Dissection 5: Earthworm

Background Information:

Specimen:
Lumbricus terrestris (Earthworm)

Habitat:
Earthworms usually live in mud around freshwater, or under to soil on land. They require moist soil in order to  thrive. Usually earthworms live within the top meter of soil, and spend most of their time just below the surface. This is an ideal area for earthworms because the soil is damp and there is plenty of food.

Food:
Earthworms feed on decomposing plant material. Living near the surface of the soil is ideal for them because there are plenty of dead plants for them to eat. This includes, grasses, leaves, and even dying roots.

Respiration:
Unlike most animals, earthworms don't have any lungs. To breathe, absorb oxygen through their skin. Oxygen absorbed through the skin does directly into the worms bloodstream. An earthworm's skin must be moist in order for it to respirate.

Fun Fact:
A worm must always be damp, but it cannot live in water. A worm's skin cannot absorb oxygen from water. This is why after a heavy rain, earthworms must surface. After a storm, the soil becomes so damp that the worms will suffocate if they do not come up to the surface to breathe oxygen from the air.

Dissection 4: Frog

Background Information:

Specimen:
Frog (Amphibia)

Habitat:
Frogs are amphibians, meaning they can live on land as well as in water. They are mainly found in marsh areas, creeks, ponds, swamps, trees, and rain forests. Their habitats must provide enough moisture to keep their skin from drying up, so frogs can only be found in wet areas.

Food:
Frogs are carnivorous predators. They mostly eat insects such as; flies, mosquitoes, moths, and dragonflies. The larger the frog, they larger the size of prey they can hunt. Bigger frogs can consumer grasshoppers and earthworms.

Respiration:
Although frogs breathe air like other land animals, they can also breathe underwater. They do this by absorbing the oxygen present in water through their skin. On land frogs breathe air, but unlike other land animals, they do this with their mouths closed. throat movements help the frog suck in air through their nostrils then into their lungs.

Fun Fact:
As an amphibian, a frog lives both on land and in water. They lay their eggs in water, and hatch as tadpoles. Eventually the tadpole will metamorphoses into an adult frog. It is only then that the frog can live on land.

Dissection 3: Yellow Perch

Background Information:

Specimen:
Perca flavescens (Fish / Yellow Perch)

Habitat:
Yellow Perches are mostly found in fresh water lakes, rivers, and streams. They require habitats with a lot of vegetation, and often live in schools (groups). Perches can live in deeper waters, but are known to reside in shallow waters during the summer months.

Food:
Perches are most actively feeding at dawn and at dusk. Young Perches eat algae and plankton, but once they mature are able to consume larger prey. An adult Perch's diet mostly consists of aquatic insects, crayfish, snails, mussels, and worms.

Respiration:
As with all other fish, the Yellow Perch gets it's oxygen by taking in water through it's mouth and filtering it out through it's gills. As water is carried through the walls of the gills, dissolved oxygen moves into the blood and travels to the fish's cells.

Fun Fact:
A notable feature of the Yellow Perch is it's large, spiny fins. These fins allow the fish to steer through the water without having to roll around. The Yellow Perch is a quick swimmer because of it's powerful fins and streamlined body shape that help it glide through the water.

Dissection 2: Starfish

Background Information:

Specimen:
Stelleroidea (Sea Stars / Starfish)

Habitat:
Starfish are only found in the oceans. They are classified as Echinoderms, which are not found on land or in fresh water at all. Starfish mostly live on the ocean floor or on rocks and reefs that line the bottom of the ocean.

Food:
Starfish are actually predators, often eating mollusks, clams, and oysters. However, their prey must be slow moving in order for them to catch their food. Other starfish eat dying fish and snails.

Respiration:
A starfish breathes through its arms. Each arm contains tubes made of very thin tissue that allow gas to travel throughout the starfish's body easily. These tubes let water in through pores so oxygen can be taken in, then carbon dioxide can be passed out.

Fun Fact:
A starfish's most vulnerable areas are located in the center of its arms, but is usually facing the surface they cling too. Once a starfish has caught it's prey, it uses its arms to break away anything it cannot digest, then pushes its stomach out of it's mouth and eats the soft tissue of its prey.

Dissection 1: Clam

Background Information:

Specimen: 
Mollusca (Clam)

Habitat: 
Different clam species can live in fresh and salt water, meaning they are found in most lakes, rivers, and oceans. Usually clams are found near the shoreline in shallow waters that are muddy or sandy.

Food:
Clams are filter feeders meaning they take in water, and filter out particles of food before expelling the water again. The particles clams ingest are usually smaller organisms such as plankton.

Respiration:
Similar to the way they feed, clams respirate by filtering water through their gills. Water is moved into the gills and throughout the body by cilia. Clams intake very little oxygen, about less than 10% of the oxygen present in water.

Fun Fact:
Clams do not have a head nor limbs, meaning they have none of our major senses. They do not see, hear, or smell anything.

Artificial Selection Lab

Introduction / Purpose:
For this experiment, each lab group in our class was given 3 different kinds of seeds. Our job was to plant and nurture them for an extended time. The end goal of this experiment was to eventually get the plants to reproduce. We would do this by artificially selecting which plants would reproduce together once they had matured. The purpose of this experiment was to demonstrate how artificial selection works, and how offspring can be specifically selected to display certain traits. It also tested how well the students could conduct a long-term experiment.

Procedure:
1. Each group was given a length of wicking core, three pots, and a cup of fertilizer.

2. Cut the wicking core into three sections and put one in each pot. Be sure to pull them through the hole at the bottom of the pot.

3. Fill each pot with fertilizer. Each pot should be roughly three-fourths full.

4. Plant three seeds of the same species in each pot. The species are: "Purple Stem, Hairy", "Non-Purple Stem, Yellow-Green Leaf", and "Non-Purple Stem, Hairless".

5. Place the pots in the tray structure, making sure the wicking core has gone through the plastic sheet and can reach the water below.

6. Water the plants everyday until the plants grow to be adults. If you are leaving the plants for more than one day, be sure to give them more water than normal.

F1 GENERATION:

F1 Day 5

F1 Day 6

F1 Day 8

F1 Day 10

F1 Day 11

F1 Day 14

F1 Day 15

F1 Day 18

7. After about 2 weeks, our F1 Generation plants died and could not reproduce or make new seeds, So we were given "cheat seeds" of what the F2 Generation should have been; "Non-Purple Stem, Yellow-Green Leaf".

F2 GENERATION:

F2 Day 1

F2 Day 1

F2 Day 39

Analysis / Conclusion:

The purpose of the experiment was to observe the generations of offspring produced from cross-pollination with the three different types of seeds that were initially planted in the pod. The F1 generation, or the first generation of offspring, grew successfully. Primarily plants with yellow petals were observed during the weeks that the F1 generation was allowed to grow. This may be due to the gene for that phenotype being dominant with the Brassica plant species.

However, no growth was observed for the F2 generation. There are several potential reasons for these results. It is possible that since five seeds were planted within the same, small space, availability of resources was limited and the seeds could not thrive without more nutrients. Another potential reason is the experimenters not watering the pod enough to provide enough water for the seeds. In order to improve the experiment, it would be suggested to more carefully measure the amount of water that is given to the plants each day, as well as allow each seed to have its own pod to be planted in. In order to control the experiment more and better observe the effects of artificial selection, it is necessary to provide the seeds with the necessary nutrients to grow, so that any growth or lack of growth observed is due to artificial selection and not another factor.

Restriction Mapping of Plasmid DNA Lab

Introduction / Purpose:
For this lab, we were asked to create and run an agarose gel through electrophoresis. We were given samples of DNA, which we loaded into the gel. This procedure allowed us to determine the size of the DNA fragments by observing where the segments were cut by restriction enzymes. Electrophoresis causes the fragments of DNA to travel through the gel. Since each fragment is negatively charged, they are drawn towards the positive end of the gel and away from the negative side. The smaller the fragment, he further down the gel it will travel. The purpose of this experiment was to give us a good understanding of restriction enzymes and how they cut DNA fragments. The gel gave us a great visualization of the different fragments and how they are not cut to be the same size.

Procedure:
*** The procedure calls for an Agarose Gel to be cast, but in our class the gels were already made for us. So that part of the procedure will be skipped in this post.

Analysis:

The results of the gel electrophoresis mainly serve to identify which strands of DNA are the longest and shortest and via this method give us a description of which DNA strands come from the same person or organism. However, for this experiment, the position of the bands on the gel electrophoresis allow us to see the cut sites for each of the restriction enzymes used and where these cuts sites are relative to one another.

As seen in the last picture featured in the procedure section of the lab report, the smallest fragments of DNA for each of the dyes was the same size. This is why there are four marks near the bottom of the gel and relatively all closer to another. The dye in the first row only had its DNA cut into two fragments, indicating that the enzyme used on it only had one cut site. However, dyes number 2 and 4 each had four fragments of DNA all relatively close to the same distance on the gel electrophoresis. This serves to indicate that the restriction enzyme for these substances had three cut sites since it was able to cut the DNA into four pieces. However, this is evidence that the restriction enzyme cut in the same cut sites for both dyes since the DNA fragments are very similar or almost identical to each other.

A similar situation occurred with dyes 1 and 3. They each had only two DNA fragments since the restriction enzyme only had 1 cut site. As with dyes 2 and 4, it is important to note that the DNA fragments are in very similar or identical spots on the gel electrophoresis demonstrating that the DNA strands are very similar or almost identical. This means that the restriction enzyme had the same cut sits when dealing with DNA strands from both dyes 1 and 3.

While the gel electrophoresis seems to have been conducted correctly, several steps may be taken to improve accuracy. For improvement in further testing it is suggested that more care be taken when pouring the dye into the gel. This way the only movement of DNA on the gel will be due to the size of the DNA fragment and not any other factor that could lead to an inaccuracy in the data.

pGLO Transformation Lab

Introduction & Purpose:

For this lab, we were trying to genetically transform colonies of E.coli so that they would display a trait that allowed them to become bioluminescent (glow) as well as become antibiotic resistant. To do this we took a gene called Green Fluorescent Protein (GFP) that is originally found in jellyfish and inserted it into the dish of E.coli colonies. We also inserted a gene that allows bacteria to overpower antibiotics. Although the E.coli bacteria were never designed to become bioluminescent, they have the ability to transfer plasmids, causing them to share the new genes we inserted into them. The purpose of this experiment was to help us understand the procedure of genetic transformation. We were able to observe how different factors allowed the bacteria to transform. We learned how to insert new genes into the bacteria, and why the bacteria colonies were able to display the new traits.   

Procedure:

Analysis:

Through the lab it was determined that E. coli can be genetically modified to glow in the dark under UV light. Through the method used, it was determined that this could be done by inserting E.coli into an agar plate that contained quantities of the plasmid known as pGLO, along with ampicillin and arabinose. The plasmid pGLO contains the GFP gene which is what allowed the E. coli to glow in the dark by coding for a green fluorescent protein. It is also important to note the total amount of growth for each plate, especially the plates that had the least and most growth.

As predicted, the two control plates, those labeled -pGLO and -pGLO LB/amp exhibited the least amount of growth, with the -pGLO exhibiting no growth. The plates that exhibited the most amount of growth were labeled  +pGLO LB/amp and +pGLO LB/amp/ara, with the latter plate having the most growth out of the four plates. This may be due to the bacterias increased resistance to ampicillin.  

 
This would also explain why the control plates has less growth than those with the pGLO plasmid. The plate with the -pGLO had no growth because it had no LB broth or arabinose to stimulate growth. The plate labeled -pGLO LB/amp did not have the plasmid necessary for antibiotic resistance to ampicillin, and therefore the E. coli could not grow. However, the plate labeled +pGLO/amp/ara had both the plasmid necessary to encode for antibiotic resistance, as well as ambroise which will induce the bacterial cell to express the fluorescent trait and grow.      

 To make the environment within the the plate most suitable for cell growth it is then necessary to add the pGLO plasmid, the ampicillin, and the arabinose. It is plausible to believe that the E. coli cells will grow with the added presence of arabinose because this chemical is what begins to stimulate the E. coli growth with both the expression of the fluorescent trait, along with antibiotic resistance. For the transformation efficiency of the experiment it was determined that there were  transformants/μg. Because it is common for the transformation efficiency calculations to result in higher numbers it is possible that there might have been an error while conducting the experiment. It is plausible to believe that too little of LB broth or arabinose was added to the agar plate. It is also possible that too much ampicillin was added.       

While we obtained the results predicted, to obtain more accurate results, it would be suggested to take more accurate measurements of the time the plates were in ice or into the warm water, along with perhaps better, more detailed written observations of the transformation and control plates. It would also be beneficial to make sure that each plate contains very precise amount of LB broth and ampicillin to get the most accurate calculations of the efficiency of transformation by getting the desired growth rate in the E. coli. To improve this calculation, it is also possible to take more care in counting the bacterial colonies on the agar plates after the experiment by using a microscope and more concentrated UV lights.

Gummy Bear Lab

*This lab was done in collaboration with Amanda Diana & Ananya Bhattacharya

1.) 30 Pink: 10 White

Hypothesis: Since pink appears to be the dominant trait, having a pink:white, 3:1 ratio, the parents of these offspring must both be carriers for the recessive white.

Analysis:

As previously stated, this group of offspring has a 3:1 ratio, exhibiting simple Mendelian dominance. In order to get this ratio, the crossed parents must be two heterozygous pink gummy bears (Pw x Pw).

The result of crossing these two parents is three pink gummy offspring (one homozygous and two heterozygous) and one homozygous white gummy offspring, or a 3:1 ratio. Thus proving that this litter of gummy bears follows simple Mendelian dominance.

2.) 15 Pink: 30 Pink-White: 16 White

Hypothesis: Here we have an interesting batch of offspring. ¼ of the offspring are pink, ¼ are white, and ½ are pink and white. This appears to be a 1:2:1 (pink: pink-white: white) ratio. The parents of these offspring most likely are carrying a gene for white and pink, and these genes can both be expressed simultaneously.

Analysis: Because approximately half of the offspring are showing both traits, it can be assumed that pigment trait is co-dominant. This means that heterozygous genotypes will code to show both yellow and white, as opposed to complete dominance, where in heterozygous genotypes the more dominant gene surfaces.The parents for these offspring are infact carrying a gene for white and pink, as is shown below.

This also supports the hypothesis because the ratio of possible offspring here are also 1:2:1.

3.) 20 Pink: 18 White: 14 Green: 19 Pink-Green

Hypothesis:

This particular set of offspring is interesting in that four different phenotypes are exhibited. Since the offspring exhibits four different possible pigmentations it is likely to believe that the mode of inheritance may be multiple alleles, similar to the mode of inheritance for blood types.

Analysis:

Due to the evidence shown in this punnett square, we can conclude that the mode of inheritance is multiple allele. All possible phenotypes are demonstrated in the genotypes of the potential offspring shown in the punnett square. There is also a 1:1:1:1 ratio demonstrated in the Punnett Square equivalent ratio for the phenotypes of the offspring, supporting the idea that the dominance for this set of gummy bear genes is multiple alleles.

4.) 38 White

Hypothesis: In this grouping, all 38 gummy bears were white. Since all of the offspring share a phenotype, we can conclude that the parents must be homozygous white. The entire litter would not be all white, since white has proven to be a recessive trait in every other litter thus far, unless both parents had a genotype of ww.

Analysis: The offspring have a ratio of 1, meaning all offspring are white. These offspring are displaying simple dominance. To yield theses results, the parents of this litter of bears must have been homozygous white (ww x ww).

By crossing these two bears we see that all the offspring will share a genotype and phenotype. (ww, white).

5.) 15 White: 15 Pink: 30 Orange

Hypothesis: In this grouping, there are 15 white / yellow gummy bears, 15  pink gummy bears, and 30 orange gummy bears. The ratio of the offspring is 1:2:1 (Red:Orange:White). From these results we can assume that both parents have a genotype of heterozygous orange. We know this because heterozygous parents will always display a 1:2:1 ratio when expressing incomplete dominance.

Analysis: The offspring have a ratio of 1:2:1, meaning the amount of orange offspring is double the amount of white and pink offspring. This litter is displaying incomplete dominance, in which the parents are heterozygous orange gummy bears (as displayed in the punnet square below, with PW = orange).

In this graph, we are comparing the phenotype frequency for each gummy bear phenotype.