Take 2

I gave the bacteria extraction from soil another try to see if I had different results. It looked as if I contaminated some of my samples and didn't use the right amount of broth. The second time around was a bit easier and quicker because I am more aware of what to do and made sure that I was very careful (learned some interesting tips two weeks ago about the "do's" and the "don't's" when going through the process). I then worked on streaking the samples on four petri dishes and wait for the results to show.

11/22/11

Well to start the day i had to write down data from the yogurt experiment and then took some picture of my experiments. Then I started to work with Rick and started to staining my yogurt bacteria that grew in the TSA media plates. After that I learned about the different types of bacteria based on the shape shown in the microscope. My bacteria was bacillus gram negative.

11.22.11 Gilbert

So on tuesday I worked on writing up my experiments that I worked on the previous weeks. When we finished the write up josh told us to stain the bacteria that was in the our yoghurt experiment. The problem with that was that we didn't know how to stain them so he asked Rick if he could teach us how to stain the bacteris properly. After Rick taught us we each did one ourselves and the end result was pretty well. I could clearly see the gram positive Bacillus bacteria in my slide.

11.22.2011

Well this was a really short day but we did do a lot. To begin we started off rewriting the little experiments that we did in the past weeks. After that, we worked with Rick in staining our yogurt bacteria that grew in the TSA media plates. It was pretty interesting and the best part was I stained my hands more than I did the actual bacteria. After that we learned about the different types of bacteria based on the shape shown in the microscope. My bacteria was bacillus gram negative.

11/23/11

Wednesday, we didn't stay that long. We learned how to gram stain bacteria and look under the microscope identifying Spirilla, Bascillus, and Cocci. My bacteria had the most common Cocci within it's view. It was fun :)

Microbes Soil Isolation Project

Josh introduced me to a new project, which was to look for a way to isolate bacteria from soil. I researched several experiments, but then I was given a mini-lesson on how to conduct this experiment with the help of Josh and Matt. Several mistakes here and there, but I eventually learned how. 

Soil Project Continued (Microbes)

Samples of soil. One is directly from the garden, and another is from a path of soil. 

What I needed to keep in mind before using the "hood".

• Make sure to clean any contamination with Windex
• What goes in, it does not come out until it is closed and finished. 
• Make sure to wash hands!

First Experiment

• Obtain 2 different samples of soil (path and garden). *Make sure to label!
• Have a test tube racket with six test tubes + cap. 
• Have the "hood" clean with Windex and have paper towels ready in case of spills. 
• Wait for 5-15 minutes with UV-ray light to clean the "hood" from bacteria.  
• Turn "blower" on and light on and get ready.
• Have Super Broth and about 4 LB Nutrient Broth in the "hood". 
• Make sure to have all materials in the "hood" and do not take anything out!
• Add soil (2 will be garden soil, 2 will be path soil, and one with garden and another with path. *Use yellow loops (do not touch the loop!). 
• Once labeled (test tubes), add 4 (2 garden soil and 2 path) 5 ml of LB Nutrient Broth to 4 test tubes. 
• *Make sure to use a pipette and graduated cylinder to take out the Broth. If contaminated (Broth), use new broth and pipette.  
• Add 5 ml of Super Broth in each test tube remaining (2). 
• Note: when taking out media (opening cap), try not to open completely or else it may become contaminated.
• Take test racket to the incubator and wait for alarm or ask. (Maybe 1 hour). 

Experiment 2

• Repeat sanitary procedures. 
• With test tubes in the hood and 6 petri dishes, use loops to swab samples for each tube and apply to each petri dish. Swab the sample in the petri dish several times. 
• Label (turn over) with date, name, and media used.  

 Results 

 Example of 1 of the 6 with bacteria and other things growing.

Last Thursday we learned how to streak plates in the Bio Safety Cabinet (with the hood) so that there is a smaller chance of contamination. I streaked two plates with buttermilk, which I then labeled and let set at room temperature. Then I made a buttermilk 10mL/milk 200mL solution which I also set at room temperature. We watched videos on Fungi and many ways it can "save the world" with capabilities such as absorbing oil.
Today I arrived to find that the buttermilk/milk solution and plates were refrigerated. Richard demonstrated to Tomie, Alex, and myself how to stain bacteria (taken from our plates), how to tell if the bacteria is Gram Positive or Gram Negative, and to identify different types such as Cocci, Spirilla, and Bascillus.

Catalase Project

Matt chose a mini project for me to work on and experiment to find results. My project was to find was Catalase was and to see if it was in potatoes. Using Hydrogen Peroxide was the key to this experiment as it gave me results to the project. 

                                      The Catalase Project

 What is catalase?
Catalase is an enzyme normally found in many plant and animal tissues, and it's purpose is to destroy toxic substances which may be introduced into cells. Also, some cells use catalse to destroy cellular debris or worn out organelles.
 Credit: chem.lapeer.org/Bio2Doccs/catalaseLab.html

Further in Research
As I was browsing for an experiment that I can conduct, I came across a site that gave great info about enzymes, which I wrote down for future reference. I thought it would be helpful to keep in mind when working on this project.

• Enzymes have five important properties that you should know:
• They are always proteins
• They are specific in their action. (controls reaction/type of)
• They are not altered by the reaction. (This means that an enzyme can be used repeatedly. It also means that enzymes appear neither in the reactants nor in the products of a chemical reaction.
• They are destroyed by heat. (This is because enzymes are proteins, and all proteins are destroyed by heat.) Destruction of protein by heat (or under any extreme conditions of pH or salt concentration) is called denaturation. 
• They are sensitive to pH. 

Credit: http://www.sciencegeek.net/Biology/biopdfs/Lab_Catalase.pdf

 Experiment 
Once I found an experiment, I gathered my materials and begun.

• Procedure
• Label 3 large test tubes hot, cold and room temperature. 
• Cut (3) 1.5 cm^3 pieces of potato with peel removed. 
• Use a mortar and pestle to mash/grind up each cube.
• Place all of the mashed potato cubes into each labeled test tube. 
• Add 1m of distilled water to each test tube with mashed potato. 
• Place the test tube labeled hot in the hot water (100 degrees Fahrenheit) both for 3 minutes.
• Place the test tube labeled cold in the cold water bath (0-4 degree Fahrenheit) for 3 minutes.
• Leave the test tube labeled room temperature in the test tube rack. 
• After 3 minutes, remove the test tube from the baths and allow the hot test tube to cool.
• Add 5 ml of H202 to each tube. 
• Wait one minute while reaction occurs then measure the height of the bubbles in each tube in cm. 

   Before hydrogen peroxide has been added

Results
Once I did this experiment twice, I found some slight changes, but usually the same.

• 1st Experiment
• Cold temperature = 5.5 cm (0-4 F)
• Room temperature = 10 cm (73 F)
• Hot temperature = 2 cm  (100 F)

• 2nd Experiment
• Cold temperature = 10 cm (0-4 F)
• Room temperature = 8 cm (73 F)
• Hot temperature = 1 cm (99.9 F)

Overall
Overall,   I found out that potato indeed has catalase, and the results with this experiment was a nice way to see how it takes effect with hydrogen peroxide. "Under the influence of an enzyme called catalase, the hydrogen peroxide is broken down into water and oxygen."

11/16-17/11

Wednesday was a very long day because I helped out Alex with finding soil for his experiment but didn't know which soil to collect so it took us awhile. I had put the numbers from the inventory taking we did our first week. It took awhile helping Alex but it was worth it because I saw the garden.

Thursday we watch videos on fungi and how it can change the world. Then I tested out my experiment with rennet and milk forming cheese. However, I ran out of time therefore I have to redo it on Wednesday(11/23/11). I also took notes on hot to streak a plate so when it comes time, I'll now how to do it.

November 16 and 17, 2011

On Wednesday, I showed Matt my findings for my potato experiment that I have done in the past. I was told to redo the projects (because it is a good idea to do it twice for comparison) and this time he will be taking pictures of before the experiment has been implemented and after the results were in. This time the experiment went a bit easier because of previous experience and I was able to get the results rather fast. I compared my results from last time to the most recent and found somewhat of a difference, but for the most part things stayed the same as expected. After, I worked on another project, which is to isolate bacteria from soil samples. I went to the campus to find samples of soil, one from the garden, and another from the path. I was to work on the project the following day.

On Thursday (today), I continued with my project, but this time I was using the "hood" for the majority of the experiment. I struggled a bit because it was my first time using the machine, but I eventually got the hang of it after the mistakes that I made. I applied two different broths, one was Super Broth and the other was LB Nutrient Broth. I applied LB Nutrient Broth to four test tubes (2 in the garden samples and 2 in the path samples) and then apply Super Broth in one test tube (path) and another (garden). After I was finished, I left it in an incubator and watched two twenty-minute videos about "Biomimicry" and another about fungi. I really enjoyed both clips and took notes which I found interesting. Mushrooms can sprout out of ants! After the videos, I continued with my project and swabbed the samples to six petri dishes and then labeled them. I should continue to work on this project next week. This is the most exciting project yet, besides Aquaponics and Hydroponics.

10/10/11

I went to Robotics and got to use hands on equipment to cut open half globe of the world. Then i got to control one of the Robots. I also removed laptops from one classroom and put them in another classroom. I also put some DI water into the testing tubes of the Baby Onions. There was a slight change in the roots and i measured then and put them back. Then i wrote down the data I took into my notebook.

11/16/11

So today I checked on my experiment with the pinneapple and the jell-o and recorded the results and also started a new batch but this time I used canned pinneapple and concentrated pinnaepple juice. After waiting a while the results of the test were as expected that the canned one would not do anything because it was cooked and also the juice didn't do anything. After checking the experiments that I did one with eggs we hard boiled some eggs and put the egg whites in a test tube and after that we smashed the pinneapple and some mango to get it juicy and stuffed it in the test tube along with the eggs to see if the protein will also eat the protein from an egg.

11.16.2011

So today was pretty interesting. I started off with one Matts little jello projects. It is a little similar to what Gilbert did with his Jello pinapple project, except I used mango. What I basically did was create an experiment to see if mango contained the enzyme protease. Protease is an enzyme or type of protien that is, in theory, suppose to hinder the process of jello solidifying. What I found out was that there is a way to stop or inavtivate those enzymes, by denaturation, which means changes shape or structure of a protien, with out chaging what it's made up of. It is said that heat will permantly inactivate the enzyme protease in mangos. In my experiment I made 3 samples of jello, one control, one with fresh fruit, and one with cooked fruit. I will see the results tomorrow.
I did another one of Matts exeriments, which is one of his most smelly ever I have to say. We had boil 12 eggs, only to use like 2 of them. Put them in 12 test tubes and add smashed pinneapple to 4 test tubes and and smashed mango to the other 4, all of this is along with the egg pieces. The last 4 were our control with nothing but pieces of egg white. The reason of this test isto see if the same enzymes we tested before will eat though egg white, which is another type of protien. That is basically all.

11/9-10/11

Wednesday I was creating a box for a family for Christmas time and made about 28 tubes with protease and 28 tubes with lysis buffer.

Thursday I helped clean a cadaver, finished making the box on all 4 sides including the lid, helped pour media in small dishes, and watched a video about education and artistic ability dwindling.

11/15/11

So today I did my Jell-o experiment for matt but I have to wait until thursday to see how it came out. Today we had a little trouble with conversions from cups to ml so Jen, Michael and I googled it and decided to print out the table. I also took one of the new tech people Michael into the cadaver room to show him the bodies and showed him how to clean them by picking out the fungus and spraying the dis-spray. Jen tought me how to use the autoclave for the dry cycle and it was fairly simple. Thats about it, it was kinda slow since I was the only one that came to ineternship today. On 11/10/11 I help the robotics get an idea of how to build R2D2 from star wars and it was pretty fun because I personally like building robots, we kinda have an idea how to build it and I think its going to look great.

November 10 - Robo!

It was a different experience in internship. Instead of researching, working on a project, helping out in the labs, I went to a Robotics meeting. I've never been to a Robotics meeting before, so I didn't know what to expect (besides robots). After some time in the meeting, I started to appreciate people who deal with machines, tools, etc. because there were some procedures that were quite dangerous (sawing that could chop fingers), and also how mathematics is prevalent. It's great to see different perspectives and see how people with different passions (whether it is engineered-focused, medical-focused, etc.) impacts our lives. I thought it was an interesting day.

November 10th Meeting

Today we cut the globe in half and reset the base higher on the PCD3 Robot. We also fixed a broken PWM cable on Bear. Next week we will add plywood and build the body. Thanks everyone!

11.8 - 11.9

Well on Tuesday I made HE media. It was quite interesting because while I was making it, it was a dark almost black liquid. When I poured the plates, the liquid turned into a greenish purple. I also got to help another intern, Gilbert, with pouring MSA plates since I have been working a lot with pouring plates. I also researched what The Belmont Report was and who it was designed mainly to protect. Which is mainly childeren, elderly, people with disabilities, prisoners and people in the army. We also worked a little bit more on my project but realized that it still is difficult. We did however get past the calibration process, which is much more difficult then it looks. Today was kind of slow for us, mainly because Josh is so busy, but I started off with pouring plates of MSA. Then I had to bag the MSA and HE that was completely dry. We helped prep a lab practical and we also tore down a lab. Oh yeah, we also cleaned 3 of the cadavers.

NEW PROJECT!!

Last week my project was completly changed. i was trying to compare
DNA from two palo verde trees. I was able to succesfully extract DNA from seeds, the next step was to pcr the DNA and cut it with enzymes. Thing was i needed the sequenced DNA of the trees in order to know where to cut, and no one has sequenced it. So my project was stalled. Josh had me talk to Dr. Hayashi about it to see how we could proceed. We looked for the DNA sequence even more but we didn't find it. Dr. Hayashi then told me that i should focus on a smaller scale, so we went with bacteria. As of now theres not a set project but so far im going to grow bacteria from soil samples collected here at PC and a Tortoise habitad we have at my High school.

11/2-3/11

Wednesday I was real sick.... I was kindly asked to leave so I didn't do much at all.

Thursday was a little more productive since I felt better. Josh had me help clean 3 cadavers and when we were done, I had to fill 192 tubes with dionized water, 32 tubes with lysis buffer, and 32 little tubes with dionized water and protease mixture. Jasmine helped me because it was a hefty task.

11/8/11

So far I have been working on many little projects for a couple of labs. I created 6 slide sets of four slides each for Mrs. chapmans class. those slides were composed of interns hair. Basically I had 3 suspects and one of those is the killer and all you have to do is match up the hairs to the corresponding suspect. I also worked with josh on testing out a new and faster DNA kit from GenoSensor Corporation we have to use sybr green which was at a concentration of 10,000 and I had to dilute it to 2/10,000. The DNA kit failed because we didn't have the adequate instructions to follow so we basically did it by what we know and it didn't work. I'm also working on an experiment for matt that consist of pinneapple and Jello and what im trying to do is to see if the pinneapple will allow the jello to solidify it all has to relate to the proteins that each of those have. Everything else that im doing is just helping out and trying to keep everything organized in the Lab. 

11/3/11

I started on my little project and that was Determining weather Onion roots will grow faster with Miracle Gro in the DI Water and I'm testing that by having two controls that can determine if they grew faster or not. I had put 24mL of DI Water in 2 of the testing tube and then i put them in a tube rack. Then i got a scale to weight out the Miracle Gro and the first one came out to .155 and then put in in a beaker and then put 24mL in a test tube and then put in the beaker with the Miracle Gro then put it back in the testing tube and place it back in the test tube rack and then  I repeated the process for the other 3 except i added .005g to them such as the 2nd one was .160, 3rd one .165, and 4th one .170 and i labeled each tube and then placed a onion on top of each one including  the controls. Then put them in refrigerator. My Prediction is that the baby onions with Miracle Gro is going to grow faster than the control and within the the ones with Miracle Gro, the one with the most will grow faster than the others and the one with the less will slightly grow faster than the controls. After i worked on my little project i took care of finishing enrolling for the class and help prep a lab for college students in a classroom. 

Sorry...

I have been a little behind on my work so I kind of been slacking on my posts. It is my mistake and I will ensure that it will not continue to happe. So, what has happend from the last time I posted till now, is a lot. First, I started getting familiar with some of the equipment that I will be using for my exeriment. We realized that in order to use the equipment, I am going to need more than one person to operate all the equipment at once, correctly. I also helped clean a lot of the cadavers. I've became really familar with cleaning the cadavers and spotting the tiny spects of white or black fungus. I have also grown familiar with the correct process of wrapping the body after it is cleaned. Oh, Josh and I also had a little "expirement" of our own, that was not even close to sucessful. We made an agar media of BBL Mannitol salt, but that wasn't the difficult part. This type of media requires that it be auto-claved at a pH of 7.2 +/- 2. In order to get this, we had to add acids and bases as needed. This really didn't work out in one of our media mixtures in particular. The pH levels were off the wall and was increasing, for some reason, the more we added acid to it. We spent at least 30 minutes trying to understand why it wasn't working and finally just gave up and created a whole new batch. This one, however, was successful, and there I was, pouring away.

November 3, 2011

Today I started with a new project. The first that I needed to find was what bacteria was common in soil. It took me a while to find the bacteria because there was a lot of types of classes. However, I eventually found that it was Pseudomonas putida. I then needed to look for a protocol for isolating bacteria in general from soil. I'm still in the process of looking for a simpler one, but I did find one that was semi-easy. I will continue to look for an easier protocol to not make things too complicated. I'm interested in this project as I want to see the bacteria from the soil and see how many colonies of bacteria there is.

November 2, 2011

What I did today in internship was that I focused on my connection endeavors project that is required for school, and with that project I should speak with one of the mentors in the lab and discuss about problems/challenges in Environmental Science. One suggestion that was brought up to me was looking in-depth with soils and its toxicity levels. I didn't think about that before, and this has helped me start my research and having something to focus on. I think speaking to someone about it has definitely helped me.