This is great :(

Well this is great, Last week I came to find out that one of the refrigerators in DB 107 broke down and with out knowing I continued to the next part in my experiment. As I finished making my PCR master mix I got up and begun to look for my DNA extraction samples that I had left in the fridge, as I opened the fridge it was completely empty which was strange, I searched for Matt to ask him if he had moved or seen my samples which then he followed by saying oh! your samples were in there? I was disappointed when he informed me that the fridge had broken down sometime last week and no one noticed until a couple days later when everything on the inside had gone to waste. Now I have to extract the same DNA again so I can proceed to running my PCR. Hopefully I am able to get it done quickly so that I may get results fast.

Protocol

PCR protocol:
PCR mix
DNA 1μl
Primer 1 2μl
Primer 2 2μl
Master mix 12μl
DNase free H2O 7μl
Total= 25μl

Cycle
1. 95°c for 3 minutes
2. 95°c for 30 seconds
3. 58°c for 40 seconds                  Repeat 2-4 35times
4. 72°c for 1 minutes
5. 72°c for 10 minutes
6. Hold at 12°c 

Well that's my PCR protocol with the cycles included but we might need to recalculate one of the temperatures because it was just and educated guess. This week we had our rough draft for our research paper due and I found it quite difficult to accomplish since I don't have any results that can help me with my conclusion but I was however able to finish part if it. Last year when I wrote my first research paper it was quite easy because I had all this information in my head and all the results it was just a matter of putting it all together, now don't get me wrong I don't think it was the best paper ever but it was a pretty good first try. Next week I will be getting some results from my project and hopefully I will be able to revise my paper and make it even better.

PCR

Currently I have 4 plants that I have extracted DNA. With those four samples I am now able to run it through the PCR to amplify the DNA the only problem is that I have no protocol for the PCR yet. The protocol is currently a work in progress as well as getting the primers ready since the primers come dry (As in they look like a powder). I know Jervana is also eager to get those things as well. As soon as I get them I will begin my PCR and hopefully yield promising results. I almost forgot that this week I am suppose to have 90 hours completed for S-STEM and I am a bit behind on that so now I will have to be at lab for a while to catch up. The picture below is how I feel right now with all the stress of classes and work.

(iFunny)

Second attempt

The extraction for the the tomato and the carrot came out really well but there was a slight problem. When I was extracting the DNA from the tomato, I didn't yield a high amount of DNA so I had roughly 0.1mL of tomato DNA and after running it through the Gel I was left with practically nothing. So the bad news is that I will have to extract more DNA from the tomato. The second part of the bad news is that when I was pippetting I accidentally tore the well in the gel where I was placing the DNA and didn't notice it so nothing came up on the gel except for the carrots DNA. Next step is to extract more DNA from more plants and then run then through the PCR to amplify it.

Good news

Well the good news is that the wizard kit actually worked and although it was a bit difficult to understand once I got it done the first time it was quite easy after that. I ran the extracted DNA in the gel box and there was some DNA present so that was pretty exciting. At first when I saw the gel it was quite disappointing but looks can be deceiving a closer look at it under a UV light showed that there was indeed some DNA present in my samples. The samples present below were that of a lettuce leaf. Now that I know it works it is time to extract more DNA from different vegetable and fruits.  

The Struggle

Well this past week hasn't been all that easy for me going back and forth on what I want to do. I have been an intern here at phoenix college for about two years now which is a very long time. Currently I have no clue if I want to continue this internship so I spoke with Amanda. I'm currently trying to find something that I'm passionate about which I have yet to find. It's a big struggle for me to find something which I am passionate about. I have done a wide range of jobs, internships, and volunteer work solely for the purpose of finding something that is interesting to me. Even though I'm in this dilemma I will strive to do my best with everything, don't get me wrong I love being in the Biosciences department but I think I may need a change of environment or maybe I'm just freaking out and there is nothing to worry about.

Electrophoresis

Well last week I began my DNA extraction protocol and found it quite easy to do, or so I thought. When the time came to using the Wizard kit it was difficult to follow the protocol that came with the kit so I was asking Matt tons of questions regarding how to use it. After a while of going back and forth with Matt I was able to write a protocol in my own words. At first it took me quite some time to get used to the process but I believe that after a while I will be able to do it in a much faster pace since everything is practically repetitive. Tomorrow I will be running my extracted DNA though a gel to find out if I have any type of DNA present in my sample. When that is complete I will be running the rest of my sample through a PCR machine.

CaMV 35S

CaMV stands for Cauliflower Mosaic Virus which is a pararetrovirus (reverse transcribing viruses because they replicate through an RNA intermediate) that infect plants. Pararetrovirus replicate through reverse transcription (Creates single stranded DNA from an RNA) but the viral particles contain DNA instead of RNA. CaMV induces a variety of systemic symptoms such as mosaic (irregular leaf mottling), necrotic lesions on leaf surface, stunted growth, and deformation of the overall plant structure. Basically scientist modified this horrible virus to make it easier for them to infect a plant with a genetic mutation to alter the state in which the plant will grow into. CaMV 35S is used in most transgenic crops to activate foreign genes which have been artificially inserted into the plant. This enables the plant to operate in a wide range of host-organism environments which otherwise not be possible.

(The Science Creative Quarterly)

 

It's time

It's about time I can start on my project. Matt just gave me the okay today since he had to figure out what type of protocol I needed to use and also all of the materials I will be using are here. This Friday I will begin going over the protocol with Matt and deciding on what food I would like to extract DNA from. Hopefully by tomorrow I will be able to begin extracting DNA from multiple plants so that I may run it with the "Wizard" kit that was purchased. The process after extracting the DNA should run somewhat smoothly since I have done PCR's and Electrophoresis numerous times it should be relatively easy. Later on as I perfect my protocol I will be able to run different types of food ranging from cafeteria food or something from the vending machine to identify the presence of CAMV35S.

(Exploratorium.edu)

Protocol?

Since most of the materials that I need aren't here yet, I started researching a way to extract the DNA from my food samples. There is a vast amount of protocols that state what needs to be done in order to extract DNA from plants and it's very difficult to pick just one. I had a discussion with Matt about what I should do because the protocol that he had sent me earlier wasn't something that I could use, well I could use it but there needed to be some changes. All the materials were ordered and should be on their way thanks to Matt. Jervana has also been waiting for the same materials since we are doing practically the same experiment I feel Jervana's eagerness to receive them.

(Courtesy of SOPACHEM.com)

What is a GMO?

GMO stands for “Genetically Modified Organism” most commonly found in plants and animals. Plants and animals are genetically altered by scientist to improve the ability for it to grow in various environments, resist pest, tolerate extreme weather, Produce more food, or show desired traits. GMO’s are like system updates on your computer, making a new version of that specific plant or animal in a lab. This semester I will be working on isolating DNA from various foods and running it through a PCR to detect foreign DNA, since most of the transgenic crops contain a CaMV35S promoter it offers a good target for DNA testing. CaMV35S promoter is derived from the phytopathogenic cauliflower mosaic virus.

Well!

It's that time again when we start going to our internships. Even though this past couples of weeks have been kind of stressful because of classes I have the task of organizing my time so that I'm able to participate in the S-STEM discussions and also getting to my internship on time for 9hr/week. I went to robotics today to help out Josh (Lab Supervisor) with the new robotics people and to also get some work done. This year's game Toss up sounds quite exciting. Below is a video describing this year’s game and hopefully we will get 1^st place. 

Rocket launching

Launching the rockets was lots of fun. The launcher that I build work great or so you can say but it did what it was needed for. The launcher was able to hold its pressure at about 80psi which was great because it made the rockets go a great distance. I had some strings attached to some rods so that we would be able to pull them when the pressure was where we wanted it but after a couple of launched it completely fail and I had to resort to hold it with my hands. Holding with my hands was a great idea at the time up until I got wet from the multiple rockets that were launched but it was worth it. It seemed like everyone was having fun watching some rockets fly and others completely failing. Josh of course won in the achieving the maximum height then Amanda's daughter and I came somewhat close to josh but we didn't beat him. Since we did fairly decent josh announced that he would be buying shirts for the people that came close. The shirt will have the robotics logo along with a sub tittle of projectile specialist. 

The video is a bit messed up but you can somewhat see how high the rockets went.

The wait is over

It took a while but I finally heard back from Estrella Mountain saying that I was accepted. Apparently they forgot about me and I probably would have never found out if I got accepted. Well at least now I know for certain that I will be attending. I was supposed to take part in both a poster and an oral presentations but since i didn't hear back from them for the longest time they told me I was just accepted to the poster presentation which I didn't mind.

The easy part of presenting at Estrella mountain is that I already have a poster from ASU the only thing I need to do is re format it to fit the specifications required since the ASU poster was 36x36in and I need a 36x48 poster. Aside from that rearranging everything on my poster was simple. I also added more things to this poster since I have more space to work with.

The difficult part to this has begun since we are required to write a lab report for our whole project it became a priority since most of us (interns) haven't started it has proven to be somewhat of a challenge. Everyone was freaking out at first because they thought we were going to be writing a 20 page report until Amanda cleared it up and I believe she said somewhere in the 8 page range.

Testing our rockets

Well it doesn't look like much but this puppy can fly, not very high but enough to make an impression. The first launch went pretty well and surprisingly as it was coming down it flew like an airplane and it was awesome. To make it go to a higher altitude I had to add weight to the nose cone and I did that by tapping washers to the cone. I had to make so that the washers sat on the outside because there was no way I would be able to put them inside. I made 2 rockets and both flew but the second was pretty crappy it was too heavy coming down like a lawn dart.
One of the challenges we had to face was in regard to the launcher it was not well designed so it wouldn't hold more than 20 psi before the rocket taking off. I had to come up with a new design that is able to hold pressure up to 80-100 psi so that we are able to achieve a greater distance.
When it comes to filling the bottle I found that it is best to fill a maximum of 1/3 of the bottle to enable it to reach a maximum height. also being able to fly straight is a result from building fins to stabilize it while it is in flight.

Bottle Rockets

This week in robotics we started working on our soda bottle rockets and well let’s just say it is going very slowly. The soda bottle launcher proved to be a bit difficult to build since we didn't let the glue dry on the PVC pipes making not hold any kind of pressure. It held a bit of pressure enough to blast the rocket but it didn't get very high. We also tried various sizes of bottles to see which one would travel the most distance leaving us with a poor demonstration. That good thing though is that we now know what not to do which will help up in the future. Everyone else should watch out because Josh and I our working on a special rocket that should theoretically blow everyone away but I can't give out any more information because it is top secret.

Calibrating the probe that I'm using wasn't as difficult as I thought well when you find the manual it isn't as difficult. Now that it is calibrated I will be able to start collecting data to help my experiment which I have been working on for almost a year.

Estrella mountain student conference is upon us, at least the deadline for the abstract just passed. I submitted my abstract on time and I will do an oral presentation. I signed up for both an oral and a poster presentation. Matt suggested that I should do the oral presentation because he thinks I will be able to get first place based upon the presentations that we viewed during last year’s conference. I am a bit scared and at the same time a bit motivated to do the presentation. The reason for why I'm scared is because presenting to a large group of people is somewhat stressful and also trying not to finish the presentation with "so umm yeah" which a lot of people tend to do.  

Not so great

The past couple of weeks haven't treated me nicely :/ My computer crashed 3 weeks ago and well it's been hard for me to do anything but at least now it's getting fixed. Also during spring break my car broke down so this week has been hard for to get to lab on time during the morning so I haven't been in lab in the morning and well I have minimal hours this week. This week I started working on the submersible attaching the probe that will be reading data from the water. There is also a camera added to the submersible so that I'm able to see where I'm going and to just get an idea of how it is. (Like in Rio Salado or Papago park) 

I also tried testing out the probe that will be attached to the robot but it didn't seem to work out so well mainly because it is old and not calibrated. My next step is to calibrate the probe and test it to see if it is going to allow me to get accurate results. Since the only outside body of water on campus is a fountain I spent a good 30 minutes or so trying to get results but since it wasn't calibrated the results were a bit weird. Everyone kept looking at me like I was weird because I was putting stuff in the fountain but I guess they were just curious heck even public safety paid me a little visit.

Thursday was very interesting because as you all know it's when we have a robotics meeting and well we have a project to try out, 2 projects actually. One of those is build a soda bottle water rocket which is somewhat simple if you don't over think it. The other is making a small boat out of cardboard that should be able to float and move.

Finally

After a long and stressful week I feel somewhat accomplished. On Saturday my team and I participated in the vex robotics competition, going in we set a low goal of only scoring 5 points and yet we went above and beyond scoring an average of 40 points per game. We made it to the finals against Scottsdale since we beat ASU's engineering team and also Embry riddle school of aerospace engineering. Over all we did great, got second place and we were only beat by 2 points.

On Monday I went back to ASU again to present my poster project. It was a long day but the good thing was that we only had to present for a short amount of time. Everyone that went did a great job and most people presented to 2 or more judges, I only presented to one but he asked so many questions, most unrelated to my project. All in all I'm glad I got it over with because I don't think I would be able to do it for very long. In the end it all worked out pretty nice, except when I found out my laptop broke which was horrible :(. Hopefully I get it replaced in the next couple of weeks so I can be able to do my work.

Now it's time to start a new project which I have somewhat started already. I will be working with submersibles to try and collect data from the bottom of a lake or pond. This next project is going to be an interesting one.

Busy week

This week has been a stressful week because of everything we had to complete for the ASU conference. The poster that was for the ASU conference was completed on time and it looks pretty good, well it looks pretty good to me at least. Also this week has been a crunch time for robotics since the week before the robot wasn't working properly after all the alterations it had, I spent a good amount of time trying to fix it and get ready for the competition this weekend on Saturday also at ASU. I feel good about the competition we have a functioning robot well we have 1 out of 2 functioning robots, and it looks like it's going to do well. I spent a lot of time helping individuals both in robotics, and lab. I helped a good amount of people that were still working on their poster as well as helping them upload them to dropbox since a lot of the interns hadn't used it before.

This week end, and next week are going to take up a lot of time. On Saturday the the vex robotics competition is going to take place at ASU, and after that I will be attending an open house on campus. On Monday the 4th I will be heading back to ASU to attend the student conference and present my poster on my project all day long. Then on Friday S-STEM will be going on a field trip to the botanical garden which is awesome because I have never had the opportunity of going, and now that I do I will not be missing out. :)

The long days have begun

These past couple of days I have arrived at school at 7am and well it's a bit exhausting especially since I end up leaving like around 5 pm. From 7am-10am or 11am I'm in the lab after that I have classes until 1pm and after that I was in the lab 'till 5pm which is a pretty vast amount of time but it has its up sides. I have a somewhat good amount of my poster finished which is a good thing because those are a pain in the butt to do, not because they're hard but extremely time consuming. Since I was the first one to start my poster and had it saved on dropbox Matt and Josh told all the interns to use mine as the template which is totally find but now everyone's poster looks somewhat to mine, since they're all related :). Tomorrow I will be searching for a new template so that there won't be a resemblance with everyone else's, lets just hope I find one otherwise it would just look funny with everyone having the same poster.

On Wednesday I spent working in robotics, fixing some of the errors that the robot had encountered, since many of people there find themselves disagreeing with one another which is fine because that is process, the only problem was that things weren't getting done. I basically took the whole top part of the robot apart and build a newer version of it which I tried to make as symmetrical as possible, while also trying not to cut any pieces so it could be easily repaired or adjusted. Today since the robotics people were meeting up I showed them what I had done, at first they seemed a bit upset that I took it a part, but they soon came to realize that it was needed, since I wasn't there today to help them they worked on it themselves and I must admit they're off on a good path. Now that we had some ideas exchanged I now know what they want to do with the robot, before everything was done in a manner were only certain people knew what to do so it was hard for others to work on the robot without someone being there.

Anyways it's interesting to see how people interact with each other. I can always help as well if they need me :)

Weird week

   This week has been pretty weird for me because of everything I have going on like my project and school work. Today I worked on the bacterial cultures I have incubated a while back and it held good results except for some unfortunate few that were contaminated but I was still able to get data from the remaining ones. Basically what I did was count every single CFU's (Colony Forming Units) present on each individual dish meaning every dot on the dish was counted. The control plates that I had were the most contaminated of all the majority of them were contaminated but for the ones that were not contaminated I counted the CFU's and took the average of all the controls which theoretically should all have the same samples.

 




I also tested out this experiment for a lab that was meant to test out the levels of oxygen ppm, Nitrogen, and phosphate. At first the experiment seemed somewhat difficult but after I got started it was fairly easy. I was also timing myself to see how long it should take for someone to do it and it took me roughly 55 minutes but I also had multiple water sources to test out: tap water, DI water, and Papago water. It held some interesting results, At first I thought I had messed up somewhere but then I realized that everything was done properly so the results of oxygen was 0 ppm for all water sources, nitrogen was also at zero, the only one that gave me results was phosphate which Papago water was rated at 2 and both DI water and tap water were rated at 1.   

The Difficult Part

So now comes the hard part after 2 weeks it's time to get samples from my test tubes and try to identify the different species of algae. Based on observation alone it seems that the treatments with Sodium Phosphate added to it has the most growth and the weird thing is that tube #1 has the most growth which is expected but tube #2,3 had growth around the same as the control and tube #4 has the second highest amount of growth. Tube #1 had 1ml of a certain nutrient + 100μl of Sodium Phosphate and tube #4 had 25μl + 100μl of sodium phosphate. The nutrient Sodium Phosphate was added to the second set 100μl in each of the test tubes except for the control which is just plain Papago water which should have some nutrients in it. below are the tubes numbered 1-6 left to right.

When taking samples and putting it under the microscope I found that it was extremely difficult to identify all of the species so what I did was take picture with one of the microscope cameras which is somewhat better because I'm able to come back to the picture and see if my observations are the same as Matts. I did however see a pattern within the different sets mainly the one where tubes #1 and 4 had the most growth even though I expected #1 to have the most growth. Below are some of the many picture I took.

After resetting the last Pea plant set I got 28/30 seeds that germinated but the reason why they didn't germinate was because one of them had mold on it and the other was just rotten. The picture to the left shows the the two different reasons. The bottom was the one with the mold and it looked really weird because of the fact that it was like spider webs with little tiny black spots on it. The optimal temperature for the pea plants to germinate in is between 20-25 degrees Celsius. Another factor that I tested out was if light had a difference in the germination rate of the plants, but I came to find that it doesn't have any kind of significant changes to the rate of germination.
     About a Week has gone by since I put my fresh set of test tubes and as you can see there is some visible growth which is a good sign so far. Based on the tubes that have some growth in it are the ones that had Sodium Phosphate added to the tubes in addition to the normal solution. Next week I will be getting some samples from the test tubes to identify the different species of algae that are present in my set. While I look at the samples I will be setting the same experiment up so that I have more data to look at and compare it to the first.

Today I also helped josh with a small little task that involved the garden. I had to create a rectangle that is 33in x 36in out of PVC pipes so that one of the classes is able to plant seed in a grid system. I made one so far but now I must wait for more supplies to finish 2 more and glue all the pieces together.  

Well it's good to be back even though I have to hit the ground running because of all the stuff I have to do ranging from my main project, and my small project to organizing things, and helping set up for labs. It has been a hectic start for the semester so far because of the difficulty of my classes.  I also applied to the ASU student conference that is on March 4th and I got an email yesterday saying that I got accepted to participate in it. During this past week I have set up a new set of algae eutrophication which takes about two week for it to develop enough for it to be visible with the naked eye. I also had to redo one of the sets of my pea plant experiment which is set at 25 degrees Celsius and the light cycle is at 12 hours light and 12 hours dark this set should run for about 1 week this allows them to germinate. The purpose of this experiment is to determine what the optimal conditions are for the best germination rate.

The current setup that I have for my project is a bit confusing because I have 6 different treatments.
Materials:

• 40-15ml test tubes
• 6- test tube racks
• Papago park pond water and RO water
• 5-125ml Erlenmeyer flask
• Green pipette, and micro pipette
• Incubator set at 32 degrees Celsius with a light cycle of 16 hours light and 8 hours dark     

Nutrients: Sodium Nitrate, Sodium Nitrite, Ammonium Chloride, and Sodium phosphate.

Treatments: Sodium Nitrate, Sodium Nitrite, Ammonium Chloride, Sodium Nitrate + Sodium Phosphate, Sodium Nitrite + Sodium Phosphate, Ammonium Chloride + Sodium Phosphate.