User:Aikerim Imanalieva/Notebook/Biology 210 at AU

5 February 2016 Exercise III- Microbiology and Identifying Bacteria Objective- the objective of this lab was to observe and identify bacteria based on their motility, gram stain, colony morphology, and sequencing of the 16s ribosomal subunit gene.

Hay Infusion Culture After a week the Hay infusion culture seemed to get lighter in color, with the soil and most of the leaves going to the bottom of the jar. However, there were some lighter in mass leaves that were still floating in the middle and the top. The smell of the Hay infusion culture seemed to worsen, a smell of poop mixed with decomposing material. I hypothesize that the smell and the appearance of the Hay infusion culture changed was because the environment’s pH and amount of material changed. Leading to microorganisms dying and changing. The Archaea did not grow on agar plates because Archaea grows only in extreme environments, which the agar plates did not provide.

Procedure I: Quantifying and Observing Microorganisms When I was recording the plates I had seen a substantial difference in the colony types between the plates with tetracycline and without tetracycline.

10^(-3)- The biggest difference observed was between agar plate with and without antibiotic was observed in this dilution. The agar plate without tetracycline contained a lawn of colonies that were dark green in color. While the agar plate without contained about 203 colonies of rod, yellow like bacteria. 10^(-5)- The colony types were similar between the one with tetracycline and without it. They looked like circular, yellow like bacteria. The only difference observed was that the one with the antibiotic had only one colony, while the one without it had about 130. In both plates Fungi was not observed. 10^(-7)- The agar plate without antibiotic had one rod, yellow like colony. While the one with antibiotic did not have any colonies. 10^(-9)- Interestingly enough the agar plate with tetracycline showed to have a fungi grown on it. While the one without tetracycline did not have anything. Antibiotics can not kill Fungi that why the colony was able to grow on the agar plate with tetracycline.

The observations confirm that the bacteria collected is not fully resistant to tetracycline antibiotic, probably gram-negative because it is more resistant to antibiotics than gram positive bacteria, reducing the amount of the bacteria colonies in those who had an antibiotic. The tetracycline however did not have any effect on the Fungus. Proving that the antibiotics cannot affect Fungal growth.

Mechanisms of Tetracycline

Tetracycline belonging to polyketide class, is widely used against bacterial infections. What it does it releases its promoter into the cell depressing the transcription of the bacterial cell that it had infected (Werten). This afterwards triggers allosteric cascade, even in the absence of magnesium, stopping bacterial protein synthesis. The bacterias that are sensitive to such antibiotic are bacterial pathogens such as Chlamydia, Mycoplasma and Rickettsia (Werten).

Werten, Sebastiaan, et al. "Tetracycline Repressor Allostery Does Not Depend On Divalent Metal Recognition." Biochemistry 53.50 (2014): 7990-7998. Academic Search Premier. Web. 5 Feb. 2016.

The PCR tubes were carefully labeled with our initials. Then 20ul of primer were aded into a PCR tube, which was then dissolved. Afterwards a bacterial colony was taken from the agar plates, using a toothpick, and put into PCR tube. After this was done, the tubes were put into PCR to let it run.

                                                                                                                       Plantae and Fungi 

Transect Sample Plants Location # in transect Description (size and shape) Vascularization Specialized Structures Mechanism of Reproduction Centifolia

Centifolia Kingdom: Plantae Family: Rosaceae Genus: R. × centifolia

Located on the NorthEast of the transcend, in front of the bench and surrounded on one side by the pathway to Gray Hall and on the other side by Rockwood Pathway. Plants are lank and open, with long floppy canes that can attach themselves to railings, growing up to 1.5-2 meters in height. On the plant there are small spines and large hooked thorns. In general centifolias are stouter and taller than gallicas, with coarser prickles, and narrower, longer leaves. They have pink blossoms that are lush and round in shape.

Plants absorb nutrients and water through their roots. Plants contain vascular tissues (xylem), which transports water and minerals up from the roots to the leaves, and phloem, which transports sugar molecules, amino acids, and hormones both up and down through the plant. The leaves of plants also contain veins, through which nutrients and hormones travel to reach the cells throughout the leaf. Veins are easy to see some leaves (a maple tree, for instance). There is also Sap, that is the mix of water and minerals that move through the xylem. Carbohydrates move through the phloem. Keeping plant hydrated and nourished. Inside the cells of the root, there is a higher concentration of minerals than there is in the soil surrounding the plant. This creates root pressure, which forces water up out of the root through the xylem as more water and minerals are "pulled" into the root from the soil. This force results in guttation, which is the formation of tiny droplets on the ends of leaves or grass early in the morning.

Unlike many type of roses, Rosa × centifolia has a thick covering of resinous hairs on the flower buds. Roses are like angiosperms. They have males who contain pollen and females who contain ovule. During spring, when insects transfer the pollen from one kind of flower to the other, the pollen joins itself to form egg cells inside the ovule, and the combined cell is considered fertilized. They develop into a rose hip, which is then ingested by birds. Who then poop it out and this poop nutrition for the seeds within the rose hip to germinate. Snowdrop

Snowdrop Kingdom: Plantae Family: Amaryllidaceae Genus: Galanthus L. Located on the NorthWest of the transect, in front of the bench and surrounded on one side by the pathway to Gray Hall and on the other side by green bushes. The bulb is spherical with the circumference of, 2–2.2 cm x 1.1–1.5 cm. While the green stalk is 7–15 cm long and is straight. The leaves are held flat against each other in the bud. They are linear and smooth, with a greenish/grey color. The flower is white in color and when bloomed hangs down in an inverted V o U shape.The flowers are composed of six white perianth segments, with a green tip.

Snowdrops are known for coming during the winter. The ability to emerge at that time is due to the leaves and stem that have hardened tips and are covered in a protective sheath. . They enable the plant to penetrate the layer of snow.

Snowdrops can reproduce sexual and asexual reproduction. Sexual reproduction occurs through the pollination of the flower, while the asexual reproduction occurs through the formation of the bulb. The bulb is formed by the leaf bases which completely encircle the short, conical stem. The part of the leaf above ground makes food by photosynthesis and sends it to the leaf bases which swell as they store the food. In the following year the stored food is used for the early growth of the bulb.

Japanese Hop

Kingdom: Plantae Family: Cannabaceae Genus: Humulus Species: Humulus Japonicus Located in the SouthEast behind the wooden bench and next to the pathway made of rocks leading to Gray Hall. The plant characteristics lies in twining, shallow-rooted vine that grow to be ten or more feet. Because it contains a rough-textured stem that is covered with short, sharp, downward pointing prickles they can attach themselves to the surfaces of the buildings. They contain male and female flowers that are greenish-yellow in color. Females contain seeds.

The leaves of the Japanese Hop are rough and toothed, in a shape of a hand with typically 5-7 lobes.

Unlike many plants, Japanese Hop are highly adaptive. They can grow in different environments, and because they require minimum amount of nutrients and water, when risen can spread very quickly. Thus stopping the growth of other plants. Reproduction in the Japanese Hop occurs by the spread of seeds that germinate in early spring. The seed is dispersed by animals (including people), machinery and floodwaters.

Daffodil

Kingdom: Plantae Family: Amaryllidaceae Genus: Narcissus L.

Located in the middle of the transect, it is surrounded by the bench on the West of it and the pathway made out of rock on the East of it. Behind the pond, covered by green bars. Daffodil is bulbous perennial with upright, strap-like, grey-green leaves. The leaves arise from the base of the stem and are up to 35 cm long and 12 mm wide, with rounded tips. During its time there is a single flower which is located at the end of the flower stalk.

The flower is made up of light brown “'trumpet' (corona) surrounded by a ring of 3 sepals and 3 petals (perianth), which are a lighter yellow.

Daffodil can reproduce either either by producing seed or bulbs. In reproduction of the seed, sexual reproduction, the flower is pollinated by insects. The pistil containing the stigma and the female gamete, is where the daffodil's ovule is found. On the stamen of a plant, pollen is produced, which contains the male gametes. When pollination occurs, the pollen is dropped into the stigma. This fertilizes the ovules of the plant, inside its ovary. A seed then develops from the fertilized ovule. When the daffodil blooms die, the tiny black seeds are dry and ready for dispersal. The seed pod (ovary) of the daffodil cracks open, and seeds either fall to the ground or are transported by wind or animals to a new location.

During asexual reproduction, the bulb at the base of the daffodil is split into two, forming bulblets. These then can become their own daffodils.

English Ivy

Kingdom: Plantae Family: Araliaceae Genus: Hedera L.

Covering the trunk of the tree it is located on the NorthWest of the transcend, in front of the wooden bench and next to the Centifolia. It is a climbing vine that attaches itself to different surfaces by root-like structures that exude a glue-like substance to aid in adherence. The leaves are dark green in color with a waxy texture and 3-5 lobes. The flowers are small, greenish-yellow and occur in globular starburst type inflorescences at tips of flowering stems. While the fruits are black with a fleshy outer layer and stone-like seeds.

English Ivy has the same basic vascularization as any plants. But because English Ivy is so mobile, it does not have an extensive root system. Instead of roots burrowing deep into the ground, the roots are on the surface, allowing for more movement to pick up nutrients from the surface rather than soil. To ensure the spread of the fruit and thus their reproduction, English Ivy developed a glycosides that can be mildly toxic, causing some birds to regurgitate them. English Ivy reproduces using seeds in the berries. The seeds in the berries are distributed by birds such as starlings, European house sparrows, band-tailed pigeons, robins and cedar waxwings. To ensure that the seed enter the soil, English Ivy developed a mildly poisonous berry, that forces the bird to vomit the seeds out into the soil.

Work Cited http://www.ivy.org/about_bv1.htm http://www.ask.com/science/roses-reproduce-b0d417afac38ec65 http://www.savanna.org.au/all/termites.html http://www.dummies.com/how-to/content/how-plants-get-water-and-nutrients.html https://en.wikipedia.org/wiki/Galanthus http://www.nps.gov/plants/alien/pubs/midatlantic/huja.htm http://www.ivy.org/about_bv1.htm http://www.biology-resources.com/plants-vegetative-reproduction-01.html http://speciesofuk.blogspot.com/2013/01/week-7-common-snowdrop-galanthus-nivalis.html https://en.wikipedia.org/wiki/Galanthus https://www.botanical.com/botanical/mgmh/r/roses-18.html