Scientists Develop New Genetic Bases

       
Chris Miller

Main Article:

          Pollack, Andrew. "Scientists Add Letters to DNA’s Alphabet, Raising Hope and Fear." The New York Times. The New York Times, 07 May 2014. Web. 23 May 2014.

Additional Sources:

Greenfieldboyce, Nell. "Chemists Expand Nature's Genetic Alphabet." NPR. NPR, 7 May 2014. Web. 23 May 2014.

Landau, Elizabeth. "New Life Engineered with Artificial DNA." CNN. Cable News Network, 9 May 2014. Web. 20 May 2014.

Malyshev, Denis A., Kirandeep Dhami, Henry T. Quatch, Thomas Lavergne, Phillip Ordoukhanian, Ali Torkanami, and Floyd E. Romesburg. "Efficient and Sequence-independent Replication of DNA Containing a Third Base Pair Establishes a Functional Six-letter Genetic Alphabet." PNAS. Proceedings of the National Academy of Science, 6 June 2012. Web. 23 May 2014.

Service, Robert F. "Designer Microbes Expand Life's Genetic Alphabet." Science/AAAS. American Association for the Advancement of Science, 7 May 2014. Web. 23 May 2014.

          Scientists from the Scripps Research Institute in California have developed two additions to life's four known nucleotides- adenine, thymine, guanine, and cytosine- known as X and Y. X and Y bases were developed after over three hundred failed base formulas and structures that simply did not work as well. The new bases are drastically different from the typical ATGC bases used by natural life. The bonding between base pairs of A-T and G-C is based on hydrogen bonds- hydrogen molecules bond strongly with nitrogen, oxygen, and fluorine molecules, pulling the bases together. However, the new X and Y bases utilize hydrophobic interactions and complementary shapes, allowing them to have similar bond strength and stability to A-T and G-C pairs. Incredibly, when an E. Coli cell was modified to include X and Y bases and supplied with free floating X and Y nucleotides, the DNA Polymerase enzyme which replicates DNA, was able to successfully copy the X and Y bases with an error rate of just .1%. The team is currently attempting to decrease the error rate to .01% using a variety of polymerases, at which point the transcription error rate would be indistinguishable from the error rate of the natural bases. However, without externally supplied X and Y nucleotides, the cell became depleted and the X and Y nucleotides were replaced with other bases. Though developing a mechanism for cells to synthesize their own X and Y nucleotides is a complicated undertaking, Stephen Benner, a researcher at the Foundation for Applied Molecular Evolution in Florida is attempting to solve the problem. Meanwhile, the Scripps research team is using a protein from algae that takes nucleotides from the material around the cell, allowing them to artificially supply X and Y nucleotides. Researchers are encouraged by the finding that due to the stability of the X-Y pair, DNA repair enzymes do not recognize the pair as damaged. This means that the DNA will not try to get rid of the unnatural X-Y pairs, silencing concerns that X-Y pairs would be excised due to their abnormal effect on DNA's double helix shape (the X-Y pairs cause the double helix shape to become slightly deformed, as seen here. Not only do the repair enzymes not harm the X-Y pairs, but the low error rate of X-Y transcription implies that the enzymes are actually repairing the X-Y pairs just as they would with A-T or G-C pairs. The researchers have not yet attempted to transcribe altered DNA into mRNA, however when they do they plan to also insert artificial tRNA which is able to recognize the X and Y bases and release a predetermined amino acid, creating all new natural proteins.

Top- X-Y bases. Bottom- C-G bases, with visible hydrogen bonds.

          At this point, the team's primary goal is getting cells to transcribe the DNA into mRNA, synthesizing tRNA that can read the new bases, and actually creating proteins coded from the new bases. Their addition of two bases to DNA's repertoire quadruples the amount of information that DNA can carry, and the team, which has since formed their own company, Synthorx, hopes to use this newfound storage capacity to expand life's typical library of twenty amino acids to a theoretical maximum of a hundred and seventy two. More amino acids would allow cells to create new proteins with vastly different functions from those available to cells today. Scientists hope that the new pair may be utilized in beneficial viruses. The requirement of externally-supplied X and Y nucleotides means that cells containing X-Y pairs in their DNA cannot accurately reproduce without a constant supply of the nucleotides. This would allow scientists to create a virus which could be used against diseases or to repair cells, then die as supplies of X and Y nucleobases are cut off, alleviating concerns that the virus could stay alive, mutate, and do damage. Advancements in this area would allow for whole new classes of revolutionary medicine- instead of slowly synthesized artificial drugs, cells could rapidly create evolving proteins to combat disease in the body. Additionally, research with the new nucleotides may allow scientists to find out why all modern life uses the four traditional bases instead of other bases. Were there originally other bases at the dawn of life? Is a four base system more efficient, or is it just how life happened to evolve? However, the research also raises ethical and legal questions. The field of synthetic biology is not heavily regulated, and lacks oversight and restrictions. This raises ethical issues as to how far researchers should go. For now though, the research is limited to the cellular level, as are most of its implications.

         Though the main New York Times article by Andrew Pollack was fascinating and inspired me to look more into the subject, the article did not include enough details. This isn't the author's fault; the complexity of the research and all the implications are difficult to summarize in a short article, and none of the other articles I looked into were able to condense everything relevant into a few paragraphs of text. The article was able to effectively summarize who did the research, exactly what was and what was not accomplished, and some of the implications of the research. However, the title of the article, "Scientists Add Letters to DNA's Alphabet, Raising Hope and Fear" seems to imply more risks than actually exist. Outside of their X-Y nucleotide rich cultures, the modified E. Coli cells will not stay modified long. Fortunately, other articles from CNN, NPR, AAAS, and more were able to fill in other details that the New York Times article missed, and the missing details forced me to look deeper into the subject than I might have otherwise.

Potential of Gene Therapy Using T Cells for Cancer Treatment

By: Caroline DePaul

DePaul, Caroline. Potential of Gene Therapy Using T Cells for Cancer Treatment. Rep. N.p.: n.p., n.d. Print.

There is a new idea for adoptive therapy for treating cancer with the use of altering your T-Cells. T-Cells are your white blood cells and each T-Cell is shaped to target a specific antigen as an immune response. The idea of T-Cell Gene Therapy is to alter the shape of the cells to target tumor antigens as a way to kill cancer cells. Adding a chimeric antigen receptor to the T-Cells would make the T-cells attack tumor antigens. However, there are some risks to adoptive T-cell therapy such as, potential toxic effects when healthy tissues express the same target antigens as the tumor cell. When the T-cell has been altered and knows to target the cancerous cells the T-cells release perforin and cytotoxins, which both work to destroy the cell. The perforin and cytotoxins enter a newly created pore of the cell and completely killing the cell. Other helper T-cells do not target cells individually but they send out chemical messages to trigger certain immune cells to replicate or produce cytokines. There have been durable remissions after the use of T-cell therapy. T-cell engineering is looking very promising for treating blood cancers like leukemia.

I think that T-cell engineering could possible be very helpful, especially in treating blood cancers. T-cell engineering has been shown to be effective because it is using the cells that target viruses and just making them target a specific antigen to kill off all the tumor cells. Though there are some down sides to T-cell engineering I think that over time scientists will be able to find a specific helper T-cell that wont cause damage to healthy tissue. Overall, t-cell engineering is an incredible new alternative to chemotherapy and other treatments, which can be very taxing on the elderly especially because their bodies are weaker. Gene Therapy is very important to today’s society because all over the world people have cancer and there aren’t too many effective options for treatment because it is such a tough disease. Having another option to treat cancer is taking us one step closer to finding a cure.

I think the poster was very well done and presented in a well-explained manner. Caroline used a brilliant combination of diagrams and graphs to help me and the other viewers understand exactly how the T-cell engineering works. I think there could have been some more explanation of what exactly the T-cells function is. Also, some parts of the poster were very wordy and included a lot of confusing different types of T-cells without any explanation. The only thing the poster lacks is some explanatory detail in few places. Other than that I think that the poster and presentation was very well done. I hope to read and hear more about T-cell engineering and be updated on the results of the treatment. I found the learning about the potential gene therapy using T-cells very interesting and I cannot wait to read up about it again!

"The Big Melt Accelerates"

Jude Bato Biology

Mrs. McClellan Due: May 23, 2014

Chang, Kenneth. "The Big Melt Accelerates." The New York Times. The New York Times, 19 May 2014. Web. 20 May 2014. <http://www.nytimes.com/2014/05/20/science/the-melting-isnt-glacial.html?ref=science>.

It is apparent that the world is getting warmer. Ice caps in the North and South poles are melting, causing sea levels to rise, with new research, many of these melted glaciers have passed a point of no return, which could set off a chain reaction for many other ice caps, and place covered in ice.

Even if global warming halted completely, the climate of the Earth had already reached a tipping point. The whole Earth climate, atmosphere and temperature have began to swag towards the more humid and wet, because of these melted sums of ice.

“We as people see it as closing doors and limiting our future choices,” said Richard Alley, a professor of geosciences at Pennsylvania State University. “Most of us personally like to keep those choices open.”

While some glaciers are holding steady or even growing slightly, most are shrinking, and scientists believe they will continue to melt until greenhouse gas emissions are halted. “It’s possibly the best evidence of real global impact of warming,” said Theodore A. Scambos, lead scientist at the National Snow and Ice Data Center.

“But the mountain glaciers have been telling scientists what the West Antarctic glacier disintegration is now confirming: In the coming centuries, more land will be covered by water and more of nature will be disrupted. A full melt would cause sea level to rise 215 feet.” He is saying that the most problematic situation is the Antarctic, because it is located near the coldest places on the Earth.

“During recent ice ages, glaciers expanded from the poles and covered nearly a third of the continents. And in the distant past there were episodes known as Snowball Earth, when the entire planet froze over. At the other extreme, a warm period near the end of the age of dinosaurs may have left the earth ice-free. Today the amount of ice is modest — 10 percent of land areas, nearly all of that in Greenland and Antarctica.” The future of this planet may lead to a new ice age, by which most, if not all, the bodies of water will freeze and cause the Earth’s median temperature to decrease dramatically.

Core Bio                                                                                              Yasmeen Fahr

Current Event                                                                                               5.21.14

Pensoft Publishers. "New species of metal-eating plant discovered in the Philippines." ScienceDaily. ScienceDaily, 9 May 2014. <www.sciencedaily.com/releases/2014/05/140509130040.htm>.

            For my current event, I read an article titled “New Species of Metal-Eating Plant Discovered in the Philippines.” As explained in the title, scientists have discovered a new species of plant named Rinorea Niccolifera that, strangely enough, feeds off of Nickel. Professor Edwino Fernando notes that this plant can ingest up to 18,000 ppm without being poisoned. This plant’s strange ability is found to be incredibly unique, with only about 450 of the 300,000 plant species displaying it. This plant has been placed under the category “hyperaccumulators” which are plants that live in soil with a high concentration of metal.

            The discovery of this plant is extremely important because it shows scientists where they should look for new plant species and gives them hints as to what these undiscovered plant species might be like. For example, now that this new species has been discovered, scientists might begin to look for more hyperaccumulators that perhaps ingest a different metal, or that ingest the same metal in higher concentrations. The possibilities are endless.

            I found this article very interesting and well written, but a bit sparse in information. The topic was extremely interesting but with limited data and facts on it. Otherwise, the article was very informative and overall a great read!

Young Blood May Hold Key to Reversing Aging

Alex Szor

5/20/14

Current Event

Young Blood May be Key to Reverse Aging

           

            In a new study done by two scientists from Harvard and Cornell, there has been an experiment done on mice to look into reverse aging. This experiment consisted of the scientist removing blood from the younger mouse and putting it in the older mouse. When testing the scientist got results that showed that when the younger blood was transfused, the older mice started to show signs of reverse aging. After the experiment was done the scientist did research on why this was happening. The scientist found that there was a protein called GDF11 that was found in the younger mouse’s blood but not the older mouse. Scientists then researched the protein and found why the protein was making such a big difference. The protein was increasing the efficiency of stem cells in the older mouse. As you get older your stem cells start to become less effective which causes aging. This protein that’s found in the younger mouse speeds up the stem cells in the older mouse, which is why the ageing process was revered. A similar study was done several decades ago on rats however the reason for the results was unknown until this study was done on mice.  Stem cells play an important role because the more efficiently they operate the faster they make cells, which is why when your younger you heal much more quickly. Since the stem cells in the older mouse weren’t growing as fast, a lesser amount of cells were being made which is why the mouse was aging.

            This is very important and could have major implication on the human race. It can help cure multiple diseases such as Alzheimer’s, heart disease, among multiple other diseases. Not only can it help medically but also it could have a huge impact on the market. Since some of the richest doctors are plastic surgeons this could be an alternate to having surgery. This could also have a negative impact because of diseases transferred through the blood. It can also leas to multiple religious debates and over population.

            I really enjoyed this article and I thought it was really well written. I liked that there was opinions from multiple different doctors from multiple different medical centers. I also like that it gave a lot of fact and really gave you the big picture of this experiment. The only thing I wish they did was added more information on the stem cells and more detail on how they lead to aging. Besides that I really enjoyed this article and I learned much from it.

Zimmer, Carl. "Young Blood May Hold Key to Reversing Aging." The New York Times 4 May 2014. Web. <http://www.nytimes.com/2014/05/05/science/young-blood-may-hold-key-to-reversing-aging.html?ref=science>.

Thousands of Toddlers Are Medicated for A.D.H.D., Report Finds, Raising Worries

Biology                                                                                                                           Mia Bettino

Current Event Report                                                                                                            5/19/14

Schwarz, Alan. "Thousands of Toddlers Are Medicated for A.D.H.D., Report Finds, Raising Worries." The New York Times. The New York Times, 16 May 2014. Web. 19 May 2014. <http://www.nytimes.com/2014/05/17/us/among-experts-scrutiny-of-attention-disorder-diagnoses-in-2-and-3-year-olds.html?_r=0>.

            This article is about young children diagnosed with attention deficit hyperactivity disorder being diagnosed with medications like Ritalin and Adderall, which some doctors find very unsafe for small children and their developing brains. Based off of a report by Susanna N. Visser, it is estimated that ten thousand two- and three- year olds are being treated with such medications. She says that families with children that have behavioral issues are coming to the doctor for help and the children are being diagnosed with A.D.H.D. instead of making an effort to change their child’s learning environment. Some children are misdiagnosed, for behavioral issues are sometimes a result of a violent or neglectful home life. Dr. Doris Greenberg, a behavioral pediatrician, says, “You have children with depression and anxiety who can present the same way, and these medications [like Ritalin and Adderall] can just make those problems worse.” A 2006 study about the effects of methylphenidate (Ritalin) showed that these medications could help with A.D.H.D. symptoms, but the study was only performed on a small number of three-year-olds. Overall, it is very controversial as to whether or not these stimulant drugs on young children with A.D.H.D., especially since so many children are misdiagnosed.

            This article is very relevant to today. I have heard a lot about more and more children being diagnosed with attention deficit hyperactive disorder and that they are often treated with these drugs, but I had no idea that children were being given these medications as young as two years old! Since A.D.H.D. diagnoses are on the rise, it is very important that doctors are careful with what they are prescribing to young children and why. Behavioral pediatrician Dr. Lawrence H. Diller said, “People prescribing to 2-year-olds are just winging it. It is outside the standard of care, and they should be subject to malpractice if something goes wrong with a kid.” Obviously, some people are taking this controversy very seriously.

            I really enjoyed reading this article. It gave me good background information about the topic and went into detail about why this is such a big controversy. I learned that one in five boys will be diagnosed with A.D.H.D. during childhood! That is a huge number – that is way larger than I expected. This article was to the point but gave enough information so that I felt well informed about this topic after reading it. One question that arose while reading the article was: What are some things that could happen to a child if they respond badly to the stimulant drugs? I thought that this was key information that the author left out. However, the article was very well-written and has made me curious to find out more.