User:Ji Won Shin/Notebook/Biology 210 at AU

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(2)Purpose: to understand the characteristics of bacteria using Gram Staining as a tool and observe their resistance to bacteria by the difference shown in seperate agar plates. Also to understand DNA sequencing as a tool of identification by preparing PCR.  
(2)Purpose: to understand the characteristics of bacteria using Gram Staining as a tool and observe their resistance to bacteria by the difference shown in seperate agar plates. Also to understand DNA sequencing as a tool of identification by preparing PCR.  
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(3)Materials and Methods:
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(3)Materials and Methods:
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Observation of Agar Plates:
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- Serial Dilutions done on agar plates last lab were seen. The colony size on each plate was counted and plates with too many colonies to count were considered a lawn. Differences between the nutrient agar plates with and without agar plates were recorded, along with what this might indicate. The effect of tetracycline was observed and colonies per mL of the culture was also observed.
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- 3 samples were collected from the plates, 2 from the nutrient agar plate and 1 from the nutrient agar plate with tetracycline, an antibiotic. The three sample colonies were recorded for their elevation, color, form, and margin. A wet mount of these samples were made, using a loop tool. The wet mount was then observed with a microscope to identify the cell shapes and motility, each at different magnifications.
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Gram Staining:
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- the 3 samples that were collected before for the wet mount were gram stained, following the instructions given in the lab manual (pg 22).
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PCR:
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- Of the 3 samples, 2 were chosen to be used for PCR, one from nutrient agar and one from the nutrient-tetracycline agar. Each colony was transferred to 100µL of water that was in a sterile tube, then incubated at 100°C for 10 minutes. The incubated tube was then centrifuged and 5µL of the supernatant in the tube was used for the PCR reaction.
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(4)Observations and Data:
Table 1:  
Table 1:  
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Figure 6: [[Image:Fusiliurm Spirilum.PNG]]
Figure 6: [[Image:Fusiliurm Spirilum.PNG]]
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(4)Observations and Data:
 
(5)Conclusions:
(5)Conclusions:

Revision as of 18:14, 16 February 2014

February 16,2014

(1)Introduction: The characteristics of bacteria will be assessed by gram staining samples from different agar plates. Since there were two types of agar plates, one with tetracycline and one without, the two different plates will be observed to compare and contrast the difference in bacteria growth. The same samples used in the gram staining will also be used to prepare PCR for the next lab's DNA sequencing.

(2)Purpose: to understand the characteristics of bacteria using Gram Staining as a tool and observe their resistance to bacteria by the difference shown in seperate agar plates. Also to understand DNA sequencing as a tool of identification by preparing PCR.

(3)Materials and Methods:

Observation of Agar Plates:

- Serial Dilutions done on agar plates last lab were seen. The colony size on each plate was counted and plates with too many colonies to count were considered a lawn. Differences between the nutrient agar plates with and without agar plates were recorded, along with what this might indicate. The effect of tetracycline was observed and colonies per mL of the culture was also observed.

- 3 samples were collected from the plates, 2 from the nutrient agar plate and 1 from the nutrient agar plate with tetracycline, an antibiotic. The three sample colonies were recorded for their elevation, color, form, and margin. A wet mount of these samples were made, using a loop tool. The wet mount was then observed with a microscope to identify the cell shapes and motility, each at different magnifications.

Gram Staining: - the 3 samples that were collected before for the wet mount were gram stained, following the instructions given in the lab manual (pg 22).

PCR: - Of the 3 samples, 2 were chosen to be used for PCR, one from nutrient agar and one from the nutrient-tetracycline agar. Each colony was transferred to 100µL of water that was in a sterile tube, then incubated at 100°C for 10 minutes. The incubated tube was then centrifuged and 5µL of the supernatant in the tube was used for the PCR reaction.

(4)Observations and Data:

Table 1: Image:100-fold_Serial_Dilutions_Results.PNG

Figure 1: Image:Plates_without_tetra.jpg

Figure 2: Image:White_Big_Swab.PNG

Figure 3: Image:Purple_Swab.PNG

Figure 4: Image:Plates_with_Tetra.jpg

Figure 5: Image:White_Swab.PNG

Table 2: Image:Bacteria_Cell_Morphology_Observations.PNG

Figure 6: Image:Fusiliurm Spirilum.PNG

(5)Conclusions:

JS February 09,2014 Identifying and Understanding of Algae and Protist through a Dichotomous Key

(1)Introduction: algae and protists in different regions of the Hay Infusion from Lab 1 will be analyzed using a dichotomous key. Hay Infusion will also be used to make serial dilutions, each dilution being smeared on nutrient agar plates and nutrient agar plates with tetracycline, an antibiotic. I hypothesize that the nutrient agar plates with tetracycline will show less growth and that the samples of differnt niches of the Hay Infusion will contain similiar organisms.

(2)Purpose: to understand how to use a dichotomous key, using it to identify algae and protists found in individual Hay Infusion, noting their individual characteristics. Making of Hay Infusion culture serial dilutions and smearing of agar plates with and without tetracycline to use for next lab, learning serial dilution method and agar plate smearing.

(3)Materials and Methods:

- observation of Hay Infusion culture made in last lab. Characteristics such as smell and appearence noted. 3 samples from different layers (Top (mold area),Middle (Near Plant),Bottom(near the dirt))taken to oberve organisms inside. Drop of each sample placed on a slide and observed in a microscope. 2 different organisms observed and recorded, totaling in 6 samples, 2 from each sample.

- serial dilution of Hay Infusion culture conducted for next lab. 4 tubes with clean 10 mL broth each are labled: 2,4,6,8. 100 µL from swirled Hay Infusion culture added to tube labled 2. 100 µL then taken from swirled tube 2 and transferred to tube 4. Process repeated until tube 8.

- 100 µL from each tube placed aseptically on surface of nutrient agar that corresponds to tube label. Same for nutrient agar with tetracycline.

Figure 1:Image:Serial Dilution.jpg


(4)Observations and Data:

Hay Infusion Culture:

Overall, the culture is yellow/brown in color, with a sour smell.

Figure 2:Image:Hay Infusion Very Top.jpg

The top layer of the Infusion has mold on top, with some plant leaves floating in between. Overall color from top is brown, riddled with some green plants.

Figure 3:Image:Hay Infusion Middle.jpg

Middle layer clear compared to top and bottom layer. Roots of plant can be seen.

Figure 4:Image:Hay Infusion Bottom.jpg

Bottom layer lined with dirt and decomposed deaf leaf, mostly solid matters with high density.

Figure 5:Image:Sample 1-3.jpg

Sample #1:

Colpidium sp(protist):

- clear
- slow, jerkey movement
- 7µm x 10 = 70µm

Gonium(algae):

- green
- immobile
- 3µm x 10 = 30µm

Sample #2:

Blepharisma sp(protist):

- yellowish
- fast
- oval
- cillia
- 5µm x 10 = 50µm

Colpidium sp(protist):

- white/clear
- oval/circular
- motile, jerkey

Sample #3:

Gonium(algae):

- green
- colony
- round
- 15µm x 2.5 = 12.5µm

Colpidium sp(protist):

- clear
- fast
- circular
- 6.5µm x 65µm

(5)Conclusion: Overall, the Hay Infusion gained the appearence it has currently because of the force of gravity and evaporation. Materials in the hay infusion culture were seperated according to their density and the water in the culture was evaporated into the air. Because the culture was not disturbed in any way, the materials and the water started decomposing due to inactivity, creating the sour smell. If the hay infusion culture had been observed for another two months, I would predict that more water would have evaporated and that the sour smell would have become stronger.

Colpidium sp meets the needs of life (energy, reproduction, cell, evolution, information) because it gains energy through consumption of materials in its surroundings. The energy gained from this consumption allows for reproduction. The unicellular cell is flat with a cytostome, nucleus, and a vacuole. It self-replicates, fulfilling reproduction and because of this they are able to evolve, which resulted in their current appearence, granting them cilliarly hair to move around with. Through these hairs, they are also able to gather information about their surroundings.

Part of my hypothesis was correct; Based on the data, colpidium sp and gonium were present in all 3 niches of the Hay Infusion culture. However, there were differences that resulted from the fact that the 3 samples were all taken from different areas. Sample #1 and #2, which was taken near the plant exhibited a lot of cell movement and a lot of organims compared to sample #3. This result would be because of the fact that the organisms feed on the plant matter. The lack of plant matter in the bottom of the hay infusion culture meant a lack of food for the organisms, making organisms to be scarce or dead. On the other hand, sample #1 and #2 with their abudant algae and plant growth created a perfect enviroment for the organsism insdie the culture. The hypothesis on the growth on the agar plates cannot be confirmed untill next week's lab.

This lab can perhaps be improved if the slides can be dyed because it was hard to see the organisms. Other than this, there seems to be nothing that I would do differently.

JS 2/6/14, lab 1 notes

Great job!!! Make sure you sign each entry at the bottom of each entry. Good work.

AP

January 31,2014: Understanding Natural Selection and Observing Abiotic and Biotic Characteristics of a Niche

(1)Introduction:observation of green algae of volvocine line and observation of niche and its biotic/abiotic factors I hypothesize that the Volvox would be the most advanced out of the three green algae that are to be observed.

(2)Purpose:to understand natural selection by looking at three green algae (Chlamydomonas, Gonium, Volvox) of the volvocine line in order to observe the selective functions that organisms have developed and to determine the biotic and abiotic characteristic of a niche in American University, forming a hay infusion at the end in order to determine organisms that exist in niche.

(3)Materials and Methods:

- observation of three types green algae, Chlamydomonas, Gonium, Volvox of the volvocine line. Each placed upon slide and observed through a microscope. Number of cells observed, Colony Size, Functional Specialization of Cell, and Reproductive Specilization (whether the cell is isogamy or oogamy) of the cell were recorded.

- journey outside in different groups to observe specific niche in American University. Topography, biotic/abiotic features of niche, Location, and specific informations about niche were observed and recorded. Samples of the niche were collected to use for hay infusion for next lab.

(4)Observations and Data:

Chlamydomonas:

- 1 observed cell with colony size of 25.
- single celled
- egg-shaped cells that are easily visible
- cup shaped chloroplast with pyrenoid
- flagella for motility
- Isogamy

Gonium:

- 5 observed cell with coloy size of 4
- colonies normally range from 4,8,16,32 cells, each able to form a new colony
- Oogamy

Volvox:

- 3 cells observed with 2.5 colony size
- thousands of cells that make up colony
- has gametes
- has anterior/posterior pole of cell
- Oogamy	                                  

Niche #4:

Description:located in area across from Katzen Art Center, across Massachusetts Ave NW. Area constructed as drainage in case of snow and rain. Because of the purpose that it was built for, niche laid out with rocks and pebbles. Types of vegetation that can live with excess amounts of water and that have great absorptivity such as cat tails. Mud and sand rather than dry dirt because of reasons mentioned before. Some grass at edge of transect. Humans and squirrels near transect.

Abiotic Factors:

- air, wind
- dirt, sand, mud
- sunlight
- rocks,pebbles
- sidewalk
- moisture,water

Biotic Factors:

- plants (grass, cat tails), dead leaves
- humans
- squirrels
- fungi (on rock)
- bugs, worms

Image of Niche #4:https://drive.google.com/a/student.american.edu/file/d/0BzQOqxfdJTX9SC1iVGhIRDlPcTA/edit?usp=sharing

(5)Conclusions: Orignial purpose was fulfiled and hypothesis was proven correct. Colony size decreased from Chlamydomonas to Volvox. The data showed that natural selection chooses characteristics that would benefit the specie and that regression does not mean evolution has not occured. It all depends on what benefits the specie in total. To improve the experimental design, the lab should be divided up because for some time, people were left waiting until the others finished to continue the lab portions. Future plans would be to use the hay infusion that was made and observe the organismss such as bacterias in the infusion. The change in the hay infusion would also be recorded.

January 22, 2014- successfully added text

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