Week 14

 

 

This week was the last week of the semester, and every one was getting ready to present their research. I saw how hard every one was working to perfect their findings and to put the knowledge that they gained together. For me personally, it was an incredible experience. I learned a lot about science through out the course, but my learning wasn't limited to just science. I met very talented people who had a great impact in my life. I learned how to be patient and how to cope with unexpected situations. I really want to appreciate every single person in S-STEM including all the professors, my mentors and also students, who help me to come along smoothly and to never feel that I'm alone.

 

Dalby Building at Phoenix College, Photo by Phoenix College



  

Week 10

 

This week I learned how to extract DNA using heat. If we have a Gram positive bacteria which has a bilayer cell wall, we can use boiling water to extract the DNA without damaging it. Extracting DNA,  using this technique can be easily done. We need enough amount of a fresh sample. Then we can pipet some of our sample into a tube, and spin it in a centrifuge. Now, pallet can be re-suspended in a new tube with some water in it. Next step is to sit the pallet in a boiling water which will break the cell wall. We, then, centrifuge the tube one more time to pallet the constituent. We keep the supernatant of the last step which is the extracted DNA.

 

                                     DNA extracted at the bottom of the tube (google image) 

Week 13

 

Staphylococcus Aureus is the major reason for “human bacterial infections” throughout the world. This bacterium can cause everything from trivial skin infections to major infections that lead to death. The reason being is that it can obtain resistance to antibiotics like penicillin and methicillin (DeLeo, 2010; Deurenberg & Stobberingh, 2008).  This “pathogenic Gram-positive bacterium” lives closer to us than what we may think. It can be found in our nasal area and also our hands can be used as vectors to transfer the bacteria. Intact skin has a smaller chance of getting infected than wounded skin. It’s communicable through close contact and will last for months on any type of surface (Wertheima et al., 2005). In order to know which antibiotic to use to treat an infection, the bacteria causing the infection should be identified.

To identify the bacteria cultured from human skin, the methodology was slightly modified from how it was conducted in Aher, Roy, and Kumar’s 2012 study, “Molecular detection of virulence genes associated with pathogenicity of Gram positive isolates obtained from respiratory tract of apparently healthy as well as sick goats.” In that research, methods included obtaining nasal swabs, bacterial isolation,  incubation at 37° C, morphological identification based on Gram's staining, biochemical identification of Gram positive, DNA Extraction, Polymerase chain reaction (PCR) for amplification, identification of amplified genes based on fragments’ size. For more definite results, sequencing the DNA was also planned.

Before DNA can be sequenced, it needs to be isolated. The course of extracting DNA from its source by separating it from other cellular constituents is called DNA isolation (“DNA Isolation Methods,” 2005). To study DNA, enough of an amount of it should be available; otherwise, DNA should be copied to obtain the amount needed. The technique used for DNA replication is called “polymerase chain reaction (PCR)” (Maczulak, 2011). Composition of DNA of a species is specific to that species and different from the others. Distinctive sequences of nucleotides give DNA its unique characteristic that serves to identify an organism from the others in the same way that a person’s fingerprint does to identify a person from others (Maczulak, 2011; DNA, 2005). Fingerprinting DNA can reveal the identity of individuals and, therefore, is used for recognition of criminals, war and accident casualties, paternity, and classifying plants or animals in forensic science. Another purpose of isolating DNA is to diagnose a genetic disorder (“DNA Isolation Methods,” 2005).

Another way to identify bacteria is based on “antigen-antibody bonding”. These rapid tests are often used in doctors’ offices to rapidly identify bacteria like streptococcus.  In this method, a specific region of bacterial or viral DNA or RNA, called “target regions,” are being spotted. Special genes are being introduced to the infected body, which code for the existence of the target region. Diagnosis of a disease can be done a lot faster using this method, comparing to the old methods of only looking for symptoms (Hoyle, 2008).

https://www.youtube.com/watch?v=EkGPOoIJCoc

 



 

 

Week 11

 

Identification of Staphylococcus Aureus is important because it’s the major reason for “human bacterial infections” throughout the world. This bacterium can cause everything from trivial skin infections to major infections that lead to death. The reason being is that it can obtain resistance to antibiotics like penicillin and methicillin (DeLeo, 2010; Deurenberg & Stobberingh, 2008).  This “pathogenic Gram-positive bacterium” lives closer to us than we may think. It can be found in our nasal area and also our hands can be used as vectors to transfer the bacteria. Intact skin has a smaller chance of getting infected than wounded skin. It’s communicable through close contact and will last for months on any type of surface (Wertheima et al., 2005).

To identify the bacteria cultured from human skin, the methodology was slightly modified from how it was conducted in Aher, Roy, and Kumar’s 2012 study, “Molecular detection of virulence genes associated with pathogenicity of Gram positive isolates obtained from respiratory tract of apparently healthy as well as sick goats.” In that research, methods included obtaining nasal swabs, bacterial isolation,  incubation at 37° C, morphological identification based on Gram's staining, biochemical identification of Gram positive, DNA Extraction, Polymerase chain reaction (PCR) for amplification, identification of amplified genes based on fragments’ size. For more definite results, sequencing the DNA was also planned. Isolating DNA and observing its characteristic and functions can be done in order to classify them or do comparison on different DNAs for different reasons.

                                         Staphylococcus Aureus (Google image)

 

 



Week 9

This week I learned how to extract DNA from my bacteria using an easy protocol that one of the scholars (Paul Cattelino) has designed. In this method, I used a big amount of my sample (500 µL) to extract DNA from, so it didn’t need to be amplified in order to be seen. I learned that for extracting DNA, we’d better to use a sample that has been cultured overnight and is fresh. Then, I ran PCR with getting help from Paul. I learned to different techniques running PCRs. The difference of two techniques was in the way of loading the DNA sample into the gels. The first technique used was the way that microbiologists use, and it’s purring the buffer first and then loading the sample. The second technique was loading the sample and then purring the buffer which is not as perfect as the first method, but it’s an easier way to load the sample. Finally, I ran the PCR with both methods, but something was done wrong because I didn’t have any DNA extracted from my samples. I will repeat the experiment next week all over again to see if I can get some results.

https://www.youtube.com/watch?v=DkT6XHWne6E

Week 8

 

I spent most of last week trying to find information from different resources for my research paper. Now, I'm piled up with lots of information that needs to be put together to build my paper. I realized that how writing a research paper can be though. But the bright side of it is that I'm learning a lot. tomorrow will be my first experience on extracting DNA, and I'm so exited about it. I hope everything goes well, and I get interesting results. As I said I'm going to see if the bacteria grown from my skin is the same as my known bacteria (staphylococcus aurous). I also incubated my samples today to grow over night, so I have fresh samples for tomorrow.

https://www.youtube.com/watch?v=azCozArFK9M

 

 

Week seven

 

Extracting DNA is one the most important scientific discoveries as it helps human and their wellbeing in numerous ways. Nowadays, isolating DNA and observing its characteristic and functions can be done in order to classify them or do comparison on different DNAs for different reasons. Some of the reasons for extracting a DNA are to find out about mutations, paternity, genetic disorders, forensic, and for diagnostic reasons. Extracting DNA opens an access to genetic material, and to study it and manipulate it in order to improve human life and the world surrounding them. My research is on extracting DNA from bacteria on human skin and staphylococcus aurous to see if the two are the same or not. Two colonies observed to be so much alike. To take a step further, more experiments are needed to be done. Colony morphology for the bacteria grown from human skin was so close to that of staphylococcus aurous. Series of tests will be done to determine the truth to this hypothesis, and to make the result definite DNAs of two species will be sequenced. If the results to any of the steps don’t support the hypothesis, further experiments will be terminated and conclusion will be made.

Google Image

     Week Six

I wanted to extract DNA out of the bacteria that I grew from my skin last week, but unfortunately I got so sick and wasn't able to do the experiment. What really interests me is extracting DNA from different people's cell and compare their different characteristic with each other. I'm really curious to see if DNA gets shorter by us aging, or if tow people that are at the same age would have DNAs of different lengths because of their different genetics. I'm really into looking at researches that have been done on how to stop shortening the DNA or how to inject foreign DNA into our DNA in order to treat a disease and be successful to pass the foreign DNA through the immune system without having to hurt the white cells. I know it sounds like a big project, but I'm considering those as a future project and for right now, I just want to start with anything that leads to that goal at the end. Below is a video that I found interesting. please take a few minutes to watch it.

https://www.youtube.com/watch?v=de0aSMxeYmg

 

Blog Bio 

My name is Mitra, and I'm from Iran. I moved here three years ago from Turkey. I lived about three years in Turkey and had a really good experience living there. I loved that country so much that I'm planning on going back and spending more time in there later on. But I have to finish schooling first if I want to live there for a while. I'm still going to visit though, sometime soon. I started attending Phoenix College a year after I got here, and I'm almost done with my associate. Now, It's time to decide about my career.

I really like doing research, but I never had the opportunity to do one before. I have a little bit of engineering background, so all I was doing was about math and physics and never really biology or anything from that kind. After having my first biology class, I started feeling even more interested in research, and it's kind of tilting my mind towards research as a career. When my family is here I'll be having more peace of mind, and that will help me to think more clear and eventually decide what I want to do with research. I'm from a big family and have four more siblings. They will be all here next year. I can't wait to see them again. They are so supportive and loving, and I'm blessed that I get to have them around me again.

I want to share a picture that I took from a stream that was running behind my house in turkey.

First Week

 

Hi everyone,

I started my lab work tow weeks in to the semester so I kind of felt that I'm behind. I also felt lost. By the time passed a little, I found myself more comfortable doing the procedures and I also got to know you and to ask your help in certain areas that I needed help with. I'm glad that I'm finally part of the program and get to learn a lot of things that I wouldn't otherwise. I'm really excited and can't wait to see how much knowledge I will gain at the end of the semester. I'll be most probably transferring next semester to ASU west campus, but if I end up staying here I hope to have enough knowledge by then to do an specific research on the possibility of stopping or slowing down DNA shortening.

 

 

A picture of our lab stockroom

 

 

Fifth week

 

 

last week I figured out that my bacteria was Gram Positive Cocci. This week, I did more tests to figure out my unknown. I added hydrogen Peroxide on my bacteria sample for Catalase Test and saw it's bobbling, so I moved to the next step. My bacteria had changed the color of the indicator dye in the glucose and lactose indicating the change of the PH in the medium, and bobbles were trapped in Durham tube. So the result was positive, and I had to look at the result on my MSA Test. Sure enough that it had turned from red to yellow. Now with having a positive result for my last test I can conclude that my unknown is staphylococcus aureus. I also incubated an MSA and a TSA plate with bacteria from my skin. next week, I will extract DNA from the bacteria that I had initially as my unknown and the one that grew from my skin to see if those are the same type of bacteria. It will be exciting if I find the similar result.

Glucose, lactose, and MSA plate after incubating my initial unknown

 MSA and TSA plates before inoculation

 

Grown bacteria that I got from my skin 

 

Inoculated broth with bacteria from MSA plate with grown bacteria from my skin

 

Fourth Week

I got the results for my inoculations and saw how the unknown was grown. I included some of the pictures dawn below. But my lab work for this week was Gram Stain. In this method I learned how to identify the type of bacteria, but I still don’t know what exactly my bacteria is. First time when I Gram stained, it all got washed off because I hadn’t heat-fixed the bacteria smear on the slide. Second time, I successfully finished the experiment and got to look at my unknown by microscope. It was purple, so I figured out that it’s Gram Positive, and from the circular shape that it had I found out it was Cocci. Then I could cell morphology by looking at my bacteria’s colony from my isolated bacteria and could see that it was circular, raised, entire type of colony. I also included a picture of my bacteria. Now, I’m looking forward to my next week experiment which is Gram + Catalase Test.

                                                                     Unknown Lab

This week was basically my first lab experiment. I learned about five I’s: inoculation, incubation, isolation, inspection and identification. I inoculated a sample from TSB (soy broth) to TSA slant (soy agar) using loop and dragging it in “S” pattern back and forth across the surface of the agar. The loop should be sterilized by heating it in Bacti-Cinerator for 5 seconds before each use. I also learned how to streak a plate in two different ways. First, I used the lawn technique. It’s basically spreading your bacteria on a petri-dish in an “S” pattern. I spread my unknown on the first region.Then turned my plate 60 ͦ and kept spreading it and did another 60 ͦ turn to make sure it’s spread really well. Next technique was isolation technique in which I divided a plate to three separate regions. Then, I spread the sample or my unknown on the first region. To go to second region, I got two lines from first region and spread those on my second region. I repeated it for third region, but getting my two lines from second region this time. I incubated them all and waiting for them to grow, so I can inspect and eventually identify my unknown. Bellow is a picture of my plate, slant tube and unknown.

Hi everyone,
I just started my lab work last week. Like any new scholar, they started me with safety videos, and I got to meet some of you and hear about your individual experiences which were really helpful. I got to watch Celena making and running gels with 2% Agarose. But because of her PCRs being so dried out the experiment wasn't successful enough. Next week they will have me going through the routines of the lab like cultivating bacteria. I'm looking forward to start my second week, and I'm sure it will be amazing working with you all. Below is the picture that I took from the experiment that Celena did while teaching me about it. and I think we are going to work together for this semester on the same project.