User:Maria Belding/Notebook/Biology 210 at AU

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1/19/15

My computer skills are on par with the average octogenarian, so I'm very proud of myself for getting this to work in only three tries.

MRB


1/26/14 Our Pet Rock

Purpose: The purpose of this second lab was to map out and explore a tract of land for biotic and abiotic features.

Hypothesis/Prediction: This semi-man made small land parcel will contain both biotic and abiotic features.

Materials and Methods:

Data:

Abiotic Features: 1.Large rock. 2.Bench 3.Snow 4.Water 5.Sign

Biotic 1.Moss 2.Dirt 3.Leaves 4.Trees 5.Shrubs

Conclusions:

MRB (to be continued)

  • 1/29/2014

Jar of Hearts (Breaking)*

Purpose: The purpose of today's lab is to further explore the microbiology of our land tract and the ecological life within. We are doing so by sampling cultures from our Hay Infusion.

Hypothesis/Prediction: We will observe more species diversity at the top of our infusion than at the bottom, as the top has more exposure to oxygen, allowing more non-aquatic species to survive or grow.

Materials and Methods: After utilizing a dichotomous key to learn to identify specific and known organisms under a microscope with control slides, we repeated the process using our own Hay Infusion culture. We drew one sample from the surface and a second from the bottom of our jar to ensure as much differentiation as possible. We then put these samples onto slides and observed with the same dichotomous key.

Data and Observations:

Top Sample: 1. Coalpidium sp. 16 um

           2. Paramecium 50 um 

Bottom Sample: 1. "Coalpidium" 100 um

              2. "Paramecium bursaria" 75 um 

Conclusions: We were supposed to find a total of six different species for this lab, three from each site. We found two each at the top and bottom - and they were the same species, although of varying sizes. Why would we have such homogeneous results from such different sample locations? One possible explanation could be how we took the initial sample that became our Hay Infusion. We included dirt, moss, leaves, grass and a little rock, all of which we found in one particular spot in our tract measuring less than six square inches. The life contained may have been diverse to the eye, but perhaps the bacterial life within wasn't.

2/5/2015

The Long and Winding Lab: Identifying Bacteria Through DNA

Purpose and Hypothesis: The purpose of this lab was to investigate the bacteria sourced from our Hay infusion and identify them by their DNA. Hypotheses/Predictions: Hay Lab: The Hay Infusion smell is more rancid than in weeks past as the overall volume depletes from evaporation and more organisms share a smaller space as they necrosis. Antibiotic Resistance: Due to antibiotic overuse, we will see little difference between the Tet-treated and non-Tet-treated plates.

Methods and Materials: We examined our Hay Infusion culture and after taking notes on changes in appearance and smell, dumped it down the drain. We then returned to our plates from last week and observed the number of colonies and lawns on each plate. (See results below.) Next, we attempted to make a wet mount and then a gram stain of our four plates, tasks we’re still not entirely sure we did correctly, and tried to observe them. Finally, to round out the lab, we began PCR reactions to pick up for our next class session.

Data and Observations:


Dilution Agar Type Colonies Counted Colonies/mL 10^-3 Nutrient 100+ (lawn) (lawn) 10^-5 Nutrient 60 60 x10^5 10^-7 Nutrient 2 2 x 10^7 10^-9 Nutrient 0 0 10^-3 Nutrient/Tet Lawn (lawn) 10^-5 Nutrient/Tet 45 45 x 10^5 10^-7 Nutrient/Tet 1 1 x 10^7 10^-9 Nutrient/Tet 0 0

Colony Label Plate Type Colony Description Gram Positive or Negative Additional Notes A 10^-2 w/Tet Lobate edge; smooth; gusting rhiziod colony Gram Negative .1-.4 cm individual colony with lawn B 10^-2 Irregular undulate; rasied; smooth; shiny Gram Negative .3 cm C 10^-4 w/Tet Circular colony; entire edge smooth; gustening pulvinate Gram Negative .5 cm D 10^-4 Circular colony; entire edge smooth; gustening pulvinate Gram Negative 8.5 cm (across entire plate)

Observations: Our hypothesis regarding Tet and its growth was correct. We saw almost no difference between the Tet-treated and Tet-free plates, underlying the severity of antibiotic resistance among these particular pathogens. In other words, tetracycline would appear to be useless or nearly-useless in fighting this bacteria, raising questions about antibiotic overuse and the development of “super bugs”.

Conclusions: Tetracycline had almost no effect on our bacterial growth. Why? Tetracycline works by stopping protein synthesis, interfering with tRNA and ribosomal activity to prevent growth (Chopra & Roberts, 2001). Since many bacteria operate in this way and are fatally affected by such an interruption in their grow, tetracycline is considered a broad-spectrum antibiotic, as it can kill many different kinds of both gram-negative and gram-positive bacteria, or at least it used to be able to. Rampant overuse has allowed millions of generations of bacteria to adapt and evolve around our medical interventions for infection, leaving us with harder-to-treat disease. This antibiotic resistance represents one of 21st-century medicine’s greatest challenges.

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. doi:10.1128/MMBR.65.2.232-260.2001


MRB


2/12/2012 The Fungi Files

Purpose/Hypothesis: The purpose of this lab is to understand the characteristics and diversity of plants along with the importance of fungi and plants.

                   We believe that we will find few variations of fungi from our transect. 

Materials and Methods: We returned to our tract with sample collection bags, gloves and a cell phone with a good camera to capture images of where we collected each sample. We then returned to lab and attempted to identify these samples.

Results:

Sample #1: (obtained 24 inches from central tree) Angiosperm. 2-4 in spear-shaped leaves with net-like veins. Vascularized via xylem. Contains specialized structures cuticles and stomata. Reproductive mechanism: dichot.

Sample #2: (obtained directly below central tree) Lycophyta. 2cm spear-shaped leaves with net-like viens and toothed edges. Vascularized via xylem. Contains specialized structure stomata. Reproductive mechanism: dicot.

Sample #3: (obtained on edge of 5th stone from sidewalk in walking path) Around 5cm spear-shaped leaf with net-like veins and smooth edges. Vascularized via xylem. Contains specialized structures cuticle and stomata. Vascularized via dicot. Reproductive mechanism: dicot.

Sample #4: (obtained near back right leg of bench) Bryphyta. 12 inch wide and circular. Vascularized via xylem. Specialized structures include rhiziods. Reproductive mechanism: haploid.

Sample #5: (obtained twelve inches north of tree directly in front of sidewalk) Angiosperm. No leaves; contains berries, branch of 1-2 cm circumference. Vascularized via xylem. Mechanism of reproduction: xylem.

(See Taylor's lab notebook for images. Not sure if OpenWetWare will allow upload of the same document even if worked on by both authors. For safety's sake I have written out each above.)

This lab allowed to understand the specifics of our transect and begin to identify the scientific names of some of the plants in our area. (Ironically, our group struggled with this until we found a children's website with diagrams that allowed us to more successfully identify our organisms.) This information should prove helpful as we move into writing our full lab report.

2/19/15 Get Out of My Dorm (And Into Our Transect

In visiting our transect over the past several weeks, we have observed a number of vertebrae wandering, flying or hopping in and out of our designated study area. For the purposes of this report, we elected to describe the species we believed we could most accurately describe and classify: a black squirrel, a brown squirrel, a brown bird, a dark gray bird and a mouse.

We know that mice live in this area, as I have had the distinct pleasure of seeing several of these creatures about twenty feet left and thirty feet up from our transect inside my dorm room. Mice love people and their food almost as much as we hate them, so for this animal to be residing in a place nearly overrun by a particular breed of human not known for their neatness while eating makes sense. Furthermore, the grass to hide in in combination with the water and natural food sources make our transect a smart place to live for our rodents. (If only we could get the ones currently living in Hughes to follow suit.) We believe this is a Common House Mouse, or Mus musculus from the rodentia order, mammalia class and chordata phylum (Animal Corner).

Research into our two different squirrels revealed that they’re not different after all. Although they represent different phenotypes, both of these nut-hunters are Eastern Gray squirrels, or s. carolinensis (genus scurius, order rodentia, class mammalia, phylum chordata). According to an information page developed by biology students in Fairfax County, Virginia (relatively close to where we are), these animals tend to build nests out of the same materials found in our transect and eat apples, seeds, bird eggs, bark and occasionally each other (Fairfax County Public Schools). Our transect has almost all of these, so making our location a home is a logical choice for this species.

We had less success with our birds. We only saw them fly by, so we had very little to go on in terms of observed characteristics. What we did remember - some colors - in addition to our location yielded one viable creature - the Brown Creeper. (species c. americana, certhia genus, passeriformes order, aves class, Chordata phylum). The Brown Creeper both lives in and migrates to Maryland this time of year, so their presence in our transect makes sense. We can’t reconcile all of the given traits - our transect doesn’t have trees big enough to support the creature, for example - but we’ve hypothesized that the birds may drop in for a bite of bark before heading off to a more permanent home more equipped for their survival needs.


“Brown Creeper” 2015. DC Birds. Smithsonian Museum of Natural History. <http://dcbirds.si.edu/bird/brown-creeper>

“Eastern Gray Squirrels” 2015. Fairfax County Public Schools. <http://www.fcps.edu/islandcreekes/ecology/eastern_gray_squirrel.htm>


“Mouse Species” 2003. Animal Corner. <http://www.animalcorner.co.uk/pets/mice/mice_species.html>

2/19/2015 Little Miss Muffets

Purpose: Appreciate and understand the key role invertebrates play in our transect.

Hypothesis: Given the massive size of our funnel and diversity of other kinds of life we’ve found, we believe we will find at least three separate invertebrate species.

Materials: Funnel, lab tape, collection sample, microscope, dissection microscope, slides Method: We examined our sample under the dissecting and traditional microscopes until we located invertebrates. We then used a dichotomous key to determine the exact creatures we had found.

Results: We found Planaria (identified by its gliding and folding movements in combination with its flat body), Annelida (characterized by its circular body and almost spastic movements), and planaria.

Conclusion: Invertebrates play a role in our environment, but either our sample didn’t do it justice or we overestimate the significance of said role. I still don’t feel like we’ve made the connection between these creatures and rest of the environment, but perhaps further research and writing as we develop our final lab report will illuminate our issues.

MRB

3/19/15 A Fish Too Far

Good news: our Zebrafish experiment is done. Bad news: they all died. Worse news: We still don't know why.

A few of the deaths can be blamed on operator error - I killed a few in transport, and Taylor was tripped and lost a few too. The other fish, however, we still can't account for. Our ehisterone treated fish definitely died before the controls, and there were clear differences between the groups. However, we can't answer our original question: does ehisterone cause a significant difference in the development and behavior of zebrafish embryos? Since our fish died before we could get an accurate picture of their developmental and behavioral characteristics, we're going to need to go back and rethink our experiment. More research and outside information may help us develop a better plan, but until then, we don't have much to go on.

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