Writing in Biology

Problems that arose during research was the lack of literature associated for each category of inasive species assessment. Solid quantifiable data such as the ratio of inasive plant species abundance to native species abundance was non-existant. For this, more research in the field is neccessary. Figures such as cost was uncertain, in terms of annual investment, there was no data, only potential costs of implication of herbicides and protective barriers. Still some insight was drawn from the minimal data that was provided. Future assessment methods can draw on the bioecomic framework, but the devised numerical value of threat determined for each invasive species is perhaps insignificant to the threats of all the invasive species combined.

The two parameters for this graph are the slope and the y-intercept. The y-intercept is voltage and the slope is the resistance. The values are as we expected, they were 96.3 for the slope and -0.0013 for the y-intercept. The error of the slope is 0.297 and the error of the y-intercept is 0.0102. The relationship that we described for question 3 matches up perfectly with Ohm’s law. We stipulated that the relationship was directly proportional and looking at Ohm’s law this seems to be true if the voltage were to increase then the current should have a corresponding increase.

This is my project abstract. There has long been a desire for genetic enhancement in order to cure genetics diseases or alter the physical appearance of someone. With modern gene editing tools it is now possible to treat disease as well as select for cosmetic enhancements. However, with the ability to alter a person’s genetic makeup, comes the question if it’s considered ethical to be changing what was naturally chosen. Scientists have discovered that part of some bacterial immune systems have CRISPRs, which are are specialized stretches of DNA. A specific protein associated with this system is Cas9, an RNA-guided DNA endonuclease that can cut foreign DNA at specific sites. Together utilizing CRISPR and the Cas9 enzyme, genome engineering is now possible. With this new biotechnology, many scientists are delaying the use of gene editing in humans for a multitude of ethical concerns. For our project we discuss the ethics and applications behind human genomic engineering, specifically when used to treat inherited medical diseases or for cosmetic enhancements. To measure the University of Massachusetts Amherst student’s public opinion a mass survey was distributed. We found that gene editing for disease prevention was considered ethical while gene editing for cosmetics was not.

Bradi1g72430 was hypothesized to play a role in cell wall biogenesis, so it was expected to be more highly expressed with increase tissue growth. We hypothesized that if Brachypodium distachyon plants were treated with indole-3-acetic acid (IAA), which stimulates root growth, we would see increased gene expression due to the increased root growth and subsequent formation of cell walls.

    We set up two 30 mL agar plates, one with 1.5 µL of ethanol (control) and one with 1.5 µL of 0.0001M IAA for a final concentration of 5 nM IAA (treated). Once set, four B. distachyon seeds were planted on each plate, and the plates were placed in the incubator for seven days, covered by a blue-minus filter, before the entire root of each plant was removed for RNA extraction. The four control plants were labeled as samples 1-4 while the four treated plants were labeled as samples 5-8. The extracted RNA was quantified with NanoDrop (Table 3) and visualized via agarose gel electrophoresis (Figure 7).

In order to gain large qualities of the DNA of interest, DNA and primer amplification is necessary. DNA and primer sequences can be amplified through polymerase chain reaction. In order to look at a particular SNPs, restriction enzymes for that SNP should be amplified using PCR-restriction fragment length, RFLP, also called cleaved amplified polymorphic sequencing, CAP. In the case that there is not a specific digestion enzyme that exists for a particular trait of interest, there is a way to create one. These enzymes are called derived cleaved amplified polymorphic sequences, or dCAPS. These reactions cut and amplify a specific single polymorphism (SNP). A dCAP is used on a mismatched PCR primer to make or get rid of a restriction site based on the particular genotype of the SNP being looked at. The primer used to create a dCAP is mismatched to create the restriction site of interest and the differing alleles are mutated. Primers used do not overlap or mutate the SNP. The restriction enzyme will cut at one site, so if the DNA sequence is cut into two fragments then both strands of DNA contain the allele. However, in the case that the individual is heterozygous, the restriction enzyme will cut only on one strand of DNA resulting in three strands of DNA. Additionally, if the DNA is homozygous for the other allele, there will be no cuts made (J. Laney, dCAPS Primer Design PowerPoint. Moodle.1, 1-16 (2018)).

    Recently, Avengers Endgame came out which has been the talk of young adults since its release. A lot of people have been trying their best to not get spoiled by the movie, while those who have already seen it are not trying to run their mouths. But why do people enjoy spoiling movies? What is the benefit behind spoiling the experience for someone else who has not yet gotten to experience it yet?  The reasoning scientifically lies behind the reward system. Those who spoil movies purposely, find joy in ruining the experience from others, and seeing that they’re able to take it away from people, they find a rush of dopamine when they ruin it. The reason why they feel rewarded, is because having the ability to take something away from another is a power move. This position of power can make you feel significantly better with the reward system, and subconsciously putting you “above” the other person. To have this power and to use it is what causes the rush of dopamine. The reward system is rewarding the spoiler for being in a position of power.

DNA sequencing is a helpful tool in determining the exact nucleotide sequence of a particular genome. The Sanger Method is a particular way this can be achieved. This method feeds off of DNA replication occurring naturally within a cell. The DNA needs a primer to begin the process but can be stopped with the addition of a dideoxynucleotide. The reason the process is stopped when a dideoxynucleotide is added is due to the missing OH group on the 3’ end. Therefore, a fragment of DNA can be sequenced with a large amount of the DNA sequence of interest, a large amount of primers, DNA polymerase, an excess of nucleotides, and a small amount of one of the dideoxynucleotides. Due to the ratio of high normal, deoxynucleotide, to low dideoxynucleotides, there will be termination of the sequence at many different places. This process can also be done with all of the nucleotides labeled with different florescent dyes. If the fragments were then run on a gel, the piece of DNA could be sequenced. The use of capillaries is a technological way of doing this (J. Laney, Sequencing Slides. Moodle.1, 1-17 (2018)).

Toluidine blue (T-blue) stains polysaccharides and phloroglucinol HCL (Ph-HCL) stains lignin. In the NaN1793 mutants, both the Ph-HCL and T-blue stains appear a much lighter color at the distal cortex as opposed to the proximal cortex (Fig. 7B, 7D). In the wild - type plants, this contrast is not observed to as great of an extent (Fig. 7). The NaN1793 mutation is predicted to be a nonsense mutation, resulting in a truncated, nonfunctional protein. This phenotypic difference suggests that Bradi1g25180 may be involved in formation of cell walls of the distal cortex.

On R, the leaf, root, and stem gene expression data were plotted (Figure 5), and a T-test was performed for both the leaf, root, and stem relative expressions and stress response gene expression data. The T-test resulted in p-values of 0.00408 for root versus stem, 0.0008745 for root versus leaf, and 8.741x10-6 for leaf versus stem. All of these p-values were lower than the Bonferroni correction p-value cut-off of 0.01667, meaning there was a significant statistical difference in all three comparisons of gene expression between the tissues (Figure 5). The T-test on the stress response expression resulted in p-values of 0.1951 for CS versus HS, 0.03036 for CS versus DS, 0.8509 for CS versus SS, 0.0069 for HS versus DS, 0.16 for HS versus SS, and 0.04488 for DS versus SS. Only the p-value of HS versus DS was lower than the Bonferroni correction p-value cut-off of 0.008333, meaning there was only a significant statistical difference between the gene expression levels under heat stress and drought stress (Figure 4).