cheetah is “punctuated” by two significant events that resulted in reduced genetic diversity.  The fossil record shows that about 100,000 years ago, when cheetahs inhabited North America alongside the puma, cheetah migrated across the Bering Strait into Asia, and ultimately into Africa, producing a series of population “bottlenecks.”  As a result, the number of animals dropped so low that the cheetah interbred to survive.  Late in the Pleistocene epoch, a global extinction caused cheetah populations to dwindle, resulting in inbreeding.  The cheetah barely escaped extinction.  The research scientists focused in on the series of mutations of a specific timetable.  The international team of geneticists calculated exactly when these population bottlenecks occurred.  They coincided with the two ancient events and pinpointed the second, Pleistocene bottleneck, 11,084 to 12,589 years ago.  The cheetah’s incredible running ability is due to natural selection.  Eleven different genes showed evidence of mutations over generations that boosted the animal’s muscle contraction, stress response, and regulation of energy-releasing processes.

This article was informative and interesting.  This scientific research is groundbreaking.  Scientists pinpointed the reason for the lack of genetic diversity in the cheetah and why the specific attributes of the cheetah exist.  The cheetah is an endangered species, as illustrated by the fossil records, because of inbreeding, due to the migration across the Bering Strait into Africa.  The cheetah is the fastest running animal on land because of both natural selection and mutation.  Eleven different genes showed evidence of mutations over generations that boosted the animal’s muscle contraction and stress response.  In addition, this research was relevant to what we are learning in class.  By examining fossils from specific periods and eras of the earth, scientists unearthed evidence of mutations and genetic diversity.

The article summarized the research concisely.  I understood all the terminology and found the description of the evolution of the cheetah’s ability to run to be very interesting.  The article could have been improved by utilizing more quotations from the scientists involved in the research.  The article could also be improved by describing prior research and whether it differs from the current discoveries.

Moffet, Barbara S. "In DNA, Clues to the Cheetah’s Speed and Hurdles."The New York Times. The New York Times, 29 Feb. 2016. Web. 01 Mar. 2016. <http://www.nytimes.com/2016/03/01/science/in-dna-clues-to-the-cheetahs-speed-and-hurdles.html?_r=0>.

"DNA Under the Scope, and a Forensic Tool Under a Cloud."

Since the 1970’s scientists have been deciphering DNA for multiple reasons including forensics, cancer biology, archaeology and evolutionary biology. Just recently Dr. Marina Stajic, the previous director of the forensic toxicology lab at the medical examiner’s office in New York City, has filed a lawsuit against NYC, claiming that “she had been forced into retirement last year in part because of a disagreement with her superiors over the accuracy of certain DNA tests.” Following the 1970’s, the tests conducted to decipher DNA have been reformed so that less DNA is required to run the tests. The original chemical process destroyed most of the DNA, making it so that scientists needed a large amount to start off with. Unfortunately, in many cases it is difficult to collect so much genetic material, making the tests impossible to complete. One of the first major improvements was made by biochemist Kary Mullis, who created polymerase chain reaction, or PCR, which allowed scientists to make copies of a gene fragment. Recently, a more “cutting-edge” technique has been used to analyze DNA, called low copy number DNA analysis. This technique requires a very small amount of DNA; just collecting some loose skin cells off of surfaces is sufficient. As low copy number DNA analysis uses such a small amount of genetic material, there are several errors that can be made, making it quite controversial. One issue is the fact that low copy number DNA analysis can detect a mix of DNA from more than one person, DNA that may be irrelevant for situations like crime scenes. Furthermore, it has been proven that people can leave traces of DNA on objects that they haven’t even touched, further jeopardizing the accuracy of low copy number DNA analysis. Another error, called allelic drop-out, occurs when so few DNA molecules are collected that they don’t react with the PCR used to duplicate the DNA. When used in forensics,  this can lead to the creation of a genetic profile that doesn’t even match the crime scene. Overall, low copy number DNA analysis has revolutionized multiple fields of science, but is still considered controversial to use due to the errors that can occur.

Low copy number DNA analysis is definitely relevant to society today. As mentioned before, this DNA analysis technique has improved police work, cancer biology, in vitro fertilization, archaeology and evolutionary biology. Fewer DNA molecules are required, making it easier to analyze DNA in situations in which a large supply of DNA isn’t available, like at a crime scene or when studying cancer cells. Without this type of testing people would have difficulty applying the use of DNA analysis, since not enough DNA would be provided at a crime scene for developing a profile for the case, or on a fossil to classify it. Low copy number DNA analysis is even being used to help identify skeletons and remains of Civil War soldiers. Overall, while it has its faults, low copy number DNA analysis has allowed the impossible to occur in multiple fields.

I found the article very informative and pleasant to read. The topic of DNA analysis and the many techniques used is so intriguing, and it was very interesting to learn about it in the article. The author did a nice job of making the topic clear and easy to understand through giving just enough detail and using vocabulary that is understandable to people who aren’t scientists. The author also included many quotes from scientists and experts, specifically from Dr. Budowle, the executive director of the Institute of Applied Genetics at the University of North Texas Health Science Center, and Stephen R. Quake, a biologist at Stanford University. This allowed me to see that the information was from a reliable source and all the claims that were made by the author could be backed up. The only thing that could have been done better would be the explanation of low copy number DNA analysis. The author did not spend a lot of time explaining what exactly this technique is, what it does, or how it works; the description was pretty vague, considering the entire article was based on this concept. I was able to get a basic level of understanding of low copy number DNA analysis, but it would have been beneficial to provide a more detailed description. However, in the end, I did definitely learn a lot from this article and found it pretty interesting.

Zimmer, Carl. "DNA Under the Scope, and a Forensic Tool Under a Cloud."The New York Times. The New York Times, 26 Feb. 2016. Web. 01 Mar. 2016. <http://www.nytimes.com/2016/02/27/science/dna-under-the-scope-and-a-forensic-tool-under-a-cloud.html?rref=collection%2Fsectioncollection%2Fscience&action=click&contentCollection=science®ion=rank&module=package&version=highlights&contentPlacement=9&pgtype=sectionfront>.