16th, 18th & 19th December 2014, "Maybe I Should Put The Same Topic As Mashi's, A Hectic Week With Dr Wan. Hehe"

Actually on the 15th, some of us attended a talk about our future career. It shows us that there are some of the fields that require us, future Microbiologists. 

The after effect of that talk was it did open my eyes a bit since I have always think that I will be only in a laboratory and do research and research and more research. But there are actually more jobs other than that (although it is still associated with researching but at least the scope is bigger now). I still do not know what I wanted to be though, for now I still have the same "working in the lab and do some research to find cure for diseases" dream~ 

This week we covered on Microbial Growth, Growth Control On Microbial Growth as well as Antimicrobial Chemotherapy.

Microbial growth covered on the suitable conditions for microbes to live. Some microbes are aerobic and some are anaerobic. And there are physical requirements and chemical requirements for them to grow. These microbes need all the physical and chemical requirements in balance. They will not be able to further their growth if there are some missing nutrients. 

Just like human, we need oxygen and food. If we have oxygen but we don't consume food, we cannot grow since we don't have any source of nutrients needed for growth. In fact, we become weaker if we don't eat. The same goes to microbes, well, sort of. Hehe. 

Besides that, we learned about how to isolate microbes. There are several techniques that can be used. And even some "precautions" that must be taken when isolating them such as for anaerobic microbes, we need to ensure that there are not even one oxygen is present around the desired microbes that we want to culture in order to not let them die. 

Other than techniques of isolating, it is also important to pick the right medium for the desired microbes that we want to culture. You might want to make sure of that before putting your desired microbes into the medium you have prepared. You might accidentally put them into a "hated" place for the microbes x'D 

Hence, your effort of collecting the sample will go to waste because you have just inhibit their production due to your own mistake which is by putting them in an undesired place for them to live. 

Also, picking the correct medium is not only important for their growth but also important to classify them. For example, putting Shigella sp. in a lactose containing agar can result in the Shigella sp. being the microbes that stand out due to their non-lactose fermenting characteristics. Hence, we can isolate Shigella sp. and leave out the unwanted microbes, right? 

So it is very important to have your aim right, in order for you to get the desired result. You definitely do not want to waste your time doing "unneeded" research right? HAA. 

Other than that we learnt how to count the generation time and also number of generation of the microbes. I managed to understand them and hopefully... HOPEFULLY! If there is a question(s) in the Final Examination asking to count their amount, I hope it is a question that is not so tricky.

And I have to admit, while doing the exercises. I miss Maths. Deeply. Sincerely. Sincerely from my heart! x'D ---> This person over here, have always been a Maths fan <--- 

Next, since we learn the requirements of microbial growth. It is only fair if we learn how to prevent them from growing too, don't you think? Hehe.

For antimicrobial treatment, there are also physical and chemical "requirements" as well as processes needed to kill or inhibit their growth. Oh, and it also depends on our aim either to kill or inhibit them. Because some of the antimicrobial treatments can kill them while others slowing down their growth. 

And the term, biocide means killing the microbes. I don't think I will ever get confused of this term with the other terms because you can see how closely related it is to the word "suicide" which means killing one self. At least, that's one of the ways to remember~ 

Talking about terms, there are a lot of terms for this topic. And I'm still having troubles remembering them. Hehe. (Except for biocide and bacteriostasis of course, since Dr Wan kept asking us/repeating over and over again the terms in class)

Lastly, we learnt about antimicrobial chemotherapy in which how to prevent pathogen form reproducing. Of course, penicillin is frequently brought up all over the topic because it is an antibiotic. Other than that, we can also observe the activity of the pathogen by doing some test such as the E-test and disk dilution test. To see the level of resistance of the pathogens towards antibiotics. 

So.... I guess from there, we can pick the best antibiotic needed to treat cases associated with the microbes that we have tested. I wonder if that's also the purpose? (Other than to determine the pathogen's activity) 

Also, other than the infamous penicillin there are also other antibiotics. For example, to prevent growth of fungus we have antifungal as well as antiviral which is to inhibit virus activity. And a lot more! That I am not familiar with.. And Dr Wan said that she is going to give us a simpler note, the current note we have is a bit detailed. Don't forget Dr~~~ :D 

That's pretty much (roughly) what we have learnt this week. 

In my opinion, the topics that cover on procedures to isolate and the requirements of microbial is a bit... hard because it consist of facts. But "dinoflagellates can cause red tides" is a fact too! But that is more interesting! Because.. it's about the microoganisms themselves. Haha. I don't know how to explain this... problem? x'D 

However, this is it. End of BMY3101 2014. 

Ah, Dr also said that it felt like it is the longest lecture. Haha. It is! But I don't mind at all since it was the last class. And class with you was always fun anyway so it's okay :D 

And by the time we have finished doing the Kahoot quiz with everyone, and you said "This is it". I was feeling so sad! x'D <---- just so you know, this is a "laughing-until-tears-came-out-of-eyes" emoticon but I strongly feel that you already know this. Hehe. 

It feels like you are our... "Guru Kelas" you know? Hahaa. I hope you will teach us again during the upcoming semesters! I will miss all the digital assignments!!

Keep being the enthusiastic and wonderful lecturer you are, Dr! I will always pray for you :D 

Thank you! LOVE YOUUU! ♥ 

8th, 9th and 10th December 2014, "Of Yakult Trip And Microbiology"

On Monday, we went to Yakult factory. It's cool really. Since we are Microbiology students and know a bit (a bit? It should be a lot, isn't it? x'D) about the microbes and at least know what Lactobacillus is, it was a memorable trip! :D

Compared to before I studied Microbiology, I don't pay any attention to what is in Yakult. Going there and hearing the talk about the ingredients of Yakult, I think it's my first time knowing that there are probiotics in it. Scratch that, I just know that Yakult is actually a probiotic drink! x'D 

I can just conclude that I have never read the ingredients of Yakult before. Or maybe I did but because I do not know what Lactobacillus is, I don't bother much about it. Hehe. 

It left a big impact on me, to be honest. While drinking the free Yakult given to us that day. In my head, "There's Lactobacillus casein Shirota" in this drink" crossed my mind x'D I became more aware of their presence. 

The representative of the Yakult factory that day also remind us not to drink Yakult mindlessly. It should be drink at least once or twice a day. If not, it would be wasteful of the probiotics included in the drink. 

Probiotics are known to be good bacteria. However, if you take probiotic in excess, they might harm you. People with weak immune system shouldn't consume them too much. 

_____________________________________________________________________________

Enough about the trip. Now we proceed to this week's lesson. 

This week, we learnt about microbial metabolism, microbial nutrition and microbial growth. 

For this week entry, I shall state informations that's not stated in the notes. Things that was discussed during class. [At least from what I managed to write in my notebook]

Microbial Metabolism 

-> Cellular respiration is a process in which energy in the nutrients in converted into energy in the form of ATP. There are three types of cellular respiration which is aerobic and anaerobic respirations and fermentation. 

-> Organism that respires by fermentation will produce ethanol however it depends on the microbe and substrate because not all fermentation process will produce ethanol as the end product. Some can produce other end products such as lactic acid and carbon dioxide. 

The products of fermentation for each different bacteria.

-> Aerobic respiration : glucose + oxygen --> carbon dioxide + energy + water [if you look closely it is the reverse reaction of photosynthesis] isn't it cool!! x'D I just realized that too! 

Photosynthesis equation

-> Other names for Citric acid cycle are Kreb cycle and tricarboxylic acid (TCA) cycle. 

-> Pyruvic acid are also known as pyruvate so they are the same thing. And pyruvate/pyruvic acid is a transition product before the final product is obtained. 

-> I found out through the Net today that two of the common types of biofuel nowadays are ethanol and biodiesel. Hence, organisms that can produce biofuels are bacteria, fungi and algae because they are able to ferment glucose into ethanol. 

-> Oil palm is the best substrate to produce ethanol because they have cellulose to ferment ethanol. [there are three basic types of EFC (Ethanol-From-Cellulose) process which is acid hydrolysis, enzymatic hydrolysis and thermochemical.]

-> Different microbes act with/ferment different substrates producing different end products. 

-> Other names for carbon fixation are Kelvin cycle and Calvin Benson cycle. [Although Dr have mentioned this before. hehe]

-> Bacteria have carboxysomes that contain enzymes that helps in carbon fixation. [I forgot this fact, to be honest. Hmmmm]

Microbial Nutrition

Dr asked us to find a way to remember the microbial nutrition since it is quite... various. Dr said it's either you remember each of the microbial nutrition or remember them by understanding them. Ah, I hope my words aren't jumbled up. x'D 

However, Dr said that this is the best table to understand/remembers them because it states the terms one by one. For example, first identify what's the energy source and then the reducing equivalent source (biosynthetic process) and then the carbon source.  

For example, I will do this randomly without looking at the correct microbial nutrition. Hehe. 

This organism, its energy source is from chemical compound (chemo-), it's reducing equivalent cource (source of electrons) is from inorganic compounds (-litho-) and it's carbon source is from organic compounds (-heterotroph). Hence, the microbial nutrition for this organism is chemolithoheterotroph. Ok? Ok. :D 

I studied this the night before the day that Dr Wan held a pop quiz (sort of) in class. I thought I have somehow mastered it (hehe) I mean, I thought I have understood it well but I was indeed wrong. During the quiz, I was not able to guess correctly what are the microbial nutritions based on the questions given D: Thank you Dr for doing the pop quiz!! Because it gave me the realization that I'm weak in determining the nutritions. I will definitely pay more attention to it!

Dr also said that we have to have good imaginations too when determining the microbial nutritions. For example, based on one of the questions that day... This organism lives on the mountain where there are no other microbes surrouding it --> from there we can know that since there are no other microbes around it that it can feeds on, thus it should be an organism that can produce its own food! 

Microbial Growth

-> The purpose of studying the growth of microbes is because when we know what can kill/help the survive, we can control the factors of their survival such as the temperature and pH in order to either stop or slow down their cell productions. 

-> The growth of microbes are not determined by its sizes but by the number of cells. 

-> When to use the terms "tolerant" and "-phile"?

tolerant : when the condition is very near to "optimum". 

-phile : when the condition is at "optimum". 

-> One of the physical requirements for microbial growth is water activity. What is meant by water activity?  

Water activity (a_w): The amount of water needed/found in substrate that is just right or enough for the microbes to grow. 

 Water in food that is not bound to food molecules can support the growth of bacteria, yeast, and mold. The term water activity (a_w) refers to this unbound water.

The water activity of a food is not the same thing as its moisture content. Although moist foods are likely to have greater water activity than are dry foods, this is not always so. In fact, a variety of foods may have exactly the same moisture content and yet have quite different water activities.

The water activity (a_w) of a food is the ratio between the vapor pressure of the food itself, when in a completely undisturbed balance with the surrounding air media, and the vapor pressure of distilled water under identical conditions. A water activity of 0.80 means the vapor pressure is 80 percent of that of pure water. The water activity increases with temperature. The moisture condition of a product can be measured as the equilibrium relative humidity (ERH) expressed in percentage or as the water activity expressed as a decimal.

Most foods have a water activity above 0.95 and that will provide sufficient moisture to support the growth of bacteria, yeasts, and mold. The amount of available moisture can be reduced to a point that will inhibit the growth of microorganisms.

Water activity can also be used to predict the spoilage of food which is by knowing the water activity that is suitable for the bacteria or any other microbes to enhance its growth. This can be prevented by reducing the water activity of the food as much as possible! 

Water activity (a_w) has its most useful application in predicting the growth of bacteria, yeast, and mold. For a food to have a useful shelf-life without relying on refrigerated storage, it is necessary to control either its acidity level (pH) or the level of water activity (a_w) or a suitable combination of the two. This can effectively increase the product's stability and make it possible to predict its shelf life under known ambient storage conditions.

Food can be made safe to store by lowering the water activity to a point that will not allow pathogens such as Clostridium botulinum and Staphylococcus aureus to grow in it. The table below illustrates the water activity (a_w) levels that can support the growth of particular groups of bacteria, yeast, and mold.

And this is some of the water activity that is suitable/optimum for the microbes~ 

The range of water activity in food that can enhance the growth of some microorganisms. 

I read about this from here :- 

http://www.foodsafetysite.com/educators/competencies/general/bacteria/bac5.html

Dr also gave us an example by asking us a question. She said that the water activity for ..

(i) bacteria : 0.91-0.97 
(ii) fungus : 0.81-0.88 
(iii) honey : 0.9 

So which of the stated can survive in low amount of water? The answer is fungus! As you can see the water activity it requires to grow is rather low compared to bacteria and honey. 

Not to forget, organisms that can withstand extreme dryness are called xerophiles~ 

-> Barophiles are organisms that can live at high pressure. 

Dr test our understanding about the temperature range by asking us a question. 

Pyrolobus fumarii can survive at 110 degree Celcius. What will happen to it when in low temperature? 

It will die. Die instantly. It will instantly die at low temperature, not inactive because it cannot survive in temperature below than 110 degree celcius. 

I guess that's all from me! I think entry like this is much more informative in form of my understanding, right doctor? Hee. I may have misunderstood the purpose of the reflective journal. x'D 


P/S
Thank you for reminding us to study hard, Dr :) I will do my best!! 

Tuesday & Thurday, 2nd & 4th December 2014

Tuesday's class went for only one hour while Thursday's class went for 2 hours. And we managed to finish learning the topic on Taxonomy. 

I concluded this week's lesson with a mindmap. 

New things that I've learnt 

1- Phylogenetic -->> study of evolutionary relationships among groups of organisms

2- Phylogeny -->> history of organismal lineages as they change through time.

3- Serology -->> The analysis of the contents and properties of blood serum

4- ELISA (Enzyme-linked immunosorbent assay) -->> a rapid immunochemical test that involves an enzyme used for measuring a wide variety of tests of body fluids. ELISA test detect substances that have antigenic properties, primarily proteins rather than small molecules and ions.

5- Western Blotting -->> An assay that detects specific proteins within a protein mixture by a multistep process.

6- Phage Typing -->> the process of identifying a species of bacterium according to the type of virus that attacks it.

7- Fatty Acid Profiles -->> considered as chemotaxonomic markers to define groups of various taxonomic ranks in flowering plants, trees and other embryophytes.

8- Nucleic Acid Hybridization -->> A technique in which single-stranded nucleic acids (DNA or RNA) are allowed to interact so that complexes called hybrids are formed by molecules with similar, complementary sequences.

9- Southern Blotting -->> a procedure for identifying specific sequences of DNA, in which fragments separated on a gel are transferred directly to a second medium on which assay by hybridization may be carried out.

10- DNA Chips (also called "DNA microarray") -->> A small solid support, usually a membrane or glass slide, on which sequences of DNA are fixed in an orderly arrangement. DNA microarrays are used for rapid surveys of the expression of many genes simultaneously, as the sequences contained on a single microarray can number in the thousands. 

11- Ribotyping -->> involves the fingerprinting of genomic DNA restriction fragments that contain all or part of the genes coding for the 16S and 23S rRNA. By digesting the genes with a specific restriction enzyme, fragments of different lengths are generated.

12- FISH (Fluorescent In Situ Hybridisation) -->> a laboratory technique for detecting and locating a specific DNA sequence on a chromosome. The technique relies on exposing chromosomes to a small DNA sequence called a probe that has a fluorescent molecule attached to it.

13- Dichotomous Keys -->> A reference tool where a series of choices between alternative characters leads progressively to the identification of them species.

14- Cladograms -->>  a diagram depicting patterns of shared characteristics of variou organisms. 

I missed Friday's class because I had to go on a trip for my co-curriculum but from the 

look of it (the assignments that my friends had been assigned to by Dr Wan) it seemed 

like they had fun with the websites that they have to use for the assignments. 

Hmmm, about Taxonomy.. It made me realized that there are actually A LOT of methods 

can be used to classify and name the microorganisms. I thought it was simple as that but 

nope, I was wrong all along. Happy learning, Dayana~