User:Caitlin G Denison/Notebook/Biology 210 at AU

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3-27-14 Lab 6


Question and Objective: The Objective of this experiment was to learn the stages of embryonic development, and to compare the embryonic development of different organisms. The experiment addressed these objectives by allowing us to observed models of embryonic development. The question for this experiment was: What effect will placing zebra fish embryos in a fluoride solution have. The prediction for this experiment was;Fluoride will disrupt the embryonic development of zebra fish. The hypothesis for this experiment was : If the zebra fish embryos are exposed to fluoride, then they will display developmental abnormalities. This addressed this question by allowing us to directly observe the effects of fluoride on zebra fish embryos.


Specific Steps Preformed: 1. 20 zebra fish eggs were placed in control plates containing only Deer Park spring water. 2. 20 zebra fish were placed in plates containing fluoride. 3. The fish were observed four times over the course of a week-- the fishes' stage of development, and physical appearance was noted at each observation 4. On day seven, tow fish from each group were fixe 5. On the final day of observation the two fixed fish were observed for developmental abnormalities.

Raw data:


Control treatment group observations: Day One: Two fish dead, 18 alive, all in 18-somite stage of development, black pigmentation Day Four: No fish dead, all in pectoral fin development stage, all displaying a fin Day seven No fish dead: all fish in protruding mouth stage, all displaying a protruding mouth Day 14: All fish dead

Experimental group observations Day one: All fish alive, all in 18-somite stage, all showing pigmentation and fin development Day Four: Four fish dead, all in pectoral fin stage, ll showing an elongated tail Day Seven: All fish alive, all in protruding mouth stage, all showing protruding mouth. Day 14: All fish dead

Fixed fish observations: Control group Average pigmentation: even dark spots Average tail length: 97.3um Average whole fish length: 240.8um Average diameter of eyes: 15.5um Average distance between eyes: 48um Fin development: large pec fin


Fixed fish observations: Experimental group: Average pigmentation: uneven dark spots Average tail length: 88.8um Average whole fish length: 238.8um Average diameter of eyes: 13.8um Average distance between eyes: 50.5um Fin development: small pec fin


Embryos787878.jpg


Conclusions and future plans: This experiment was successful in allowing us to observe the stages of embryonic development. The experiment was also successful in answering the question. It was determined that fluoride does cause developmental abnormalities in zebra fish embryos. In the future the experiment should be repeated with a larger sample size in order to confirm results.

2-22-14 Lab 5

Objective: The objective of this experiment was to understand the importance of invertebrates, and to determine what invertebrates inhabit the transect. In this experiment we observed different types of worms in order to better understand the different modes of locomotion employed by invertebrates. We also collected samples of invertebrates using the berlese funnel set up last week. Tis allowed us to observe and characterize the various invertebrates living in the transect.


Specific Steps Preformed: 1. Coelomate, acoelomate, and psudeocoelomat worms were observed under a microscope 2. The invertebrates that were collected using the Berlese funnel were observed under a dissecting microscope. 3. The species of the different invertebrates was determined based on morphological characteristics. 4. A food web including all of the organisms that might live in the transect was created

Raw Data:

-Movement of different worms

Coelomates: move by contracting their muscles and pulling themselves along. This is relatively complex movement. The worms are able to do this due to their long, muscular bodies. The worms have two different types of muscles; one that allows for the contracting movements, and another that allows for the elongating movements.

Pseudocoelomate- Moves by slithering side to side. This movement suggests a less advanced musculature. This type of worm cannot make the fine muscle movements a coelomate can.

Acoelomate- These worms move by gliding. There is no evidence of complex muscle movement. Due to the complete lack of a coelom, these worms don’t have much of a support structure and can’t contract their muscles like the pseudocoelomates or coelomates.

Invertebrates found in transect-

Ground Spider- .5cm long, Description: 8 legs, hairs on legs, black spots on abdomen

Biting lice (Mallophaga)- .3cm long Description: oval shaped, little hairs on body and legs, brown colored

Primitive Springtail- .2cm long, description; 3 segments, grey colored, hairy, two large antennae

Springtail- .1 cm long, Description- 6 legs, 3 segmented body, 2 antennae, chewing mouthparts, little hairs on body and legs

Porturan- 0.05cm long, Description- 4 segments, 6 legs, 2 antennae, stinger on rear end, abdomen has stripes.

Flea (Diptera)- .01cm Description- oval shaped, 3 segments, plump abdomen, 2 antennae, 2 large eyes, 6 legs, dark brown colored

    • We were not able to find any more organisms

-The sizes of the organism ranged from .5cm long to .01cm long. The largest organism was the spider and the smallest was the flea. The organisms that were most common were springtails.

-Some vertebrates that might inhabit the transect are; robins: Chordata, Aves, Passeriformes, Turdidae, Turdus, T Migratorius

Cardinals: Chordata, Aves, Passeriformes, Passeri, Cardinlidae, Periporphyrus, Cardinalis



Mocking birds: Chordata, Aves, Passeriformes, Mimidae, Mimus, Mimus polyglottos


Rabbits: Chordata, mammalia, Lagomorpha, Leporidae, Nesolagus Timminisi


Northern Brown snake: Chordata, Reptilia, Squamata, Colubridae, Storeria, S Dekayi

-Robins would benefit from the invertebrates living in the transect, which could provide food. They would also benefit from the leaf litter, which could serve as nesting material. Man made materials could also be useful to the birds for nest building.

Cardinals would benefit from the invertebrates in the transect- especially worms, as well as the nesting material such as leaf litter, and man made materials that were left in the transect.

Mocking birds would benefit from the edible invertebrates living in the transect, as well as the nesting materials, such as leaves and man made objects.

Rabbits would benefit from the green plants growing in the planting boxes. They could also benefit from the fence that encloses the transect; while the rabbits might be able to burrow under the fence, large predators may not, providing the rabbits with a safe living area.

Northern Brown Snakes would benefit from the small mammals that might be living in the transect. They could also benefit from the sunny location of the transect.

Foodweb.jpg


Conclusions and future plants: This experiment was successful in allowing us to gain a better understanding of invertebrates, it was also successful in allowing us to determine what sort of invertebrates are present in the transect. It was very helpful to be able to observe the organisms in person, instead of just reading about them. In the future further experiments should be carried out to learn more about the various invertebrates and how the interact with the other organism and abiotic factors of the transect.

CD

2-18-14 Lab 4


Objective: The objective of this lab was to determine what sort of plants are present in the transect,to understand the characteristics and diversity of plants, and to appreciate the function and importance of fungi. This experiment will address this objective by allowing us to directly collect and observe any plants and fungi that are in the transect. This observation will help to give us more insight into the function and importance of plants and fungi.

Specific Steps

Specific steps preformed: 1. The bacteria plates were observed for evidence of fungi growth. 2. Five plant samples were taken from the transect. 3.The plant samples were examined under a microscope for distinguishing features. 4. The Plants were classified based on morphological features. 5. A Berlese funnel was constructed by: placing a funnel containing a screen, in the neck of a beaker filled with ethanol. 6.placing the beaker under a light 7. Placing dirt and leaf litter in the funnel


Raw Data:


Table 1: Transect plants Plant 1- Angiosperm: Found growing in a planting box. Description: Growing with other similar plants, greyish leaves with soft lumps on them, very woody stem. Vascuaralization: Dicot, vascular bundles Leaves and Special characteristics: Lumpy, soft, oval-shaped leaves, growing alone on stem. Contains, guard cells, stomata, and soft fuzz on leaves. Seeds/ evidence of flowers or reproductive parts: No evidence of flowers or seeds was observed.

Plant 2-Angiosperm:found growing in a planting box. Description: Growing close to the ground in clumps, soft leaves, leaves turning brown at ends. Vascuaralization: Dicot, vascular bundles. Leaves and special characteristics: Leaves are wide, grow in threes, and browning at the edges. Contain a thick, waxy cuticle. Seeds, evidence of flowers or other reproductive parts: No evidence of flowers or seeds was observed.

Plant 3- Pterido-phyta: Found growing in a planting box. Description: Found growing with other similar plants, has long roots, and fern-like leaves. Vascuaralization: Dicot, vascular bundles. Leaves and special characteristics: Leaves are branching and grow from a bundle in center of plant, many leaves are yellowing. Contains cuticle, guard cells and stomata. Seeds, evidence of flowers or other reproductive parts: No evidence of flowers or seeds was observed.

Plant 4-Angiosperm: Found growing in a planting box. Description: Found growing with other similar plants, has small, round leaves, many leaves are yellowing. Vascaralization: Dicot, vascular bundles. Leaves and special characteristics: Leaves are round and grow along a long stem. Contain; cuticle, guard cells and stomata. Seeds, evidence of flowers or other reproductive parts: No evidence of flowers or seeds was observed.

Plant 5-Angiosperm Found growing in a planting box. Description: Found growing with other similar plants, has small purple and green leaves, leaves have soft fuzz on them. Vascuaralization: Dicot, vascular bundles. Leaves and special characteristics

Leaves are round and grow along a long stem. Contain; cuticle, guard cells and stomata. Seeds, evidence of flowers or other reproductive parts: No evidence of flowers or seeds was observed.


      • Note: The plants observed were growing in less than ideal conditions and did not appear to be very healthy-in many cases the plants were mostly dead. The unhealthy plants may not have been producing seeds or flowers, or may have been producing very few. The lack of observable reproductive structures made identifying the plants very difficult. It was assumed that all plants, with the exception of number 3, were flowering plants. Due to lack of identifying features the genera of the plants was not able to be determined.

-Fungi Sporangia are formed from hyphae and contain spores that can be released to preform asexual reproduction. Without these structures, the fungi would not be able to reproduce.

-No fungi were found on our agar plates.

Note: All of this information was originally in a table as the lab suggests, but when put on open wet ware, the formatting was messed up.


PS:Photos are working now!!

Conclusions and Future plans: This experiment partially met the objective of the experiment. The experiment was successful in allowing us to observe plants and gain a greater understanding of plants. It was not successful in allowing us to observe fungi due to the fact that there were no fungi present on the plates. Additional experiments should be carried out in order to determine what sort of fungi is present in the transect.


CD


2-18-14 Lab 3

Objectives: The objective of this experiment was to determine what type of bacteria is present in the transect, to understand the characteristics of the bacteria, to observe antibiotic resistance and to use DNA analysis to identify bacterial species. In this experiment we used agar plates to observe the bacteria-including some species that are resistant to antibiotics,  and PCR in order to determine their species. 

Specific Steps preformed: 1. The bacteria from the serial dilution were observed, and colonies were counted. 2. Three samples of bacteria from the plates were smeared on a plate 3. The bacterial smear was covered with crystal violet for one minute 4. the smear was rinsed with water 5. The smear was covered with Grams Iodine mordant for one minute 6. The smear was rinsed with 95% ethanol for 10 second 7. The smear was covered safranin for 20 seconds 8. The smear was rinsed with water and rinsing the slide again. 9. To prepare a PCR, a colony of bacteria was placed in a 100ul of water in a tube 10. The tube was incubated at 100°C for ten minutes, 11. The tube was centrifuged 12. 10ul of supernate was isolated

Raw Data:


-I think it is possible that some archaea may have grown on the plates. Archaea are capable of living in very hostile environments, so it makes sense that they would be able to survive on the plates. Of course, the plates are not designed to match a hostile environment a species of archaea is adapted for, so if there are archaea there may not be many and they may not have a very high fitness.

-The smell of the culture may change from week to week due to the continued decomposition of the plant matter within it, and the continued growth of new and different organisms.


Table one: Table one: Dilution 10^-3, nutrient agar, lawn, too many bacteria per mL to count Dilution 10^-7, nutrient agar, 180 colonies, 18,000,000 bacteria per mL Dilution 10^-9, nutrient agar, 18 colonies, 180,000,000,000,000 bacteria per mL Dilution 10^-3, nutrient agar+tet, 53 colonies, 53,000 bacteria per mL Dilution 10^-5, nutrient agar +tet, 4 colonies, 400,000 bacteria per mL Dilution 10^-7, nutrient agar +tet, 0 colonies, 0 bacteria per mL



-The differences between the colonies on the non-tet and tet plates are; the tet colonies tended to be larger than the non-tet colonies, most of the colonies on the tet plates were orange, while the colonies on tet non-tet plates came in a variety of colors (including orange).

- The lack of color variety indicates that only a select few types of bacteria were able to grow on the tet plates. The larger size of the tet colonies indicates that the organisms that were able to grow on the tet plates were better suited for growth on the tet plates than on the non-tet plates.

-The tetracycline limited the number of bacteria. Note that the maximum number of colonies on non-tet plates was 180, whereas the maximum number of colonies on the tet plates was 53. There were no fungi found on either plate.

-Based on our observation of the color and shape of the colonies, it was determined that 2 species of bacteria were unaffected by the tetracycline

-Tetracycline is an antibiotic that works by inhibiting protein synthesis in bacteria. It inhibits the binding of t-RNA to the ribosome. Both gram-positive and gram negative bacteria are susceptible to this antibiotic. Some specific types include; chlamydiae, mycoplasmas, rickettsiae, and protozoa. (Chorpa, Roberts, 2001)

Colony 10^-9: Tet -, Pink, circular colonies, 2 colonies, 200000000 bacteria per mL, small, non-motile, pill shaped cells, often found in pairs. Gram positive. Colony 10^-7: Tet-, Yellow circular colonies, 6 colonies, 6,000000 bacteria per mL. Small irregular shaped cells, non-motile. Gram positive. Colony10^-3:Tet+, Orange circular colonies, 8 colonies, 8,000 bacteria per mL. Pill shaped and non-motile. Gram negative


- Based on the results of the PCR it was determined that the bacteria Janthinobacterium, lividium strain and Streptomyces, narbonensis strain are present in the transect. References Roberts, M. R., & Chorpra, I. C. (2001). Tetracycline antibiotics: Mode of action, applications, molecular biology, and epidemiology of bacterial resistance. Microbiology and molecular biology reviews, 65(2), Retrieved from http://mmbr.asm.org/content/65/2/232.full

Bacteriasketch.jpg


Conclusions and future plans: It can be concluded that a variety of bacteria are present in the transect, including some that are resistant to antibiotics. It can also be concluded that this experiment was successful in meeting its objectives, since is allowed us to observe and classify several types of bacteria. In the future, more extensive analysis of the bacteria should be done in order to determine how the bacteria survive in the transect, and how they interact with the other organisms. CD



2-6-14 Lab 2 Identifying algae and protists

Objective: The objective of this experiment was to observe the algae and protists living in the transect, and to better understand the characteristics of algae and protists. Through this experiment, we will collect samples of protists and algae, this will allow is to observe their characteristics, and determine their species.

Specific Steps: 1. Water samples from two different areas of the hay infusion culture containing algae and protists were observed under a microscope. 2. 100ul of water from the hay infusion culture was mixed it with 100ul of broth, and added to a test tube. 3. The solution was then used to fill six more tubes with a hundred-fold decrease in concentration for each tube. 4. The tubes were then used to inoculate seven agar plates, three of which contained the antibiotic tetracycline.

Raw Data:

Description of hay infusion culture:

The culture has a thick, light brown film on the top. On top of the film lie some black mold spots. There is lots of darkly colored, slimy debris at the bottom of the jar. The culture is foul smelling; it smells a little like mold.

-Organisms might differ depending on whether they are near to plant matter or not, because some organisms have evolved to live in areas with lots of plant matter. These organisms may use plants for shelter or food. Other organisms have evolved to live away from plant matter; perhaps they need to live at the surface to get more sunlight.

-Organisms observed in culture:

Area 1: Surface:

1. Peranema, mobile, protist, not photosynthesizing, 50um 2. Euglena, mobile, protist, can photosynthesize, 40um 3. Actinoshpaerium, mobile, protist, not photosynthesizing, 75um

Area 2: Middle of jar

1. Peranema, mobile, protist, not photosynthesizing, 50um 2. Colpidium, mobile, protist, not photosynthesizing, 60um 3. Actinoshpaerium, mobile, protist, not photosynthesizing 75um

Note: We were unable to find 6 different species in our sample. Many of the organisms that were living at the surface, were the same species as the ones living at the surface.

How Paranema meets all the needs of life:

1. Energy-Paranema is heterotrophic and therefore must consume other living things to survive. Paranema capture prey such as bacteria to provide energy.

2. Cells- Paranema is made of a single cell.

3. Information-Paranema is able to take in information from the environment and adapt to it. One example of paranemas’ ability to process information is its ability to sense and respond to changes in light.

4. Replication-Paranema is able to reproduce through binary fission.

5. Evolution- like all living creature, paranema is subject to the pressures of natural selection. This pressure and the ability to mutate, allow the organism to evolve.

-If the hay infusion culture were to be observed in another month, I suspect there would be less visible plant matter, because the leaves etc., would have begun to decompose. I also suspect that if the nutrients in the jar have not started to run out, there would be more mold on the top of the culture, and there would be more protists. If the nutrients in the jar have started to run low at this point, then I suspect there would be fewer protists and only the strongest, healthiest protists would still be living.

-The selective pressures that affected our sample were: temperature constraints, limited nutrients, predation by other organisms, and limited living space. The organisms had to compete to gain access to these resources, and the ones that were best able to adapt to their environment survived.

Sketch of organisms:

Organisms626262.jpg

Sketch of serial Dilution:

Serialdilution887878.jpg

Great job, the pictures didn't upload, try again. 2/18/14 GHH

Conclusions and Future plans: This experiment was successful in allowing us to observe the various protists that live in the transect. The experiment was unsuccessful in allowing us to view algae. Next time this experiment is preformed it would be advisable to take a wider variety of samples, in order to find some algae to observe.


1-28-14 Lab 1 Lab 1 Diversity of Life at AU

Objective:  the objective of this experiment was to determine what biotic and abiotic characteristics are present in the transect. A visual survey was used to determine what characteristics are present. Knowledge of these characteristics will help us to better understand the organisms we discover. Additionally a hay infusion culture will help us to observe biotic factors more in depth. 


Specific Steps Preformed:

1. The transect was observed for abiotic and biotic factors. 2. leaf litter and dirt samples were collected. 3. 10-12 grams of soil/leaf litter were placed in a jar containing water and 0.1g dried milk. 4.The culture was then mixed for 10 seconds 5. The culture was allowed to sit unsealed for a week.

Raw Data:

Characteristics of Transect:

The transect is located on the south side of campus, near Beegly Building. The area consists of six wooden planting boxes, with dirt separating the boxes and a chicken wire fence surrounding the plot of land. The ground is flat and the soil is dark, with many bits of mulch and leaves mixed in.

Abiotic features:

1. Planting boxes 2. Dirt 3. mulch 4. rocks 5. chicken wire

Biotic features:

1. leafy, green plant 2. grey colored bush 3. leaves 4. weeds 5. small, green bush-like weeds

Transectdrawingsketch123456.jpg


Conclusions and future plans: Through the survey of the transect, we were successfully able to determine what abiotic and biotic features are present in the transect. A number of small, green plants are present, as are man made features such as planting boxes and chicken wire. Additionally there are natural feature that have been placed here by humans such as dirt, mulch and rocks. During future experiments, I believe we should look more in depth at the biotic features discovered and determine how they interact with the abiotic features in the environment. CD