Writing in Biology

Clostridium difficile is the inflammation of the colon caused by the clostridium difficile bacteria. The symptoms occur when there is a lack of healthy bacteria in the body. Symptoms often include diarrhea, stomach pain, and fever. The common method for treatment, as with most bacterial infections, is to use antibiotics; however, even with antibiotics, the risk remains for the infection to come back. In recent years, researchers and scientists have consulted a different treatment approach with fecal transplant. The fecal matter from a healthy person can potentially restore the healthy bacteria in the infected colon of a patient with C.diff, or Clostridium difficile. It is an effective combination of antibiotics destroying bacteria, both healthy and infectious, and the fecal matter restoring only the healthy bacteria to reduce the risk of the disease resurfacing. So far, this process has been shown to be successful, however, critics are concerned about the pricing for patients. Additionally, while not necessarily a concern, rather an unknown, the methods are still under review by the FDA. This breakthrough has helped patients feel better within hours after a single treatment, and can be administered via colonoscopy or capsules containing fecal matter.

On the synthesized cyclohexene, gas chromatography was performed. At least one compound was present because there was one peak observed. The gas chromatography had a retention time of 0.386 seconds and the large peak was recorded at 0.386 seconds. The area of the peak is 10,530 and has 100% of the area, suggesting that the cyclohexene was very pure.

Infrared spectroscopy was also performed on the same cyclohexene end product. The peak for the alkene group was seen at about 2,800 1/cm. The graph for this compound has a major peak at about 2840-3000 1/cm, suggesting that the cyclohexene contains both alkenes and alkanes and that the experiment was successfully performed. Moreover, the frequencies of the infrared can determine the bonds as different interatomic bonds do not all vibrate the same. More specifically, double bonds have higher stretching frequencies than single bonds.

Eating local honey seems like it would not do much for someone who has allergies, however, a recent study proves this to be wrong. Volunteers with seasonal allergies were told to eat a tablespoon of local honey every day or told they were eating a tablespoon of honey every day when in reality, they were eating cornstarch and artificial flavoring. The results showed that the people eating the real versus fake honey had no difference in their allergies. The effects of the honey were a placebo. However, scientists are not convinced that honey has the same effect as artificial. Scientists believe that there would be a significant difference when comparing the type of honey. Meaning, local honey versus commercial honey may have drastic effects on people with allergies.

          In this experiment, an acid-catalyzed dehydration of cyclohexanol using phosphoric acid was performed in order to synthesize cyclohexene. Following fractional distillation, the product resulted in 28% yield of cyclohexene. This low yield could have been caused by insufficiently thorough mixing during the wash or incomplete removal of impurities. This product was analyzed through a series of tests to detect the presence of alkenes that would be expected in a successful reaction. The two chemical tests confirmed the presence of alkenes by exhibiting the expected color changes. In the bromine dichloromethane test, the vial containing the product remained clear despite the dropwise addition of the brownish-red chemical, indicating that the alkene reacted with bromine to form a colorless dibromide. In contrast, the vial containing cyclohexane briefly turned a reddish-orange color upon the dropwise addition of the chemical, indicating no reaction. In the potassium permanganate test, the vial containing the product turned brown, indicating the purple chemical reacted with the alkenes to produce a colorless diol and a finely-divided brown precipitate of manganese dioxide. In contrast, the dropwise addition of the chemical into the vial of cyclohexane resulted in a purple solution, indicating no reaction. The product was further analyzed by gas chromatography. The resulting GC trace displayed only one peak of 0.299. IR spectroscopy was also used to analyze the sample. The known absorption frequency for an R-C=C-H bond is approximately 3083, and the experimental absorption frequency was 3063.09. The known absorption frequency for a C=C bond is 1644, and the experimental absorption frequency was 1653.07. The experimental values were close enough to the expected values to confirm the presence of cyclohexene. 

If there was a new retrovrius killing domestic dogs, but we could save one pregnant mother. The breed of dog we should save is the Poodle. These dogas are both family friendly and highly intelegent. These dogs would make good family pets because they are loyal, alert, and trainable. Poodles are hypoallergenic, which would allow people with allergies to dog hair to also be able to have a dog as a pet. They are highly intelligent which means they could be trained easily and could be used as service dogs and support animals. They were originally bred to be hunters, which could be useful if there were ever times of food shortages. 

The ab initio program FGENESH predicted that the mRNA will be 2229 base pairs spanning 7 exons and the protein will be 742 amino acids long.  The homology-based program Phytozome predicted that the mRNA will be x base pairs and 847 amino acids long. The discrepancy between the two peptide sequences lies after amino acid 437 (Figure 2).  FGENESH predicts the following sequence to be KSLQ, while Phytozome predicts the sequence to be a set of 109 amino acids, nowhere containing KSLQ in sequential order. The sequence towards the C terminus of this discrepancy is in agreement.  21 ESTs were found in the Brachypodium distachyon genome with an Ident greater than 95%.  These ESTs were imported into CAP3 software to form contiguous sequences. Two contiguous sequences were created from the ESTs (Figure x and Figure x), and all ESTs contributed to the contigs; there were no singlets.  There is a very slights gap between the ESTs, but other than that they cover the whole cDNA found.

Another idea that my group had for the proposal was involving the decomposition of fruit. There were a few topics within this umbrella topic that really interested me and I want to hopefully have the rest of the class look at it. One idea was to test organic versus non-organic and see if the decomposition rates between the two were different. I work at whole foods so this would be particularly interesting to look at and see if paying the extra money for organic will actually get you a product that lasts longer. I kind of feel like organic products will actually have a shorter shelf life just because they aren’t allowed to have any additives or herbicides applied to them. Another thing we wanted to look at was if the origin of the fruit mattered to shelf life. Does my avocado last longer if it is from Mexico or California? I think that this answer might be found within the composition of soil, if that even has any affect on shelf life at all. And even if the soil is different will the fruit that is produced by the plant in that soil be so drastically different that it will decompose faster than another fruit of the same variety. Another thing that we wanted to test was if the size of the fruit had any affect on how fast or slow it decomposed. In my opinion this project has many easy divided sub projects that would be easily testable by the class.

The Arctic is currently undergoing the most dramatic impacts of climate change. These changes not only have a drastic effect on the environment but also the people who live there, the Inuit’s. The land is vastly made up of land, sea ice, and open water. This region is highly dependent on the wintry conditions so warming poses an obvious threat. The Inuit people have been rerouting their daily trails in order to surpass the melting and this has not been easy on them. The trails are essentially unmaintained but are essential for them to use as they gather their food and hunt in these areas. However, one surprising finding in a recent study is that the people are moving around a lot more, just in different means. Instead of using the sea ice trail, they are now using the open water to their advantage.

           A hot plate was turned on and set to 250 °C. Cyclohexanol (2.0 grams, 20 mmol) was pipetted into a 5 mL round-bottomed (RB) flask RB flask. A buret was used to add phosphoric acid (0.5 mL, 9 mmol) to the RB flask. Boiling chips were added to the RB flask. A fractional distillation was performed on the liquid mixture inside the RB flask at a rate of one drop every 20-30 seconds. The temperature was recorded at the time of the first drop, and again once every four drops after that. The distillate was collected at 68°C. The liquid mixture was distilled until approximately 10% of the original volume remained in the flask. The contents of the collection vial were pipetted into a test tube, and a work-up was performed. The mixture was washed by adding 1 mL of water to the test tube, mixing thoroughly, and removing the lower, aqueous layer. This process was repeated with 1 mL of NaOH and 1 mL of NaCl. The contents of the test tube were pipetted to a new vial. Several CaCl2 spheres were added to the vial until the CaCl2 spheres no longer clumped together. After being transported to a third and final vial, the mass of the liquid was recorded. Samples were taken of the liquid to be analyzed by gas chromatography and infrared spectroscopy. With the remaining contents of the vial, two chemical tests were performed. First, 0.5 mL of cyclohexene product was added to one vial, and 0.5 mL of cyclohexane was added to a second vial. Three to four drops of bromine in dichloromethane was added to both vials and the resulting color changes were recorded. Finally, 0.3 mL of cyclohexene were added to one vial and 0.3 mL of cyclohexane were added to a second vial. Two to three drops of potassium permanganate were added to both vials and the resulting color changes were recorded.

To find the official identity of the RZW gene, we performed a Phytozome BLAST search of the RZW genomic DNA with Brachypodium distachyon v3.1 as the target species.  The best match to the query sequence was Bradi1g25180.1, and the predicted protein sequence was saved. The FGENESH and Phytozome predicted protein sequences were compared and the working map was updated.  From the Phytozome locus page, the functional annotation was saved as a graphic showing domains. The link to Uniprot was followed and there were 16 annotations that contained information about different domains.  We used NCBI BLAST to perform two Standard Nucleotide BLAST searches using the Nucleotide Collection (nr/nt) database and the Somewhat Similar Sequences (blastn) algorithm. Max target sequences was set to 1000, and the expect threshold was set to 1.  The first search was of our genomic RZW sequence and the second was of the Phytozome predicted coding sequence. We used NCBI BLAST to perform a Standard Protein BLAST using the non-redundant protein sequences (nr) database and the protein-protein BLAST (blastp) algorithm.  Max target sequences was set to 1000, and the expect threshold was set to 1.