User:Nouf Abuladel/Notebook/Biology 210 at AU
Feb 16th, 2014 | lab# 3
INTRO: After observing several types of micro organisms within our transect and incubating the plates for a week, it is the time to look at bacteria and understand its characteristics. The further we study bacteria the more we get to learn about its cells and be able to distinguish between gram positive and gram negative. That would, also, help in examining the antibiotic resistance and observe its affects on bacteria. Additionally,we'll be sequencing DNA from our Hay Infusion in preparation for next lab.
METHODS: The very first procedure of this lab was to examine nutrient agar and tetracycline plates. We were asked to count the total number of colonies on each plate.
Then , we chose three plates that we wanted to study their colonies. We labeled a place of interest on each of the three plates, so, we have labeled them as (10^-3, N three guys), (10^-3, T) and ( 10^-5, N). the identifications are based on colony description in terms of color, shape and texture, number of colonies, cell description in terms of shape and arrangement, and wether it's gram positive or negative. In order to see those micro organisms closely, we observe them under the microscope after we've spread a sample of the place that we labeled on the plates on a slide. Also,the slides were heated with the bacterial smear side up after that we coated the smear with crystal violet for a minute and rinse it off with water. next, the smear was covered with iodine for a minute and rinse gently after that, moreover, the smear was decolorized with alcohol for 20 seconds and , then, covered with safranin for 25 seconds and rinse gently again. Finally, the slides were dried from excess water carefully with paper towel.
The very last step was to prepare PCR for DNA sequence Identification. That's by choosing one of the plates that has the best characteristics to examine. A single colony of bacteria was added into 100 ul of water in a tube and it was incubated at 100 degrees celsius for 10 min. That tube, later on, was centrifuged. 5 ul of the supernatant was used for PCR.
OBSERVATIONS: The smell and appearance of the Hay Infusion keep changing from week to week and even its concentration seems to be increased over the days. That is due to the fact that some of some microorganisms in the jar might have died or grown and, in fact, the bad smell is from the growth of bacteria. The plates with antibiotic had less bacterial colonies while the plates without antibiotic had more colonies. So the effect of tetracycline on the number and the type of bacteria was definite and that shows that the antibiotic was effectively working. Tetracycline works by interfering with the ability of bacteria to produce proteins that are essential to them. Without these proteins, bacteria cannot grow. Moreover, after observing our slides we had two gram positive cells and one gram negative cell.
CONCLUSION: Summing up, this lab was helpful in understanding bacteria, observe its cells more closely and learn about the antibiotic's affects on bacterial colonies' color, type and numbers. So, now we have considerable amount of information about the bacteria of our transect. Moreover, in this lab we make PCR sample of our Hay Infusion so that for next week we'll be able to run the PCR products on an agarose gel if the DNA looks good. Thus, we are going to analyze the DNA sequences from our transect.
Feb 9th, 2014 | lab# 2
INTRO: This lab is all about identifying algae and protists. The identifications are based on the morphological characteristics such as shape, size and motility. Thus, we're using a tool called a "Dichotomous Key" to make the work easier in identifying the group of organisms from our Hay Infusion.
METHODS: Before we use our Hay Infusion, we looked at known samples of organisms, such as Gonium, under the microscope and that is just to get practiced and familiar with the tool "dichotomous key". After that, we divided the work on our group so that each individual observes a specific niche, such as, surface or near-vegetation niche. My part was to identify the organisms that are in the bottom of the jar.
Lastly, in order to prepare for lab# 3, we obtained four 10-ml-sterile-broth tubes to prepare the dilutions. 100 micro liters of the Hay Infusion was added to the first tube (10^-2). Also, we took 100 micro liters from the first tube and added it to the second tube. The process were repeated for the third and fourth tubes. Next, we obtained four nutrient agar plates labeled -3, -5,-7 and -9, additionally, three tetracycline plates labeled T-3, T-5, and T-7. we took 100 ul from the first tube and pour it into the plate (-3). By using a spreader, the 100-ul of the dilution was spread in the plate. [Exact procedure was repeated for the rest of the plates]. These plates will be incubated at room temperature over the next week.
OBSERVATIONS: Hay Infusion smells awful, some mold appeared on its surface and no green shoots. Also, the concentration of the Hay infusion has decreased. That's because some the organisms in the system died. Temperature and light are some the selective pressures that affected the compositions of the samples. Since we observed different niche from our transect, there were many different organisms such as two of Euglena (size=7 um), Stentor (size= 10 um), Paramecium (size= 80 um), Actinosphaerium (size= 50 um) and Gonium (size= 65 um).
CONCLUSION: All in all, we, now, know how to use dichotomous key to identify different micro organisms. also, we further understand how selective pressures affect a particular system and can lead to evolution. the plating procedure will, also, be helpful to understand the characteristics of bacteria in the upcoming lab.
2/6/14, lab 1 notes
Great work! Some notes: -Include subject headers such as "introduction", "methods", etc
-Make sure pics are included by Sunday
-Start working on building a map of your transect to detail your land and where your samples are taken from. We will talk about this more Wednesday
Good job! AP
Jan 31st, 2014 | lab# 1
INTRO: The purpose of this lab is to understand the meaning of the neutral selection and evolution. From those concepts, organisms that live in a niche (biotic and abiotic) can be observed through the lab. Also, we can see how these organisms change their behaviors from time to time and from place to place. So, now, we can look at our transect and be able to identify different organisms.
METHODS: Prior to preparing our transects, we had a chance to look at different types of algae by using the microscope: Chlamydomonas, Gonium, and Volvox. Thus, we identify the size, number of cells, reproductive type and functions.
Then, the transect was prepared from a place that has vegetation around it near Bender Arena which can help in preparing the Hay Fusion. That is by taking some of the vegetation and putting it in in a sterile 50ml conical tube. The Hay Fusion 500ml of water was added, 0.1 gram of powdered milk, in addition to the contents of our conical. After that, the Hay Fusion content was transferred into a jar.
OBSERVATIONS: Plants, bird and shrubs were our biotic. Abiotic factors that was observed were wet mulch, soil, sunlight, cigarette buts, rocks, a sprinkler,and a coca cola paper cup.
CONCLUSION: All in all, this lab will help us in studying microorganisms in the transect and in upcoming labs. Also, definitely, there will be a diverse of organisms that might be living in the surface and the bottom of the jar.
Jan 22nd, 2014 successfully entered text and username