Eudicot identification:

Phylum: Anthophyta

Species: Dianthus chinensis

Monocot identification:

Phylum: Anthophyta

Species: Hemerocallis lilioasphodelus L.

Monocot flowers:

Dicot flowers:

Difference between monocots and eudicots:

1. Dogwood fruit is a compound berry that is derived from multiple ovaries of one flower.
2. A Japanese quince is a simple fruit as it develops from one ovary. It's flesh has a sweet taste similar to that of an apple or pear which attracts pollinators and helps in the dispersal of seeds.
3. The Gingko biloba produces a simple fruit. Within the fleshy seed is a nut-like structure, but the seeds have a foul odor when they are ripe, so male ginkgoes are preferred for planting.

Lily dissection with major structures labeled:

Life Cycle of a Lily:

Life Cycle of Lily vs. Fern:

When comparing the life cycle of lily with that of fern, there are a few major differences that can be seen. One difference is that the spores of a lily come from the pollen grains of the anther while the spores of the fern are located within sporangia. Also, the spores of a fern go on to germinate and form the prothallus while the spores of a lily land on the stigma and grow a pollen tube that transports the sperm to the egg. Additionally, the lily must go through double fertilization in order to produce a zygote while the fern only has to go through fertilization. Because of that, the lily produces a seed that contains an endosperm (food supply/protection) and the embryo. On the other hand, the zygote of the fern begins its development inside the archegonium of the prothallus rather than inside a seed. The life cycles are similar, however, in that both consist of a diploid sporophyte generation and a haploid gametophyte generation.

Phylogenetic tree including seed plants:

Major Trends in Plant Evolution:

1. The dominant generation has transferred from the gametophyte to the sporophyte
2. The size of the gametophyte has gone from large (majority of the plant) to very small (almost invisible)
3. The size of the sporophyte has transitioned from very small to very large (majority of visible plant is the sporophyte generation)
4. The protection of the embryo has increased from minute coverage to significant protection

Evidence:

1. Nearly all of the plants that we observed in labs one and two were in their sporophyte generations. The ferns and the lilies are examples of plants that were in their sporophyte generation.
2. We viewed mosses in lab one which have a large gametophyte and compared them to flowering plants where the gametophyte is nearly hidden.
3. The size of the sporophytes in moss were much smaller than those of ferns that came later in time as shown by the phylogenetic tree above.
4. The embryo in gymnosperms went from being unprotected to being protected with by a seed with an endosperm in angiosperms. Gymnosperm seeds are not protected by thick flesh like those that are contained within fruit like apples or peaches.

LAB 3: Lichens as Bioindicators of Air Quality and Fungal Diversity

Why are lichens susceptible to air pollution?

Lichens are so susceptible to air pollution because their main constituents are cyanobacteria and/or green algae that undergo photosynthesis. Because the lichen is a partnership between a fungi and a photosynthetic cell, the environment that it is growing in has a large effect on the health of the organism. As a whole, lichens are able to take in pollutants from the air, which improves the quality of the soil surrounding them, but hurts themselves. According to www.air-quality.org, lichens have an adverse reaction to excessive amounts of sulfur dioxide found in polluted air and in water. They are so sensitive to this compound because they have structures that allow for very efficient absorption of materials and sulfur begins to accumulate within them. After long exposure to high levels of sulfur dioxide, the algae or cyanobacteria is unable to go through photosynthesis because their chlorophyll is extremely damaged. This can lead to the bleaching and potential death of the fungus and algae. Because of that, lichens are unable to live in areas where air pollution levels are high.

Encountered lichens:

Encountered fungi:

1. Coltricia perennis (Tiger's Eye)
2. Trametes ochracea (White-rot fungus)
3. Pholiota squarrosa (Shaggy Scalycap)

Click here to view the super helpful website that helped me in identifying the fungi above!

Hypothesis/Prediction:

I believe that the lichen air quality index will be able to indicate the quality of the air surrounding the Penn State Beaver campus and I predict that we will find the air quality of this region to be moderately low despite the the presence of lichen.

Excel Graph:

Conclusion based on graph (Figure 1):

It appears that there is basically no correlation between the lichen air quality index and the distance that the tree is from the origin. However, it seems that as the distance from Walmart increases, the lichen air quality index decreases.

Pittsburgh’s Air Quality:

The website www.lung.org provides numerous statistics and rankings for the air quality throughout Pennsylvania. When looking at the particle pollution data, Allegheny County (Pittsburgh region) receives a grade of F which is a failing annual grade. On the other hand, the grade for Beaver County is a B which is a passing annual grade. Particle pollution is referring to the amount of harmful particles floating in the air that come from sources such as the exhaust of trucks.

Pittsburgh's Air Quality vs. University Park's Air Quality:

As mentioned above, Allegheny County receives an air quality grade of F for particle pollution. In comparison, Centre County (State College, PA) receives a C for particle pollution in the area.

Accuracy of lichen survey:

I feel as if our lichen survey was fairly accurate. Because of the presence of foliose lichens, we know that the air quality in this area must be moderately high with a lower amount of pollution in order for those lichen to grow. We did not find any fruticose lichens, but that does not mean that the quality of the air is extremely poor, it just means that the particle pollution was not low enough for those lichen to thrive. Based off of that, I feel that our survey matches the ranking of a B for Beaver County because we were able to observe a decent amount of foliose lichen which are indicators of moderate air pollution.

Other factors affecting air quality:

Nature: ozone produced from lightning strikes, volcanoes, carbon dioxide from wildfires

Transportation: cars, buses, airplanes, semi-trucks

Agriculture/land: methane from livestock, byproducts from fertilizers, oil and gas drilling

Stationary: power plants, sewage treatment facilities, industrial factories

Improvements to survey:

To improve our survey, a larger transect area could be examined in order to record more data. Also, the transect areas could be placed farther apart so different parts of the trail were examined. We could have increased the accuracy of our survey by being sure of what each tree species was that we were examining. Having unknown tree species in our survey resulted in lost data points when tree species in particular were being compared.

Would our campus still be a suitable location for people with respiratory issues?

Based off of the reading, I think that our campus could still be a suitable location for people with respiratory issues, but the quality of the air is not as high as it used to be at the time when the Beaver County Tuberculosis Sanatorium was up and running. I think this because we were able to find a lot of lichen when completing our survey. Because there was a decent amount of lichen present, that means that there is low pollution in the air. If the level of pollution is low, then those with respiratory issues should be safe breathing in the air.

LAB 4: Protist Diversity and Introduction to Microscopy

How are protists taxonomically defined?

Protists were originally grouped together as one kingdom, but DNA evidence has revealed that some protists are not similar in their evolutionary lineage. In reality, they are a unique group of organisms that cannot be described as monophyletic and must be classified with other eukaryotes like animals, plants, and fungi. Because of that, protists are taxonomically defined as supergroups which are in between domain and kingdom in the hierarchy of taxonomy. Overall, there are five supergroups and each represents a different evolutionary lineage. The five supergroups are Archaeplastids, SAR, Excavata, Amoebozoa, and Opisthokonta.

Protist Locomotion (ciliate):

Protist Identification:

Supergroup: SAR

Species: Stentor

Special structure(s): gullet, oral groove, contractile vacuole

Supergroup: SAR

Species: Spirotostotum

Special structure(s): oral groove, cilia

Supergroup: Archaeplastids

Species: Volvox

Special role(s): live as colonies that contain daughter colonies within them

Supergroup: Archaeplastids

Species: Chara

Special structure(s): cell walls, chloroplast

Supergroup: Archaeplastids

Species: Red algae

Special role(s): used as an emulsifyer in chocolate and various makeup products, used to make agar which goes into products like vitamin capsules and bacterial culture mediums

Special structures: contain red and blue accessory pigments, has a filamentous structure

Supergroup: Excavates

Species: Euglena

Special structures: chloroplast are surrounded by three membranes and have an area known as the pyrenoid that produces paramylons, two flagella are present for help with locomotion, eye spot enables protist to see light

Ecologically/Medically Important Protist:

Diatoms: Diatoms are ecologically important because of their role as photosynthetic producers. They are stramenopiles that contain special, golden chlorophyll pigments that gives them a yellow-orange hue. They provide oxygen and and are a food source for freshwater and marine heterotrophs because they make up a majority of the plankton in those waters. The remains of these organisms (diatomaceous earth) can also be used as abrasives in toothpaste.

Plasmodium: Plasmodium is an apicomplexan (sporozoan) that is important in the medical world. Because it is an apicomplexan, it contains an apicoplast which aids in the infection of a host. In particular, Plasmodium is the cause of malaria in humans. It infects red blood cells and causes them to burst, releasing releasing toxins into healthy blood. This protist makes such an impact because over 200 million people are infected by it each year. Almost 50% of the world's population is at risk for getting malaria.

Zooxanthellae: Zooxanthellae are ecologically important dinoflagellates that help maintain coral reefs. They are endosymbionts that live within their hosts and provide them with organic nutrients. In return, the coral provides the zooxanthellae with protection, food, and a place to live. Zooxanthellae are also what gives coral their vibrant colors and can result in bleaching if water conditions become unfavorable and they expel themselves from the coral.

Lab 6: Phylum Porifera and Phylum Cnidaria

Phylogenetic tree showing relationship between classes Calcarea, Demospongiae, and Hexactinellida:

Distinguishing features of sponges:

1. Sponges possess choanocytes which are specialized flagellated cells that cover the inside body cavity of the sponge. The flagella of these cells creates a beating motion which draws water into the middle of the sponge resulting in the capture of food particles.

2. Sponges possess a unique water canal system. They are able to draw water into and out of their bodies through pores.

3. Sponges lack true tissues and are therefore the simplest animals of the Metazoa. They do, however, have specialized cells that are capable of recognition. This allows for reformation of the sponge if part of it were to break off.

Key features of Cnidarians:

1. All Cnidarians have radial symmetry which allows their entire body to interact with their environment.

2. Cnidarians possess special cells that are used to sting their prey. They are called nematocytes and house a small, sharp dagger that is expelled violently from the cell and into the flesh of the predator.

3. Cnidarians have gut cavities where enzymes aid in the digestion of food. This allows nutrients to be directly absorbed by the cells surrounding the cavity.

4. Cnidarians have a unique life cycle in which they can alternate between a medusae and a polyp stage. Medusae are umbrella-shaped and have tentacles with nematocytes hanging down. Polyps have a cylindrical, tube-like shape as shown in corals and Hydra.

Hydra feeding on Daphnia: A Closer Look

In order to kill its prey, the Daphina, the Hydra uses its long tentacles that are lined with stinging cells called "nematocysts" to grab the food and paralyze it. Once the nematocysts have taken affect on the Daphina, the Hydra pulls it closer towards its mouth. At this point, the Hydra is able to push the food into its mouth with the help of its tentacles. This desire to eat is caused by the presence of GSH, or glutathione, which is released into the surrounding water when the Daphina is killed. At this point, the Daphina enters the interior gut cavity of the Hydra where extracellular digestion can take place. During this time, enzymes are secreted from the epidermis cells into the gut cavity to aid with digestion. If there is any food that remains undigested, it is removed back through the mouth of the Hydra, as that is the only opening available for materials to move both in and out.

Mutualistic relationship between zooxanthellae and coral:

Zooxanthellae are are a form of photosynthetic algae that live within the cells of coral. The coral provides a home for the zooxanthellae to live in, and in return, the zooxanthellae produces food for the coral and provides oxygen which aids in the removal of waste. On top of that, zooxanthellae are responsible for the stunning colors of coral that can be seen below the water. These vibrant colors can fade, however, when the temperature or pH of the ocean water changes. The phenomenon of coral turning white is called “coral bleaching” and is caused by an increase in temperature or pH of the water which distresses the zooxanthellae and causes them to be expelled from the coral. Once zooxanthellae are evacuated from the coral cells, the coral no longer has a source of food or a source of color. If coral goes a long time without zooxanthellae, it will die. The changing ocean acidification and warming of water is a major problem in maintaining coral reefs.

Lab 7: Phyla Mollusca and Arthropoda

Mollusks

Distinguishing features of Polyplacophora:

The class Polyplacophora consists of organisms called “chiton” that have a shell made up of eight calcaerous plates as shown below. Chiton are marine mollusks that prefer to live in rocky areas where they can hide and blend in. They have radula which they use to eat algae and barnacles, and they move using their foot. A benefit of their unique shell is the ability to wrap tightly around irregular surfaces when moving across rocky terrain.

Distinguishing features of Bivalvia:

The organisms within the class Bivalvia have a unique shell that is composed of two clacareous halves connected in the middle like a hinge. Examples of bivalves are oysters, mussels, and clams. To move, these animals can quickly open and close their shells (valves) to propel them through the water. They live in a marine or freshwater environment and take in nutrients via filter feeding.

Distinguishing features of Cephalopoda:

Members of the class Cephalopoda are organisms such as squids, octopuses, and nautiluses. Cephalopods are distinguishable from other mollusks due to their large brains and lack of a true shell. Instead, these animals have a mantle cavity that has been modified and allows for jet propulsion through water with the help of their tentacles. Another unique feature is the presence of two beaks for biting off pieces of prey after they have been captured by the tentacles. Most cephalopods also have radula which are tongu-like organs that act as teeth to scrap algae from the surface of rocks.

Distinguishing features of Gastropoda:

The organisms within the class Gastropoda are among the most recognizable and common mollusks. Snails and slugs are examples of animals that are classified as gastropods. In these organisms, their mantle produces the hard shell which provides a home and protection. To move, Gastropods use their strong foot to grip the surface they are moving across and pull themselves forward. Like cephalopods, gastropods have radula which aid in the consumption of food.

Arthropods

Distinguishing features of Chelicerata:

The subphylum Chelicerata houses organisms like sea spiders, horseshoe crabs, and arachnids. These animals are unique due to the presence of chelicerae, which are located at the front of the body and act as pincers. The body is divided into two distinct sections, those being the anterior prosoma and the posterior opisthosoma. The prosoma has the four sets of walking legs attached to it while the opisthosoma holds the reproductive organs. Most chelicerates are terrestrial, but some live in freshwater and others are marine like horseshoe crabs and sea spiders. A majority of these animals are carnivorous, but must release digestive enzymes to break down their food before it can be eaten.

Distinguishing features of Crustacea:

The subphylum Crustacea is composed of animals like shrimps, crabs, barnacles, and lobsters (all marine) and fresh water crustaceans like crayfish. Pillbugs are also considered crustaceans, but they are terrestrial. Some crustaceans have a unique structure in which the cephlon and thorax are fused to produce a cephalothorax, but most have three distinct regions. These organisms are special due to the presence of two sets of antennae. Most have three sets of appendages for handling food and multiple sets of legs attached to their abdomen and thorax. For larger crustaceans, respiration takes place through gills that are located by the base of their legs. The larva, which are nauplius, are a defining feature of all members of Crustacea.

Gram Staining of the Bacteria in Aged Whole Milk

0 Days: After being left out for only a few hours, the whole milk had a pH of 7 and just smelled like normal milk. It still had a homogeneous white color and consistency. After doing a gram staining of the bacteria from this sample, we found that there was only gram positive coccus-shaped bacteria in the milk. They seem to be in clusters, rather than chains.

1 Day: After being left at room temperature for a full 24 hours, the pH of the whole milk was 6 and the milk itself had a slightly unpleasant odor. The milk had begun to separate into a cloudy white liquid with chunks of white solid throughout. Once the gram staining was complete, we found many rod-shaped bacteria that were gram positive. It also looks like there could be a few gram negative coccus-shaped bacteria as well.

4 Days: After being left out at room temperature for four days, the pH of the whole milk was 5 and the unpleasant odor was much stronger than the one-day-old milk. The milk separated even further and there was much more white solid within the the yellowish/clear liquid. Once the gram staining was complete, we found that there were still rod-shaped and coccus-shaped bacteria, but the the rod-shaped bacteria were now gram negative. The coccus-shaped bacteria were far more abundant in this sample when compared to the one-day-old milk sample as well. Overall, the amount of bacteria present in the milk greatly increased after being left out for four days.

8 Days: After being left out at room temperature for eight days, the pH of the whole milk was 5 and there was a clear liquid surrounding white solids that were pooled in the middle of the flask. This sample of milk did not have a completely unpleasant smell; it almost smelled like cheese to me. Once gram staining was complete, we once again found gram negative rod-shaped and coccus-shaped bacteria. However, there was much, much more of each bacteria within this sample of milk.

Overview of Change in Community Composition: Over the course of eight days, the types and amount of bacteria changed dramatically throughout the whole milk. When refrigerated, there were many clusters of gram positive coccus-shaped bacteria in the milk. Once left out at room temperature for a day, there was much more bacteria in the sample and it contained a large amount of gram positive rod-shaped bacteria and a few gram positive coccus-shaped bacteria. After being left out at room temperature for four days, there was a significant change in the composition and amount of bacteria. At this point in time, the bacteria had gone from being gram positive to being gram negative. The coccus-shaped bacteria became more abundant and the overall amount of bacteria increased as well. This would show that the community would have had to been changed enough by the gram positive bacteria to make conditions unfavorable for their survival, but favorable for the gram negative bacteria, leading to their survival. The last sample of whole milk that had been left out at room temperature for eight days had a very large amount of gram negative bacteria. The shapes of the bacteria remained the same, but there were even more coccus-shaped bacteria in the eight-day-old milk. The picture below shows how the amount and types of bacteria changed overtime.

Whole Chocolate Milk

Gram Staining of the Bacteria in Whole Chocolate Milk

Comparison of Whole Milk and Whole Chocolate Milk Bacterial Communities