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Results draft

Submitted by jonathanrubi on Fri, 02/23/2018 - 00:27

DIfferences were observed between the original figure and the figure replicated by following the given methods. Structural differences between the two figures were noted. In the replicated figure, there was no blank white space in between the separate panels, which was seen in the original figure. The letters labeling the different panels (A,B,and C) in the replicated figure are slightly larger and bolder as well as above and below the panels as opposed to on the sides. Differences were also seen between the content of the panels in the figure. In terms of differences in angles and distances of the panels, the flower shown in panel A of the replicated figure encompasses a larger surface area of the plant and is taken from a position lower and further to the right. The color of the flower in the replicate figure is also beige and appears to be more creased and drier as opposed to the yellow and pink flower color in the original. In panel b of replicated the replicated figure, more plants and pots are present in the background of the photo than the original. Also, the photograph was taken from an angle further to the right than the original. One of the flowers is also completely wilted and the two large leaves protruding from the stem of the plant appear to be resting at a lower angle and a lighter tinge of green than in the original figure. Panel C of the replicated figure does not include Brazil, Peru, and Bolivia as native countries of the Rhyncattleanthe Momilani species, while the original figure does.

Methods Introduction

Submitted by jonathanrubi on Fri, 02/23/2018 - 00:24

The Methods section of a scientific paper allows for the reproduction and verification of any given experiment. In order to do so, a carefully thought out narrative must be developed with clear explanation of materials and subjects, as well as experimental design including variables and controls and procedure. In this study we examined how to write an accurate methods section by having a peer follow a set of methods detailing the construction of a figure and subsequently comparing the two figure in order to determine the clarity and accuracy of the provided methods section.  Our findings show that small details, variables and controls not accounted for in the methods section of a paper can lead to deviations in the reproducibility of a given experiment. This is important for any scientific paper and provides it with legitimacy.


Methods Abstract

Submitted by jonathanrubi on Fri, 02/23/2018 - 00:23


    We tested the hypothesis that given a detailed and accurate methods section the construction of a figure could be repeated with precision. In order to test this, methods were provided for the construction of a figure to a peer without knowledge of the original figure in order to determine the efficacy of the methods in providing an accurate template for exact replication. We observed differences between the overall structure of the replicated and original figure in multiple areas. These results suggest that the provided methods did not take into account all possible variables as well as controls for the reconstruction of the figure.


Discovery of the Structure of the Ribosome

Submitted by jonathanrubi on Fri, 02/16/2018 - 13:01

Yonath, Steitz, and Ramakrishnan dedicated over 20 years to discovering the structure of the ribosome. Using X-ray crystallography provided tremendous hurdles for Yonath when trying to figure out the atomic structure of the ribosome, which is a complex structure containing two subunits each with thousands of nucleotides of RNA and 32 and 46 proteins respectively. However, using ribosomes taken from bacteria living under tremendously harsh conditions in the dead sea, a high-salt environment, helped to provide the stabilization needed to  obtain a detailed mapping of the atomic structure. Still problems persisted, and it was Steitz who used both images generated by Yonath and electron microscopy from Joachim Frank that provided the information needed. After years of collecting additional data, and the structure of the small subunit of the ribosome from Ramakrishnan, it was finally possible to map the functionality of the ribosome at the atomic level.

Scientific History leading up to discovery of ribosome

Submitted by jonathanrubi on Thu, 02/15/2018 - 16:14

In understanding the importance of the discovery of the structure of the ribosome, it is imperative to understand the groundbreaking experiments that led up to it. Prior to Avery, Macleod and McCarty’s experiment showing DNA as the transforming principle, it was widely assumed that proteins carried the hereditary information that encoded life. This was due to the fundamental understand of protein and DNA at the time. Chargaff had discovered that the composition of DNA varied from species to species, however containing only four alternating bases, DNA was seen as too simple to carry the complex information that encodes all of the information across life. Proteins on the other hand, were known as incredibly complex and variable in an infinite way. The Avery-Macleod-McCarty experiment, later repeated and verified by Hershey and Chase as well as X-ray crystallography experiments performed by Rosalind Franklin provided the clues needed for Watson and Crick to hypothesize about the structure of DNA, which was only later proven by Meselson and Stahl, who’s experiment showed the semi-conservative replication of DNA that provided a model for the successful replication and thus hereditability of DNA. In the early 1960’s, Nirenberg and Matthei were the first to crack the genetic code, using synthetic poly-uracil RNA, which showed that RNA controlled the production of specific types of proteins. Roughly 50 years later, the detailed mapping of the structure of the ribosome provided the last link to the puzzle.

Conclusion for Paper on Discovery of Structure of Ribosome

Submitted by jonathanrubi on Thu, 02/15/2018 - 16:13

Providing the structure of the large and small subunit of the ribosome allowed for the development of a whole new class and specificity of drug targeting. The ribosome has been a target for antibiotics, however bacteria have become increasingly resistant to these developed antibiotics. The specific mapping of the ribosome can now be used to develop new antibiotics targeting different and new mechanisms in the ribosome, previously not known.


PP - Protein misfolding disease

Submitted by jonathanrubi on Fri, 02/09/2018 - 12:22

Protein misfolding can occur through a number of mechanisms and lead to a large variety of disease and misfunction. One pathway for protein misfolding and pathogenesis is improper degradation of proteins. Improper degradation occurs when proteins that are partially functional and can actually benefit cellular processes are degraded despite it being detrimental to the cell. This is seen in the case of cystic fibrosis, where a deletion of a phenylalanine in CFTR leads to partial functionality but is still targeted for degradation by CHIP, a molecular chaperone which ubiquitylates the protein. CFTR is an important membrane channel for the production of mucus, which is why this improper degradation is seen in a large number of cystic fibrosis patients.  Another way in which improper folding can lead to disease is through improper localization. Improper localization occurs when misfolded proteins cannot get to where they need to go, leading to not only a loss-of-function but potential toxicity if aggregated in the wrong place. One example of this is misfolded antitrypsin, which becomes retained in the ER of liver cells and accumulates, preventing synthesis of other proteins resulting in liver damage. Also, since antitrypsin does not get secreted to its proper location, it is unable to inhibit protease activity in the lungs leading to damage in the alveoli and emphysema. Another mechanism for pathogenesis as a result of protein misfolding is dominant-negative mutations. Dominant-negative mutations are characterized by mutant proteins that compromise the function of wild-type proteins, most often in a dimer or quaternary structure. An example of this process is seen in the connective tissue disorder epidermolysis bullosa simplex. When mutant forms of keratin proteins are present, they disrupt the function of the entire keratin composed filament, leading to fragile skin that blisters easily in response to minor friction. Gain of toxic function and amyloid accumulation are two other mechanisms for pathogenesis as a result of misfolding and play a big role in neurodegenerative disorders.

Draft of Paragraph for internship cover letter

Submitted by jonathanrubi on Thu, 02/08/2018 - 13:54

Over the past few semesters, excelling in courses such as Biology of Cancer and AIDS, Genetics, and Cell and Molecular Biology has expanded my skills and knowledge and excited me about the possibility of doing research related to oncology. Last summer I received tremendous experience and exposure in the field of oncology, shadowing a pulmonologist. I was able to review malignant CT scans, observe various procedures and sit-in on Thoracic Pulmonology Board meetings at New York Presbyterian – Queens. After gaining experience in the field of oncology both academically and clinically, I am interested in gaining valuable research experience as well.


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