Difference between revisions of "User:Matthew Bugajski/Notebook/Biology 210 at AU"

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== DNA analysis ==
The nucleotide sequence acquired from the microbiology experiment was run through the NCBI Blast web page.[[http://blast.ncbi.nlm.nih.gov/]] From the website, it was determined that the black bacterial colony was that of Janthinobacterium lividum.
== Lab 6; Embryology ==
The purpose of this lab was to assess vertebrate development. To accomplish this objective, zebrafish embryos were studied. The treatment selected for my group was the effect of salinity of development.
Developing zebrafish are very sensitive to the environment; therefore are affected by the surroundings.
The optimal environment for zebrafish embryo:
* Can survive 10 days without food
* 28-29 degrees Celsius
* pH = 7 - 7.5
* Paramecium as food: They can survive up to three weeks
Embryonic development in zebrafish proceeds rapidly: within 24 hours of blastulation, the basic body plan of the embryo can be observed. Within 48 hours, pigmentation appears. Within 72 hours, the mouth of the embryo protrudes. For these reasons, it is an effective model organism.
Hypothesis: if the salinity of their environment is increased, zebrafish embryos will not be able to develop and mortality will increase.
We predicted that the zebrafish would survive in the control solution, but would not develop in high-salinity water
'''Experimental Design'''
* Three treatments and one control group were prepared: solutions of 3%, .3%, and .03% NaCl, and distilled water.
* About 25 zebrafish eggs were added to each petri dish.
* The hypothesis appeared to be accurate. More zebrafish survived in the control group than any treatment.
* In both trials, all zebrafish in 3% salinity died before developing, reflecting the results of the embryology paper about salinity.
The extent to which zebrafish raised in saline solution was further than initially expected. Also surprising was that salinity had a measurable effect on the size of the measured zebrafish embryos.
Future experiments could extend longer than the time period used for this class, in order to evaluate whether salinity causes effects on development that are not evident until later in life.
Additionally, a larger sample size would ensure that the observations made were not simply due to chance.
With human development impacting existing sources of freshwater, these findings are important to keep in mind.
*Climate change may eventually affect ocean salinity.
**even if these changes are minute, they could have surprisingly large effects on fish
Future studies should evaluate a more nuanced range of salinities, in order to determine the threshold at which the mass death of embryos occurs.
== Lab 5; Invertebrates ==
The purpose of this experiment was to evaluate invertebrate life in the transect and characteristics of various types of worms.
Worm movements
* Acoelomate (Planaria)
** The worm slides along the dish
** This reflects the simplicity of its body plan
* Pseudocoelomate (Nematodes)
** Side-to-side movement -- they thrash about
** They still lack a true coelom, so internal specialization is too limited for more advanced movement
* Coelomate (Earthworm)
** Movement by contraction
** Forward and lateral movement
** Reflects development of coelom and muscle layers -- movement unhindered by any lack of mechanism
Our group did not observe any invertebrates through the use of the Berlese funnel. We considered and discussed potential reasons for this:
* Type of biome: we have the prairie biome, and took dirt mostly from under the rose bushes. It is possible that the biome itself was lacking in invertebrates, or the area from which we took most of our soil.
* Weather: although other groups did find some invertebrates, the weather could have played a role, especially considering that the prairie biome did not have any structures or trees shielding it from wind, snow or rain.
* Setup: our funnel was set up correctly, but since it was on the edge of the array of funnels, it's possible that it did not reach an ideal temperature, so the organisms were not driven out of the soil into the alcohol.
Future experiments will move on from the transect, looking at the development of vertebrates.
== Lab 4; Plantae and Fungi ==
The objective of this experiment was to observe properties of various plants found in the transect.
'''Plant 1''' - flower from bush in middle of transect
* Angiosperm
** xylem/phloem to transport nutrients and water
* thorns/spiky petals
* reproductive parts in middle of flower
**dicot (five petals)
'''Plant 2''' - Leaf from soil under bushes
* Angiosperm - '''Black Oak'''
* 5 lobes on leaf
* broad leaf with waxy cuticle, stomata evident
* dicot
** no visible reproductive parts in observed speciment
'''Plant 3''' - Long grass under bush
* Angiosperm
* monocot
** appears to have parallel veins, long, narrow leaf
* waxy cuticle, stomata unclear
* stem has phloem/xylem
'''Plant 4''' - cloverlike plant under bush
* Angiosperm
* dicot
** netted venation
* green/purple leaves, thick and waxy
* broad network of roots
'''Plant 5''' - 3-leaf clover
* Angiosperm
* small, green plant
* netted venation
* small but broad leaves
** indicates is probably dicot
Fungi sporangia are globelike structures which contain spores, which are released when they open. This is a reproductive mechanism for the sponge.
We observed a black bread mold, an ascomycete. We observed the mycelium and sporangia, tangled together in a randomly arranged web. It is an ascomycete because it does not fulfill the characterists of a basidiomycete or a zygomycete.
Future experiments will evaluate the diversity of plant life in the transect.
== Lab 3; Microbiology and Identifying Organisms with DNA ==
The objective of this experiment was to observe the microorganisms cultured, originally from the transect.
The hay infusion appeared to have less water, less organic growth, and less of a smell. The sediment at the bottom of the jar seemed to be more settled. These changes may be due to a food source running out, causing the protists that had flourished in the bottom of the hay infusion to have died off.
'''Table 1 - 100-fold Serial Dilutions Results'''
{| {{table}}
| align="center" style="background:#f0f0f0;"|'''Dilution'''
| align="center" style="background:#f0f0f0;"|'''Agar'''
| align="center" style="background:#f0f0f0;"|'''Colonies Counted'''
| align="center" style="background:#f0f0f0;"|'''Conversion Factor'''
| align="center" style="background:#f0f0f0;"|'''Colonies/mL'''
| 10^-3||nutrient||500+||x10^3||500,000
| 10^-5||nutrient||50 (+mold)||x10^5||5,000,000
| 10^-7||nutrient||10||x10^7||100,000,000
| 10^-9||nutrient||1||x10^9||1,000,000,000
| 10^-3||nutrient/tet||100||x10^3||100,000
| 10^-5||nutrient/tet||(mold/cannot count bacteria)||x10^5||n/a
| 10^-7||nutrient/tet||1||x10^7||10,000,000
'''Table 2 - Selected Colonies'''
{| {{table}}
| align="center" style="background:#f0f0f0;"|'''Colony Label'''
| align="center" style="background:#f0f0f0;"|'''Tet'''
| align="center" style="background:#f0f0f0;"|'''Morphology'''
| 1 (-5 plate)||-||circular, entire, raised, white
| 2 (-5 plate)||-||irregular, lobate, convex, black
| 3 (-5T plate)||+||circular, entire, convex, orange
The plates that do not have the antibiotics clearly have a great volume of bacterial colonies, and do appear to host different types of colonies. The black-colored colonies were far more prominent in the non-tetracycline treated plates than in those treated with tetracycline. The orange colonies were the only type that appeared to be more prevalent in the plates treated with tetracycline, suggesting that the antibiotic affects some types of bacteria more than others. The plates with tetracycline appeared to have more mold, however, than those that weren't, suggesting that it may not kill off fungi as effectively as it does bacteria.
Upon further research, I found that tetracycline binds to microbial ribosomes, prevent the attachment of a specific type of tRNA. (http://www.chm.bris.ac.uk/motm/tetracycline/antimicr.htm) Tetracycline works against both gram-positive and gram-negative bacteria, but is limited in effect against some antibiotic-resistant strains of bacteria.
In future experiments, other characteristics of other organisms of the transect will be observed.
== Lab 2; Identifying Algae and Protists - January 27 ==
The objective of this experiment was to identify algae and protists living in the assigned transect. This was achieved through the use of a hay infusion.
'''Culture Observations'''
* The culture primarily consists of murky, slightly brown water
* The culture does not have a strong smell.
* There is a ~1 inch layer of dirt/mud on the bottom, with small pieces of plant matter mixed in
* On the top, there floats a translucent film, which may consist of or contain microorganisms
Two samples were obtained: one near the bottom, with the dirt and mud, and one near the top. One was taken from the top, since we suspected the film could have been a result of organismal activity, and the other sample was taken due to the possibility of organisms living near the plant matter mixed into the mud.
'''Organisms observed'''
* Paramecium aurelia - 110 micrometers
** Bottom sample
** Elongate shape
** Mobile (no visible flagella; uses cillia)
** Protozoa
** Heterotrophic; no evidence of photosynthesis
* Colpidium - 100 micrometers - 100 micrometers
** Bottom sample
** Rounder shape
** Mobile (cillia)
** Protozoa
** No chloroplasts of other evidence of photosynthesis
* Amoeba - 30 micrometers
** Top sample
** mobile (no cilla or flagella; presumably uses psudeopoda)
** Protozoa
** No chloroplasts -- does not photosynthesize
''Note: after extensive searches of multiple samples from each selected region of the culture, no other protozoans were located''
'''Paramecium aurelia'''
1. Energy
* Paramecium consumes smaller bacteria and other organisms to acquire energy
2. Cells
* Paramecium is a single-celled organism, with a cellular membrane
3. Information
* Paramecium contains DNA in its nucleus, which hold genetic information
4. Replication
* These organisms replicate through mitosis
5. Evolution
* Through the mechanisms of mutation and natural selection, paramecium populations can evolve.
If the hay infusion culture had been observed for another two months, I predict that protozoan life would greatly decrease. Since there were no autotrophs observed, eventually the population of protozoan heterotrophs would run out of food sources and die. If the system was exposed to some sort of fungi, perhaps that would flourish for a while, but without any external input the system would eventually become devoid of life.
Our samples were composed only of organisms that could survive for the week between the collection of the sample and the observation. Additionally, smaller organisms that may have initially existed could have hidden in a different area of the culture than the ones that we observed.
In future experiments, other aspects of the transect will be analyzed.
'''Good job, but don't forget the last item in red about the serial dilution. 2/18/14 GHH'''
== Lab 1; Biological Life at AU - January 16 ==
'''Transect observations'''
The objective of this experiment was to observe the biological properties of the assigned transect.
Located in the middle of the quad, between Hurst and Batelle, the transect is a flat 20x20 piece of land. The transect includes a concrete path, some bushes, and the grass of the quad. The contents of the transect can be separated into biotic and abiotic content:
* Bushes (may be dead)
* Grass
* Woodchips
* Soil + associated organisms
* Small pieces of vegetation in soil
* Stone path
* Concrete bush
* Plastic/metal divider between path and bush/soil area
* Gum wrapper (garbage)
In the future, more in-depth properties of the transect and its biotic components will be analyzed.

Revision as of 08:47, 7 May 2014