User:Mary Simcock/Notebook/Biology 210 at AU
Lab Day: 2.26.16 Entry #: 7
Purpose
The purpose of the procedures performed today was to continue the study of our Zebrafish embryos. Observations were made regarding size, shape, pigmentation, and overall health of each Zebrafish. Observations of the Zebrafish continued throughout the week through 3.4.16.
Materials and Methods
Upon retrieving our plates of Zebrafish, we proceeded to observe each well under the compact microscope. Observations regarding size, pigmentation, health, shape and any other notable appearances of the Zebrafish were recorded. Growth stage and any developmental factors for each Zebrafish were noted. Each well containing a live Zebrafish was then fed with 15 microliters of brine shrimp. Furthermore, the bacteria for our transect (#4) were identified to the best of our ability based on previously determined DNA sequences.
Data and Observations
https://docs.google.com/document/d/1zAPnS6hQ3O4nS7XYjTje3NSobay-4g08jLyCM8BTfwM/edit
Identification of Transect bacteria based on DNA sequencing:
- Mary Simcock 22:48, 3 March 2016 (EST): Mary Simcock
Lab Day: 2.19.16
Entry #: 6
Purpose
The purpose of today's experimental procedures was to set up and start the initial data collection for our Zebrafish experiment. Compounds to expose the Zebrafish embryos to were determined by each group and our control and treated plates were set up with each containing a Zebrafish embryo.
Materials and Methods
First, two plates were obtained containing 24 wells each, only 20 of which were used. One plate was to be used for the control (just water) and the other plate was for the treated embryos. For the control plate, only water was placed in 20 of the 24 wells followed by the placement of one Zebrafish embryo in each well. For the other plate, an androgen antagonist was added to each of the wells followed by a Zebrafish embryo being placed in each of the 20 wells. Originally, my group had planned on adding an estrogen agonist, a mixup occurred with the compounds. Initial data was recorded, which just included the current stage of growth of each of the embryos. Throughout the week, data will be collected as to the growth stage of each embryo/Zebrafish on the day they are observed as well as any supplemental observations that may indicate a change in their growth due to the androgen antagonist. 10 microliters of Brine Shrimp were fed to the Zebrafish on Wednesday and Thursday.
Data and Observations
https://docs.google.com/document/d/1zAPnS6hQ3O4nS7XYjTje3NSobay-4g08jLyCM8BTfwM/edit
Conclusions and Further Directions
Based on the data we have collected so far, we can tentatively draw the conclusion that the androgen antagonist has indeed thus far had an effect on the growth of the Zebrafish. As the data suggests, a large number of the zebrafish exhibited abnormal growth in comparison to the healthy Zebrafish in the control wells, such as much clearer complexions, decreased or increased size, and a much more slender body frame. Further experiments will allow us to look more closely at the effect of the androgen antagonist on Zebrafish development, such as analyzing heartbeat and size of important structures.
- Mary Simcock 10:46, 26 February 2016 (EST): Mary Simcock
Lab Day: 2.12.16 Entry #: 5
Exercise V: Invertebrates and Vertebrates
Purpose
The purpose of this experiment was to identify the invertebrates found in our transect from the Berlese funnel that was constructed last week. A number of procedures were employed in order to accomplish this task as well as to enable us to describe our organism in terms of phylum and class.
Materials and Methods
Before actually observing the invertebrates within our Berlese funnel, the class was allotted 10 minutes to observe the same organisms in the back of the classroom from each of the five major classes of anthropoids: arachnida, diplopoda, chilopoda, insect, and crustacea. Our goal was to try and identify which one was which. Doing this exercise would later aid us in the identification of our own invertebrates from the Burlese funnel. After looking at the sample organisms, each group retrieved their Berlese funnel and poured the top 10-15 mL of the 50% ethanol and organisms into a petri dish. The remaining liquid was then poured into a second petri dish. Each petri dish was then analyzed via microscopy and three organisms from the first petri dish and two organisms from the second petri dish were identified using a dichotomous key and recorded. The phylum and class, length in mm, number in sample, and a description of the organism were all recorded in the data table provided below in the data and observations section.
Data and Observations
Conclusions and Further Directions
Based on the invertebrates discovered in our transect and their phylum and classes, we can conclude that our transect contains a rather diverse number of invertebrates. The phylum of Arthropoda is highly represented in the classes diplopoda and insects. Furthermore, the phylum Nematoda, which is mainly composed of earth worms, is represented in the classes Enoplia. Also, our data shows that the phylum Nematod, the earth worms, were more abundant in the top layer of our 50% ethanol, whereas the bottom layer contained majority phylum Arthropoda, such as the millipede. In addition, the conclusion can be made that a majority of the organisms observed have developed internal organ/tissue organization due to their bilateral symmetry. As far as vertebrates found in our transect, we have not found much evidence. We can assume that birds are present in our transect, though, as they are everywhere on campus and it is more likely than not that they have at one point found themselves in our transect. Furthermore, as indicated by our data, there are many earthworms present in our transect, most likely due to the fact that a large area of our transect is covered in soil, and birds feed on earthworms so our transect could provide them with a food source. Other than this assumption, no footprints (other than human) have been observed in our transect.
- Mary Simcock 23:46, 18 February 2016 (EST):Mary Simcock
Lab Day: 2.5.16
Entry #: 4
Exercise IV: Plantae and Fungi
Purpose
The purpose of this experiment was to, through a number of procedures, identify and study the plants located in our transect and to set up a Berlese funnel in order to collect invertebrates from our transect for later observation. PCR was also run on our serial dilutions to that will later be analyzed for the 16S gene.
Materials and Methods
The first of the day's procedures involved running the PCR gel in which each group loaded their two serial dilution samples from their transects into the gel. Once all of the samples had been loaded, the TA ran the gel. Results were not analyzed today. Following this each group returned to their transect to collect five plant samples and placed them in a Ziplock bag. The collected plant samples were to then be characterized in three ways: plant vascularization, presence of specialized structures, and mechanisms of plant reproduction. In order to obtain this data, sections of at least three of our plant samples were observed via microscopy. To get a more in depth look at the structure of each plant on a microscopic level, razor blades were used to chop up leaves, stems, or buds containing the reproductive systems. Each sample observed under the microscope was photographed. After careful observation, the vascularization, specialized structures, and mechanisms of reproduction were all identified for each of the five samples and recorded in table 1. Upon completion of the characterization of our plants, a Berlese Funnel was set up for the purpose of collecting invertebrates in our transect. For this part of the procedure, 15 mL of 50:50 ethanol/water solution into a 50 mL conical tube. The purpose of the ethanol mixture is to kill the invertebrates that filter into the conical tube. Next, a piece of screening material was taped into the bottom of the funnel and the leaf matter we collected from our transect was packed into the funnel to fill it up about halfway. Parafilm was then wrapped tightly around the bottom of the funnel to connect the conical tube to the funnel and to ensure its security. The parafilm was made sure to be applied very tightly to prevent the evaporation of the ethanol. Once the conical tube had been secured to the funnel, the funnel was then attached to a ring stand underneath a 40 watt lamp and an umbrella of foil. The Berlese funnel set-ups were left under these conditions until the next lab period upon which the invertebrates in the conical tube will be analyzed.
Data and Observations
We did not observe any fungi sporangia under the microscope, but we can provide information as to why they are important. As sporangia mature from small, black, globelike structures the become black, thus lending itself to the common name of fungus. Inside the sporangia are cells called spores, which are released upon the opening of the sporangia.
Conclusions and Future Directions
Based on our data and observations, we can conclude that our transect exhibits diversification in the way of plant life. Based on the identification of vascularization, specialized features, and mechanisms of reproduction, we can make the claim that Angiosperms (samples #1,5) are existent within our transect as well as many plant types that exhibit vascularization and evolutionary specialized structures, such as reproductive organs and stems to obtain nutrients. We also drew the conclusion that all of the plants in our transect were vascularized and vascularization was the first evolutionary indicator of the transition from water (algae) to land plants, meaning that all land plants exhibit vascularization. No seeds were collected from our transect nor were any fungi observed/noted within our experimental procedures.
- Mary Simcock 01:00, 12 February 2016 (EST): Mary Simcock
