User:Taylor R. Hendrickson/Notebook/Biology 210 at AU

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March 18, 2015

Zebra Fish: No Stripes, Just Fins

The purpose of this lab was to get experience was developing original experimental research. This process allowed to design our own experiment and purpose. For my groups lab, we decided to focus on the effects of ehisterone on the development of the physical attributions of the fish. We chose to stay away from behavioral traits due to the limited time and resources.

For 14 days, we alternated visits and took our own notes. We collaborated our findings between each other and with the other group who was developing the same experiment. Attached below is a PDF accumulation of all of those notes. The findings included body measurement of the eyes, dorsal fin, body ect.. as well as alertness ratings of the reactions of the fish, notes of any abnormalities or very obvious behavioral differences (although it wasn't the focus of the experiment), as well as the death rate and survival rate of the fish. On certain days the lab manual required us to take out dead fish, add paramecium, take out old liquid and put new in.

Based on the results we received, show not clear or conclusive answer to our hypothesis or prediction. The exactness and promptness of our work hindered the success of the results. So, we have no proper lead to make a conclusion off of. There were a few instances in the design of the lab where a member tripped on a book bag, spilling parts of the samples, between transferring samples under a microscope some were killed and entire samples were spilled and ruined in the storing bin by other people. Also, there were a few instances where we weren't able to record notes at all, such as the weekend when the lab is closed and two days where we were not able to enter the lab room due to testing of other classes. The death and survival rate could have been a results of many different factors because the professionalism behind the experiment was lacking, leaving us with no clear lead. It could have been a result of the extra movement from other groups moving around the other samples in the bin, lack of food, bad temperature environment and so on. The findings were interesting but still inconclusive to any final results. This lab should be redesigned and done again. I do believe however the sample size was good to work with. It's not too much to keep track of but not too little, so it didn't give a larger significance of the experimental results.

March 2, 2015

The purpose of the culminating collection, analyzation and 16S sequencing of our unknown bacteria was to create a better understanding and mostly learn about bacteria as a whole. The most important and most exciting part of this to me was going about the whole process. We could have easily read all of this in a book or been lectured about it. But instead, we had hands on work with how you collect a sample, the process and importance of a Hay Infusion, the use and creation of agar plates, and a review of PCR reactions. As a whole, this lab was a dragged out one across many weeks, but nonetheless a very important want to understanding the basics and introduction to bacteria.

A few labs ago, we took cultures from our petri dishes that grew bacteria from our Hay Infusion on Tetracycline and non- Tetracycline agar plates. We were able to examine the colony size, shape, texture and visual characteristics but, we still couldn't determine which bacterium they were ourselves. We set up a PCR for the 16S sequencing of the unknown bacteria collected. The following week we ran the PCR products on an agarose gel. The two that came of the clearest/best were the ones we chose to be sent off for professional sequencing. Once we received the sequencing, we copy and pasted the results into an online database called After pasting, the nucleotide blast was selected. After a few minutes, the database gave us the best match to a known bacteria. To do this, the program basically aligned our sequence going one direction and searched through the archives for matches not of the exact same sequence but of the opposite strand. The result that fit best like a puzzle piece was the one we chose to identify our bacteria as.

For us, our results were 

"Variovorax sp. ML3-12 16S ribosomal RNA gene, partial sequence" and "Chryseobacterium sp. MH gene for 16S rRNA, partial sequence". I looked up the two bacteria to get a general idea of what they were. For the Variovorax, I found a scientific study of isolated soil from a greenhouse, upon investigation they found their bacterium to be of the same kind. Their examination included the following characteristics: A Gram-negative, rod-shaped, non-spore-forming bacterium with irregular light yellow colonies. The description of the colony matches with our results as well. Variovorax sp.. For the Chryseobacterium we found that it is, "yellow pigmented, Gram-negative filamentous, non-motile rod and can be found in soil, plants, foodstuffs and water sources, rod bacteria of approximately 0.5 µm in diameter and 1.0 – 3.0 µm in length, [and visually] circular, convex, entire, smooth and up to 2 mm in diameter with an aromatic odor colonies". Chryseobacterium The visual descriptions of the colonies matches with our findings as well. We are confident that these are the correct bacterium in our cultures. As seen in our chart from a previous lab, Bacteria Characterization we used vile A and D which were the 10^2 Tetracycline plate and 10^4 no Tet.

Sequence for Vile A


Sequence for Vile D


There are current technical difficulties uploading the screen shots of the ID's from the website, however the identification is given in the lab explanation. Unfortunately, our group was unaware of the future lab report concerning this final journal, so we did not keep a picture of the agarose gel results. We do remember however that the two not chosen weren't very clear or good to use for sequencing. We do however, have a picture of the original agar plates used where you can locate the exact plates we took our cultures from and the relationship between the visual characteristics here and the characteristics given by my outside sources.

Agar Plates

'"February 18, 2015I spy a Vertebrate

To take our transect one step further we examined the area for vertebrates.

Inside our transect, at different points in time we have seen two types of birds, two types of squirrels and mice. Mice are usually located around humans because of food and shelter. It is common to have mice in the neighboring building, which leads us to believe, even though tiny and hard to spot, there are plenty of mice utilizing our transect. Mice, are in the Chordata phylum, mammalia class, rodentia order, family muridae and species Mus. The mice benefit from the abiotic factors such as the bench and sign for shelter, protection and a place to hide and the biotic factors of water, grass and leaf litter (camouflage). The Black Squirrel of our transect is actually the same species of squirrel as the other one we found- Eastern gray squirrel. The Black Squirrel only has a color variation. Both are in the Phylum Chordata, class mammalia, order rodentia, genus scurius and species s. carolinensis. Each squirrels utilizes the biotic factors of the transect such as trees for shelter and nesting, the leaves and twigs for building a nest berries, nuts and seeds for feeding and the water source. The abiotic factors used by the squirrels are the stones to also aid in shelter construction, the bench for climbing/jumping/escaping and often the trash laying around you see them snag and go with. There were two different types of bird seen in our transect. But being able to get a close enough look to properly identify what kind of bird was a long-shot. However, after some research online, we believe we have come as close a possible to identifying them. First, we think one is a Brown Creeper. This kind of bird is both a resident and migrator during the winter to Maryland. The use their beek to get within bark to snatch bugs. Although no trees large enough with bark are present in our transect, the Brown Creeper may be a friendly visitor to it. Brown Creeper This bird is the the Chordata phylum, aves class, passeriformes order, Certhia genus and and c. americana species. The Carolina Wren is though to be the second type of bird. It is a permanent resident of the Eastern states and is non-migratory. They tend in inhabit bushy areas with shrubs with small insects and berries in the winter. This makes sense to us because there was a tree with berries in our transect that may have attracted the bird. The Caroline Wren benefits from the same biotic and abiotic factors as the Brown Creeper. Carolina Wren The only classifying different between the Brown Creeper and the Carolina Wren, is that the Wren is its in the Thyrothorus genus and T. ludovicianus species.

Food Web- This is a PDF illustrating our food web based on all the organisms we came arose. The insects and plants were generalized because we never come to an exact identification on what kind of invertebrate or plant they were. However, the mine idea of the functioning trophic levels is expressed and understood.

Whether their only niche, or apart of a bigger one, vertebrates play an important role in the giant mix of the living variables present. They all play a role in the community of the transect/ campus environment. With many different types of animals in Maryland, the habitats on campus attract certain ones only until their carry capacity so food and other resources don't become too scarce. Because of campus being a certified arbitration, many different species are attracted to living on campus. All of the invertebrates found were herbivores, which are under tertiary and secondary carnivores and above decomposers and primary producers. The animals found at the middle ground of the food chain. Which, makes them all the more important.

February 17,2015 Creepy Crawlers

This lab shifted our focus onto the importance of invertebrates. The goal was to learn how the first simple system's evolved into more complex ones. To do so, we used what come out of our Berlese funnels constructed last lab to better understand soil invertebrates- specifically the ones located here on AU's campus. My group's leaf litter was a large collection, and we were the only group given a considerably large funnel to work with. Thanks to this, we had high hopes of finding various creatures. My group and I hypothesized that we would find at least 3 different invertebrates- large or small- within our funnel collection. We were worrisome however that due to the cold conditions of our transect, the amount of invertebrates found would be much fewer than if taken during the spring.

Materials: Berlese Funnel- microscope-slides- cover slips- petri dishes- dissecting microscope- ruler with cm- notebook

Method: The method of the lab was not very complex. If anything, it was up to us. It was mostly each group member trying to look for some kind of invertebrate in our funnel collection and taking a closer look at the organism under one of the microscopes. This was not a step-by-step kind of lab. Upon finding an invertebrate we took various notes such as the length, kind of organism based on the questions on the dichotomous key and general questions about the organisms found as a whole like, what kind of organism was most common? The only listed instruction to follow exactly was pouring the funnel collection liquid into a petri dish and search under the dissecting microscope for invertebrates. When one was found, I carefully sucked up the organism with a pipette and transferred the drop onto a slide so we could take a closer look at the characterizations under a microscope. Then, we used a the dichotomous key to better understand what kind of invertebrate it was. Dichotomous Key Used

Invertebrate Table- This is a PDF organizing and analyzing the 4 different invertebrates found in our leaf litter.

We observed the acoelomate, Planaria and the coelomate Annelida. The Planaria moved more in a gliding and folding fashion with a flat body type while the Annelida moved its round body in a weight transfer motion of contracting motions due to its lack of cilia and legs. I couldn't tell exactly but I would predict based on the Planaria's movements that it has very small cilia helping its movement. We were ale to find only 4 different kind of invertebrates in our transect unfortunately. The one we predicted to be a flea of some sorts was the most common- we found 2. The organisms found were large enough to keep the microscope at 4X. The organisms ranged from 2 cm (spider) to as small as 37 um (flea?). It was difficult to find a definite answer as to what the organisms were. There was a few times where the end result of the dichotomous key was way off based on the pictures provided. So, I had to go back and use scholarly intuition to try to get the closest result possible. Although the dichotomous key was close, our group still believes that the bug could be labeled otherwise ( as seen in the PDF chart).

To close, our group realized that we originally thought bugs were very simple creatures. However, after finding these 'basic' invertebrates we soon realized that they are complex in ways we didn't originally think could be possible. There's not just one fly and one mosquito but various different kinds based on certain characteristics. Filling out the dichotomous key, I was surprised by how many questions there were- even ones I didn't know to ask myself when looking at the organism. It is interesting to think about the kinds of roles these small invertebrates play in such a comparably large habitat/environment.


February 9, 2015 Plants and Fungi, Oh My!

By using out designated transect location, we ventured back outside to analyze and take note of the plant diversity. Along with this, we were able to take a closer look at the characteristics of specific samples taken by our own hands. Fungi, which were never previously stressed before in any of my Biology classes, were a denoted for investigation in this lab as well, for, they have specific functions and importance too. Due to the cold weather, my group hypothesized that although the temperature was not idea, we would still be able to find just enough samples to properly go about the lab. Variety we predicted, would be very limited as well as the characterization of them because they were in their winter condition- which lacks many of the characteristics seen during warmer weather (For Example, reproduction methods (flowers) and some specialized structures).

Materials: transect location- 2 plastic baggies- 5 different plant samples- microscope- notebook- camera


To begin the lab, we prepared to head outdoors to our transect on campus. We made sure to bring two baggies, one for the representative samples from five plants and the other for the gathering of leaf litter, a camera to take picture of the source of our samples and a notebook to help organize where out samples were from. When taken back to the lab, we examine each of our samples vascularization, specialized structures and mechanisms of reproduction. Next, we moved on to examining fungi- learning about the parts and the importance. We looked at a mushroom underneath the microscope to get a better understanding of this type of fungi. Next, we set up a Berlese funnel to collect invertebrates from of leaf litter. To do this, we started with pouring 25mL of a 50:50 ethanol/water mixture into a 50 mL conical tube. We placed a screening material at the bottom of the funnel to stop any leaf chunks from going into the preservative. We taped the conical tube with parafilm to the funnel and then gently put in our leaf little collection. We placed our final device underneath a lighted 40 watt lamp with a incandescent bulb approximately 1-2 inches from the top of the funnel and gently covered everything with foil. Now, the Berlese Funnel will sit for one week in hopes that the light will force any invertebrates down into the preservative.

Plant Sample Chart - Full detailed description/ pictures of plant samples

Britannica Kids Leaf Chart - This is an image taken directly from the Britannica Kids website that we used to help characterize our plants.

Mushroom Image- This image was taken during our examination and analyzation of the mushroom under a microscope.

The PDF file above is an organized chart including pictures of the specific samples of each plant, the plant of origin, as well as a full description of the genus, vascularization, method of reproduction and physical characteristics. We collected mostly angiosperms, but were lucky enough to not only find a moss but also a berry from one of the tree samples. We brought this berry back to examine the seed. The seed ended up being too small to create a usable cross section, but, we reference our Professor and came to the educated conclusion that its dicot. A few of the plants that we said were angiosperms we assume flower during their prime season. We used a concise and simple chart from Britannica Kids online to help characterize our plants and leaves. When we moved on to looking at the mushroom, we developed a better understanding of Fungi. Fungi's sporangia are important because they are a cell containing the spores until they are mature enough to be released in order to reproduce. This is key to Fungi because its a specific characterization defining them because they don't produce seeds. We took a close look as a mushroom and looked for these key traits We found out the mushroom is a Basidiomycota, which is a terrestrial fungi- most commonly a mushroom. Another important characteristic of mushrooms is the hyphae, a network of fine threads. This means, a mushroom cannot be considered a plant because they don't have roots. Spores are a microscopic feature importance to mushrooms as well. These are located inside the sporangia on the underside of the cap in branches called basidia and are released when the sporangia opens. (Source: Descriptive Characteristics of Mushrooms)

Overall, the lab provided a great way to analyze plant types specific to our transects as we learned about the specific parts and functioning of them. I feel as if this lab was less hands on and more learning the vocabulary and contractions of plants in general. However, it still proved to be valuable information and gave meaning to the samples collected. I would have been more fun and valuable if the weather was better so we could better answer the questions pertaining to the plants while they are in full bloom or at their prime.


February 3, 2015

This lab was constructed in order to better understand and work hands on with the concept of microbiology, specifically pertaining to bacteria, their DNA sequences and possible resistance. Last lab, we placed bacteria from our transect onto agar plates. This lab we finally had the chance to take a closer look. My group and I were very confident that we would see the growth of bacteria in large colonies and possibly smaller to no colonies based on the dilution of the tetracycline. We do not predict however that we will find any Archaea in the mix. Even though we did take our transect sample at a time of very cold weather and snow, we don't believe the conditions were extreme enough to find any.

Material: Agar plate samples with varying dilutions- microscope- lens oil- loop- flame/ Bunsen Burner- slide- cover slip- water- crystal violet- Gram's iodine- 95% alcohol- safranin strain-kim wipes


To begin, we just examined our agar plates after letting them sit in varying dilutions of nutrient and tetracycline since last class. We took note of the colonies within each agar plate as well as the conversion to colonies/mL. Looking under one of the less sophisticated microscopes we filled out a chart noting the plate types, colony description including diameter, color, shape, texture, as well as the GRAM + or -. For the wet mount procedure, we sterilized a loop over a flame and picked up a tiny amount of growth from the surface of the 10^-2 Tet, 10^-4 no Tet, 10-4 Tet and 10^-2 no tet. We chose these plates to work with because they had the most growth to analyze. After taking the small sample, we mixed it with a small drop of water onto a slide and covered it with a slip.We made sure to mark with a sharpie on the plate where we got the samples from. Next, we viewed each slide under 10X and 40X objective. For the next gram stain procedure, we sterilized a loop once again and scraped up samples from the same marked areas that we took the samples from before to make sure we were working with the same materials. We mixed a drop of water and the sample on a wet mount with no cover slip. Next, very careful not to burn/ kill the bacteria, we waved the wet mount three times over the flame to evaporate the water with the bacterial side up. Next were a series of strains. First, we covered the smear with crystal violet for 1 minute and rinsed the stain after that time with water. We did this same process but with Gram's iodine next. Following this, to decolorize, for 10-20 seconds we rinsed the smear with 95% alcohol until the mixture flowing off stopped giving off color. Afterwards, we covered the smear with safranin stain for 20-30 second and rinsed it off with water. We blotted the excess water with a kimwipe and allowed the smear to air dry. We looked at a gram on a low magnification without a coverslip. We observed only at 40X although the directions wanted to view the smear under 100X as well. But, we realized that in order to use the 100X we needed oil, but we couldn't use a cover slip on the gram stain, and putting the oil directly on the gram would have hurt our progress.

Below are the charts and examinations of what we saw with our eyes and well as under the microscope during our wet mount slides and gram stain slides.

100-Fold Serial Dilutions Results

Bacteria Characterization Chart

Agar Plates Image This image shows the complete set of agar plates and depicts the reason why we chose to use the four that we chose to work with as well as the descriptions chosen.

Possible Bacteria Under 100X This image is the best view we could get of anything significant at 100X with no gram stain.

10^-2 No Tet Image This image is the agar plate that was 10^2 with no tet under the less sophisticated microscope that allowed us to get a better look at the colonies.

Before going to Procedure 1, we made a last observation of our Hay Infusion Culture before we threw it out. We noticed first that there was a lot less water in the container. The smell was still the same (sewage smell) and everything settled to the bottom and the top water appeared clearer. We believe that the water was evaporating as it sat there and since the infusion sat for awhile all the organisms and materials inside settled to the bottom the same way that they would in a stagnant pond/swamp. Now, we hypothesize that most of the bacteria are located in the bottom sewage. In comparing the Agar plates we noticed that the plates with the tetracycline as well as the nutrient, compared to just the nutrient plates with the equivalent dilution, had less colonies. The tetracycline killed off whatever bacteria was present without the resistance gene. This indicates that within out culture, there were both resistant and non resistant genes. However, we didn't predict that there would be so many that did in fact have the resistance. I would have thought that there would be less with the resistance because I was under the impression it was a rare thing. We believe that the antibiotic killed off the gram positive bacteria because in our gram evaluation all of them turned out to be negative. It's possible that the tetracycline was only effective on the gram positive bacteria. After looking through the following website: Tetracycline, I found out that tetracycline is effective in killing both gram-positive and gram-negative bacteria by attacking the synthesis of proteins and both positive and negative gram bacteria have developed a resistance. This leads to be believe that possibly somewhere in our agar plate there could be gram-positive bacteria that we just didn't take a sample of or it's a coincidence that we ended up just finding gram-negatives in each agar plate.

The lab at hand fails to report the drawings of the specific bacteria found and its type of motility. This is one failure of the structure of the lab. The whole lab class had a very difficult time trying to locate the small bacteria to a close enough extent to examine it and report its details. The best we could do as a group, is make sure we understood the concept behind what we were trying to do and its importance even though the microscope analyzation of the bacteria proved to be unachievable.


January 27, 2015

This lab was designed to examine the traits of algae and protists, specifically unidentified ones from our transect. This was a good opportunity to introduce and become familiar with the dichotomous key to identify unknown organisms. My group members and I predicted that after taking samples from both the bottom of the transect jar and the top, then we would be able to find a larger abundance and more variety of organisms on the top of the transect. Our hypothesis was that the organisms would be closer to the top for oxygen and easier survival.


Transect/Samples- two slides/ two cover slips- dichotomous key- notebook


After taking a sample from the bottom and the top, we closely examined the living organisms in each. To identify a chosen organism, we followed the steps of the dichotomous key. The dichotomous key functions by a series of questions labeling the characteristics of the organism. Eventually, the questions lead you to an answer and hopefully the correct one. To check the answers, we referred to the pictures on the back and compared it to the organism in the microscope and then properly measured them in um.

Transect Organisms Image

Upon retrieving the transect and being sure not to disturb anything inside, we noticed a sewer-like smell and muggy, dirty, and swamp like features. There was a stagnant thin layer on the top of the transect similar to a out in nature swamp with no water movement. The organisms we found in Niche 1 and Niche 2 were very similar. For example, we found different kinds of paramecium in the top niche and the bottom niche, but they were all mostly paramecium. The paramecium were motile, protists, and don't use photosynthesis but eat algae. However, we did find the Blepharisma in the bottom niche. After doing some research I found that they are 'photophobic', meaning they try to stay away from light, which makes sense because we found them in the bottom niche where there was more mud, leaves, sticks and various things that packed together to form a darker area. Also, the Colpidum was found in both niches. Colpidium are protozoa usually found in moist soil- explaining why we had the appearance of them in both niches.

If the transect were to sit longer and given more dry milk, I believe that no new organisms would arise just an over abundance of the ones already there would occur. Although our lab lacked variation, we still learned how to properly use a microscope to track organisms as well as properly identify them with a dichotomous key. One probable cause of the the scarce types of organisms could be the temperature/time of the year we took the transect samples from. It's possible the cold weather hinders the existence/ flourishing of the other organisms. Also, the fact that our transect had no ponds, lakes streams or any consistent water source within the environment, could also be a contributing factor.


January 25, 2015

This lab was developed in order to take a closer look at a local ecosystem within AU's campus grounds. By looking closer at our assigned transect, we will later be able to examine different life forms whether it be a species or a specific population. To fully understand an ecosystem, we also needed to take note of any biotic or abioitic factors within the transect environment; for all of these factors have an important interplay of importance. We expect that many different types of organisms are present within out transect and we chose specific sample locations to get the best results. If we take samples of Area 2, then we will find a multitude of different organisms.

Materials: - notebook - sterile 50 mL conical tube -10-12 grams of a transect sample - 500 mL of Deerpark water - .1 gm of dried milk

Methods: To begin, we took note of and analyzed Area 2 to get a better understanding of our designated location, for example: abiotic, biotic, trees, shrubbery and ground. After doing so, we developed a detailed map labeling a birds eye view and topography of the area. After we chose two locations to take samples from to put in the 50 mL conical tube, we labeled the location of each on the map. Once the sample was brought back to the lab room, we took 10-12 grams of the transect and mixed it with 500 mL of Deerpark water and also mixed .1 gm of dried milk for 10 seconds. The jar in which all of these were mixed was then set aside for farther use for the following week.

Transect Map Area 2

After the lab, we took away that even 20 by 20 ft area can be very dynamic and has an interesting set up, even on a scale the naked eye cannot see. We predict that when we take a closer look under the microscope, our sample will have many different types of organisms present and living together.


January 20, 2015

This website is already confusing.