Showing posts with label microbiology. Show all posts
Showing posts with label microbiology. Show all posts

Monday, December 13, 2010

Electrophoresis

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Here I will write about presenting data of electrophoresis and also the calculation. What you have is the picture of the gel. You have to make that picture become informative. These are the information that you have to add to the picture:
  1. Make the picture in correct direction.
  2. Name all the well: well of marker/ladder, purified protein, PCR product, negative control, positive control.
  3. Name all the marker/ladder size.
  4. Point out the line of your expected protein/DNA. By the way.. how do you know your sample contained the expected protein/DNA?
Here's, an example from my lab result 5 years ago... but I just edited about 2 hours ago, I didn't point out the expected protein..

Uhm... where's the negative control?? Not remember..

Now, the calculation... Most of you do the wrong calculation for DNA electrophoresis. Okay, I know you got wrong directions... So, now I tell you the correct one. Calculation of DNA and Protein electrophoresis are the same. You have to make calibration curve of the electrophoresis., Log of molecular size against to Migration distance. It supposed to be linear curve.. if you didn't get the linear one.. that's okay. My friend said it usually happens in lab. practice..

Now, about presenting data again.. remember.. informative data.

Table 1. Protein electrophoresis data


Protein Marker size (kDA) Migration distance (mm) Log molecular size
16.6 57 1.220
18.4 47 1.265
25.0 32 1.398
35.0 25 1.544
45.0 17 1.653
66.2 8 1.821
116.0 2 2.064

Then, generate the curve and the linear regression.

Figure 1. Protein Electrophoresis Calibration Curve

Got the linear regression equation --> from computer or calculator.
*It's better if you can operate your calculator to find out the linear regression equation*

Where's the sample? Which line was your expected protein/DNA? Measure its migration distance. Do substitution to the equation, then you will get its molecular size...


Then what should you do with the molecular size?
You've been told what protein it was. Find out from the literature what is the size of that protein.. Then compare your result with it.

What should you conclude?
The identity and the size of the sample...


Simple :D

Monday, December 6, 2010

Microbial Contamination/Limit Test

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Here's I copied the objectives from the lab guidance:
In this experiment, students should be able to estimate the number of viable aerobic microorganisms present in pharmaceutical products, food, and drinks.
What will students do in this experiment?
Students will be given (or they bring their own) a sample of pharmaceutical products, food or drink that will be examined for its number of viable aerobic microorganism. In microbial contamination test, we want to know how much microbial contamination in a products. In limit test, we examined the sample then compare with the limit that state in requirement, then conclude if the products fulfill the requirement or no. Both tests use the same method.

How?
If the sample is solid or semisolid, we have to dissolve it first, using certain buffer (see in Pharmacopoeia). If the sample is liquid we continue to next step. The sample or sample solutions then are diluted to certain concentration using NaCl 0.9% solution (with the certain amount for example, we use 1 mL of sample, after that continue with the dilutions). The concentrations used are exponential, 10-1, 10-2, 10-3, 10-4, ..., ..., ... (start and continue as needed). 1 mL of each concentration is transferred to each Petri dish that already contain Agar (we use NA for bacteria and SDA for fungi). If the materials are enough, do replicate for each series. Then, we incubate all of them (NA in 37oC and SDA in 25oC). Do observation for 7 days. Count the colonies formed 7 days of observation.

Pick one Petri Dish that contain colony amount in range 30-300 (why should 30-300? It is statistical reason). For example your data is like this: Colonies formed in 10-1; 10-2; 10-3; 10-4 dilution respectively are 500; 380; 250; 15, then obviously, pick the dilution that produced 250 colonies (10-3). If the data became like this (in the same order of concentrations), 500; 380;250;70, which data that you pick??? Hmm.. take whole data ranging 30-300 that is 250 and 70. Calculate the cfu for each series. So, you get 25000 cfu/mL from 250 colonies in 10-2 series and 70000 from the other one. Calculate the mean, you will get 160000 cfu/mL. Don't forget to count the colonies in the replicate series too.. (from the same concentration from the first one)

How to do the calculations?
After you get the data, for example 250 colonies (from dilution in 10-3 1st series) and 239 colonies (from dilution in 10-3 replicate series). Just simply calculate the average then times with the dilution factor. The average is 244.5, times with 103 then you got 244.5 x 103 cfu. Because we use 1 mL of sample then 244.5 x 103 cfu is the amount of viable aerobic microorganisms present in 1 mL of sample --> 244.5 x 103 cfu/mL. Simple :D

If you got two data that ranging 30-300, just do calculations for the cfu for each series. So, you get 25000 cfu/mL from 250 colonies in 10-2 series and 70000 from the other one. Calculate the mean, you will get 160000 cfu/mL. Don't forget to count the colonies in the replicate series too.. (from the same concentration from the first one)

Then what does that number means?
That number means, in each mL of products, there's (about) 244.5 x 103 microbes that will form colonies. Each product has its own requirement... let say the requirement for our products is:
Viable microbes max. 103-104 aerobic bacteria per mL
Was your sample fulfilled the requirement?

What should I conclude?
Read the objective! "to estimate the number of viable aerobic microorganisms present in pharmaceutical products, food, and drinks". Report the number then :D


It's simple, isn't it?
Hope all of you understand and can make a good report of this module and also succeed in the lab exam.. :D

image taken from University of Cincinnati Clermont College. Open the link please, read the article, hope you will get more understand.

Friday, December 3, 2010

Microbiology Lab. Note

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I've been told that some (or maybe all) of you don't understand about the note that I wrote in your microbiology discussion paper. Yeah, I know it's late as you have to submit the report tomorrow :P. Hope this note can help you.

  1. The inhibtion zone diameter dimension changed to mmx10. Well, I don't know either the exact reason. I think it's only statistical reason. You used the caliper to measure the inhibition zone diameter and you got the measure for example 2.45 cm. The decimal shows the degree of accuracy. On the other side, biological assay has low accuracy (because of the biological variation). Because of that, you need to convert the diameter to mmx10 that is 100 times than the diameter measured to delete the "point" sign.
  2. Generate callibration curve. The calibration curve generated from YL, YH value and log of concentration. After that, find out the line equation, you can use calculator or Microsoft Excel. Most of you reported the same wrong equation, without asking anyone of you I already know the reason why -_-'.
  3. The uses of this experiment for diagnostic purpose. Well, I know diagnostic things are for community and clinical pharmacy, not for you that majoring pharmaceutical science and technology but there's no wrong to know more isn't it? I guess you don't have any idea of this part.. so I generously give some hints: "Hospital", "Infectious diseases"
  4. Attach the requirement for Ampicillin trihydrate in USP 32 or Farmakope Indonesia 4 and sumarize the data that useful in this experiment. This experiment also useful for quality control for the antibiotic. In quality control of course there are quality standard. USP and Farmakope Indonesia provide the standard of Ampicillin trihydrate potency. You can access USP 32 or Farmakope Indonesia IV in our library if you don't have those books (Well, I belive you don't have them :P so stop by to our library). Then conclude whether the sample fulfil the requirement or not.
  5. For the procedure, please write exactly the same as what did you do at the experiment day. How much you weigh to make the main standard, how to make S1-S5, what is the concentration S1-S5, the lab apparatus that you used, how long was the pre-incubation, how long was the incubation, etc.

As you are international students that use English as the report language, please don't take any advantage of it by only copy-pasting english internet article to your report.. please rewrite with your own words the article that you think correlate with your report.

About the references:

  • Laboratory guidance, lecture notes, blog posts can't be used as reference.
  • Please write the references in right way, especially for references from internet article. You can check here how to write references properly.-