Writing in Biology

Most of the bodies blood is in the viens of the systemic system. The venus reserve can mobilize blood when there is vasoconstriction. When someone exercises the sympatic nervous system is activated and the viens are constricted which in turn increased the blood returned to the heart. This increased the end diastolic volume of the heart, the SV, cardiac output, and blood pressure. Blood flow is proportional to a change in pressure over resistance. The more pressure there is the greater the blood flow, and as resistance increases blood flow also increases. Resistance is proportional to 1/r^4 therefore doubling the radius of the vessel is equal to 16x more resistance. 

To a tared flask, 2.003 g of cyclohexanol and 0.5 mL of 85% phosphoric acid were added with boiling chips. A fractional distillation column was setup to purify the cyclohexene. The purified sample was then extracted and placed in a reaction tube with 1.0 mL of distilled water. A bottom layer formed, it was thoroughly mixed and then left still to settle. The bottom distilled water layer was removed with a pipette and placed in a bin marked as waste. The sample was extracted with 1.0 mL of sodium hydroxide in reaction tube and thoroughly mixed. The lower layer was removed with a pipette and placed into the waste bin. The same procedure was repeated with 1.5 mL of saturated aqueous sodium chloride. The organic phase was then transferred to a clean vial. For the dehydration, calcium chloride spheres were added and left to dehydrate for five minutes. Once completed, the organic layer was pipetted into a clean vial that did not contain calcium chloride. Gas chromatography analysis  was then performed to determine the purity of cyclohexene. Infrared analysis was then used to determine which functional groups were present. The end product was used in two chemical tests to determine the functional groups present. In the first test, 4 drops of 3% dilute bromine solution in dichloromethane was added dropwise to the cyclohexene product, about 0.25 mL, where no color change was observed. However, in cyclohexane, about 0.25 mL, a red-brownish color was observed. In the second test, 2 drops of 1% potassium permanganate and 10% sulfuric acid was added to cyclohexene product, about 0.25 mL, where no color change was observed but there was a brown precipitate. 1% potassium permanganate and 10% sulfuric acid was added to cyclohexane product, about 0.25 mL, and a purple color was observed.

On the Phytozome locus page for the unknown gene, the “UniProt” icon was selected. There, we learned more about the gene’s predicted biological process, cellular component, and molecular function. Under Function, “View the complete GO annotation on QuickGO ...” was selected and studied as well.

Our unknown gene’s DNA-level similarity to other genes was compared by performing a Nucleotide BLAST with the “Nucleotide collection (nr/nt)’ database and the BLASTN algorithm. The algorithm parameters were set: Max target sequences to 1000 and E threshold to 1. This search strategy was saved. In the output, repetitive sequences in noncoding regions, sequences that match all or most of our gene’s exons, and strongly conserved regions were noted. The species the matching sequences came from were also noted.

The process of photosynthesis is the method in which photoautotrophs such as plants and algae harvest energy from light and convert it to a usable form of chemical energy in the form of glucose. In the chloroplast of plant cells are stacked structures resembling disks which are called thylakoids, containing chlorophyll, a pigment responsible of light absorption. The granum, or stacked thylakoids are surrounded by a liquid known as the stroma. The structure of the chloroplast is crucial for the two parts of photosynthesis that biologists refer to as the light-dependent reactions, which occur in the thylakoid membrane, and light independent reactions (Calvin cycle), which occur in the stroma.

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.