User:Lauren Healey/Notebook/Biology 210 at AU

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'3/22/14: Embryology Lab
Intro: It is important to study zebrafish because their embryonic development is rapid and easy to see because of their translucent body. The effects of caffeine on embryonic development are widely unknown because they are rarely studied. For this experiment we treated the zebrafish embryos with caffeine to see how they would vary from the control group who were in just water. According to the paper we read prior to completely the lab, the zebrafish treated with caffeine should be smaller in size and have slower motor skills.'
Methods:
Day One:
1. Collect 20 zebrafish that be put in a control system with just water.

2. Collect 20 zebrafish to be treated with the variable caffeine, making sure they are alive. 

3. Observe the zebrafish making note of what stage in the lifecycle they are in, how many are hatched, viability, movement, yolk, eye, pigmentation, heart rate, and structures.
Day 3:
1. Observe the zebrafish making note of what stage in the lifecycle they are in, how many are hatched, viability, movement, yolk, eye, pigmentation, heart rate, and structures.
2. Replace 5mls of deerpark water in the control and 5 mls of caffeine solution into the caffeine treated petri dish.
Day 7:
1. Observe the zebrafish making note of what stage in the lifecycle they are in, how many are hatched, viability, movement, yolk, eye, pigmentation, heart rate, and structures.
2. Replace 5mls of deerpark water in the control and 5 mls of caffeine solution into the caffeine treated petri dish.
3. Remove any dead cases and dispose of them.
Day 9:
1. Observe the zebrafish making note of what stage in the lifecycle they are in, how many are hatched, viability, movement, yolk, eye, pigmentation, heart rate, and structures.
2. Replace 5mls of deerpark water in the control and 5 mls of caffeine solution into the caffeine treated petri dish.
3. Preserve 1-3 embryos in the formaldahyde solution.
Day 11:
1. Observe the zebrafish making note of what stage in the lifecycle they are in, how many are hatched, viability, movement, yolk, eye, pigmentation, heart rate, and structures.
2. Replace 5mls of deerpark water in the control and 5 mls of caffeine solution into the caffeine treated petri dish.
3. Preserve 1-3 embryos in the formaldahyde solution.
continue these for two weeks, making sure to preserve enough embryos from observation at the end of the experiment.

Results
https://drive.google.com/file/d/0B-ntMxISdJd6U0ZuMWh2RmQ2QWM/edit?usp=sharing We sometimes had a hard time taking the heart beat of the zebrafish because they were swimming so quickly around in the slide. The most significant findings of ours was that the fish were smaller in size and they died way faster than the control fish. We also found that their movements were a lot less. It was hard to get conclusive data because all of our treatment group died along with all but 2 of the control group.
Discussion
From this lab I can conclude that when treated with caffeine, it appears to shrink the size of the zebrafish. It was also observed that the heart rate of the zebrafish was much higher than the heart rate of the control group. This make sense because it is a symptom of caffeine consumption in humans. I think that it is possible that caffeine stunts growth in all organisms including humans. For future experiments, I would like to observe the zebrafish in a temperature controlled environment so they do not die prematurely because of the quick development. I would also like to look at the effects of caffeine on an animal closely related to humans to see how it changes development.



3/16/14 DNA Sequencing Lab
Objective: The objective of this lab was to use DNA sequencing to identify the types of bacteria found in our transect. Once we identified the bacteria, we would be able to use knowledge of that bacteria to make other observations about our transect.
Methods:
1. send PCR reaction to Genewiz Inc. for DNA sequencing.
2. Input sequence into NCBI blast to identify the sequence.
Raw Data:
Unfortunately, our PCR reaction did not come back with a DNA sequence so I used the sequences from another lab group.
I used S1-T3-4 and S1-T3-3 which were a different lab section but from the same transect.
S1-T3-4 when ran through the NCBI blast came back as Uncultured bacterium clone ncd900g07c1 16S ribosomal RNA gene, partial sequence.
S1-T3-3 when ran through NCBI blast came back as Uncultured Bacteroidetes bacterium clone MA161A12 16S ribosomal RNA gene, partial sequence.
Conclusion:
This lab demonstrated that different types of bacteria can grow in one transect of the university. The results of the PCR reactions were not taken from our PCR because there was not enough product to do so.
LH


2/28/14 Lab 5
Question/Problem/Objective: The objective of this lab is to observe, identify, and understand the importance of invertebrates. The objective is to identify invertebrates found in the transect.
Steps Preformed: Procedure 1:
1. Observe the acoelomate, Planaria under the microscope. Observe the type of movement and how it reflect the simplicity of the organism.
2. Observe the cross-sectional slide of the Planaria. Observe the digestive track of the stained organism.
3. Observe the nematodes and the cross-sectional slide. Again, observe the type of movement.
4. Observe the coelomate Annelida. Look closely at the internal organs and layer of muscle.
Procedure 2:
1. Break down the Berlese setup and move the preservative solution into a petri dish.
2. Try to identify the main groups of invertebrates.
Procedure 3:
1. Think about what invertebrate would inhibit and pass through the transect.
Raw Data
Earth Worm Observations: The earth worms move by bending their entire body.
https://drive.google.com/file/d/0B-ntMxISdJd6WkVxQ3dUcERSZGc/edit?usp=sharing
https://drive.google.com/file/d/0B-ntMxISdJd6dWhEaVZCSU5udHc/edit?usp=sharing
The largest organism that we measured was the coleoptera. The organisms had a large size range. Some were extremely small and not visible with the microscope while others were very visible with the microscope. The smallest was the . Mites are very common in leaf litter.
https://drive.google.com/file/d/0B-ntMxISdJd6Q1BObmh3QVFoVWM/edit?usp=sharing
https://drive.google.com/file/d/0B-ntMxISdJd6d0gxei1fSnVDT0U/edit?usp=sharing
Conclusion:
From this lab I can conclude that there are a wide variety of invertebrates within the transect. For future experiments, I would like to look into what makes the transect a livable environment for the invertebrates that we found in the transect.
LH

2/16/14 Lab 4
Question/Problem/Objective: The objective of this lab is to observe the function and diversity of plants and fungi. For this lab, we will collect plant samples from the transect and attempt to identify them. We will then observe fungi under the microscope and attempt to identify it.
Procedure 1:
1. Bring three bags to the transect.
2. Obtain a leaf litter sample from a site at your transect.
3. Take representative samples from five plants in the least damaging way.
4. Take a photo of the whole tree when taking samples from trees.
5. Find any seeds, pine cones, flowers, ect. from the plants and bring them back to the lab.
6. Describe the five plants and where they were found in your notebook and use the information to identify the genera.
Raw Data:
https://drive.google.com/file/d/0B-ntMxISdJd6V0xlU3NXS3A5c00/edit?usp=sharing
Legend:
1. Pith- the soft, spongy interior substance of plants and animals.
2. Protoxylem- the part of the xylem that developes first, consists of narrow, thin walled cells.
3. Xylem- the vascular system of plants that consists of tracheids, vessles, and sometimes both. Conducts water and dissolved materials but also aids in support and food storage.
4. Phloem- conducts food made in the leaves to other parts of the plant.
5. Sclerenchyma- cells that support the plant. Ground tissue that are neither vascular or dermal.
6. Cortex- cells laying between the epidermis and the endodermis. Capable of growth.
7. Epidermis- single layered group of cells that make up the outermost layer of the plant's flowers, roots, stem, and leaves.
Fungi Data:
Fungi sporangia are the organ in which spores are produced. They are important because spores are needed for fungi reproduction. Sporangia can be the site of meiosis or mitosis.
https://drive.google.com/file/d/0B-ntMxISdJd6Uml4M0hFTlZRZGc/edit?usp=sharing
Conclusion/Future Plans:
From this lab, I can conclude that there is a lot of diversity among the plants in my transect. I can also identify different types of fungi. I found it very interesting that it was so hard to identify some of the plants in our transect. I figured that they would be fairly common plants but I was wrong. In the future, I would like to look more into the fungi that is in my transect. We looked at the bacteria and I would be interested to see what type of fungi is growing in the transect.
https://drive.google.com/a/student.american.edu/file/d/0B-ntMxISdJd6bFd6bkVlbUdPb0U/edit?usp=sharing
LH


2/16/14 Lab 3
Question/Problem/Objective: The objective of this lab was to characterize bacteria, observe the antibiotic resistance and understand how the use a PCR reaction to identify species. I think that as the dilution of the plate increases, the amount of colonies will increase. By taking some bacteria and allowing it to culture, containing different dilutions of the nutrient and different levels of tetracycline we will be able to observe whether the bacteria behaves in the nutrient at different levels and how it reacts to the tetracycline.

Methods:
Procedure 1:
1. Count the total number of colonies in the petri dish
Procedure 3:
1. Observe a prepared slide containing different types and shapes of bacteria.
2. Make a wet mount of a growth from the petri dish and observe it under the microscope.
3. Determine the cell shape and if the organisms are motile.
Gram Stain
1. Label the slides
2. Heat the dried slide by passing it through the flame 3 times.
3. Stain the smear with crystal violet for 1 minute
4. Rinse the stain using the wash bottle
5. Cover the smear with Gram’s iodine mordant for 1 minute. Rise gently.
6. Decolorize by flooding the smear with 95% alcohol for 10-20 seconds. Rise. Decolorization occurs when the solvent flows colorlessly from the slide.
7. Cover with safranin stain for 20-30 seconds. Rinse.
8. Blot water carefully with a paper towel and air dry.
9. Put the slide under the microscope and observe the stain under 40x and the oil objective.

Raw Data:
https://drive.google.com/file/d/0B-ntMxISdJd6a1NWOVdVMHZWX28/edit?usp=sharing
I do not think that any Archaea species will have grown on the agar plates because they tend to grow in the most extreme environments and none of our petri dishes were put in extreme environments.
Procedure 1:
The appearance might change because the contents of the hay infusion may change along with the smell because the contents of the hay infusion might be decaying and mold might be growing in the jar.
Observations of the Hay Infusion: thin film on the top, smell is not too strong and a little musty, still reddish brown in color.
Antibiotic Resistance:
The colonies with the Agar are white and orange where as the colonies in the tetracycline are orange colored. The tetracycline kills the fungi but not the bacteria.
The tetracycline has less bacteria than the Agar plate and less fungi.
There is one species not effected.
There are more bacteria in higher concentrations of both agar and tetracycline.
Many organisms have acquired a resistance to tetracycline as an antibiotic and grow in the presence of it regardless. Staphylococcus and Streptococcus both have tetracycline resistant strands. Bacteria usually acquire resistance from horizontal transfer of a gene.

Conclusion and Future Plans:
From this lab I can conclude that bacteria grows better in higher concentrations of agar and tetracycline. Using a gram test, I was able to identify the makeup of the bacteria’s cell wall (presence of peptidoglycan). I was able to identify different bacteria based on characteristics and observe an antibiotic resistant strand of diplobacilli, which grew in the presence of tetracycline. As for future experiments, I think it would be interesting to see how these bacteria get from the soil into humans. I also think it would be very interesting to see he effects of the bacteria on organisms in the transect. The objective was addressed.







2/9/14 Lab 2 Objectives: To understand and use a dichotomous key to identify organisms. Also to identify the characteristics of Algae and Protists. By observing three different sections of our sample, we will be able to observe different types of organisms and hopefully use a dichotomous key to identify these organisms.
Hypothesis: If we take samples from 3 different areas of the hay infusions, then there will be different types of organisms found in each area.
Methods:
1. Bring the culture to the work area without disturbing it. Note the smell and describe the appearence.
2. Take a few samples for microscopic evaluation. Take organisms from two different niches.
3. Note exactly where you obtain these samples in the culture.
4. Use a dropped to place a small drop of liquid from the culture onto a microscope slide and then place a cover slip on top.
5. Draw pictures of the organisms.
6. Characterize at least 2 different organisms from each of the two areas of the culture.
7. Measure the size of these organisms with your micrometer.
Raw Data:
https://drive.google.com/file/d/0B-ntMxISdJd6Ujl5ZmRrWDdDYlU/edit?usp=sharing

There were no green shoots or mold on the top of the hay infusion when first viewed.
Organisms that are closer to plant matter may vary from organisms farther away because certain organisms may feed on said plant attracting them to it. In my hay infusion, there were mostly protists.The paramecium are protoza and I could not find what the copidium were. The copidium, blepharisma, and paramecium have cilia. None of the organisms I found are photosynthetic.
Paramecium fit the definition of life because they gain energy by feeding on bacteria, algae, and yeast. It is a uni-cellular organism that is membrane-bound. They reproduce asexually by binary fission through mitosis. They have cilia that have evolved from the need to move.
Conclusion:
From this lab I can conclude that organisms in different parts of the hay inclusion can be the same. For example, I found copidium in both the bottom section of the hay infusion and the middle. I also found it interesting that all of my organisms were motile. I was able to use a dichotomous key to identify the organisms I observed but I did not observe any algae in my hay infusion. For future experiments, I would like to wait a couple of weeks and see if any mold forms or new organisms grow in the hay infusion.




2/6/14, lab 1 notes

Great job, Lauren!

Some notes:

-Make sure each lab entry is dated and bolded. This should be the first thing to appear.

-I can't see your pics :( Make sure you have pics from lab 1 and lab 2 by Sunday. Email me if you need help!

-Organize lab writeups with labels like "Introduction", "Methods", etc. Refer to email with attachment I sent out on notebook organization.

-Start working on building a map of your transect to detail your land and where your samples are taken from. We will talk about this more Wednesday

Awesome job!!!

AP


The objective of the lab was to understand the interactions between a community living in an ecosystem on January 15th 2014. In groups of three, we analyzed our assigned transect, a 20 by 20 piece of land on the American University campus, observing the biotic and abiotic factors. By observing the transect, we will be able to determine how the different organisms and species interact and how there organisms effect the characteristics of the specific organism.

1. Walk outside to the assigned transect. 2. Observe the general characteristics of the transect, making sure to note the location, topography, ect. 3. Using a sterile 50 ml conical tube, take a soil and ground sample. 4.Weight 10-12 grams of the soil/ground sample and place in plastic jar 5. Add 0.1 gm dried milk and gently mix it all up for about 10 seconds 6. Remove the top of the jar and place the jar, open, in the back of the lab. 7. Label the jar

Image:hay1.jpg Image:hay2.jpg Image:hay3.jpg

Image:hay4.jpg

The general characteristics of the transect are that it has a lot of dead trees, the area is covered in dead leaves and dead plants. The transect is located next to Hughes. The transect contains what appears to be a man-made garden. The biotic contents of the transect are: a male cardinal, trees, bushes, and berries. The abiotic components of the transect are a soda cup, the birds nest, and a street light.

The objective of observing a transect in order to determine the interactions between the community living in an ecosystem was accomplished. We were able to take a soil and ground sample and we are currently analyzing the contents of it. As a future experiment, I think it would be interesting to observe the interactions between two specific organisms in the transect. For example, I would like to observe the effect of a certain bacteria found in the transect on an organism in the transect, such as a tree.

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