Thursday, May 9, 2013

A new discovrery: Fractals




Recently, I was told about something very cool in Math that i did not know exist before. I found it very amazing so I decided to share it with my peers. I am talking here about fractals. According to Wikipedia, a fractal is a mathematical set that has a fractal dimension that usually exceeds its topological dimension and may fall between the integers. In another fractals are mathematical repeating patterns that we have in nature. We see those patterns in our everyday life, but we do not really pay attention to them to see catch the pattern that was buried inside
Monday april 1, the STEM Program with me include we decide to inform students about fractals in our rubric ASK ME ABOUT STEM
A lot of students did not know about the existing of something called fractals and they were very amazed by looking at the pictures and then watching the videos.
We set up a boot at the sophomore square to illustrate the fractals and to students about it.
Here is a picture of me demonstrating to students how to do fractals by hand.








During our rubric ASK ME ABOUT STEM, we also did some other activities such as DNA extraction from strawberries, some experiments in Chemistry presented by Dr Ed ONG and also we looked at some plants and insects under a microscope with Elena Ortiz, a Biosciences department faculty member. the purpose of these activities is to get students interested and major in the STEM related career fields in order to increase the number of graduate in STEM. I think we reached our goal in a certain way because we got a lot student signed up during those activities and we just need to follow up with them next to see how they are doing.

As usual, I was in the STEM Program last week helping student with their and any questions they might. last week was the week before finals so it was little busy. everybody was trying rushing to finish their late assignment and have them submitted before deadline. I myself was busy. i had some stuff to submit too. it was little rough but we went through it and survive. It is a great pleasure for me to be able to impact students' life and give them the taste of success. I really enjoy doing that! One more week and can't wait for my graduation!!!








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Wednesday, May 8, 2013

Struggling with a software

I have been working on the second part of my project few days after i presented the first at ASU conference. When I was at that conference, one of my judges gave me a brilliant ideas of how to quickly realize the second part of easily. he showed me the NCBI website where i can get the sequences of my bacteria ready to be used. He also showed me a software called CLUSTAL W which i can used to build my phylogenetic tree. when i started the experiment, I had trouble finding the same 16S sequences for all the bacteria in the right format. After many attempts,  and after been very consistent, I finally get the same 16S for twelve bacteria out of fifteen. For the other three bacteria, (pseudomonas mirabillis, staphilococcus epidermis, Proteus vulgaris) I could not find any 16S at all. Now that I get the sequences, I need to aligned them in order to build the phylogenetic tree. This was my biggest struggle. Everything that I try did not give me any result. They all came out blank saying there was formatting errors. This means that I am not putting the sequences in the proper format and I could not figure out the right format. I looked online and I tried everything i got from but it did not work. I asked help from my mentors and apparently they have not used this software before so they was unable to figure it out too. I was stocked on this software for almost a week trying to figure out how to do. After many research and many attempts, I finally figured out the proper format in which you need to submit the sequences in order to get them aligned and then build the phylogenetic tree. It was a very though week for but i was glad that it ended happily.
After that i knew how to use this software, I was very amazed about all the other things you can do using this software. I found it very cool and useful.
Below is the fruit of my struggle--- my beautiful tree

Friday, April 19, 2013

A tour to Desert Botanical Garden

On Friday, April 12th, the S-STEM Scholars with our mentors Matt, Josh and Dijana led by John Schampel, a Biosciences Department faculty member went to the Desert Botanical Garden (DBG) for a tour. We left the the Biosciences Department around 12:30 pm and arrived there around 1:15 pm. Once there, we got our admission tickets which was paid by the S-STEM and started a quick tour to one side of the garden while waiting for a presentation at 2:00 pm given by Dr. Kim McCue, Interim Director of Research at Desert Botanical Garden. She gave us an overview of all the different types of research that are going on at the Desert Botanical Garden and also talked to us about the research and internships opportunities that are available there.
After that, we continued our tour to rest of garden. During the tour, we saw different types of plants that grow in a desert.

We also took a tour to the Butterfly Exhibit where we got to see various types of butterflies. They were very cool.

 While we were touring this beautiful garden, there was a plant that I saw more than once that capture my attention. This plant was Opuntia sulphurea aka Pricklypear.

Pricklypear also known as nopales or paddle cactus belongs to the kingdom of Plantae, the order of Caryophyllales and the family of Cactaceae. It is the only genus in the cactus family.
Pricklypear are native only to the Western Hemisphere. They were first introduced to Australia in 1788 and then to the rest of the globe later. Pricklypear species are found in abundance in Mexico and in the Mediterranean region of Northern Africa especially in Tunisia. They are found in the Sonoran Desert located 25.3 degrees to 33 degrees North and 105 degrees to 118 degrees West. Pricklypear typically grow with flat rounded cladodes that armed with two kinds of spines. Most of the species are cold tolerant in general extending then into western and southern Canada. They produce a fruit that is commonly eaten in Mexico.
They are many adaptations that they Pricklypear has to the Sonoran Desert. They reduced their leaves to spines to reduce water loss and also to protect the cactus. Their roots are also made for very dry environment to help adapt to the deserts hot weather. Usually plants in the desert do not require much water or they need a way to store it for a drought. For the case of Pricklypears, they used thier pads to store water and then used it when they need in a drought.


 


Wednesday, April 10, 2013

Another conference

I came to lab last Friday and I was told by Matt that by Matt that we have to go to another conference at Estrella Mountain Community College. So, we need to submit an abstract and it was due on the Monday following the Friday he was talking to me. The good thing for is that I don't have to write a whole new abstract but I just need to add and modify the old abstract that I already have. This is because I am continuing the second part of my project which consist of extracting the DNA from the bacteria I used in the first part of my experiment and sequence the DNA to have a sequence of the base pairs and then be able to compare these sequences to find which bacteria is related to which one. So, this was my task in the lab this whole week.
Due to many reasons and the short time I have ahead of me before the conference, I can not be able to do the actual DNA extraction from the bacteria and send them to a place for sequencing. But thanks to my judge from the ASU conference who showed a website where I can get the 16S rRNA for most of my bacteria and also he showed another software that I can used to build the phylogenetic tree. So, I spent the whole trying to find the 16S sequence of the 15 species of bacteria that I am using. I used the NCBI website to find these sequences and I searched for the FASTA format of these sequences.
After several hours of research and after being very consistent, I found the 16S rRNA sequences for 12 bacteria out of the 15. The bacteria sequences that I was able to find are: Salmonella, Bacillus subtilis, Enterococcus faecalis, Enterobacter aerogenes, Escherichia coli, Pseudomonas aeruginosa, Staphilococcus aureus, Micrococcus luteus, Providentia stuartii, Serratia marcescens, Streptococcus mutans and Streptococcus salivarius. The three that I could not find are a consistent sequence for are: Pseudomonas mirabillis, Staphilococcus epidermis, Proteus vulgaris.
Honestly, I found it very awesome that we can we have access to those sequences online by simple clicks. It really helps save times during your research.
For the ones that I could find a sequence for, I asked my mentor Matt to give the opportunity to do the actual DNA extraction and sequencing of these bacteria. So, now I am looking for primers for these bacteria and he is going to place an order of these primers and then I can be able to start. The sequencing part is not to be done here in lab because we do not have a proper equipment so after DNA extraction and PCR, we will it to a company for sequencing. I am very excited to do such experiment and be able to find the sequences of the 16S rRNA of these bacteria.
Below is the screenshot of the 16S sequences for Salmonella from NCBI website. Just to give you guys an idea of what the 16S looks like and how to find it.



Wednesday, March 27, 2013

Presentation day at ASU

On Monday March 4th,  I was at ASU Main Campus in Tempe for my poster presentation. Registration is supposed to begin at 7:15 am. I left my house at 6:30 and get there by 7:06 and I have to look for parking. Fortunately for me I found a place where they will let me park for five dollars the whole which i thought was great compared to eight dollars in some places around the campus. After that, I looked for the place called Memorial Union on the campus where the conference will be taking place. After a long walk, I finally found the place. When I got there, there were a lot of people already waiting in line to register. I did the same thing, find the appropriate line and then line up. At the registration, a badge was given to me along with bag containing the schedule of day, information about where i will put my poster for presentation and also some paperwork and fill out and sign by the end of day. After the registration, I went to the big hall where we will be present the poster. Inside the hall, there was breakfast composed of fresh fruit, bagels, juice and coffee on table and everybody was helping themselves. First, I looked for my presentation board number and put up mu poster. After that, I went grab some fresh fruit, some juice and bagels and then enjoy a nice and healthy breakfast. Then after, I was walking around meeting people and looking at others posters to see what kind of research they have going on and they new discoveries in Sciences. There was six of us from Phoenix College to attend the conference. We met there, helped each other set up the poster and then just hanging around waiting for the first talk of the day. At 9, we had the first talk which was about convincing the undergraduate to go for a PhD. It was presented by a teacher from ASU who shared his own experience of how he ended up going to graduate school. Two other teachers also shared their experience on the same topic. After the talk, everybody went back to his/her poster waiting for a judge to come so that you can present him the poster and answer his/her questions. I was waiting and after awhile a judge came to me asking me to tell him about my poster. I was anxious at first but i took a deep breath and started to present him my poster. He was really interested in the research and he even gave me ideas on the second part of my project which consists of sequencing the DNA of the bacteria and then compared them. he gave a me website where I can easily find the sequences of most of my bacteria and then a program to build a phylogenetic tree with the sequences. I was very excited! I believe this was the best experience I ever received in college and I am very grateful to everybody that help me accomplish this.

Here is the picture where we did the conference: Memorial Union



Friday, March 22, 2013

Finally done...

I am very excited to let you guys know that i finally finished my poster for the ASU conference presentation. It was not easy at all and I believe it was the same for my other peers. Now, I am glad that I am done with the hardest part. Remember that I told you guys that I was having trouble writing the introduction because I could not find any references or somebody that has done something similar to my project. Well, I finally came up with a good introduction for my project. This was the last component I wrote for my project and i was very glad that I ended up with something good. Now, it is over with writing and drawing, I am getting ready for the ASU presentation this Monday coming up March 4th. Like we all know it is not easy to stand before a lot people to do a presentation or to speak. Until now I do not know if we are going to present one by one or if we are just going to stand near our poster and people will stop by and ask questions. Hopefully it will be the second one. Anyways, I am getting ready for both. I am more than excited to be there on Monday and meet these varieties of people from all over the place and see what kind of research they are doing and also find out about the new discoveries in science. On Friday afternoon around two, Dijana brought the printed posters in the lab. They were looking very nice in the 3x3 size. I looked for mine and it was looking perfectly great and exactly like I wanted it. Supposedly, one person will bring the poster to ASU on Monday and we will get it from there but I preferred taking mine home in order to practice at home and then know pretty much that I have on the poster and also be ready for eventual questions. Now, I believe everything is ready and I am just waiting for Monday to go present. I am very excited and I am looking forward to doing good on my presentation. Wish me good luck guys!!!

Below is a picture of my poster


Thursday, February 14, 2013

What a week!

This week was a rough week for me. Everything started first with a cold that I caught and which did not give me any chance to breathe just for a second. And on top of that I lost my cell phone in the library downstairs and i have not found it until now. It was horrible! Anyways life goes on and I have to be strong and fulfill my engagement. Since I finished the practical part of my research project, I was in lab this week trying to finish up writing my lab report and the poster for the presentation at ASU conference. It is on march 4th and it is around the corner so I better work hard to get it done on time. I spent this week in lab trying to write the introduction. But unfortunately, I could not figure out something good. For some reason, I am still having trouble writing the introduction of my project. I spent countless of hours trying to research if anybody has done a similar research but unfortunately I did not see anything similar. Last week, I started with the material and methods part which I finished it this week. After that, I began the results and discussion part. I have all the results of my tests recorded in my lab notebook so I used it to create a spreadsheet on Microsoft Excel in which I documented my results. Now I just need to insert this spreadsheet in the results and discussion part along with my two phylogenetic trees that I already made. After that I will focus on drawing a conclusion of my experiment and then go back to the introduction. I hoping by that time I will have the inspiration to figure out something good. As usual, I was in the STEM Program this week helping student with their and any questions they might. It is a great pleasure for me to be able to impact students' life and give them the taste of success. I really enjoy doing that! For next week in the lab, I will try to finish the component of my poster presentation and start to build the actual for the conference. I am looking forward to finishing this poster in the next two weeks so that I can have some time to revise before March 4th.
Below is the picture of a tree similar to the one i constructed.