User:Student 59/Notebook/Biology 210 at AU: Difference between revisions
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To take a closer look at the seeds we brought back from our transect, we dissected them to find out if they were monocot or dicot. A table of results is below. | To take a closer look at the seeds we brought back from our transect, we dissected them to find out if they were monocot or dicot. A table of results is below. | ||
TABLE | TABLE Image | ||
'''Procedure 5: | '''Procedure 5: Observing Fungi''' | ||
The fungi that we observed was a fungi called Rhizopus Stolnifer. They are a part of the Ascomycota group since it is bread/yeast. Below are images of what we observed. | |||
Image of fungi name | |||
Image of fungi through microscope | |||
Image of fungi description | |||
'''Procedure 6: Setting Up the Berlese Funnel to Collect Invertebrates''' | |||
To set up the Berlese Funnel for next week's lab, we took a 50 ml conical tube and poured 25 ml of the 50:50 ethanol/water solution. We cut out a piece of screening material and put it in the bottom of the funnel and taped the sides so it did not move. Then we put the leaf litter on top of the funnel and set it all on a ring stand. We taped the funnel and tube together and placed it under a 40 watt lamp to be observed next week. | |||
Image of Berlese Funnel | |||
'''Conclusions and Further Direction''' | |||
From this lab, we were able to | |||
CLS | |||
Revision as of 15:25, 11 February 2016
Caroline Sell
Bio 210 - 007
Lab 5: 02-11-16
Lab 4: 02-04-16, Plantae and Fungi
Purpose
The purpose of today's lab was to examine plants and fungi, especially plants found in our transect, to understand their diversity of appearance and function. By dissecting plants, we can see the intricate differences that make each plant important for the ecosystem they are living in.
Materials and Methods
- 3 Ziploc bags
- phone camera
- 50:50 ethanol/water solution
- conical tube
- screening material
- scissors
- tape
- funnel
- ring stand
- 40 watt lamp
- foil
Like last week, this lab consisted of multiple procedures and they will be described below with their corresponding data and observations.
Data and Observations
Procedure 1: Collect 5 plant samples from transect
We took 3 ziploc bags and our phone cameras back out to our transect #2 to collect samples. We found an area with soft soil (everything was pretty soft since it had just rained/snowed) and picked up dead leaves for our leaf liter sample. We collected about 25-30 leaves (~500g). We also searched for representative samples from five plants and collected a seed, a flower bud, a bushel of flower petals, a long leaf, and a short leaf. The images of the organisms are below along with a map of where they were found:
Procedure 2: Plant Vascularization
Of the specimens we collected, we took a closer look at the vascularization of each one and recorded it in the table in procedure 4
Procedure 3: Presence of Specialized Structures
The leaf litter we collected consisted mostly of large maple-type leaves. They covered the entire soil in our transect, as the trees were leafless since it is winter. Also since it had rained/snowed recently, they were very wet/damp.
Procedure 4: Mechanisms of Plant Reproduction
To take a closer look at the seeds we brought back from our transect, we dissected them to find out if they were monocot or dicot. A table of results is below.
TABLE Image
Procedure 5: Observing Fungi
The fungi that we observed was a fungi called Rhizopus Stolnifer. They are a part of the Ascomycota group since it is bread/yeast. Below are images of what we observed.
Image of fungi name Image of fungi through microscope Image of fungi description
Procedure 6: Setting Up the Berlese Funnel to Collect Invertebrates
To set up the Berlese Funnel for next week's lab, we took a 50 ml conical tube and poured 25 ml of the 50:50 ethanol/water solution. We cut out a piece of screening material and put it in the bottom of the funnel and taped the sides so it did not move. Then we put the leaf litter on top of the funnel and set it all on a ring stand. We taped the funnel and tube together and placed it under a 40 watt lamp to be observed next week.
Image of Berlese Funnel
Conclusions and Further Direction
From this lab, we were able to
CLS
Lab 3: 01-28-16, Microbiology and Identifying Bacteria
Purpose
The purpose of today's lab was to take a closer look at the bacteria present in our culture, now that we understand more about the specific microorganisms from last lab. There is great diversity in bacteria, and bacteria are everywhere in the world. We will be able to categorize the types of bacteria based on shape, motility, gram stain, and antibiotic resistance.
Materials and Methods
- Hay Infusion Culture (*prepared previous week)
- Latex Gloves
- Microscope
- (8) Slides and slide covers
- Transfer pipettes
- Dichotomous Key (*aid in identifying microorganisms)
- Crystal Violet
- Distilled water
- Alcohol Decolorizer
- Iodine
- Safranin
There were multiple parts to this lab. But before we describe the processes, it is first important to note that before we did anything, we observed our Hay Infusion Culture one last time. As of today, it has been sitting for 2 weeks. There were no changes in smell but the appearance did change. All the organisms we saw growing at each layer were nearly gone. There was a lot of dirt that had sunk to the bottom, and the top layer was extremely reduced. We observed that 50% of the water had evaporated. We hypothesize that there was a change in appearance because there were no more nutrients left in the culture and everything died. However, we did see that there was growth on our agar plates because there were nutrients present allowing bacteria to cultivate.
There were 5 procedures to complete for this lab. The descriptions are below with their corresponding data and observations.
Data and Observations
Procedure 1: Quantifying and Observing Microorganisms
We used colony morphology to help determine the type of bacteria growing on our plates. We counted the colonies on each plate, and made sure we divided by 100 to keep the units the same (colonies/um) since we made the cultures with 100 μL.
According to this table, there were no results for the 10^-5 tet, 10^-7 with and without tet, and 10^9 with and without tet plates.
Procedure 2: Antibiotic Resistance
Based on the table above and the images of the plates below, we saw that for the previously mentioned plates, there was no growth at all. The only plates we could compare tet/no tet were the 10^-3 plates and we saw that the growth looked slightly different. The colonies on the plate with tet were larger, more spread out, and brighter in color whereas the colonies on the plate without tet were smaller and covered more of the plate. Neither of these was quite enough to be a lawn. The differences in colony type could indicate that the antibiotic did not allow for as many smaller colonies to grow as we saw with the plate without tet. As seen in the table above, there were significantly fewer colonies on the plate with tet than on the plate without tet. There appeared to be presence of some fungi on each of the plates where there was growth.
Tetracycline is a broad-spectrum antibiotic that inhibits the protein synthesis in bacteria, which prevents it from growing. It can be used on both gram positive and gram negative bacteria such as chlamydiae, mycoplasmas, rickettsiae, and protozoan parasites. However, there has been resistance to tetracycline since 1953 with the Shigella dysenteriae bacterium and now there are 29 different genes in bacteria that have tetracycline resistance as well as three oxytetracycline resistance genes. While tetracycline is is a good antibiotic used for many infections (Streptococcus pneumoniae, typhoid, urinary tract infections, etc.) when there is antibiotic resistance, it makes it much harder to handle the infection.
(Chopra, 2001)
Procedure 3, part 1: Bacteria Cell Morphology Observations
To observe the bacteria from our sample plates, we used a toothpick to pick up a colony of bacteria from 4 plates (10^-3 with tet, 10^-3 without, 10^-5 with tet, 10^-5 without tet) and put them on slides with a drop of water. We placed a cover slip on top and used a compound microscope to take a closer look at the shape and mobility of the bacteria. Below are the images we collected, all at 40x magnification:
Procedure 3, part 2: Gram Stain
To perform the gram stain, we had to first make a wet mount by sterilizing an inoculation loop over a flame and let it cool before picking up a small amount of the sample from our plates. We mixed this with a drop of water on a slide and heat fixed the air dried slide by passing it over the flame. Then we started dying the slide, first using crystal violet (1 min), rinsing, then iodine (1 min), rinsing, then decolorizing with 95% alcohol (10-20 sec), rinsing, and finally with safranin stain (20-30 sec), and rinsing. Any excess water was blotted with a kimwipe and when we went to look at the slide under the microscope, no cover slip was used. Below is a table of the results we found for our slides:
Procedure 4: PCR setup for 16S Amplification
We selected to compare the 10^-3 without and 10^-3 with TET samples for our PCR test. To prepare for the test, we labeled 2 PCR tubes with our transect (group) number and colony identifier (10^-3 with and without). We added 25 μL of primer/water mixture to a labeled PCR tube and flicked/mixed the tube to dissolve the PCR bead at the bottom. Then, with a sterile toothpick, we touched a bit of a bacterial colony from each respective plate we were observing and mixed it in with the primer/water mixture of the PCR tube. Then we capped the tube and placed it in the PCR machine to be used for next lab.
Conclusions and Future Directions
We saw that the higher the dilution, the less likely we were to see bacteria, especially when there was tetracycline. This means that a lot of the bacteria was not resistant to the antibiotic. Perhaps we diluted too much which is why nothing showed up in many of the plates. However, we were still able to learn a lot about the bacteria present in our samples from our transect. They were different shapes, sizes, and had different patterns of motility. There is always a reason that organisms look and move differently based upon their function, and we saw this in our lab today.
Works Cited:
Chopra, I., & Roberts, M. (2001). Tetracycline Antibiotics: Mode of Action, Applications, Molecular Biology, and Epidemiology of Bacterial Resistance. Microbiology and Molecular Biology Reviews, 65(2), 232–260. http://doi.org/10.1128/MMBR.65.2.232-260.2001
CLS
Lab 2: 01-21-16, Identifying Algae and Protists
Purpose
The purpose of this week's activity was to identify the microorganisms present in our given transects. We learned how to use a dichotomous key to identify microorganisms from different layers of last week's Hay Infusion Culture: top, middle, and bottom layers. It is important to know what exactly is present in the transect to better understand how everything in the area lives together. Below are images of the Hay Infusion Culture after one week of sitting out on the lab bench.
Materials and Methods
- Hay Infusion Culture (*prepared previous week)
- Latex Gloves
- Microscope
- (6) Slides and slide covers
- Transfer pipettes
- Dichotomous Key (*aid in identifying microorganisms)
We made wet mounts for microscopic observation of the culture with samples coming from each of the three layers (top, middle, and bottom). Once we looked at them with the microscope, we took pictures of the microorganisms and attempted to identify what they were by using dichotomous keys for Free-Living Protozoa and Algae.
Data and Observations
When we observed the Hay Infusion Culture, we did not notice any particular smell. There was also a bit of mold on the top of the culture. We noticed some plant matter (algae) near the top of the culture and this would be because of the need to perform photosynthesis and there is more light on top. Along with the algae at the top level we also was Paramecium, which would need the nutrients to survive.
Below are the images of the organisms found at each level (top, middle, and bottom) along with their size and name.
Paramecium: As per the Freeman text, paramecium are protists that are motile. They are a single cell, part of the Alveota lineage, and have 1 macro and 1 micro nuclei. They can reproduce asexually by binary fission or sexually with conjugation. In order for them to survive, they must consume the nutrients surrounding them in their environment, which is why we found them with the diatoms at the top of our culture.
Conclusions and Future Directions
It was interesting that we found diatoms on each level, but this is probably because we took a sample of the water from the creek which would contain this type of algae. We found the most microorganisms at the top of the culture, probably because there is more access to light for the algae to perform photosynthesis and continue to grow. If the Hay Infusion "grew" for another two months, we would expect more growth of algae such as diatoms. We already saw these on each level of our culture. However, there was only 0.1 grams of dried milk and at some point the nutrients would run out and nothing else would be able to grow in the culture (carrying capacity). In terms of learning how to use the dichotomous keys, it was not as easy as it sounds because you have to be very specific when describing the microorganisms or you could end up with the wrong name.
For next lab:
We also prepared and plated serial dilutions using our Hay Infusion Culture. This will be used to take a closer look at the specific bacteria in our culture.
CLS
Lab 1: 01-14-16, Examining Biological Life at AU
Purpose
The purpose of this lab was to take a closer look at the biological life around us here at AU. While we study biology, it is important to understand the biological life we interact with each day. This semester, each group will examine a select 20x20 transect located on campus. We had transect #2 which is located by the Amphitheater and Hughes/McDowell Hall. There is a creek, many rocks, bushes, and trees. Below are images and a diagram of the transect. For this week's activity, we collected samples of all elements found in the transect to make a Hay Infusion Culture in lab. We also took notes to describe the biotic and abiotic components of the transect.
Materials and Methods
- 1 Gallon Ziplock Bag
- Latex Gloves
- Flashlight (*transect observed after dark)
- Camera/camera phone
- Glass Jar (w/ 1L capacity) with lid
- 500ml of purified water
- 0.1 gram of dried milk (*sustenance for living organisms in hay infusion culture)
- Sharpie
- Painter's tape or labels
We observed our transect by collecting many elements from the transect and putting them all in a gallon size ziplock bag. Then we took 10-12 grams of the material (soil, leaves, water from the creek, etc.) from the bag and placed it in a glass jar with 500 ml of purified Deer Park water and 0.1 grams of dried milk. We covered the jar to shake it, and then left the lid off for a week so we could come back the week later and observe the organisms.
Data and Observations
Biotic: bush, trees, moss in water
Abiotic: rocks, sticks, dead leaves
Conclusions and Future Directions
By doing this lab activity we found that our Transect #2 had a lot of water, soil, and dead leaves since there was a creek that ran right through it and the leaves had fallen since it is winter. When we look for organisms in our Hay Infusion Sample next week, I expect to see a good variety of microorganisms that live in the water since our location must rely on the water to produce life in the area.
CLS
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