User:Mones jana/sandbox

8.6 Rodents
Legend has it that there is an underground city of rats living in the walls of the New York City subway. According to a two-year study done by the Bloomberg Administration, rats do exist in the subways, however not to the extent to which they are rumored. The study was sponsored by the city of New York, in other words, the cost for the study was fronted by the taxpayers as the city saw the rodents as a growing issue. 18 stations were surveyed, finding that rats were not present at every station. Those stations were rats were present were also found to have overflowing trash bins and litter, leading food for the creatures. A key component in fighting the pests is reducing litter. Poisons have proved to be ineffective, as the rats have grown an immunity. Dr. Robert M. Corrigan, the head rodentologist who lead the study, works as a research scientist for the New York City Department of Health and Mental Hygiene. He concluded that stations should bait the “refuse room” (a storage room where garbage is held before it is picked up). Rats are drawn to the room for obvious reasons; free-for-all for food..

The infestation of rats in the subways has been equated partially to the unsuccessful poisoning formulas. A 1976 study recreated the conditions of the underground New York Subway system and put rats found above ground into the controlled environment. As a control group, rats found from the subway system were also placed in an identical recreation of the environment. A majority of the rats from above ground died, whereas those originally from the subway survived. In appearance, both groups of vermin were identical. Given the observation that there are still rodents living in the subways, it can be concluded that the pests have adapted. As noted in Darwin’s theory of evolution, the rats in the subway system are a species variation of the free range rats.

==== 8.7 Bed Bugs ==== For years, New York City has been attempting to combat the pestilence of bed bugs. Taking on the challenge, researchers from the American Museum of Natural History paired with Weill Cornell Medicine. They set out with the goal of finding a pesticide that could limit the spread of the bed bugs. The study was done by collecting DNA and RNA of both male and female bed bugs spanning from 1973 to present day, optimizing the accuracy of the results. A bed bug has six stages of life, throughout the before and after of blood meals. Multiple samples were taken of microbes at the different stages. The extracted samples of DNA and RNA observed over 1,500 genes. Bed bugs were taken from over 1,400 locations around New York City, however focusing primarily in the subway system. Across the subway lines, the scientists were able to differentiate the genetic makeup of the bedbugs on the east-west compared to those on the north-south lines. Even further, they were able to find specifics among boroughs living on distinct locations in the subways (e.g., benches, turnstiles). Depending on the stage of the cycle that the bed bug was in, different genes were expressed. Being able to track the way the bug’s body is changing will enable pesticides to develop that can infect and kill them more accurately than before. The study also found a connection in genomes among the common bed bug to the kissing bug (Rhodnius prolixus), and the body louse (Pediculus humanus).

The most basic results of the study identified bacteria that is beneficial to the growth of bed bugs. To control the population of bedbugs, scientists suggest creating pesticides that kills bacteria that the bugs thrive on, which would ultimately kill of a portion of the population. Differences in the genetic sequences among the subway lines will enable the city to pinpoint the source of the outbreak, if one were ever to occur. Pest control would then be able to go to the center of the epidemic.

8.8 Bacteria
The genome mapping project of bacteria and microorganisms was conducted by Cornell Weill Medical after lead scientist, Professor Christopher Mason began the study by swabbing handrails in the NYC subways. With growing curiosity, Mason sought out to develop a map of the New York City subways, gathering specimen from turnstiles, benches, handrails, garbage cans, Metro Card Kiosks, and the doors, poles, handrails, and seats on the trains. Species found in each station were found to match the DNA of the neighborhoods in the general area of the station. Of all of the New York City boroughs, the Bronx was found to have the most diverse microbial species. The Bronx was followed by Brooklyn claiming second, Manhattan taking third, then Queens and Staten Island. Of the top 50 busiest subway stations, Manhattan takes claim to 40 of them. With Manhattan’s annual ridership numbers exceeding all of the other stations, makes it surprising that it does not have the most diverse bacterial growth.

Upon analyzing the swabs, Mason found that 48% of the collected data did not match any known organisms. Of the collected samples, only 12 percent could be linked to a disease and only 27 percent was live and antibiotic resistant. Nevertheless, none of the bacteria found poses a direct threat to society any more than being in any other public space would.

To compare the results, the study also took samples from Union Square, which is an outdoor park. Approximately the same percentages of bacteria species were found both in Union Square and the average of all of the subways. The samples were analyzed using two different methods, Sanger and Pyrosequencing. Sanger is the simpler form of analysis, giving a broader range of the most basic DNA similarities. Pyrosequencing further breaks down the DNA interpreted during the Sanger sequencing. As seen by the charts, Union Square Park and all of the subways charts for Sanger sequencing are quite similar, with the exception of Chloroflexi and Archaea segments. To be expected, the pyrosequencing shows deeper variances between the bacteria types at each location. Pyrosequencing takes the sequence of multiple sequences at once, where Sanger sequencing can only focus on one section of a DNA strand per sequence. Ultimately, both forms of sequencing shed light on the little need for fear to arise from the mutations and volume of bacteria developing in the subways.



Alike the analysis done of the bed bugs and rats, each station has been found to contain its own genetic variances. In the event of a large outbreak, such as the flu, or an extreme case, a form of the plague, scientists hope to utilize the subway system to trace the source. The information is not insinuating that such a disaster will occur, however in the event that it did, scientist are confident that they would be able to trace areas at high risk.