Drafts

Next, a prediction of the protein sequence was made using the BLAST tool on the Phytozome website with Brachypodium distachyon set as the target. The best match shown in blue under the Query View was selected, and the protein sequence predicted from that Bradi1g72430 gene was viewed and saved in a new text file named “AHP-Phytozome-ProteinSequence.” Back in the Phytozome genome browser, “Log-Scale RNA-Seq Coverage” was selected on the left to view the normalized number of times a sequence was counted. This diagram was saved as “AHP-Phytozome-RNA-seq.”

The Working Map File was altered to factor in all the learned information. Positions of the exons and introns, the beginning and end of the coding sequence, and the poly-A tail were marked using the FGENESH output. Additionally, restriction enzyme recognition sites of 6 base pairs or more were marked. The predicted protein sequence was also highlighted, deleting all frames that were incorrect and all translations in noncoding regions.

The Basic Local Alignment Tool (BLAST) on the National Center for Biotechnology Information (NCBI) website was used to find expressed sequence tags (ESTs) that match the sequence of our unknown gene. A Nucleotide BLAST of the unknown sequence was performed, setting the database to “expressed sequence tag (est)” and the organism to “Brachypodium distachyon.” The sequences that had an Identity number of at least 95%, meaning they perfectly or near perfectly matched cDNAs, were selected and saved in a new file as “Unknown-AHP-ESTs-fasta.txt.” Consensus sequences (contig) of the ESTs were formed using the CAP3 web server at the Pasteur Institute. The contigs were saved in a new text file named “AHP-CAP3-Contigs,” and the sequences of ESTs that were not contig’ed were saved in another text file named “AHP-CAP3-SingleSequences.” A full-length cDNA of the unknown sequence was then found by performing a Nucleotide BLAST with the “Nucleotide collection (nr/nt)’ database instead. Once a cDNA sequence for the gene was found, it was compared to the contigs from CAP3 through a Nucleotide BLAST. The cDNA sequence was pasted as the query sequence, the contigs were pasted as the subject sequence, and the “Align two or more sequences” box was selected. The resulting comparison was saved as a new file named “AHP-Contig+cDNA-fasta.txt.”

Recently, scientists observed a meteor exploding over the Bering Sea with the energy adding up to approximately 10 atomic bombs. It is the second largest meteor of its kind and had the third largest impact. Scientists were not expecting this to happen at all. The meteor exploded not even 16 miles above the surface. Military and civilian instruments were able to spot the explosion right after it happened with many monitoring stations around the world. This type of meteor with this size only happens two to three times in a century. The article pointed out the fact that we’re rather lucky the meteor hit the sea rather than land/over a populated area. We need to develop better technology to map out objects in the solar system so we know far in advance when things may hit us.

To improve the quality and consistency of the experiment and cell counts across the class, the exact regions of the brain to be counted (e.g. telencephalon, posterior recess, etc.) could be encircled first. Implementing a standardized system for identifying regions of the brain is crucial to both accuracy and precision of experimental technique. This has already been partially started, but could be expanded upon and continued. Level of consistency in the brains obtained could also be improved. Because of low fish survival, salt-treated brains were obtained from a separate experiment, which may have led to differences in cell numbers, affecting the accuracy of the results. Perhaps less strong salt concentrations can be used when allowing embryos to grow to improve survivability. Salt-treated brains from the same experiment as the system H2O and nanopure brains can then be dissected and counted. Any group with extra salt-treated brains can give them to groups that do not have as many. Perhaps this may improve the accuracy of cell counting on the whole. Fixing protocol of the zebrafish larvae could also be changed to improve ease of dissection, allowing more time to run the experiment. After break, weaker salt concentrations could be experimented with and an improved protocol could be run, or a different variable could be tested. pH could be an interesting variable to explore with the zebrafish. Could slight changes in pH alter cell proliferation rates in the brain, and if so, would these changes occur in the same regions?

The unknown DNA sequence was saved as “AHP - Gene Sequence” as a text file on Microsoft Word and translated using the Bioline Six-Frame Translation website with the following settings: Output: 20 amino acids in one line, code: one letter, frame number: all. The whole map under “Sequences alignment” was copied, pasted into a new document, and saved as “AHP, Angela Park - Working Map File” in Microsoft word format, changing the font to 10 point Courier and the side margins to 0.7”. In order to obtain predictions of its structure, protein sequence, and coding sequence, the unknown sequence was then ran in the FGENESH website, selecting “Brachypodium distachyon” as the organism and choosing “print exon sequences for predicted genes” in “Advanced options” to get sequences of all the predicted exons separately. The diagram under “Show picture of predicted genes in a pdf file” was saved as “FGENESH Prediction Diagram - AHP.” The protein and coding sequences were then separately saved into new text files as “FGENESH Protein Sequence Prediction - AHP” and “FGENESH CDS Prediction - AHP” respectively.  

Vaccines are only as effective as their delivery system. Many vaccines employ the use of adjuvants or additives that help to deliver the antigen to the host. What the adjuvants are supposed to do is activate an immune response so that the host can fully recognize the antigen and properly recognize to create a lasting immunity. You can think of adjuvants as the coating of a multilayer pill. Many pills have a layer that dissolves and releases compounds that will create and ideal setting in which your body can take in the actual active drug that the pill contains. The drug itself is pretty much never directly used just because without other compounds interacting with it it will never reach the destination where it is supposed to absorbed by the body or it will never actually be absorbed at all. Adjuvants are used in vaccines today primarily because of the way that vaccines are produced. Vaccines used to be made using killed or weakened whole cells, now they are made with parts of the antigen that produce strong immune responses. These vaccines are usually much safer and are generally produced more efficiently. However because it is only parts of the antigen they must be presented to the immune system in a different way. Most modern vaccines contain 25% or less of the active ingredient, parts of the antigen, and the rest is adjuvants to help present the antigen to the immune system. If you are curious about what adjuvants are in the vaccines you are receiving you can visit the the CDC website for a full list of ingredients as this information must legally be disclosed.

The heart requires its own blood supply, stemming from the aorta is the coronary artery which splits into left and right. The right coronary artery on the right side of the heart. The marginal artery branches off and supplies the right atrium with blood. Continuing along to the posterior of the heart. The posterior interventricular artery supplies the ventricles with blood. The left coronary artery is on the left side of the heart. The circumflex artery branches off and wraps around to the posterior of the heart, supplying the left atrium with blood. The anterior interventricular artery, which is branched off the left coronary artery goes down the anterior side of the heart supplying the atrium and left ventricle with blood. All the deoxygenated blood is then drained by the cardiac vein. From the cardiac vein the blood goes into the coronary sinus. From the coronary sinus the blood goes into the right atrium.

A petri dish containing only duckweed and a separate dish containing only salvinia are used for the control groups. The mass of the plants were initially all weighed the same. A third petri dish housed both species. Given all the same variables (besides space), the plants were subject to the same amount of light (14 hours) a day, same amount of distilled water as well as liquid fertilizer. Over the course of one week, the growth and the mass of the plants were monitored. By the end of 7 days, we observed the change in each species growth using their biomass, identifying the difference between the mass of the plants grown in the same environment, as opposed to grown separately.