Drafts

          In A High-Coverage Genome Sequence from an Archaic Denisovan Individual, the authors used samples of bone powder from a phalanx fragment found in the  Denisova Cave in the Altai Mountains in southern Siberia. The draft nuclear genome sequence retrieved from the Denisovan phalanx revealed that Denisovans are a sister group to Neandertals, with the Denisovan nuclear genome sequence falling outside Neanderthal genetic diversity, which suggests an independent population history that differs from that of Neanderthals. Also, whereas a genetic contribution from Neanderthal to the present-day human gene pool is present in all populations outside Africa, a contribution from Denisovans is found exclusively in island Southeast Asia and Oceania. To verify this, they sequenced the genomes of 11 present-day individuals: a San, Mbuti, Mandenka, Yoruba, and Dinka from Africa; a French and Sardinian from Europe; a Han, Dai, and Papuan from Asia; and a Karitiana from South America for comparison. They conducted a direct estimation of Denisovan heterozygosity indicating that genetic diversity was extremely low, detailed measurements of Denisovan and Neanderthal admixture into present-day human populations, and generated a near-complete catalog of genetic changes that swept to high frequency in modern humans since their divergence from Denisovans (Meyer et al. 2012).

Each resulting immunogenic neoantigen sequence from this extensive screening process will then be incorporated into a single gene with the fascin promoter and edited into the genome of differentiated dendritic cells via CRISPR (Population 1). The fascin gene promoter is highly active in mature dendritic cells, making it an ideal element of the researchers' neoantigen gene construct (Bros et al. 2003). A second gene construct identical to the first but including a signal sequence directed to the endoplasmic reticulum (ER) will be edited via CRISPR into a second population (Population 2) of differentiated dendritic cells. These two populations will be kept together in vitro and all dendritic cells will be treated in solution with Poly(I:C), a toll-like receptor 3 (TLR3) agonist shown to induce activation of dendritic cells (Garzon-Muvdi et al. 2018). Since the fascin gene promoter is active in mature dendritic cells, expression of these genes in both dendritic cell populations will result in expression of both endogenous and exogenous neoantigen peptides. In population 1, the expressed endogenous neoantigen peptides will be processed by the proteasome and subsequently move to the ER, bind to MHC class I, and display on the plasma membrane. In population 2, the addition of the signal sequence to the ER will result in the secretion of neoantigen peptides, which then can be recognized by population 1 dendritic cells as “exogenous.” While displaying these same neoantigens on MHC class I, these dendritic cells will also phagocytose the neoantigens secreted by population 2. Since these neoantigens are exogenous relative to population 1, they will be displayed via MHC class II on the plasma membrane.

While the PBMCs are differentiating and through the use of comparative DNA isolated from PBMCs, the researchers will identify all nonsynonymous mutations through whole exome sequencing of biopsied pancreatic cancer cells (Cullinan et al. 2018). Comparing normal exons to those found in pancreatic tumors not only allows for scrutinization of potential neoantigens, but also allows for more treatment flexibility as whole exome sequencing is less expensive than whole genome sequencing. Whole exome sequencing also allows for the inference of HLA types from exon sequences (Cullinan et al. 2018). Expression of identified nonsynonymous mutations can then be verified with cDNA capture. From these expressed mutations, potential neoantigen sequences will be further scrutinized through multiple MHC class I epitope prediction algorithms. The NetMHC algorithm has been previously utilized in analysis of Panc02 tumor cells to predict neoantigens (Kinkead et al. 2018). A Random Forest-based computational algorithm has also demonstrated an immunogenicity prediction accuracy of 83% and an HLA binding prediction accuracy of 97.4% (Wilson et al. 2018). Therefore, the researchers will use the NetMHC and Random Forest algorithms to screen for tumor-specific neoantigens in individual patients. Additional filters can be applied to these algorithms to eliminate epitopes predicted to be poorly processed by the immunoproteasome and those with lower binding affinities than the corresponding wild-type sequences (Gubin et al. 2014). These filters will discern any potential neoantigens that would not be broken down effectively to be displayed via MHC complexes. These filters also eliminate any neoantigens outcompeted to bind to MHC complexes by the wild-type sequences and assure that resulting candidate neoantigens are sufficiently different from self-antigens (Hopkins and Jaffee, 2018). A common method for evaluating immunogenicity and further scrutinizing final candidate neoantigens is interferon-gamma enzyme-linked immunospot assay (Cullinan et al. 2018). This assay allows for the quantification of cytokine secretion [interferon-gamma] within a specific cell. The researchers will perform this assay in undifferentiated PBMCs taken from the patient with the candidate neoantigens to determine immunogenicity.

The methods project was the most difficult project assigned. I thought that it was difficult because it introduced the idea of precise scientific writing and the procedure on how to write a proper methods section. The project had several components including; thinking of a figure to photograph, collecting the digital elements for the figure, creating the figure, constructing the methods section, following someone elses methods, and analyzing the results from someone elses methods and yours. Because the project had several components, being able to effectively organize and plan ahead were essential and was where I struggled. I would consider the methods section of a research paper to be one of the main components and also one of the most elaborate sections of a paper. I learned from writing the methods that you need to be clear and concise with every component of your procedure, but you want to explain what you did instead of giving directions. Comparing the two creations of multipanel figures made this clear as there were multiple differences when looking at the two figures. 

Forty UMass students were surveyed regarding their ethical beliefs and understanding of genetic engineering in foods. We researched the background of GM foods, consumer acceptance, and the overall public opinion on this controversy. The survey consisted of ten questions highlighting various aspects of GM foods in regards to: knowledge, government regulation, risks/benefits, and safety. Survey options included the following; strongly agree, slightly agree, slightly disagree, and strongly disagree. Implementing this Likert-scale allowed for the data to be easily analyzed and displayed in a histogram model. Students individual responses to each of the ten questions were analyzed. We designed the survey, grouping questions that presented the same idea together. Question 1 introduced the topic of GMOs. Questions 2 and 3 were aimed towards government regulation, questions 4-7 asked about different influential motives for modifying these foods, and questions 8-10 explored the relation between knowledge and attitude in respect to GM technology. The histogram model presents a simple visual representation of the data. Analyzation of the data retrieved from the surveys simplified the process in making conclusions on college students opinions on GM foods and their regulations.

Hemp is known for being one of natures best sources for a plant-based protein as it is full of essential fats and vitamins. Hemp protein contains all 20 amino acids and is able to supply the body with nutritional fiber and minerals. There are various benefits to consuming this hemp protein as it boosts the immune system, increases energy levels, reduces inflammation and improves digestion. Hemp protein contain edestin and albumin which are globular proteins that make up various enzymes, antibodies and hormones that our body uses daily. The ability for hemp to increase energy levels is a perfect substitute for caffeine. The fatty acids that are in the hemp produce twice as much energy as carbohydrates as they take longer to break down in the body and sustains the energy throughout the day. 

In plants, DNA methylation also occurs at CpNpG trinucleotides, where N represents a nucleotide with any base. Some DNA regions have many CpG dinucleotides and are referred to as CpG islands. In mammalian cells, CpG islands are often located in or near the promoters of genes. These CpG islands are usually not methylated when genes are being actively transcribed. However, methylation of CpG islands near a gene leads to repression of transcription. Cells repress and activate genes by methylating and demethylating cytosine bases. Enzymes called DNA methyltransferases to methylate DNA by adding methyl groups to cytosine bases to create 5-methylcytosine. Other enzymes, called demethylases, remove methyl groups, converting 5-methylcytosine back to cytosine.

At the start of the class, the idea of having to write multiple drafts a week seemed daunting and not particularly doable. As the semester got underway though and I started writing and posting drafts I realized that having drafts “due” pretty much every day of the week was actually very helpful in making me stay aware of my writing. I did miss a few weeks, but overall writing multiple drafts, even if they were about different topics or for different subjects, made me take more notice of how I was writing and how long it would take me to write something. Looking back at the start of the class I felt like I was spending a lot of time on each draft trying to get it to be as good as possible, and then struggling to turn one draft a week into a Perfect Paragraph seeing as I had already spent so much time on editing and perfecting while writing the initial draft. I soon realized that this was an inefficient way to be going about this, especially considering we had to write multiple drafts a week. Eventually I started to become more aware of how much time writing tends to take me, as I unconsciously attempt to simultaneously write something from scratch and edit it. Although I still find myself doing that, I have noticed that the necessity of writing multiple drafts a week has made me better at just putting all my thoughts on a page and then going back later to fine-tune things—and this is where the Perfect Paragraphs were helpful.

As a theoretical concept I think Pleistocene Park is very interesting, but although premise behind grasslands slowing the Arctic thaw may hold merit, I don’t think it’s feasible as a solution for climate change at present. Climate change is such a time-sensitive and pressing concern, and the proposed project could take decades upon decades, with no certain guarantee of success—time which we no longer have. Although we can approximate most of the megafauna that actively drove the expansion of the Pleistocene grasslands, we cannot reintroduce the exact same species and this could mean failure of the project. There is no guarantee that introducing all the components of a Pleistocene ecosystem (or as close enough as we can get) will result in an identical recreation, and we may instead z be left with an ecosystem that resembles neither the Pleistocene, nor any modern-day ecosystem.

In addition to the opposing Republican views on universal healthcare, the American Medical Association insists that the ACA suits the American population better for low-income residents. The ACA provides affordable healthcare to patients with lower incomes and therefore wants to protect their patients from increased taxes and instead “seeks to enhance patient choice and encourage patients to be conscious of health insurance costs, while also maintaining innovation in the private sector” (McCanne, 2008). They believe the single-payer system would prevent better healthcare and decrease the quality of healthcare to its patients. Lastly, insurance and pharmaceutical companies are also against a single-payer healthcare system because they believe it could increase “wholesale bureaucratization of the health care system by the federal government”(Galea, 2017). The pharmaceutical companies are extremely involved in the U.S. healthcare because they sell drugs and treatments to patients with different insurers and consequently, based on their experience with customers, want to ensure that everyone can have access to acquiring necessary medications. As the different groups continue to assert their claims on the best healthcare method, Americans are starting to assess how other countries manage their healthcare system.