User:Janelly Gonzalez/Notebook/Biology 210 at AU
Zebrafish Ongoing Project
Purpose The purpose of this study is to monitor the developmental effects and reactions of the protein source ovalbumin on zebrafish, starting from the embryonic stage.
Material and Methods Embryos of twenty zebrafish were placed in water and twenty were placed in 2 mg/mL of ovalbumin liquid. Once the embryos hatched, the fish were fed shrimp brine every other day. They were monitored and observed over a period of six days. Because the fish in ovalbumin deceased, on the seventh day, eight new fish were put in a mix solution of .5mg/mL ovalbumin for the next five days. Differences in growth were assessed to explore the possible changes in body composition and what exactly the ovalbumin protein influences.
Data
Figure 1
Protein fish day 5 before dead first batch
Figure 2
Disintegrated new batch fish at day 10
Figure 3
Control fish on the last day, day 14
Conclusion Although zebrafish hatched from the embryo and grew quicker than the control group, zebrafish in the water, they disintegrated. A second batch of fish was tested on and with a lower concentration of ovalbumin and although they grew quicker and died than the control fish, the skeletons remained. Ovalbumin made the fish grow quicker and made it hard for them to swim when they were alive. It was determined that ovalbumin is a glycoprotein used in vaccinations.
March 18th: Vertebrate Analysis and Food Web
Purpose The purpose of this lab entry is to explore the different vertebrates that are in the transect. In doing so the food web could be determined. This will help figure out what type of vertebrates can live in the specific transit and how they contribute to the ecosystem. The food web illustrates the different roles of organisms as food sources and competition.
Material and Methods Vertebrates determined by seeds, plants, and observational studies.
Data File:March17OWWFoodwebentry.pdf
Conclusion Identifying the vertebrates and mapping out the food web helps understanding the entire ecosystem from the microscopic biodiversity to the macroscopic level. It is evident that the terrestrial's food chain is a hierarchy and every organism has a specific function and place in the food web and in the transect.
March 4th: 16S Sequence Analysis
Purpose PCR was conducted on grown bacterial colonies to identify strain of bacteria that devleloped in Transect One.
Materials and Methods After observing bacteria colony grow, samples were taken from the two colonies and inserted into a Polymerase Chain Reaction gel sample. The goal is to then observe the expression sequences of specific genes in bacteria.
Observations Transect one did not produce the bacteria necessary to create a polymerase chain reaction, Eric Mconough's transect was examined to provide the PCR data Transect One should of had. The transects were similar biomes. "Samples 1 and 4, which were run on agarose electrophoresis gel last week and then sent out for sequencing, returned the following sequences, in which N represents unidentified base pairs. Sample 1: TGNANGCCNANCGNGTNAGANGANCGNNNTNCTGNGGNANNCTNTGNGNNAGCGNGNTGATACGGGTGCGGAACACGTGTGCAACCTGCCTTTATCAGGGGGATAGCCTTTCGAAAGGAAGATTAATACCCCATAATATATTGAATGGCATCATTTGATATTGAAAACTCCGGTGGATAGAGATGGGCACGCGCAAGATTAGATAGTTGGTAGGGTAACGGCCTACCAAGTCAGTGATCTTTAGGGGGCCTGAGAGGGTGATCCCCCACACTGGTACTGAGACACGGACCAGACTCCTACGGGAGGCAGCAGTGAGGAATATTGGACAATGGGTGAGAGCCTGATCCAGCCATCCCGCGTGAAGGACGACGGCCCTATGGGTTGTAAACTTCTTTTGTATAGGGATAAACCTTTCCACGTGTGGAAAGCTGAAGGTACTATACGAATAAGCACCGGCTAACTCCGTGCCAGCAGCCGCGGTAATACGGAGGGTGCAAGCGTTATCCGGATTTATTGGGTTTAAAGGGTCCGTAGGCGGATCTGTAAGTCAGTGGTGAAATCTCATAGCTTAACTATGAAACTGCCATTGATACTGCAGGTCTTGAGTAAAGTANAAGTGGCTGGAATAANTAGTGTANCGGTGAAATGCATAGATATTACTTANNAACACCAATTGCGAAGGGCAGGTCNCTATGTTTTAACTGACGCTGATGGACGAAAGCGTGGGGAGCGAACAGGATTANATACCCTGGTNGTNNNNGCCGTANACGATGCTNACTCNTTTTTNGNNCTTCNGATTCAGAGACTAAGCNAAANTGATAGTTAGNCNNCCTGGNGAGTNCNTTCNCAANAATGAAACTCANAAGAANTGACGGGGGNCCCNCNCANCCGTGNATTATGTNGTTTAATTCANNNNNCNNNNGNANCCTTNNCNACGCTTAANNGGGATTGNGGGGGNTTAGANNNNANNNGTCTCNNCATTTCNANNTTCTNCNNGGGNNGNCGGNGGNTGGTCCCCCNNTGTANGNN NNGGTCAAGNACNNGNNGNNCCCNNT Sample 4: GCAGTCNAGCGGATGANANNAGCTTGCTCTTCGATTCAGCGGCGGANGGGTGAGTAATGCCTAGGAATCTGCCTATTAGTGGGGGACAACGTTTCGAAAGGAACGCTAATACCGCATACGTCCTACGGGAGAAAGCAGGGGACCTTCGGGCCTTGCGCTAATAGATGAGCCTAGGTCGGATTAGCTAGTTGGTGAGGTAATGGCTCACCAAGGCGACGATCCGTAACTGGTCTGAGAGGATGATCAGTCACACTGGAACTGAGACACGGTCCAGACTCCTACGGGAGGCAGCAGTGGGGAATATTGGACAATGGGCGAAAGCCTGATCCAGCCATGCCGCGTGTGTGAAGAAGGTCTTCGGATTGTAAAGCACTTTAAGTTGGGAGGAAGGGTTGTAGATTAATACTCTGCAATTTTGACGTTACCGACAGAATAANCACCGGCTAACTCTGTGCCANCAGCCGCGGTAATACAGAGGGTGCAAGCGTTAATCGGAATTACTGGGCGTAAAGCGCGCGTAGGTGGTTCNTTAAGTTNNATGTGAAATCCCCNGGCTCNACCTGNNAGCTNCNTTCNANACTGTCNNGCTANANTATGGTANANGGTGCTGGAATTTCCTCTGTNGNNNNNCAAATNNNNANATANANNATTGAACNNNNNTGNCNANNNGNNNNCCTCCNCTGNTNGNCNANNCNNGTATNCGCNCCNTGNGNGNGAAACACNNGNGGNTNGNCTCCNNCGCCACNGNGTNTNCNANATNTACNANCCTTTTCGNTGNGNTNNNNNNNTATTNCNCNGNCTCNCCNNANANNTNNACNNNCANNNTNNNGNNNNGNCCNCCCTGGGGGCTCNNCNNGNNTTTTTNNNTGNCNNGNGCAAGNAANNNNNGNGGGNGTTGNNGCTNNNTNNNACAAAANNANNNNANCGCCCCNTGGTNNNGNNCNGGNNNANGGNNNNTAANANNTGGNNTGGNNNCCTNCGGGNACCNAAANNNNNGGNNGNA NNGNANNNCNNNNNCTCCCNNNCCNANNNNGGTTGG
Sample 1 was considerably more definitive than Sample 4, which ultimately could only be fit to a best match of 59% due to the large number of unidentified base pairs. The table below presents the findings when each sample was run through the GeneWiz and Genomic Blast programs. Sample # Number of base pairs Identity of Bacteria % match? Sample 2 1386 Chryseobacterium sp. WR1 80% Sample 3 1397 Pseudomonas sp. Ata11 59% Sample 1 was identified as Chryseobacterium with an 80% match to the known genetic code. Chryseobacterium is gram-negative, rod-shaped, and yellow-pigmented. It is found in environments much like that of this transect, including in soil, plants, and wastewater. This sample had been characterized under the microscope as coccus-shaped, gram positive, and orange-yellow in color. As the color matches, and sample is matched relatively well to the known genetic code, it is likely that this sample is indeed Chryseobacterium, and that some error was involved both in observing the shape of the bacteria under the microscope (identification is difficult for such small organisms without use of an electron microscope) and in the gram stain procedure. Sample 4 was identified with less certainty (59%) as Pseudomonas. Pseudomonas are gram-negative and rod-shaped. As this sample was characterized under the microscope as rod-shaped but gram-positive, and the percent match to the known genetic code is so low, it is likely that this is not a correct identification of this bacteria."
Conclusion Because Transect One did not produce desired results, no concrete conclusion could be made.
Feb. 18 Lab Entry #5
Feb. 12 Lab Entry #4
File:LabExcerciseIVPlantaeFungi.docx
Jan. 29 Microbiology Lab 3
'''Materials and Methods for Gram Stains''' In order to pick up a small amount of bacterial growth from the agar, a loop was sterilized first over a flame from a bunsen burner and then cooled. This small amount was then placed on a slide along with a drop of water over it. A circle was drawn on the opposite side of the labeled slide to indicate where the sample was. The water was evaporated by passing the slide through the flame using a tong, bacterial sample right side up. Once it cooled a drop of crystal violet was put on top of the smear and left there for a minute then rinsed with water. The same was done with Gram’s Iodine. A drop of 95% alcohol was applied for 15 seconds and then rinsed. A drop of safranin stain was applied next and left for 25 seconds and then rinsed. With a kimwipe the rest of the water was removed.
Materials and Methods for DNA Isolation and PCR Amplification From two different agar plates, one containing tetracycline and one without , a toothpick was used to remove a sample from a bacteria colony. The sample was put into a PCR tube that contained 20 microiliters mixture of primer and water. Before adding the sample, the tube was mixed to get rid of the PCR bead. Once the sample and the mixture was combined it was inserted into the PCR machine.
Media:Microbiology_Lab_Data.pdf
File:Gram stain, tet 10-5 40x File:Gram stain 10-7 40x No tet File:Gram stain no tet 10-5 40x File:No gram stain 10-7 40x No tet File:No gram stain Tet 10-5 40x File:Gram Stain Tet, 10-7 40x
