User:Matthew Holland/Notebook/Biology 210 at AU

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Lab 6: Embryology & Zebrafish Development: 2/24/15

The purpose of this lab is to watch the stages of development from embryonic conception, through development, and up till the organism (zebra fish) has reached its full growth. It was not only to look at the stages of development but also to see what the affects of various chemicals have on these organism when they are exposed to through out development. Prior to the experiment with the Zebra fish, we were responsible for deciphering how: starfish, frog, chick, and human egg embryos developed. The general trend was that the frog and starfish eggs were more closely related to each other while the chick and human embryos were more similar to one another. Even to someone who does not know the complexity of the eggs there are huge differences in the organisms but being that they are all animals there are similarities. The fertilization takes place externally with starfish and frogs where as in humans and chickens the fertilization is internal. The amount of yolk and distribution in starfish and frogs is holloblastic (amount) and telolethical (distribution) where as it is meroblastic(amount) and isoethical (distribution) in chickens and humans.

The reason that we are using zebra fish is because they are inexpensive, easily available, easily affected by the presence or absence of certain chemicals, and the maturation rate does not take that long. Two petri dishes were taken and had 25mLs of either distilled water or 25mLs of water/retinoic acid (vitamin A) poured into them using a electronic droppers. 20 eggs were then placed in each dish after they had been fertilized for somewhere between 18-36 hrs and they were observed bi-daily. Other than the liquid the fish were developing in everything was kept as similar as possible (temperature, food supply, water level, etc.). Every 4 days the liquid was changed to prevent disease and they were feed 2 drops of paramecium every 4 days. During the observations that were made every 2 days we were responsible for removing any dead fish, egg shells, large pieces of mold, anything that was not liquid or fish.


Day 1: 2/18/15

Control: -Clear circle -No visible features in egg -Most likely in zygotic stage -0 movement

Test: -Clear circle -No visible features in egg -Most likely in zygotic stage -0 movement

Friday Feb. 20 2015

Test group: bodies have begun to form there is the head, body, and tail. 2 black lines run down each fish and make it look like it is developing legs a sack under the head and is filled with black dots. 48 hr stage H in back of book Control group: appear to be at the same level of development as the test group. test group does not show signs of any mutation yet

Monday Feb. 23 2015

Control group: fully formed bodies developed eyes not easily agitated clear bodies with spots probably 2mm long 17 still alive Test group: 15 still alive some bodies are deformed they curve to the right and left various levels of severity appear more yellow than clear in color cant really swim they try to move but just squirm in place or they move but sporadically requires more to agitate them probably the same lenght as the control group but deformed larger bottom bulge deformed fins

Wednesday Feb. 25 2015

Control group: more developed moving around with more ease small black node on the bottom of the fish where the empty sack used to be. possibly the heart some are have a yellow tint but are not as yellow as the test group probably .5-.6 cm long all 20 are still accounted for have more spots tails have tapered down to one

Test group: 3 dead slow moving, still mostly vibrate in place "heart" is less developed and has a hole through the middle not as yellow more clear concave eyes and are moving irregularly have more spots tails have tapered down to one

Feb. 27, 2015

Test group: small body return to yellow tint 5mm long probably more fish shaped black hole in body is still not 100% solid erratic/twitchy movement right eyes appear to be more deformed than the left 7 are alive

Control group: bodies are transparent with black spots eyes are very developed and large on some of the fish the sac at the bottom is solid and others not so probably 5mm long more fish shaped movement is fluid and streamline

Mar. 1, 2015

Test group: all dead

Control group:

bodies appear to be more developed still some yellow tinted bodies but most are clear eyes well developed and you can see eyes tracking other objects still about 5mm long movement is very fish like

Lab 5: Invertebrates: 2/17/15

During week 4, we made a Berlese funnel to collect invertebrates from our transect. One of the bags that we collected leaf litter and other specimens in was taken back to the lab and placed in a funnel that had a screen taped to the inside of it preventing large chunks of debris from falling into the attached beaker that was filled with 25mLs of 50:50 water/ethanol. The funnel was then placed 2-3 inches under a 40 watt incandescent that was covered with foil for one week. After the week of incubation, during the lab in week 5 we broke down the funnel and poured out the liquid and organisms into petri dishes. We observed using a dissection scope: 4 Springtrail Xs (Kingdom:Animalia, Phylum: Arthropoda, Subphylum: Hexapoda Class: Entognatha Subclass: Collembola) that ranged from 1-6mm in length, 1 Thrios that was about 3.5 mm in length, 1 soil mite (Kingdom: Animalia, phylum: arthropodia, subphylum: chelicerate, class: arachnida, subclass: acari, superorderL acariformes, order: oribatida ) that was about 1mm in lenght, 2 ants (kingdom: animalia, phylum: arthropoda, class: insecta, order: hymenoptera, suborder: apocrita, superfamily: vespoidea,family formicidae) approximately 2mm in length, and 2 nemadoe worms (kingdom: animalia, Clade: nematoida, and phylum: nematoda) about 2mm in length. The lab provided several known specimens for us to observe: the planria had and arrow head and moved in a serpentine fashion while the nematodes resembled leaches and moved more in a forward inching motion. Even though this environment seems to not have that many components to it there are still and ample amount that if some were to disappear there would be an affect on the stability of the ecosystem. Currently there is an abundance of dead (abiotic factors) plant leaves in the garden and on the lawn. These are just as essential for suntanning the life of the invertebrates as the live plants (biotic factors) are in the warmer months. Following is a food ranking with the producers at the top and omnivores at the bottom

Live plants, leaf litter, plant material, feces, algae, fungi

Springtails, nematodes, ants, soil mites, Thrios

Worms, spiders, insects

Robins, cardinal, Sparrow

Fungi, other decomposes and scavengers

All of the organisms listed in this food ranking are in the manicured grasslands transect at AU but it does not include all of them. There are different numbers of each organism need to sustain life in this environment and if any is disproportionate there is potential for an issue. The carrying capacity can fluctuate a little but not too much for if it did the trophic levels of one species would rise and the others would fall. As humans we have ways of intervening and manipulating these variables but in nature it is up to the surrounding environment to keep everything in check.

Lab 4: Plantae and Fungi: 2/10/15

Saying that something is a plant is a very generic/broad term. It hints at certain characteristics but exact phenotypic characteristics are still left unsure. In this lab we returned to our transects to collect plant specimens and examine their characteristics so that we could see the different plants that all live in the same environment as well as what makes them unique. One of the main characteristics that differentiates plants is whether or not their is a vascular system for transporting fluid and or waste into/out of the plant. Mosses, lichen, and similar sprawling type plants do not have a vascular system; plants that are more vertical do have a vascular system. Using a magnification tool, we were able to see the rhizoids, xylem and phloem on the samples provided. We collected a large amount of leaf litter from the transect as well as some grass clippings, twigs, and buds. The bud that we collected was from a rose bush - it was 2/3 eaten by a squirrel. The five samples that we chose to examine were: grass, a clover, a stem from a tall grass plant, the flower bud, and a pointy leaf. File:Unamed All of these samples had vascular systems even though the rose and pointy leaf reproduced via pollen and the other three reproduced via seeds. These were the plants we examined, there were also fungi provided by the lab. We were able to observe the fungi's sporangia which are vital to the posterity of the fungus. The sporangi hold and release spores when it is time for the fungus to grow/move. The most visible sporangi were the ones on the under side of the basidiomycota. The flaky tissues were these spores were kept. --A side bar that I know about basidiomycotes, the under side of them is similar to a human finger print, no two are the same if you were to stamp or scan them.--

Lab 3: Microbiology and Identifying Bacteria with DNA Sequences: 2/2/15

The major differences between bacteria and archaea are: the chemical make up of the cell wall, how the organism grows and reproduces, and the preferred habitat. Even though archaea prefer more extreme environments, I believe that it is safe to say that archaea will grow on the petri dishes with agar because the gel is designed to be the perfect environment for growing microorganisms. The final observation of the Hay Infusion looked similar to the one the prior. the differences were that: there was more mold growing on the surface of the water, the water in the middle of the jar was a clearer shade of brown, and there was more debris collected at the bottom. IMG 0911.jpgIt still smell did not change it was still reminiscent of nasty pond water. We took samples from the hay infusion and placed them on two different types of petri dishes one with only agar and another that was agar combined with the antibiotic tetracycline. Colonies grew on both dishes but there was a larger number of white colonies on the dish with tetracycline. This suggests that the white strain was an antibiotic resistant form of the mold where as the orange (sunset) color was not. The trend on both dishes was the same: in the less diluted solutions there were more colonies and as the dilution increased there were fewer however, the math suggests that there would be more. The math makes sense. With less organisms in a larger space not having to compete as much for resources, eventually there would be more bacteria in the diluted dishes. The tetracycline did have an affect on the number of bacteria colonies that were able to grow and be observable to the naked eye but the trend was the same. I was able to speak with a pharmacist and have them explain to me how tetracycline works. From what I was able to understand, the way that the antibiotic works is by using the OH double bonds to chelate on cell wall of the bacteria and then lysis the bacteria. The pharmacist then proceeded to tell me that tetracycline is capable of binding to pretty much any part of the body which makes it slightly "iffy" to use. For example: If taken as a child it can bind to the enamel of the teeth giving them a gray tint. The though that the white strains of the mold were genetically different from the sunset colored ones makes sense but the reason that both grew in the presence of the antibiotic could have been the result of multiple things. It could be that tetracycline was not that effective at killing the bacteria, the mold exceeded the minimum inhibitory concentration, or that not many mutations were needed to make the bacteria immune. We also went through the process of staining them to see what the cell wall was composed of. We only selected four of out of the eight; two with agar and tetracycline and another two with only agar. Only one cell was negative for the gram stain. Now, as i look at my data, it is the only one that was random and by random I mean that multiple descriptions accurately described what the cells looked like.

Lab 2: Identifying Algae and Protists: 2/1/15

For this lab, we used the micro organism collected from the previous week's transect. We let them grow for a week in a cleaned out peanut butter jar filled with water and milk protein power so that we could create an ideal environment for the organisms to grow. We were trying to observe what type of organisms grew in our environment. We used a dichotomous key to help differentiate what organism was what. The first organism that was observed was 50 nano meters long, clear, sporadic/fast moving, oval shaped, and they extended their whole bodies to move; we concluded that it was a paramecium multimicronucleatum. The escond was 230 nano meters long we though it to be a colpidium. It was pieced together that the third was gonium, and the forth was bilephaisma. IMG 0861.jpg

The hay infusion looked like a suspension with a little bit of mold on the surface, dirtier water in between and then a collection of debris at the bottom. It smelled like a nasty pond (very still, dirty, vial water)

Lab 1: Biological life at AU: 2/1/15

First, we observed Chlamydomonas, Gonium, and Volvox to see the relationship between the three as proof that evolution does take place. As we examined them under the microscope, it was more evident that these cells were related. The data that was collected also suggests a relationship. (not sure how to make a chart on here so i could include the information). The niche at AU we were assigned to collect samples from was "manicured grass" or the quad. Some Abiotic components observed were: snow, dirt, mulch, fallen leaves; some biotic factors observed were: a rose bush, berries, tall grasses, etc. Below is a hand drawn diagram of the transect. File:IMG 0959.jpg