User:Skyler Trice/Notebook/Biology 210 at AU

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March 7, 2014 Lab #6 - Embryology and Zebrafish

-The purpose of this lab is to observe the effects of fluoride on the development patterns in zebrafish embryos - I will use two sets of 20 zebrafish, one acting as a control just submerged in water, while the other embryos will be experimental and submerged in water mixed with fluoride. -Over the next week of observation I will try to identify the development differences between the two groups of zebrafish embryos. After reading previous experiments done on the effects of fluoride on embryonic development, I predict that the experimental group of embryos will have growth deformations.

-To begin the expedient I filled two petri dishes with 20 milliliters of water. Then 10 milliliters of fluoride was added to the experimental petri dish.Then from the large pool of embryos, I selected 40 healthy embryos and transferred 20 embryos into each petri dish.

-I observed the embryonic development of the zebrafish at intervals of 1, 2, 4, and 7 days. All 40 embryos survived until sometime around day 7. After each observation session it was clear that the experimental group was developing much larger than the control group specifically in their had region. At day 7 measurements of the embryos were taken and the experimental group had on average heads .2 um larger than the control group, and were 1 um longer in length.

-The experimental group also appeared to have lived longer than the control group because they were not as denigrated.

-Results proved my hypothesis to be correct in that fluoride did appear to have an effect of embryonic zebrafish development. The experiment showed that head deformations occurred as a result of the added fluoride and length was increased as well.

Data: Day 1: Most in 10 to 12 hour stage. All alive. Day 2: Most in 14-16 hour stage. All alive. Day 4: Most in 48 hr-72 hour phase. All alive. Day 7: Almost all zebrafish in 120 hour phase. All dead.


February 29, 2014 Lab #5 - Invertebrates

-The purpose of this experiment was to understand the importance of invertebrates and their various characteristics.

-In the experiment we observed dead and preserved unidentified arthropods and classified each group such as millipedes, centipedes, arachnids, etc. After observing the arthropods, we observed the invertebrates that we collected from our Bernese Funnel in a petri dish. Under the microscope we tried to identify the invertebrates using a dichotomous key.

-We only found two invertebrates from our Bernese Funnels. The first organism we believe was a flea from the phylum siphonaptera. We observed small black wings which helped in the classification. The organism was approximately 3 mm. The second organism we we believed was a soil mite because it had many legs and a segmented body approximately .5 mm in length. 1-3 millimeters was the size range of the organisms we found. SWT

February 25, 2014 Lab #4 - Plants and Fungi -The purpose of this experiment was to understand the various characteristics of plants and to observe the function and importance of Fungi.

-Our group collected various plants from our pine transect and characterized them.

-First, we went to the transect and collected five different types of plants. We then took them back to the lab for observation. After looking at them under the microscope we characterized the plants based on their different classifications. We were able to observe different types of characterized plants to help us with the classification process.

-The first station observed was plant vascularization. We looked at mosses and plants and were able to find their xylem and phloem. In the second station we observed plant specialization. We looked at different types of specialized cells in the plant such as the stomata and the guard cells. In the third station we observed plant reproduction. We also observed diagrams of plant reproductive organs and looked at plant reproductive organs underneath the dissecting scope. At the last station we observed appreciating fungi underneath the dissecting scope.

-At the end of the lab we concluded that most of the plants found in out pine transect have very similar characteristics likely due to the fact that similar plants characteristics thrive in similar environments.SWT

February 15, 2014 Lab #3 – Microbiology and Identifying Bacteria with DNA

-The objectives of this lab were to understand the characteristics of bacteria, observe antibiotic resistance, and understand how DNA sequences are used to identify species.

Procedure 1: Quantifying and Observing Microorganisms

First, we checked on the Hay Infusion Culture from last week an the only noticeable change was that the smell was better. The plant matter sill looked the same. The smell probably changed from the microorganisms living and interacting with matter in the culture.

Procedure 2: Antibiotic Resistance

Upon observing plates, I noticed the plates without the antibiotic had a significantly larger amount of growth compared to the plates with the antibiotic. This indicates that the antibiotic was successful in killing the bacteria and preventing reproduction. The tetracycline significantly reduced the number of bacteria and fungi. Very few species were unaffected by the tetracycline. Tetracycline works by inhibiting a lot of enzyme reactions essential for processes of bacterial cells. The synthesis of protein is the most sensitive biochemical reaction that is inhibited. Tetracycline binds to the 30S ribosome of the bacteria which prevents the attachment of the aminoacyl tRNA to the RNA-ribosome complex.

Procedure 3: Bacteria Cell Morphology Observations

First we observed prepared slides with different types and shapes of bacteria on them. Then we used the oil immersion objective lens to observe the samples of bacillus, coccus, and spirillum shaped bacteria. In the second part od procedure 3, we made wet mounts from the nutrient agar plate and the nutrient agar plate with tetracycline. These samples were also used to make a gram stain. When the sample were gram positive it was a violet color, while the gram negative was a pink color because it didn’t retain the dye. We then determined the cell shape and motility of the organisms.


Black Colony 10^-5: (nutrient) -Dark purple -Round shaped colony -Dipococcus colony shape -Circular morphology with slightly raised edge -Cell wall - Coccus - Single celled colony -Non moving - Gram Negative


Orange Circle Colony 10^-7: (nutrient)

-Circular colony shape - Orange -Raised, convex - Entire edge - No visible cell wall -Coccus - Light elevation -Non moving - Gram Negative


Orange Circle Colony T-10^-3 (tet)

- Circular colony form - Egg yolk color - Raised elevation - Entire Edge - No visible cell wall - Coccus - Smooth - Gram Negative Colony 3.jpg

Procedure 4: PCR

In this part of the lab we isolated DNA from the bacteria in the colonies and used two primer sequences of 27F and 519R to selectively amplify the 16S rRNA gene. In next weeks lab we will run the PCR products on an agarose gel to see if it is good enough for sequencing.


February 8 : Lab # 2 - Identifying Algae and Protists

The objectives of this lab were to understand the characteristics of algae and protists, as well as how to use a dichotomos. This was accomplished by completing the procedures written below.

Procedure 1: How to Use a Dichotomous Key

In order to identify the organisms on our wetmounts we described what each organism looked like, how big it was, and then used many questions and images on the dichotomous key to conclude what organisms we were looking at.

Wet Mount #1: Bottom Sediment Sample

Organism 1:Paramecium - Threadlike - Not moving - 40um Organism 2: Gonium - Many cells clumped together - Round shape - Greenish color - 50um

Wet Mount #2: Middle Sample

Organism 1: Spirostomum - Unicellular - Long needle shape - Green color - Visible peristome - 5mm Organism 2: Gonium - Many cells clumped together - Round shape - Greenish color - 40um Organism 3: Chlamydomonas - Motile - Flagella - Unicellular - Oval shape - 5um

Wet Mount # 3: Top Sample Organism 1: Gonium - Many cells clumped together - Round shape - Greenish color - 70um Organism 2: Bursaria Truncatella - Oval Shape - Cilia - Motile - Visible peristome - Many vacuoles - 725um Organism 3: Volvox - Round shape - Green - Many colonies of cells - 400um

Procedure 2: Hay Infusion Culture Observations

In this section of the lab the Hay Infusion Culture that we made the previous lab was observed. Observations were written down, and wet
mounts were taken from the Hay Infusion to see what organisms were present in the transect. We observed the different organisms
from each wet mount, one from the bottom, middle, ant top of the Hay Culture. Organisms closer to the the plant matter on the
bottom tended to be photosynthetic.  Different organisms were found in the top, middle, and bottom of the culture because
different materials were in each level of the culture. Below is what we observed in the Hay Culture. 

Appearance of Hay Culture: - Smells terrible, like rotten leaves - Many pine needles - Murkey - Sediment at bottom - Foamy surface residue (possibly from milk)


January 31st - Transect Lab #1 - Biological Life at AU - Group #5

The objective of this lab is to understand the biotic and abiotic characteristics of a niche, and to better understand natural selection. To better understand the process of natural selection we observed the driving forces which are the interactions between the biotic and abiotic factors in our transect and their interaction with the physical environment.

Transect #5 a 20 by 20 foot transect located right in front of Hurst and across from Battelle. Half of the transect was covered by the cement walk area and the benches and the other half was covered by rose bushed, trees, and grass.

Steps Performed: 1) Locate Transect and set detentions with 4 popsicle sticks 2) Observe the transect- noting the location of the transect, and the topography 3) Draw a picture of the transect 4) Observe and record four biotic and five abiotic factors 5) Take notes on the surroundings of the transect 6) Take a soil sample and vegetation sample in a 50 mL conical tube 7) Return to lab to make a hay infusion culture

Biotic Factors: -Rose bushes -Grass -Bugs -Squirrel

Abiotic Factors: -Stone -Rock -Bench -Stone Sign

Future Plans: This lab allowed me to understand the biotic and abiotic characteristics of a niche by observing our transect. In order to fully reach the objective of this experiment and better understand natural selection, further experiments and observations will need to be made by observing the Hay Infusion culture in Lab #2.

ST 1/31/14