User:Devki Gami/Notebook/Biology 210 at AU

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3/19/14 BIO-210

Lab 6: Embryology and Zebrafish Development

Question: How does placing zebrafish in complete, continuous darkness affect their development?

Hypothesis: Zebrafish placed in complete, continuous darkness will develop slower than zebrafish placed under normal light conditions(control).


Two petri dishes were filled with 20 mL of water in each. 20 undamaged zebrafish eggs were placed in each dish. One dish was put in a drawer to implement the dark treatment. One dish was left on the lab table to serve as the control. Zebrafish observations were made on days 4, 7, 12, and 14. One zebrafish from the dark treatment and one zebrafish from the control were put into depression slides and observed under a microscope using 40X objective. Qualities that were observed included the number of zebrafish unhatched, hatched, alive, and dead, movement, yolk sac size, eye movement, pigmentation, heart rate, development of the swim bladder, and development of the pectoral fins. Each observation day, dead zebrafish and empty egg cases were removed and more water was added to the dish. On Day 7, three zebrafish from the control and three zebrafish from the dark treatment were fixed using tricaine solution and paraformaldehyde.


Table 1: Zebrafish Observations


This table shows the observations made on days 4, 7, 12, and 14 of the zebrafish development for the dark treatment and control.


Based on the observations seen in Table 1, the initial data supported the hypothesis that the zebrafish in the dark treatment will develop slower than the zebrafish in the control. Overall, the zebrafish in the dark treatment hatched slower and were much less active than the control zebrafish. When the fixed samples were examined, the dark treatment zebrafish was one ocular space smaller than the control zebrafish. However, the larger lesson learned is that once the yolk sac of the zebrafish is absorbed any time after day 7 of development, additional food is necessary to keep the zebrafish alive. Because the zebrafish were not fed on time, all except 1 from the control died. However, 13 of the zebrafish in the dark treatment survived. It is proposed that because the zebrafish in the dark were developing slower, they still had their yolk sacs, whereas the zebrafish in the control that were developing at a normal rate did not have their yolk sacs anymore. In the future, this experiment could be conducted again with the zebrafish being fed on time to get results where the dark treatment was the only variable affecting the zebrafish development.

2/23/14: BIO-210 Lab 5

Procedure 1: Observing Acoelomates, Pseudocoelomates, and Coelomates

Objective: Observe and describe the movements of Acoelomates, Pseudocoelomates, and Coelomates.

Acoelomates: Planaria


Movement: gliding

Pseudocoelomates: Nematoda


Movement: whip-like

Coelomates: Annelida


Movement: moves different parts of body at different times

Procedure 2: Analyzing the Invertebrates Collected with the Berlese Funnel

Objective: Observe the invertebrates from the transect collected with the Berlese Funnel and identify them.

Table 1: Invertebrates Collected from Transect


All of the organisms we measured were less than a mm. Arthropods are supposed to be most common in leaf litter.

Procedure 3: Vertebrates and Niches

Objective: Identify five vertebrates that might inhabit the transect and create a culminating food web.

Species 1: Spizella arborea (Spizella arborea)

Common name: American Tree Sparrow

Phylum: Chordata

Class: Aves

Order: Passireformes

Family: Emberizidae

Genus: Spizella

Biotic factors that the American tree sparrow will eat include the invertebrates and seeds found in the transect (Spizella arborea).

Species 2: Setophaga pinus (Dendroica pinus)

Common name: Pine Warbler

Phylum: Chordata

Class: Aves

Order: Passireformes

Family: Parulidae

Genus: Setophaga

Biotic factors that the pine warbler will consume include the invertebrates found in the transect. The pine warbler will also look for food on the pine tree (Dendroica pinus).

Species 3: Sciurus carolinensis (Sciurus carolinensis)

Common name: Eastern Gray Squirrel

Phylum: Chordata

Class: Mammalia

Order: Rodentia

Family: Sciuridae

Genus: Sciurus

Biotic factors that the eastern gray squirrel may use to build nests in include the sycamore and holly trees (Animal Diversity Web). The pine tree can provide food for the gray squirrel (Animal Diversity Web).

Species 4: Peromyscus maniculatus (Peromyscus maniculatus)

Common name: North American Deer Mouse

Phylum: Chordata

Class: Mammalia

Order: Rodentia

Family: Cricetidae

Genus: Peromyscus

Biotic factors that the deer mouse can use for food include weeds, seeds, and bark, and the vine groundcover and fallen sticks and branches can be used for shelter (Deer Mouse (Peromyscus maniculatus)).

Species 5: Canis familiaris (GAWW: Classification of Animals)

Common name: Dog

Phylum: Chordata

Class: Mammalia

Order: Carnivore

Family: Canidae

Genus: Canis

Dog feces has been seen near the transect so biotic factors that the dog may enjoy include the pine, sycamore, and holly trees, and the vine coverage on the ground.


Animal Diversity Web. (n.d.). ADW: Sciurus Carolinensis: INFORMATION. Retrieved February 23, 2014, from

Deer Mouse (Peromyscus maniculatus). (n.d.). Deer Mouse (Peromyscus Maniculatus). Retrieved February 23, 2014, from

Dendroica pinus. (n.d.). Encyclopedia of Life. Retrieved February 23, 2014, from

GAWW: Classification of Animals. (n.d.). GAWW: Classification of Animals. Retrieved February 23, 2014, from

Peromyscus maniculatus. (n.d.). (Deer Mouse, North American Deermouse). Retrieved February 23, 2014, from

Sciurus carolinensis. (n.d.). (Eastern Gray Squirrel, Gray Squirrel, Grey Squirrel). Retrieved February 23, 2014, from

Spizella arborea. (n.d.). Encyclopedia of Life. Retrieved February 23, 2014, from

Food Web


2/23/14: BIO-210 Lab 4

Procedure 1: Collecting five plant samples from the transect

Objective: Collect and identify five plant samples from the transect. Collect a leaf litter sample from transect to be used for Berlese funnel.

See Table 1 for data.

Procedure 2: Plant Vascularization

Objective: Determine the vascularization of each plant sample collected from the transect.

See Table 1 for data.

Procedure 3: Plant Specialization

Objective: Determine the shape, size, and cluster arrangement of the leaves from the transect plants.

See Table 1 for data.

Procedure 4: Plant Reproduction

Objective: Identify the seeds brought back from the transect as monocot or dicot. Determine if there is any evidence of flowers or spores.

See Table 1 for data.

Pictures and Data

Pineconee.jpg Sample 1

Pineneedless.jpg Sample 2

Bigleavess.jpg Sample 3

Smallleavess.jpg Sample 4

Mediumsizedstick.jpg Sample 5

Table 1: Transect Plants (#1-5)


Procedure 5: Observing Fungi

Objective: Observe Rhizopus stolonifer under a microscope.

Rhizopus.jpg Rhizopus stolonifer

Sporangia are black, almost spherical structures that are formed by hyphae filaments of the fungus. Sporangia are important because they contain fungal spores.

Procedure 6: Setting up the Berlese Funnel to Collect Invertebrates

Objective: Use the leaf litter sample acquired from the transect to set up a Berlese funnel to collect invertebrates for next lab.

The funnel, light, and flask were set up as seen in the diagram below. The leaf litter sample was placed inside the funnel and covered with foil.


Conclusions: Five plant samples were collected and identified from the transect. Rhizopus stolonifer was observed under a microscope. The leaf litter samples was used to set up a Berlese funnel. Next week, we will identify the invertebrates collected from the Berlese funnel.

2/15/14: BIO-210 Lab 3

Procedure 1: Quantifying and Observing Microorganisms

Objective: Observe the bacteria growing on the agar plates from the hay infusion culture last week.

Seven plates were observed and colonies were counted for each one. Three of the plates had tetracycline.

Table 1: 100-fold Serial Dilutions Results


Procedure 2: Antibiotic Resistance

Objective: Compare the bacterial growth on the agar plates with tetracycline to bacterial growth on the agar plates without tetracycline.


As seen in Table 1 above, the plates with the tetracycline have less bacteria colonies than the plates with equivalent dilution that do not have tetracycline. This indicates that some of the bacteria that grew on the normal agar plates are not resistant to tetracycline, although the bacteria that did grow on the tetracycline plates are resistant or insensitive to the tetracycline. The effect of tetracycline on the total number of bacteria is to decrease the total number of bacteria. The effect of tetracycline on the total number of fungi is to prevent any fungi from growing. Based on the appearance of the bacteria growing in the tetracycline plates, one species in particular from the hay infusion culture is unaffected by tetracycline.

Klajn, R. (n.d.). Tetracycline - Antimicrobial properties. Tetracycline - Antimicrobial Properties. Retrieved February 16, 2014, from

According to Klajn, tetracycline stops bacteria from making proteins by connecting to its 30S ribosome, which halts the entire process of protein synthesis. According to Klajn, tetracycline can also affect the bacteria's cytoplasmic membrane and lead to a loss of nucleotides. According to Klajn, both gram positive and gram negative bacteria can be sensitive to tetracycline, including richettsia, spirochetes, and more specifically, Escherichia coli and Haemophilus influenzae.

Procedure 3: Bacteria Cell Morphology Observations

Objective: Observe slides of bacteria selected from three different colonies on three different agar plates under a microscope. Gram stain each bacteria sample selected to determine whether the bacteria is gram negative or gram positive.

Bacterial slides were prepared and viewed using the 100x oil immersion objective lens. Bacterial slides were gram stained and observed under a microscope.

Table 2: Bacteria Observations


Procedure 4: Start PCR Preparation for DNA Sequence Identification

The DNA from the selected bacteria was prepared for PCR next week by amplification of the 16S rRNA gene. This gene varies significantly between species of bacteria and will help identify the colonies.

Conclusions: Different colonies of bacteria were observed from the agar plates, with the tetracycline plates having less bacterial growth on them due to antibiotic sensitivity. Bacteria from specific colonies on three plates, specified in Table 2 in Procedure 3 above, were observed under a microscope and gram-stained to determine that the plates contained gram-negative bacteria. The bacterial samples with the amplified 16S rRNA gene will be run through PCR next week to help further identify them.

2/9/14: BIO-210 Lab 2

Procedure 2: Hay Infusion Culture Observations

Objective: Observe the hay infusion culture made last week using plant and dirt samples from the transect.

General observations: The hay infusion culture has a strong, pungent, and unpleasant smell. The dirt has settled to the bottom of the jar and some of it has acquired a gooey texture. There is a filmy layer on the top of the liquid and the plant matter has begun breaking down.

Samples were taken from the dirt matter near the bottom of the jar and plant matter near the top of the jar. The organisms near each sample will differ because plants and dirt form different niches. Slides were prepared from the dirt sample and plant sample and observed under a microscope.

Table 1: Dirt and Plant Slide Observations and Measurements


The only organism identified was Chlamydomonas, which is a type of green algae. It is single-celled, acquires energy through photosynthesis, and processes information using DNA. If the hay infusion culture were to be observed for the next two months, I would expect more decomposition to occur, especially in the plant matter. I would expect the smell to get stronger and for some organisms to die as they run out of nutrients from the dried milk in the infusion culture and for some organisms to thrive in the decomposition. As far as the selective pressures in the hay infusion culture go, the organisms that could best utilize the dried milk for nutrients were more likely to survive, as well as organisms that thrive in an aqueous environment and in the plant and dirt matter.

Procedure 3: Preparing and Plating Serial Dilutions

Objective: To make serial dilutions of the hay culture infusion to grow bacteria to observe next week.

100-fold serial dilutions of the hay infusion culture were prepared and plated on 8 agar petri dishes. Four of the dishes had the antibiotic tetracycline in addition to the agar.

Figure 1: Serial Dilutions


Both objectives for procedures 2 and 3 were met. 6 organisms were observed and measured from the plant and dirt samples of the hay infusion culture. 8 agar plates were prepared and inoculated with serial dilutions of the hay infusion culture so that bacteria growth can occur. Next week, the plates will be observed to see which bacteria grew on the plates and if any are resistant to tetracycline.

1/31/14:BIO-210 Lab 1

Procedure 1: The Volvocine Line

Objective: Observe the Volvocine Line under a microscope to view the differences in evolutionary complexity between samples of green algae.

Chlamydomonas, Gonium, and Volvox slides were prepared.

Table 1: Evolutionary Specialization of Members of the Volvocine Line Volvocinetable.png

Procedure 2: Defining a Niche at AU

Objective: Describe and diagram the transect. Collect soil and plant sample from transect to make a hay infusion culture.

Location: Seminary (off-campus)

Topography: From an aerial view, the land slopes downward and has two types of vines covering the ground. The front half of the transect is covered in ivy-like vine leaves while the back half is covered in vines that have rounder leaves. Many of the vines in the back are brown and dead. There are three trees in the transect: a holly tree in the bottom left corner, a pine tree in the bottom right corner, and a sycamore tree in the back towards the right.

Abiotic factors: tennis ball, bench, bag of dog poop, flag marker, aluminum foil

Biotic factors: pine tree, sycamore tree, holly tree, grass, vines

Hollyy.jpg Holly Tree (tree pictured in the front)

Sycamore.jpg Sycamore tree

Pine.jpg Pine tree

Sample.jpg Transect area where sample was taken from

A sample of soil and plant was taken from the transect. 11.65 grams of the sample was placed in a plastic jar with 500 mL of water and 0.1 grams of dried milk to make a hay infusion culture. The culture will be examined for protists in the following lab.

Excellent start. Good description and analysis of work undertaken. Plenty of detail and nice images. SK