User:Maeve Alterio/Notebook/Biology 210 at AU

From OpenWetWare

< User:Maeve Alterio(Difference between revisions)
Jump to: navigation, search
Current revision (15:46, 22 March 2014) (view source)
 
(16 intermediate revisions not shown.)
Line 1: Line 1:
-
'''February 16th, 2014'''
+
 
-
''Lab 3''
+
== '''Embryology Lab''' ''March 22nd, 2014'' ==
 +
 
 +
 
 +
 
 +
''Introduction''
 +
 
 +
 
 +
Embryology is a vastly diverse and ever growing field that focuses on the development of animals. For our study we studied the affects of nicotine on the development of zebrafish. Zebrafish have long since been used as a model animal for the affects of alcohol on development, however this study was to test whether zebra fish would be a good model for the affects of nicotine on development.
 +
 
 +
 
 +
''Procedure''
 +
 
 +
 
 +
We started with 20 zebrafish in the control group and 20 zebrafish for the nicotine group. The 40 fish were from the same batch in order to control for fertilization differences. The nicotine fish were placed in water containing 10-50 mg/liter of nicotine. Then observe the fish for two weeks taking note of dependent variables such as movement, amount of yolk, eye-pigmentation and eye movement, morphological development, heart rate, body structures, tail length and total body length. Additionally every few days the 10ml of water was taken from the container and replaced with fresh water in order to prevent too much bacterial
 +
 
 +
 
 +
''Data''
 +
 
 +
 
 +
see link
 +
https://drive.google.com/file/d/0B-ElHswoadloMkVFWmVqbENGZkMydkxPLWRVMndpNUdZOXJF/edit?usp=sharing
 +
 
 +
 
 +
https://docs.google.com/document/d/11sMmKlW95p3bF4b0xTKJBCrqSe35dC7j-1QMTNDYp8M/edit?usp=sharing
 +
 
 +
 
 +
 
 +
''Conclusion''
 +
 
 +
 
 +
Although all of the fish died at the end of the experiment, and the second to last data point had more nicotine fish alive than the control, it was mostly due to the fact that the fish did not have food, and since the control fish were more active, they most likely starved quicker than the nicotine fish. The nicotine fish were struggling to stay upright, they did not have even distribution of color pigment cells, and their coloring was otherwise duller than that of the control fish. The nicotine therefore is detrimental to the development of the fish. For further study, I would suggest the increasing the amount of nicotine as well as making sure the fish have food to get a better data set. 
 +
 
 +
 
 +
 
 +
 
 +
 
 +
 
 +
 
 +
== '''March 7th, 2014''' ''Lab 6: Mini DNA Lab'' ==
 +
 
 +
 
 +
 
 +
''Introduction''
 +
 
 +
This lab is a continuation from Lab 4 when we collected bacteria from our transect. We then sent the PCR products to Genewiz Inc. to be sequenced. This lab was to observe the sequences and determine what kind of bacteria was sequenced.
 +
 
 +
 
 +
 
 +
''Procedure:''
 +
 
 +
1. We took the DNA from our bacteria, and ran PCR on the genome.
 +
 
 +
2. Then the PCR products were sent to Genewiz Inc. for sequencing
 +
 
 +
3. We analyzed the sequences once they were returned to us. See Table One in link
 +
 
 +
 
 +
''Data''
 +
 
 +
See link
 +
 
 +
https://docs.google.com/document/d/1_7mZ4iNAccOrJU_2PJNFkMUAIeXlTNogUzfybOKnWsg/edit?usp=sharing
 +
 
 +
''Conclusion''
 +
 
 +
Our in class observations match with the googled observations of the bacteria identified by the genome. Our group was lucky in that both of our sequences worked, and our observations matched the known characteristics of the bacteria. It was very interesting to discover the exact species of bacteria from our transect.
 +
 
 +
 
 +
 
 +
 
 +
 
 +
MA.
 +
 
 +
 
 +
 
 +
 
 +
 
 +
== '''February 28th, 2014''' ''Lab 5: Invertebrates ==
 +
 
 +
 
 +
 
 +
''Introduction'':
 +
 
 +
 
 +
In the last lab, we set up a Berlese Funnel with leaf litter and debris from our transect. This funnel enabled us to be able to collect and observe some of the invertebrates in our transect, even though it was winter and the invertebrates were most likely hibernating. The classification of invertebrates gave us a better insight to the transect.
 +
 
 +
 
 +
''Procedure'':
 +
 
 +
 
 +
In order to get a better understanding of the possible invertebrates that we may see in our Berlese Funnel, we had to observe three different types of invertebrates, Planaria, Nematodes, and Annelida.
 +
 
 +
 
 +
In order to observe the invertebrates from the Berlese Funnel we had to transfer the preservative solution into two separate petri dishes, one for the top half of the preservative liquid and the other for the bottom half of the preservative liquid. Then observe the two petri dishes under the dissecting microscope. Use a dichotomous key in order to help identify the organisms. 
 +
 
 +
''Data'':
 +
 
 +
 
 +
see attached link
 +
https://docs.google.com/document/d/1_7mZ4iNAccOrJU_2PJNFkMUAIeXlTNogUzfybOKnWsg/edit?usp=sharing
 +
 
 +
''Conclusion'':
 +
Through this lab we were able to get a better understanding of the invertebrates and vertebrates that live in our transect. Although our transect is relatively small there was a great deal of diversity due to the three trees and plant life in the area.
 +
 
 +
 
 +
MA
 +
 
 +
 
 +
 
 +
 
 +
 
 +
 
 +
== '''February 28th, 2014''' ''Lab 4: Identifying Transect Plants, Observing Fungi, and Berlese Funnel Preparation:'' ==
 +
 
 +
 
 +
''Introduction'':
 +
 
 +
 
 +
This lab was designed to help understand the characteristics and diversity of plants as well as to understand and appreciate the function and importance of fungi.
 +
 
 +
 
 +
''Procedure'':
 +
 
 +
 
 +
The first step is to go to the transect and collect one bag of leaf litter, and fill the other two bags with dirt and other plant matter from around the transect. There must be five different representative samples of plant life from the transect.
 +
 
 +
The next step, observing fungi, involved observing different types of fungi, as well as observing and classifying a black bread-mold.
 +
 
 +
The last step was to prepare the Berlese Funnel to be observed next week. First pour 25 ml of the 50:50 ethanol/water solution into the bottle. Then put the screening material into the base of the funnel, securing the funnel into the neck of the square-sided bottle. Place the leaf sample in the funnel and place the 40 watt lamp above the leaf sample. The final step is to cover everything with foil.
 +
 
 +
 
 +
''Results'':
 +
 
 +
 
 +
Table 1: Transect Plants (located in attachment)
 +
https://docs.google.com/document/d/1_7mZ4iNAccOrJU_2PJNFkMUAIeXlTNogUzfybOKnWsg/edit?usp=sharing
 +
 
 +
 
 +
''Conclusion'':
 +
 
 +
 
 +
This lab was just one of the many steps we are following in categorizing and analyzing the transect. We learned about fungi in the chance that we have fungi present in the transect. We learned about different factors of plant life, in order to help categorize the plants found in the transect. Next week we will continue our analysis of the transect by observing the Berlese funnel.
 +
 
 +
MA
 +
 
 +
 
 +
 
 +
 
 +
 
 +
 
 +
== '''February 16th, 2014''' ''Lab 3'' ==
 +
 
''Introduction'':  
''Introduction'':  
Line 7: Line 158:
''Procedure'':  
''Procedure'':  
 +
 +
Part 1: Quantifying and Observing Microorganisms
Part 1: Quantifying and Observing Microorganisms
- obtain the handout describing colony morphology as well as your plates.  
- obtain the handout describing colony morphology as well as your plates.  
Line 23: Line 176:
''Data'':
''Data'':
 +
 +
Hay Infusion:
Hay Infusion:
Still pungent smell, however no fungal layer at the top. Water is darker in color as well as there is a ticker layer of dark foliage on the bottom of the jar. The appearance or smell may change week to week due to the different growth rates of the different organisms.
Still pungent smell, however no fungal layer at the top. Water is darker in color as well as there is a ticker layer of dark foliage on the bottom of the jar. The appearance or smell may change week to week due to the different growth rates of the different organisms.
Line 33: Line 188:
''Conclusion''
''Conclusion''
 +
 +
This lab helped to give a better idea on bacteria, as well as understanding antibiotic resistance. For further study I would isolate colonies from the agar plate and plate them on tetracycline plates.  
This lab helped to give a better idea on bacteria, as well as understanding antibiotic resistance. For further study I would isolate colonies from the agar plate and plate them on tetracycline plates.  
-
''Attempt 3 for lab 2 due February 6th''
+
MA
-
'''February 6th, 2014'''
+
 
 +
 
 +
 
 +
 
 +
 
 +
 
 +
== '''February 6th, 2014''' ''Lab 2'' ==
 +
 
Line 76: Line 240:
AP
AP
-
'''January 31, 2014'''
+
 
-
[[Biological Life at AU]]
+
 
 +
 
 +
== '''January 31, 2014''' ''Biological Life at AU'' ==
 +
 
 +
 
 +
 
''Introduction''
''Introduction''
The purpose of this study was to identify different types of algae as well as observe our transect which we would be studying. In order to become comfortable with identifying organisms under a microscope, we observed ''Chlamydomonas, Gonium,'' and ''Volvox''. We then observed our transect and collected samples that we would later test.  
The purpose of this study was to identify different types of algae as well as observe our transect which we would be studying. In order to become comfortable with identifying organisms under a microscope, we observed ''Chlamydomonas, Gonium,'' and ''Volvox''. We then observed our transect and collected samples that we would later test.  
Line 111: Line 280:
''Conclusion''
''Conclusion''
Although the three types of green algae we looked at were different, there was a surprising amount of variation in the size, shape and function of each type of algae. Each species had a different size, motility, and different characteristics. Looking at the different types of algae will come in handy when analyzing the different organisms collected in the transect.  
Although the three types of green algae we looked at were different, there was a surprising amount of variation in the size, shape and function of each type of algae. Each species had a different size, motility, and different characteristics. Looking at the different types of algae will come in handy when analyzing the different organisms collected in the transect.  
 +
 +
MA
 +

Current revision

Contents

Embryology Lab March 22nd, 2014

Introduction


Embryology is a vastly diverse and ever growing field that focuses on the development of animals. For our study we studied the affects of nicotine on the development of zebrafish. Zebrafish have long since been used as a model animal for the affects of alcohol on development, however this study was to test whether zebra fish would be a good model for the affects of nicotine on development.


Procedure


We started with 20 zebrafish in the control group and 20 zebrafish for the nicotine group. The 40 fish were from the same batch in order to control for fertilization differences. The nicotine fish were placed in water containing 10-50 mg/liter of nicotine. Then observe the fish for two weeks taking note of dependent variables such as movement, amount of yolk, eye-pigmentation and eye movement, morphological development, heart rate, body structures, tail length and total body length. Additionally every few days the 10ml of water was taken from the container and replaced with fresh water in order to prevent too much bacterial


Data


see link https://drive.google.com/file/d/0B-ElHswoadloMkVFWmVqbENGZkMydkxPLWRVMndpNUdZOXJF/edit?usp=sharing


https://docs.google.com/document/d/11sMmKlW95p3bF4b0xTKJBCrqSe35dC7j-1QMTNDYp8M/edit?usp=sharing


Conclusion


Although all of the fish died at the end of the experiment, and the second to last data point had more nicotine fish alive than the control, it was mostly due to the fact that the fish did not have food, and since the control fish were more active, they most likely starved quicker than the nicotine fish. The nicotine fish were struggling to stay upright, they did not have even distribution of color pigment cells, and their coloring was otherwise duller than that of the control fish. The nicotine therefore is detrimental to the development of the fish. For further study, I would suggest the increasing the amount of nicotine as well as making sure the fish have food to get a better data set.




March 7th, 2014 Lab 6: Mini DNA Lab

Introduction

This lab is a continuation from Lab 4 when we collected bacteria from our transect. We then sent the PCR products to Genewiz Inc. to be sequenced. This lab was to observe the sequences and determine what kind of bacteria was sequenced.


Procedure:

1. We took the DNA from our bacteria, and ran PCR on the genome.

2. Then the PCR products were sent to Genewiz Inc. for sequencing

3. We analyzed the sequences once they were returned to us. See Table One in link


Data

See link

https://docs.google.com/document/d/1_7mZ4iNAccOrJU_2PJNFkMUAIeXlTNogUzfybOKnWsg/edit?usp=sharing

Conclusion

Our in class observations match with the googled observations of the bacteria identified by the genome. Our group was lucky in that both of our sequences worked, and our observations matched the known characteristics of the bacteria. It was very interesting to discover the exact species of bacteria from our transect.



MA.



February 28th, 2014 Lab 5: Invertebrates

Introduction:


In the last lab, we set up a Berlese Funnel with leaf litter and debris from our transect. This funnel enabled us to be able to collect and observe some of the invertebrates in our transect, even though it was winter and the invertebrates were most likely hibernating. The classification of invertebrates gave us a better insight to the transect.


Procedure:


In order to get a better understanding of the possible invertebrates that we may see in our Berlese Funnel, we had to observe three different types of invertebrates, Planaria, Nematodes, and Annelida.


In order to observe the invertebrates from the Berlese Funnel we had to transfer the preservative solution into two separate petri dishes, one for the top half of the preservative liquid and the other for the bottom half of the preservative liquid. Then observe the two petri dishes under the dissecting microscope. Use a dichotomous key in order to help identify the organisms.

Data:


see attached link https://docs.google.com/document/d/1_7mZ4iNAccOrJU_2PJNFkMUAIeXlTNogUzfybOKnWsg/edit?usp=sharing

Conclusion: Through this lab we were able to get a better understanding of the invertebrates and vertebrates that live in our transect. Although our transect is relatively small there was a great deal of diversity due to the three trees and plant life in the area.


MA




February 28th, 2014 Lab 4: Identifying Transect Plants, Observing Fungi, and Berlese Funnel Preparation:

Introduction:


This lab was designed to help understand the characteristics and diversity of plants as well as to understand and appreciate the function and importance of fungi.


Procedure:


The first step is to go to the transect and collect one bag of leaf litter, and fill the other two bags with dirt and other plant matter from around the transect. There must be five different representative samples of plant life from the transect.

The next step, observing fungi, involved observing different types of fungi, as well as observing and classifying a black bread-mold.

The last step was to prepare the Berlese Funnel to be observed next week. First pour 25 ml of the 50:50 ethanol/water solution into the bottle. Then put the screening material into the base of the funnel, securing the funnel into the neck of the square-sided bottle. Place the leaf sample in the funnel and place the 40 watt lamp above the leaf sample. The final step is to cover everything with foil.


Results:


Table 1: Transect Plants (located in attachment) https://docs.google.com/document/d/1_7mZ4iNAccOrJU_2PJNFkMUAIeXlTNogUzfybOKnWsg/edit?usp=sharing


Conclusion:


This lab was just one of the many steps we are following in categorizing and analyzing the transect. We learned about fungi in the chance that we have fungi present in the transect. We learned about different factors of plant life, in order to help categorize the plants found in the transect. Next week we will continue our analysis of the transect by observing the Berlese funnel.

MA




February 16th, 2014 Lab 3

Introduction:

This lab, Microbiology and Identifying Bacteria with DNA, was to understand the characteristics of bacteria including drug resistance, and to understand how DNA sequences are used to identify different species. There is expected bacterial and fungal growth on the agar plates, however Archaea is not expected to grow as they are “extremophiles” and the conditions were average.

Procedure:


Part 1: Quantifying and Observing Microorganisms - obtain the handout describing colony morphology as well as your plates. - Count the number of colonies on each plate Part 2: - Using the plates as well as the agar plates to evaluate the antibiotic resistance of the colonies Part 3: - obtain a prepared slide and classify the different types and shapes of bacteria - pick two colonies from the agar plate and one from the tetracycline plate. - Make a wet mount of the colonies and observe under a microscope using both the 10x and 40x objectives. - Next, gram stain the three colonies so that it will be easier to identify. - Observe the gram stained slides under the 40x objective. Part 4: - Transfer a single colony of bacteria to 100 ul of water in a sterile tube - Incubate for 10 minutes at 100C then spin in centrifuge.

Data:


Hay Infusion: Still pungent smell, however no fungal layer at the top. Water is darker in color as well as there is a ticker layer of dark foliage on the bottom of the jar. The appearance or smell may change week to week due to the different growth rates of the different organisms.

Chart 1 (google drive) Chart 2 (google drive) https://docs.google.com/document/d/1_7mZ4iNAccOrJU_2PJNFkMUAIeXlTNogUzfybOKnWsg/edit?usp=sharing

There were obvious differences in the two types of plates, nutrient agar as well as the nutrient agar and tetracycline plates. There were more colonies on the nutrient plate. This indicates that the antibiotic worked and killed some of the bacteria. Tetracycline is a broad range antibiotic produced by the Streptomyces genus. It works by inhibiting protein synthesis. Its common uses are to treat bacterial infections such as urinary tract infections, gonorrhea, and chlamydia. There are many different species of bacteria that are not affected by tetracycline.

Conclusion


This lab helped to give a better idea on bacteria, as well as understanding antibiotic resistance. For further study I would isolate colonies from the agar plate and plate them on tetracycline plates.

MA




February 6th, 2014 Lab 2

Introduction: The purpose of this experiment was to get familiar with a dichotomous key, a key that helps identify any group of organisms. The other objective of this experiment was to understand the characteristics of different algae and protists.

Process: In the first part of this lab, we were given two known organisms. After making wet mounts of the two different organisms, we were to characterize them as well as use the key to identify the organism. In the next part of the lab, we were instructed to take three samples from within our hay infusion and observe two different types of algae or protists in the sample. We collected from three different locations, the surface of the water, right against a leaf, and right by the mud. This should theoretically give very different species due to the location. Each location varies in regards to light amount, as well as food source. Finally, the last part of the experiment was to prepare and plate a serial dilution. We took the samples and diluted it 10-2, 10-4, 10-6, 10-8. We plated our samples on two different plates, normal plates as well as on tetracycline plates. We then left the plates to incubate for a week.


Data: Hay Infusion: the hay infusion was settled, with the mud on the bottom, along with composted leaves and twigs. There was what appeared to ne a fungal layer coating the top of the water, as well as a pungent earthy odor. Had this been given a longer period of stagnation, there would be significantly more growth as well as a variety of species.

Name Characteristics Slide 1: A gonium Large sphere, 37.5 um Slide 1: B Colpidium Larger, lighter than other, colorless, medium body, covered in cilia 50um Slide 2: A Bursaria Truncatella White, cilia present, oval, large body with large mouth. 400um Slide 2: B Didinium Cyst Little to no movement. 17.5 um Slide 3: A Stentor Many small dots, colored, dark blueish. 50 um Slide 3: B Colpidium Colorless, cilia present, oval shaped, small body, fast swimmer, 50um, darker than other


Conclusion: In this lab, we were able to successfully identify some of the different microbes present in our transect. For future study, I would suggest more tests on the organisms found in the transect. This would give a clearer understanding of the organisms present.


2/6/14, lab 1

Good job!! Some notes:

-Make sure you include pics from lab 1 and lab 2 by Sunday

-Try pressing "enter" two times to insert a break between paragraphs and lists.

-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

Great work!

AP



January 31, 2014 Biological Life at AU

Introduction The purpose of this study was to identify different types of algae as well as observe our transect which we would be studying. In order to become comfortable with identifying organisms under a microscope, we observed Chlamydomonas, Gonium, and Volvox. We then observed our transect and collected samples that we would later test. Process First, we observed three different types of green algae, Chlamydomonas, Gonium," and "Volvox. After gathering the data on all three members of the Volvocine line, we left the lab and went to collect data as well as samples from our transect. Finally after collecting data, we set up our hay infusion cultures. Data Characteristics Chlamydomonas Gonium Volvox Number of Cells 18 10 4 Colony size 7.5 μm 17.5 μm 200 μm Describe any functional specializations of cells flagella Moved quickly Flagella, pilli Describe any reproductive specialization isogamy isogamy oogamy

cell specialization occurs mostly in multicellular organisms as they are able to carry out different tasks without compromising the vitality of the organism itself. The three genera have specialized their abilities to their environment. Evolution does not always move towards and increased complexity, in the case of the algae, it is which organisms and which traits are most suited to their environment and therefore have a better chance of passing their traits on to the next generation. Part 2: Transect 5 Biotic components: -holly tree -dead sycamore tree -pine trees -leaves -ivy -grass

Abiotic components: - soil - air -light -minerals -rocks

Transect: Transect five was off campus located at the nearby seminary. The transect was located on a downward slope with a building off to the left, a statue behind it, and a communal area in front. The transect had three trees, a holly tree, a pine tree and a dead sycamore tree. The ground had a thick covering of ivy as well as decomposing leaves and pine needles. Just to the left of the dead sycamore tree was a fallen branch.

Conclusion Although the three types of green algae we looked at were different, there was a surprising amount of variation in the size, shape and function of each type of algae. Each species had a different size, motility, and different characteristics. Looking at the different types of algae will come in handy when analyzing the different organisms collected in the transect.

MA


January 22, 2014 Successfully entered my first post. Maeve Alterio

Personal tools