User:Julia C. MacDougall/Notebook/Biology 210 at AU

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Lab 6, "Embryology and Zebrafish Development," was performed on February 19th, 2014.

Introduction: This lab taught students the stages of embryonic development, pushing them to compare the development of different organisms.

Animals that reproduce sexually begin as a zygote which then develops through growth, differentiation, and morphogenesis. For most animals, the beginning stages of development are similar, and differences emerge later in development. Fertilized eggs can have their yolks distributed in different ways, such as isolecithal (evenly throughout the cytoplasm) or telolecithal (development takes place off center). The cells will then either divide holoblastically (distinct, separate cells), or meroblastically (uneven masses of yolk and cells). Organisms that lay eggs are oviparous, and organisms that feed directly from a placenta are viviparous. Development takes place in three main stages: fertilization, cleavage, and gastrulation.

Table 1: Comparison of Embryological Features of a Developing Sea Star, Frog, and Chick ComparisonJCM.png

Table 2: Comparison of Ecological Aspects in Starfish, Frogs, and Chick Development EcologicalComparisonJCM.png

Conclusion: From this lab, it is obvious that animal share many traits during development, but also differ depending on the organism.

Lab 5, "Invertebrates," was performed on February 12th, 2014.

Introduction: Lab 5's intents were to understand the importance of invertebrates and to learn how simple systems evolved into more complex systems. Invertebrates are a very diverse group, including Porifera, Cnidaria, and Ctenophora. Invertebrates can either have radial symmetry, meaning they will be symmetrical no matter how you cut them in half, or bilateral symmetry, meaning they can only be cut one way to generate two symmetrical parts. Cnidaria and Ctenophora only have ectoderm and endoderm germ layers, while bilaterally symmetric invertebrates also have a mesoderm. When developing, the ectoderm forms the skin, the mesoderm forms the muscle, and the endoderm forms the gut.

Many organisms have a coelom, or fluid-filled cavity; they are called coelomates. Organisms without a coelom are called acoelomates, while organisms that have incompletely lined body cavities are called pseudocoelomates. Many arthropods live in an on soil, so it is expected that they will be discovered in the soil samples from the transect.

Materials and Methods: Observe Planaria, nematodes, and Annelida, and their types of movement. Then, disassemble the Berlese funnel and try to identify the invertebrates. Then, try to predict what types of vertebrates might be in the transect.

Data and Results: Planaria (acoelomates) glide through the water, using their cilia. Nematodes (pseudocoleomates) have muscles throughout their body which contract and release, allowing them to move. The Annelida (coeolomates) move by pulling themselves forward, contracting their midsections with coeloms while also using their other muscles.

Image 1: Planaria Cross Section PlanariaJCM.jpg

Image 2: Nematodes NematodesJCM.jpg

Image 3: Annelida AnnedlidaJCM.jpg

Table 1: Identifications of Organisms

Kind of Organism Length in mm Brief Description of Organism
Arthropoda 10 ocular spaces at 30X orange, 4 legs, bigger body and smaller head
Arthropoda 50 ocular spaces at 30X spider-like, clear, 6 legs
Arthropoda 15 ocular spaces at 30X clear, many legs, large central body with small head. The specimen was somewhat crushed so not completely obvious
Arthropoda 255 mm long, thin bilateral body, yellow/brown color, many legs
Arthropoda 200 mm wings, 6 legs, 2 antennae, body 3 times size of head

The largest organism measured was 255 mm long, and it was a brown beetle. The shortest organism was only 10 ocular spaces long at 30X, and it was a soil mate. Arthropods are abundant in the transect.

Table 2: Possible Organisms that Could Be in Transect PossibleOrganismsJCM.png

Image 4: Possible Food Web for Transect #3 PossibleFoodWebJCM.png

Lab 4, "Plantae and Fungi," was performed on February 5th, 2014.

Introduction: The two main objectives of Lab 4 were to understand the characteristics and diversity of Plants and to appreciate the function and importance of Fungi. The plants and the fungi are both very diverse groups. The major groups of plants include non-vascular plants (including bryophytes), seedless plants, gymnosperm seed plants, and angiosperm seed plants. In this lab, samples will be examined in terms of vascularization, specialized structures, and reproduction.

As far as vascularization goes, most bryophytes have rhizoids to anchor them to the ground, allowing them to grow securely. Angiosperms, on the other hand, have stems which allow them to obtain water and nutrients through the xylem and phloem layers.

Plants will become more specialized as they get more complex. Among different plants, leaves will be different. All leaves have a waxy layer, the cuticle, protecting them and preventing water from exiting the plant. Stomata and guard cells also play a role in maintaining water levels.

Plants can be either gametophyte (haploid) or sporophyte (diploid); land plants can switch back and forth between these stages, exhibiting what is called the alternation of generations. Angiosperms are heterosporous; they have microspores containing megaspores, anthers producing and containing pollen, stigmas, and styles. Flower ovaries contain the ovaries. Cotyledons provide nutrients in an embryo; they can be monocot, having only a single cotyledon, or dicot, having two cotyledons.

Fungi are decomposers that retrieve their nutrients by absorbing nonliving organic matter or by feeding on living organic matter. There are three major groups of fungi, the Zygomycota, the Ascomycota, and the Basidiomycota. Fungi consist of masses of hyphae, organized into a mycelium, and small sporangia, which contain spores.

Materials and Methods: Three bags of leaf litter and soil were taken from the transect, as well as seeds, leaves, and flowers. Where these were found was noted. The major groups and, if possible, genera were identified using resources. Mosses and angiosperms were compared and examined to learn more about plant specialization, giving particular attention to the stomata and cuticle, as well as vascularization. A lily was dissected to identify the flower parts, and corn and beans were identified as monocot or dicot. Fungal organisms were examined, identifying hyphae and sporangia. A Berlese funnel was set up to collect invertebrates, putting 25 mL of the ethanol/water solution into a funnel with screening material, leaf litter, and a light, positioned over a funnel to collect the invertebrates.

Data and Results: Most of the leaves found in the transect were in leaf litter because they had already died due to the winter weather. Many of the leaves were slim, green, and pointed, with red berries. Others were larger and more rounded. All of the leaves found were seed plants; some where gymnosperms, while some were angiosperms. It was difficult to determine whether the red berries were monocot or dicot because they were no longer alive.


The plants can be seen in the following images: Sample 1 American Holly I.JPG

Sample 2 Greenleaf.jpg

Sample 3 Yellowleaf.jpg

Sample 4 Brownfungi.jpg

When examined, the corn was found to be monocot, having only one cotyledon, while the bean was a dicot, having two cotyledons.

MonocotCorn.jpg DicotBean.jpg

An example of the black bread mold can be found here: [[1]]

Conclusion: This lab demonstrated the diversity of Plants and Fungi, showing the importance of such organisms in the ecosystem. In the next lab, we will examine the organisms collected from the Berlese Funnels. JM

2/13/14 Lab 3," Microbiology and Identifying Bacteria with DNA," was performed on January 29th, 2014. The intentions of this lab were to understand the characteristics of bacteria, observe antibiotic resistance, and understand how DNA sequences are used to identify species.

Materials and Methods: Examine the agar plate dilutions prepared in Lab 2. Determine how many colonies have grown on each plate. Compare the plates with tetracycline and without it. Examine the bacteria from four plates by preparing wet mounts and then prepare Gram stains for all four. Then select the two best samples and prepare them for PCR to identify the DNA sequences.

Data and Results:

Table 1: 100-fold Dilutions Results Dilution Agar Colonies Counted Conversion Factor Colonies/mL 10e-3 Nutrient Lawn X103 Lawn- 1000s 10e-5 Nutrient 120 X10e5 1.2e7 10e-7 Nutrient 13 X10e7 1.3e8 10e-9 Nutrient 0 X10e9 0 10e-3 Nutrient + tet 400 X10e3 4e5 10e-5 Nutrient + tet 14 X10e5 1.4e6 10e-7 Nutrient + tet 1 X10e7 1e7

There were differences between the plates with tetracycline and those without it. In the tetracycline e-5, the colony was yellow, convex, round, smooth, and shiny. The plates with just nutrients (dilutions e-7 and e-5) were brown, round, flat, smooth, and shiny, and convex, white, undulate, and circular, respectively.

In the tetracycline plate, we were able to identify tiny individual cocci, single bacilli, and diplobacilli, all of which were motile. When gram-stained, both gram-positive and gram-negative bacteria were present. This was somewhat unusual, for gram-negative bacteria are usually easy to kill because of their low levels of peptidoglycan, and tetracycline is supposed to be effective in killing both Gram-positive and Gram-negative cells. Tetracycline prevents bacteria from synthesizing proteins and also can cause the cellular membrane to leak ([2] The least-concentrated tetracycline plate still had 400,000 bacteria, but this was much lower than the complete lawn in the non-tetracycline plate of the same dilution. At least 3 species of bacteria were unaffected by the tetracycline.

When the PCR was run and put through Blast, the bacteria isolated were identified as Uncultured soil bacteria/uncultured gamma proteobacterium and Flectobacillus.

GramStain JCM.jpg This is a depiction of our bacteria once they were Gram stained. The colorless ones were probably colorless and Gram-negative because they were decolorized for too long. JM

2/5/14: Lab 2 Lab 2, performed on January 21st, 2014, was titled "Identifying Algae and Protists." The two purposes of this lab were to understand how to use a dichotomous key and to understand the characteristics of Algae and Protists. We examined various organisms and identified them using the dichotomous key, and we then prepared serial dilutions of our Hay Infusions on nutrient plates.

Materials and Methods: Make a wet mount of the known sample, examine and identify two organisms using the dichotomous key. Then, from the Hay Infusion prepared on 1/13/14, take samples from 2 different niches (we used three) and then observe and identify the organisms living there. Finally, put hundred-fold dilutions of the Hay Infusion into 4 test tubes, which have dilutions of 10e-2, 10e-4, 10e-6, and 10e-8 by taking 100 microliters from the original sample and then innoculate each subsequent tube to prepare the dilutions. Using 4 nutrient agar plates and 3 agar plus tetrcycline plates, plate the dilutions. Label the plates and then directly spread the dilutions onto their respective nutrient agar plates, with the further spreading causing the dilutions to become 10e-3, 10e-5, 10e=7, 10e-9. For the agar+tetracyclin plates, spread the dilutions to make plates that are 10e-3, 10e-5, and 10e-7. Incubate the plates. JCMdilutions.jpg

Data and Results: From our wet mount of the known sample, both Euglena and Paramecium multimicronucleum were identified. EuglenaParamecium.jpg

When the Hay Infusion was examined, it was found to be brown/amber colored, with leaves at the bottom, a film on top, and both brown and white spots throughout. Organisms were taken from the top of the water, the middle of the water, and from the bottom near the leaves. This was due to the fact that different organisms could be found near the leaves because there would be different nutrients contained within the leaves. Six mobile protozoa were identified: Peranema sp. and Colpidium from the middle, Colpidium and Paramecium Aurelia from the bottom, and Paramecium Bursaria and Peranema sp. from the top. There was also one nonmotile organism found in the middle that could not be identified. HayInfusionSamples.jpg

The needs of life outlined by Freeman are capacity for growth, reproduction, functional activity, and continual change preceding death. Paramecium will reproduce asexually, resulting in more paramecium, if there are adequate nutrients and space. Paramecium moves using cilia, and can avoid any stimuli that it wants to avoid, making it functional. These features also allow it to constantly change.

If the hay infusion were to be observed for two more months, I would expect the infusion to get even cloudier and grow more mold. If there were any antibiotics in the soil, the antibiotics would have acted as a selective pressure in the sample. JM

1/28/14 : Lab 1 Transect Inspection Introduction: The lab performed on 1/15/14 was titled "Biological Life at AU." The purposes of this lab were to understand natural selection and to understand the biotic and abiotic characteristics of a niche. We examined our assigned niches, making observations, and then observed samples of green algae, looking at how the Volvicine Line has changed over time.

Materials and Methods: Draw a map of niche, noting topographical features as well as other defining features. Note the biotic and abiotic features (5 each). Think about what animals could possibly live there, even if they are not visible. JM Continued, 1/30/14

Data: The transect, transect #3 ("tall bushes") is located near the American University amphitheater. This transect consists of both concrete sidewalks and soiled areas. Map of transect: Transect3 map jcm.jpgFive abiotic factors that were identified were pebbles, concrete, 2 lamp posts, cigarette butts, and mulch (note: originally listed mulch as abiotic, but now realize that it is really biotic but dead). There were many biotic factors including mid-sized trees, low bushes, ivy bushes and berries, weeds, and grass. Upon a second visit to the transect, birds were also found in the trees. Other possible animals include insects and rodents. Views of the transect: Transect3 snow1 jcm.jpg , Transect3 snow2 jcm.jpg JM

Good start and nice images. Could be improved by including some more text describing the important part of the lab and describing the observation of the volvocine line and including discussion of the questions and points made in red in the handbook. SK

1/23/14 Test -JM