With Environmental DNA, Small Water Samples Can Find Really Big Animals

In an article posted by SciTechDaily, a team of scientists from California State University (CUNY), the Wildlife Conservation Society (WCS), and Columbia University used an emerging genetic tool to detect whales and dolphins in the New York Bight. This technique searched for environmental DNA (eDNA), or trace amounts of genetic material left behind by wildlife in the water. The results of this study were published in the journal Frontiers.

The scientists said that eDNA can be used to support other efforts to locate whales and dolphins, such as visual observations and acoustic monitoring. According to the study’s lead author, Dr. Elizabeth Alter, “Determining how cetaceans and other threatened marine animals use coastal habitats is critical to their effective conservation. By generating eDNA data in parallel with survey data, it will be possible to gain a clearer understanding of how this tool can be used in management…”

This technique also detected baitfish present in the area preyed on by whales and dolphins in addition to finding the mammals themselves. The authors claim that in the future, as technology improves, this technique could eventually be used to identify individual animals. Because eDNA drops to lower levels over time, the authors also state that additional research is needed to better understand how behavior and oceanic conditions contribute to the longevity of eDNA signals.

Though there are some signs of promising recovery for many whale populations, whales continue to face a range of modern-day threats such as ship strikes, ocean noise, entanglement with nets, and a general loss of habitat. For example, there are currently plans to scale up massive renewable energy projects to meet energy demands in the United States, including a wind energy auction for more than 488,000 acres in the New York Bight. The use of emerging techniques such as eDNA can provide a new perspective on the current status of whale populations and their prey in and around lease areas as offshore wind operations scale up along the east coast. The WCS has also extended these eDNA techniques to detect critically endangered wildlife such as Swinhoe’s softshell turtle, in the Bolivian Amazon, and in some of the most rugged areas on the planet including Mt. Everest.

Related article: https://www.forbes.com/sites/grrlscientist/2018/05/18/the-power-of-environmental-dna-for-monitoring-whales/?sh=64ccf93f264c

How the Brown Rat Conquered New York

Rats are known to contaminate the places that they inhabit with feces and urine in addition to viruses and bacteria. In many ecosystems they even threaten other species with extinction. They have managed to inhabit wherever humans have. Dr. Munshi-South, a biologist at Fordham University and his colleagues conducted an in-depth genetic study on brown rats after they posed to question “What is a New York rat?” They found that once brown rats settle into a new city, they repel newcomers.

            In order to conduct the study, the team contacted researchers from all over the world in order to compare DNA of rats from around the world to rats in New York. They ended up analyzing the DNA samples of 314 brown rats from thirty countries; from this data, they were able to conclude that different population of rats mixed together over time in order to produce the brown rat. They found that brown rats originated in northern China or Magnolia even though it was previously believed that the brown rat originated in Norway. Farming societies and widespread trade became more and more popular and rats began to migrate, which gave rise to the rats that we know now.

            A biologist at Rice University, Michael Kohn, said that that the brown rats are territorial, so it is hard for other types to get in. Many of the rats that he and his team examined were missing eyes, tails, and had scars that looked like they had been in a brutal fight. He said that this is most likely why we do not see many different kinds of rats in that area. I used to live in New York and now that I am thinking about it, all of the rats that you see in subways, all did look the same. It is cool though that the rats are so territorial that they do not let other types of rats into the city. 

Genetics Show How the Brown Rat Conquered New York City

Big cities like New York are riddled with millions of brown rats. They are considered a nuisance by the many as the rats spread disease, damage property, and basically just make a big mess of things. However, a recent study conducted by Dr. Munshi-South and his colleagues may have discovered an upside to having these undesired pests around. It all started when Dr. Munshi-South wanted to answer the simple question of “what is a New York City rat, and where did it come from?” so he asked researchers around the world if they could send him DNA samples in order to could compare the DNA of rats from different areas to the DNA of rats he had captured in New York. Many samples come in from all over inspiring him to discover not just where the New York brown rat came from, but where the world’s brown rat came from.

After analyzing all the samples it was discovered that the brown rat originally came from China. They started off wild but as farms began to form they moved to these farms as it was a more reliable food source. Eventually they began expanding further, inhabiting places all around the world. They either traveled on land or stowed away on ships, which carried them overseas. The brown rats that made it to Europe managed to spread across the world the most because when Europeans began to colonize the West the rats colonized with them. This is still happening today, as rats from different countries continue to arrive in New York. Surprisingly enough though, there is very little sign of any genetic mixing in rats from New York.  It is theorized that the New York brown rats are keeping migrants out. This can be attributed to the fact that brown rats are very territorial, which means they are stopping any foreign rats from getting in. This is where the possible bright side of having rats around comes in. Thanks to them, other brown rats that might be carrying foreign diseases are unable to get into cities.

The results of this genetic research puts a positive spin on brown rats that are normally regarded with great animosity. It makes me think that brown rats might be worth keeping around instead of exterminating them. They might not be clean, they might cause damage, but if the theories here are correct then they are also the reason that diseases far worst aren’t spreading through our major cities.

http://www.nytimes.com/2016/10/28/science/brown-rat-new-york-city.html?rref=collection%2Fsectioncollection%2Fscience&action=click&contentCollection=science&region=rank&module=package&version=highlights&contentPlacement=1&pgtype=sectionfront&_r=0

http://rspb.royalsocietypublishing.org/content/283/1841/20161762

How the Brown Rat Conquered New York City

The brown rat has managed to populate New York city by the millions, with billions more in other cities across the world. They contaminate crops and food supplied and destroy wires, walls, and cars, while spreading bacteria and disease. However, scientists are not entirely sure as to how Rattus norvegicus became so rampant. Dr. Munshi-South and colleagues finished a study of brown rats that began to answer the question of what is a New York city rat and where did it come from? They found that these rats began spreading slowly for thousands of years, but in the past three centuries they spread much more rapidly. Dr. Munshi-South contacted researchers from around the world and obtained DNA from hundreds of brown rats, from Japan, New Zealand, Brazil, and the Galapagos Islands to name a few,  to compare to that of the rats of NYC. The study revealed that brown rats originated in northern China or Mongolia and fed on wild plants and small animals, until farming in China began, during which rats found a reliable food supply and moved from open plains to farms and villages. The rats then began to expand to other parts of Asia, and eventually west to Europe. It is these rats that are the ancestors of the inhabitants of New York today. As European countries colonized the Western world, they took the rats with them.

Dr. Munshi-South thought that he would find that New York's rats have a mix of genes from ancestors from all over the world, but he found little evidence of genetic mixing in New York or any other city. It seemed that there was not many migrants that arrived and reproduced after a city was already populated with rats. This could be because brown rats are territorial and simply mean, as noted by missing eyes and scars observed by Dr. Mushi-South in many rats. The theory is that the first rats to arrive in a city reproduce rather quickly, so when new rats come along, they are no match for the residents that have already inhabited the city. This is a good thing because it is unlikely that new diseases on new rats can come into a city that is already populated with rats.
Based on the results of the study, I think that we should not take action to eliminate brown rats. Although they do spread bacteria and destroy wires and walls, they are keeping out lots of potential disease because of their territorial nature.

Mystery Microbes Among DNA Diversity on NYC Surfaces

A recent study published in Cell Systems found that several organisms on the NYC subway and other places in the city, match no other known organisms. Over a 17 month period, Researchers at Weill Cornell medical college went throughout the city (above and underground) swabbing benches, handrails, poles, and doors. They found that almost half of the DNA they discovered had been completely unknown to science. 

Along with the mysterious DNA, researchers found recognizable DNA such as bacteria and viruses, both being mostly harmless. They also identified small particles of DNA from anthrax and the bubonic plague. Overall they found that only 12% of the thousands of Bacteria and virus samples discovered, were associated with diseases. The most common microorganism found was Pseudomonas studtzeri, a rod-shaped bacterium known for its flexible metabolism that can cause infection in humans.

         The researchers also found that human DNA found in subway stations aligned with the ethnicity of people living in that area. Samples taken in the subway near a neighborhood with high numbers of Hispanic residents, yielded a large amount of Hispanic and Asian genes. Samples from the Brooklyn neighborhoods turned out to host genes specific to British, Tuscan and Finnish heritage. These researchers now say that by understanding the normal population of microorganisms in the city, they now have a baseline to compare new samples against in the case of bioterrorism or a disease outbreak.

I find this study very interesting because of how much researchers can find out about a city just by looking at DNA swabbed from random places. Also, how they found a sample related to the plague was very interesting, (but also a bit scary). 

Original Article

Favorable CETP Variant Can Signify A Longer Life

        A new study found that people with a particular gene variant, in the gene CETP, may survive the longest. CETP, cholesteryl ester transfer protein, is located on chromosome 16. It is a plasma protein that facilitates the transfer of cholesteryl ester from high density lipoprotein (HDL) to other lipoproteins. HDL is known as the "good" kind of cholesterol, and an increase in the blood levels of HDL is caused by the favorable variant of the CETP gene.  

        For a long time, researchers knew that people with this gene variant have a better chance at living longer than 95, and sometimes even 100, years. A new study, presented by Dr. Sofiya Milman, shows that when comparing elderly people above the age of 95, the people with the advantageous variant of the CETP gene outlive the other elderly people. This study expands on the work began at Einstein College of Medicine in New York City in the 1990s. When describing the centenarians she has studied, Milman says, "They don't only live longer, they live healthier too."
        Before conducting the study Milman was aware that the CETP variant was found to be related to decreased rates of heart disease and strokes and sharper mental function. Milman conducted the study by gathering 400 ninety-seven year old New York residents and following them for about one to eleven years. The researchers found evidence confirming that people with the favorable CETP variant and higher HDL levels lived longer.

 

        CETP and HDL are not the only keys to a long life. Exercise, healthy eating, and adequate sleep are still some very important aspects to a long and healthy life. Understanding CETP, HDL, and other "longevity" genes are still important and may open many doors in the research world. "Down the road, it might be possible to develop therapies that mimic these genes' effects," Milman believes.

        This article stood out to me because the subject of long life is really interesting to me. As a child, I always believed that researchers would eventually invent a "magic potion" that caused everybody to live forever. Hearing there is a gene that effects one's life span and that drug companies have already started working on CETP inhibitors, makes my childhood assumption sound closer than ever. Now that I think about everybody living forever, it might not actually be a good thing. Overpopulation would be an extreme concern and resources would diminish even quicker. This article is still very fascinating and makes me wonder if I could possibly have the favorable CETP variant.

Main Article:  http://medicalxpress.com/news/2014-11-longevity-gene-key-life.html
Related Article: http://www.sciencedaily.com/releases/2010/01/100112165234.htm

Spit out your gum and become a sculpture

Ever wounder what happens to that piece of gum you spit out on the sidewalk or that used tissue you threw away well wounder no more. Heather Dewey Hagborg , Ph.D. candidate in Electro Arts at Resselaes Polytechnic Institute, who is living in New York is putting all of those used tissues and chewed pieces gum to good use. Hagborg uses the chewed gum to retrieve DNA, by genetic analysis, from the person who chewed it and uses 3D printing techniques to creates a 3D facial sculpture of that person without ever having to meet that person in person. Hagborg gets most of her art materials from public sidewalks, subways, and public bathrooms in New York. She mostly uses items people have left saliva or DNA on like gum, cigarette butts, used tissues, and what ever else she can find. With all the items she finds she creates a exhibit of anonymous strangers. Hagborg does not create an exact copy of the persons face, but she creates more of a resemblance of the person.      

I found this to be very interesting because I never really thought people would want to use someones used and chewed gum to create a sculpture of them. It also interested me because the creator of the sculptures was using pretty much anything that people had left their spit on to create an exact 3D sculpture of their face.

http://www.cnn.com/2013/09/04/tech/innovation/dna-face-sculptures/

Artist Creates 3-D Faces from DNA Left in Public

3-D faces created from DNA samples found in public. 

                A New York Artist Heather Dewey-Hagborg picks up things people leave in public, extracts their DNA from it and creates a 3-D face that looks like the DNA owner. This project is called “Stranger Visions”, where portrait sculptures are completed from the bits of genetic material that are collected in public. Heather got the idea for this project from the appeal of a single hair; it was then turned into a research project to discover as much as she could from someone by an artifact they left behind.

                The process begins with finding a sample in a public place. These samples could be a strand of hair, a chewed piece of gum, and even a cigarette butt; it has to be something that contains cells from a person’s body.  Heather then takes this sample to a community biotechnology, called Genspace. At this lab a standard DNA extraction protocol is used to mine the DNA, purify it, and use it in polymerase chain reactions. After the sequencing information is obtained, the traits form the individual’s DNA and deposits it into a computer program that generates a 3-D model of a face. This process takes about 8 hours to print one of the faces in NYU’s Advanced Media Studio. The print looks like a block of powder; the face is then dug out, baked, and hardened with a superglue-like structure.

                

                There are limitations behind these masterpieces. These faces are not exact replicas of the strangers DNA that has been found. Heather insists that it is more of a family resemblance. Also, the age of the DNA’s unknown donor cannot be determined from the DNA samples. This project was started from Dewey-Hagborg’s own DNA self-portrait two years ago. People have had different opinions of how the DNA is found for these portraits; some people feel that this is unethical. People feel that you should not be able to just take some ones DNA from things just because it is in public. They feel that their privacy is being taken advantage of. This art project is the connection between art, technology, and science. 

               I found this absolutely amazing. If is extraordinary that just from a piece of gum or strand of hair someone can make a 3-D image of what you would look like. In a way I do find it to be a little creepy. It makes you think twice what you will spit out or leave behind. The persons DNA that you are using did not give you permission to use it, though it is left in a public place. I feel that this could cause a lot of controversy with people. But, in all I think this is brilliant and I would love to have it done to me, with my permission.   

http://www.cnn.com/2013/09/04/tech/innovation/dna-face-sculptures/index.html?iref=allsearch

http://www.nydailynews.com/new-york/artist-creates-3d-models-faces-discarded-dna-article-1.1384149