On the Origin of Life: Studying how the First Biomolecule Self-Replicated

Researchers propose that RNA is the "mother" molecule that led to the formation of life.  In order to reproduce; plants, animals and other organisms need to make copies of their DNA and pass it on to the next generation.  This is possible with the aid of enzymes and through Watson-Crick Base Pairing (genetic material is made up of nucleotide bases which match to one another in a specific order).  Scientists hypothesize that before life began, there had to be one molecule that was able to replicate without any help.  They suspect that this molecule is RNA due to its ability to specific base-pairing like DNA, and catalyzing reactions like an enzyme.  Jack Szostak and colleagues used X-ray crystallography to monitor how free nucleotides interacted with a short piece of RNA.  They did this to investigate how RNA matches up with free base pairs.  The RNA formed the expected Watson-Crick pairs as well as other different match ups that may have stopped replication.  This information led scientists to believe that steps toward life may have taken much longer than expected.

https://www.sciencedaily.com/releases/2016/11/161102085329.htm
https://www.acs.org/content/acs/en.html

Running Out of Hard Drive Space? Use Your DNA.

Running out of space on your hard drive or memory card? Scientists at the University of Washington partnered with Microsoft have discovered a new way of storing electronic information such as pictures or vides, and the method of storage is anything but technological. It is a memory device of a more organic form, DNA. Their successful system allows for the upload, storage and retrieval of digital data using a DNA molecule as the storage device. 

Technological advances are growing everyday and people everywhere are becoming more dependent on technology. The amount of digital data worldwide is expected to hit the trillions within the next five years, so finding a more efficient method of data storage is becoming a crucial issue. DNA can hold data much more efficiently than any technological device. DNA decays at a much lesser rate than any hard drive or memory card, so data can be stored for centuries as opposed to decades. Also DNA can hold an unexpectedly high amount of data, 10,000 gigs to be exact. This large amount of data does not require more than a small amount of DNA for storage, just enough to fill the very bottom of a test tube is plenty to store 10,000 gigs. In this study scientists successfully encoded four photos as nucleotide sequences of synthetic DNA. Once encoded the photos were successfully retrieved in a reverse process from a larger pool of DNA strands. The resulting images were amazingly reconstructed in their entirety, not a single piece was missing. 

This method of data storage seems to be extraordinarily promising, however the scientists do not mention how long data encoding and retrieval takes. As an increasingly impatient species people may be resistant to using this method if storage and retrieval takes days or even just hours to achieve. I am interested to see where the studies on this method go, it seems like a promising method. DNA stores an astonishing amount of genetic information on it, so the thought that I can someday store my thousands of pictures on a DNA molecule is quite intriguing. 

"AAAAA Is for Arrested Translation"

In a post by Ruth Williams focusing on recent research results, a study conducted on the halt of protein translation found that multiple adenosine nucleotides in messenger RNA was the reason behind the interruption. The finding contradicted the idea that protein sequences were responsible. The importance behind the failure of the ribosome protein to translate the codon sequences of mRNA into amino acids lies on the fact that the mRNA and developing protein are degraded during the process.
Due to Rachel Green and her research team at Johns Hopkins University School of Medicine, it was found that there is a significance in the difference between mRNA sequences and associated amino acids. Bacterial ribosomes were found to halt on lysines in the presence of AAA codons as opposed to AAG codons. The research team, utilizing human cells, went on to find that reporter gene constructs with lysines encoded by AAA sequences had far less protein production then lysines encoded by AAG, as well as arginines encoded by AGG and CGA codons.
Two outcomes from this research were particularly important- bioinformatic analyses of vertebrate genomes proposed that the AAA codons are not favored evolutionary, and previously thought silent mutations may actually alter protein expression. The AAA sequence was thought to not be favored, being that the chance of lysines encoded by such a sequence was much lower than the chance of being encoded by AAG codons. The rejection of the silent mutation inference to instead be of greater importance, stemmed from mutating AAG codons to AAA codons and finding a decrease in protein expression. The opposite result was found from mutating AAA codons to AAG codons.
It is particularly interesting how failing to discover one tiny aspect of the translation process could later result in finding reasons behind translation failure. This may suggest that silent mutations are even more rare than previously thought, and that perhaps these mutations are simply misunderstood rather than inactive in many processes.

DNA Sequencing improved by lower speed

DNA sequencing has long suffered from inaccuracy and mistakes in readings despite leading technology. Nanopore sequencing is what researchers and professionals use today. DNA strands are passed through a nano-sized pores. Each of the four nucleotides have a unique characteristic that allow them to be read. Because the pores have an electrical current, the nucleotides will block the current in distinctive ways when they pass through. The method is revolutionary, without a doubt, but it is highly prone to mistakes because DNA strands pass through way too quickly.

This issue came to the attention of Aleksandra Radenovic's lab at EPFL's Institute of Bioengineering. With the help of researchers who led the project, Jiandong Feng and Ke Liu, they discovered a viscous liquid, capable of slowing down the process by a 1000 times, increasing the accuracy by a huge magnitude.

First they created a film made of molybdenum disulfide (0.7 nm thick) and made a nanopore in the film about 0.3 nm wide. Then, they dissolved DNA in a liquid, classified as a room temperature ionic liquid (salt dissolved in a solution). By altering the liquid's molecular structure, they were able to bring it to a more preferable level of viscosity to read the DNA more accurately. The researchers have used this test on nucleotides but they are still aiming to read whole DNA strands using this method.

I think this research is highly innovative and points us towards better technology in the field of genetics. The researchers are very passionate about their findings and hope that it can make DNA sequencing more effective and cheaper. This is an important discovery to me because genetic sequencing is the backbone of genetics; everything originates from the molecular level and to improve this technology can mean improvements in health as well. Maybe one day genetic sequencing can become more widespread and easily accessible if we have technology that  is quick,

Original Link

A New Discovery May Open Doors for Possible Treatments for Alzheimer's Disease

        A group of researchers, led by Andrew J. Saykin, Psy.D and Vijay K. Ramanan, PhD, recently completed the largest genome-wide study of human memory. Andrew J. Saykin, Psy.D is the director of the Indiana Alzheimer Disease Center and the Indiana University Center for Neuroimaging. Vijay K. Ramanan is a Indiana University School of Medicine post-doctoratal researcher and a medical student. Together, Saykin and Ramanan, led a research team have identified a gene that they believe is associated with better memory performance and has not previously been associated with cognition. They found this gene as a result of analyzing genomic data and memory test from more than 14,000 older adults.

Andrew J. Saykin, Psy.D

        A change in the DNA on chromosome 2 was found to be linked to better performance on episodic memory test. Usually, a G nucleotide had replaced the more common A nucleotide in the FASTKD2 gene. This single nucleotide polymorphism was also found to be linked to a larger hippocampus and more dense grey matter. The FASTKD2 gene is found in the inner compartment of mitochondria and is responsible for producing an important protein involved in mitochondrial apoptosis.

 

         Since Alzheimer's disease is associated with hippocampal atrophy and the inability to recall recent events, this drug is believed to point the way for drug developments and further studies on memory impairments caused by Alzheimer's disease. "Although the influence of FASTKD2 was modest, there are parallels to research in diabetes, cancer, and hypertension that uncovered genetic variants with similar effects that turned out to be targets for drugs that are now commonly used," Dr. Saykin said.

        This article stood out to me because a couple people close to me had Alzheimer's disease. It's amazing that even though many scientists research the same subject, new discoveries still occur frequently. This FASTKD2 gene should be researched more. Although memory is not controlled by a single gene, this SNP could possibly be the answer to a lot of questions about memory loss. It would be amazing if the FASTKD2 gene led to a drug protecting against memory related issues in Alzheimer's disease.

Main Article: http://www.sciencedaily.com/releases/2014/11/141112115934.htm
Related Article: http://news.medicine.iu.edu/releases/2014/11/saykin-memory-snp.shtml

mbPAINT and Genetic Diseases

    This month, ScienceDaily shared an article about DNA mapping. With high-tech optical tools, researchers of Rice University have now found a way to pinpoint the location of specific sequences along single strands of DNA. This technique has been proven to someday help diagnose genetic diseases. Chemist Christy Landes, a lead researcher, identified DNA sequences as short as 50 nucleotides at room temperature using a technique called super-localization microscopy. This would be impossible to see with a standard microscope because it cannot comprehend such small targets. Also, it cannot be done with electron microscopes because it requires the targets to be frozen. Super-localization microscopy has been known about for a while but is just now being used in biosensing. For a while now, scientists have been able to see double-stranded DNA molecules, but Landes says the ability to see single-stranded DNA is a new victory in science. Landes and her researchers call their technique the "motion blur point accumulation for imaging in nanoscale topography," or mbPAINT. This technique has allowed them to resolve structures as small as 30 nanometers by creating a movie-like drift of fluorescent DNA probes flowing over a known target sequence along an immobilized single strand of DNA.



    To create effect, the probes were labeled with a fluorescent dye that lights up only when attached to the target DNA. Normally, they would flow unseen, but a few would bind to the target just long enough to be captured by the camera before they were pulled away by the moving liquid. The processing of these images will allow researchers to image extremely small objects, smaller than the natural diffraction limit of light-based imaging. To the naked eye, in real time you would only see a line due to the rapid speed of the probes. This technology allows researchers to see biological processes of nano-sized objects. It shows as they happen in water, with salts, at room temperature and even in a cell. So, what is planned for the future? Landes hopes to be able to someday map even smaller fragments of DNA. Instead of seeing 50 nucleotides, she hopes to be able to look at only a few. Landes stated, "Some diseases are characterized by one amino acid mutation, which is three nucleotides, and there are many diseases associated with very small genetic mutations..." With this being said being able to get it down to just a couple nucleotides could become extremely helpful with genetic disease study.

In my opinion I feel that this new development in DNA strand study can become extremely beneficial to not only the field of science, but also human health. For many years researchers have been studying genetic diseases but can only go so far. Super-localization microscopy has now offered many people hope to finding specific mutation in genetic diseases that have not yet been identified. If Landes and her researchers were able to identify DNA sequences as short as 3 nucleotides, it would be an amazing scientific find, especially considering a great amount of genetic diseases have small, localized mutations. In addition, the mbPAINT method is very cost-effective.

Article: http://www.sciencedaily.com/releases/2013/10/131009111151.htm

Link: This is a video of what it looks like to see the single-strand  localization http://www.youtube.com/watch?v=dc6i3ZkZhd0&list=PL46869D7222684E1A