Reflection on Virtual Microbe 2016

Assalamualaikum, and a very good afternoon (it's noon at the moment) to you who is reading this. I hope you're having a good day. 😊

Oh, let's not forget to say Hi, Dr. Wan! 😁

Today is Sunday, 20th Nov 2016. And as you are informed, third year students who took Virology course are having their Test II today. I just got back (3 hours ago) from the test too. Alhamdulillah, it went well. 

I would like to take this opportunity to say my thanks to Dr. Eddie as well! Thanks to him, I now have a better insights to the virus world. Also, thank you to Prof. Azeezah. Their way of teaching is very good that I will feel troubled or guilty if I dozed off during the class (it's not because they're boring, really no! It's me, I have been sleeping late haha) 

Ok. Now I will talk about my experience with Virtual Microbe! 

To be honest, during the first briefing I do not really understand how the flow of this activity. The rough idea that I managed to get that day is that we as well as other university students will have to do a virtual meeting and discuss about the questions provided in the module of this activity. It is kind of like UPM's LAX course, you have to do a group meeting every week, discuss the progress of the activity that we're asked to do and finally produce a final product. The difference is that this has to be done 'virtually' via any application that can provide video conference. 

The idea appeals to me, but I'm also nervous because during the starting of this semester, I know my ability, that I have very low knowledge about viruses compared to the other microbes. Hence, when Dr. Wan said that the third year students have to work on the virology part (because we're currently taking that course), I think that I will not do well because I feel like I won't be able to talk much about viruses. You know that feeling, right? So, I imagine that the other university students will talk 'fluently' about the mechanism and life cycle etc of viruses and I will not be able to understand immediately or slow to catch on. 😐

However, as time goes by and weeks passed, one to two video recordings passed, I think I managed to grasp the idea of this activity. My knowledge on viruses is gradually increasing too because Prof. Azeezah and Dr. Eddie taught us well! They explain each of the viral processes in depth and clearly, so while doing this activity; Virtual Microbes also give me the confidence to talk about viruses because it feels right to talk about something that you have knowledge on. 😊 It is also easier for me to find and extract information from the Internet or from the journals when gathering information about the virus of our choice because I have managed to familiarize with the terms used in virology. 

As for the final products; montage video and infographic. We divided the task among ourselves and agreed that the UPM students will work on the montage video while UKM students will work on the infographic. By now, we, the UPM students should be familiar already with this kind of task, thank you very much to Dr. Wan! 😄 My skill in using the applications improved from semester to semester. At this point of our study year, it doesn't feel hard anymore to use these helpful applications (unlike the very first time during Adopt-a-Microbe and so on, it felt impossible to finish haha).

Aside from the output of this activity, the input is actually the most important thing in order to get a good output, right. Just like what Dr. Wan always reminds us at the beginning of this collaboration that this is a platform and an opportunity for us to connect with the people outside university besides it is also a peer teaching activity. 

It taught me how to communicate and tolerate well with people in our surroundings. Besides that, it is very important to cooperate with others when engaging in an activity in which we have to plan properly such as ask when every members of the group are available to do the video conference. Also, like Dr. Wan said it is a preparation for us, the third students that will go for our internship later on. This activity managed to give us the experience on how to work and deal with people out of our circle and also cooperate with each other as a team in order to get a desired output. If everybody put their very best effort in a group work, the outcome will come out good as well, so everybody will feel satisfied and proud of their group work at the end of the activity. 💟

We have reach the end of my reflective post on Virtual Microbe 2016, I would like to thank Dr. Wan as well as the other lecturers involved for giving me/us the opportunity to do this activity in collaboration with other university students. It gives us exposure as well as guides us to manage our time efficiently.  

Next, thank you to my group mates, from both UPM and UKM for the efforts in finishing this activity successfully. I also want to apologize for all the miscommunication occurred. It's regretful, really, but I hope we can all learn from this and improve ourselves in the future. 😺 I really really really hope that we all can end this activity on a positive note and if we ever meet outside the 'virtual world', do not hesitate to say 'Hi'. ✋

If there is another collaborative activity in the future, or Virtual Microbe 2017, it would be a nice experience for me to join as I can improve myself. 🙆


P/S 
If this makes you feel good, Dr. Wan, I downloaded the Zoom app on my phone and on my little sister's tab so that I can video call her when I'm in UPM. There's this one night, I used Zoom to 'see' my family at home because I miss them. Even though we are just 40 minutes away. I'm excited to use it! 😂

Reflective Journal on Microbes and Us Project and Microbial Ecology

Assalamualaikum w.b.t. and a very good day to those reading this

The first part of this reflective journal will be covered on the learning outcomes and what have I learned throughout this course. The most unforgettable (but also quite hard to remember all of them) part during learning Microbial Ecology is knowing all the microbial habitat. To be specific, it was during Dr. Amalia that there were so many new things I learnt, such as the aquatic habitat and atmosphere habitat. Before this, it was not elaborated in depth, but throughout this course, it was elaborated and I somehow know a lot more thing better. I will take atmosphere habitat for example. Before this I only think that atmosphere is a method of transmission of microorganisms. However, after learning the topic of Atmosphere Habitat, I now know how to prevent the presence of airborne microorganisms.

As for the experience in doing the Microbes and Us project, it was fun knowing in depth about a certain microbe of choice. We picked Toxoplasma gondii as our microbe of choice. Initially, it was because all of the members of our group seem to be fond of cats, so we all agreed immediately. As for me, I never know about the occurrence of Toxoplasma gondii on cats. Some of our group members have read about it and suggest that we study about this microbe further. I read about it and was also interested with the topic since I never consider about the possibility that microbes can actually ‘control’ our minds in which the article explains that the minds of infected rats become attracted to cats, that’s why they are consumed by the cats. Although there are times where we also have problems to understand the microbe such as its life cycle, every members tried hard to understand and explain to the members that didn’t quite catch it.

Besides that, I think I am getting better at finding journals. Haha. And also reading one!

Some of our lecturers throughout this semester frequently remind us that we have to familiarize ourselves with reading journals. Thus, this project somehow has managed to make me more ‘comfortable’ when reading journals. The thought that I have to find the answers to certain questions is what driven me to read as many journal  I can to find the best journal that can answer our questions and that we can refer to.  However, I also came across journals that are still hard to understand, and I guess it is just a part of learning.

As usual, after every project that involved a particular microbe that can cause infection will make me more cautious around the possible method of transmission, as the effects are sometimes worrying (usually diseases). Thus, I’m seeing cats with a new ‘point of view’ now.

For the fourth question on how do I relate Microbial Ecology to other microbiology courses that I have covered throughout the two years as a Microbiology students are I can relate on the characteristics of the microbes and its pathogenicity(if it is a pathogenic bacteria) and its natural habitat or ecology. The characteristics were further discussed in Bacteriology course and I can understand more clearly (although there are more things to be remember now) on how and why they are pathogenic.

Besides that, the characteristics sometime show the ecology of the microbes. For example, photosynthetic bacteria are usually found on the surface of water while the bottom of the ponds, lakes or even sea are where the anaerobic bacteria lives or thermophiles that can be either bacteria or archaea live in very hot temperature such as the hydrothermal vents.

Therefore, it is important to know the natural habitat and requirement of each type of microbes such as its favourable temperature, nutrition and even by-products, so that we can isolate the microbe of interest and grow it (in-vitro) according to its natural habitat. If we manage to provide a suitable environment for the microbes to live, we can get the by-products produced by the microbes that might be of used to the industry or health purpose.

I think it is important nowadays to culture microorganisms and to find more species or strains that can benefit us.

Awesome Microbes Carnival (19 & 20 November 2015)

Assalamualaikum w.b.t.

It’s been few days after the much anticipated “The Awesome Microbes Carnival”.

I will now write my reflective journal upon the event, covering the period before and after the carnival; from my point of view.

I did mention about this carnival during the first week of Semester 3, in my first entry. Ring a bell? The one that Dr. Wan suggested during semester break.

Well what do you know, it’s actually happening. To me, everything went well. I had loads of fun! :D

PREPARATION FOR THE EVENT

Before the event was held, there were few meet up’s involving the whole Microbiology students from first year until final year, even the lecturers and lab assistants were there to listen to a little brief about the event by Dr. Wan.  

There were also few meetings involving only the higher up(s) and committee in charge.

(My name was actually randomly picked and put under the “Social and Activities Committee”.)

I don’t intend on joining the event by being one of the committee but I do want to contribute to this event either directly or indirectly.  I think it’s a good opportunity for me to learn a thing or two about handling an event. Even just being in charge for the activity part.

It sounded easy and simple, right? For me, it’s not because we have to think and discuss on what activities that would be suitable and at the same time fun for the visitors.

Also we have to consider about the target visitors, which is primary and secondary school students in which we have to lower down our ways of thinking and try to imagine being in the students’ shoes on things such as questions for quizzes; whether they can answer it or not and etc.

It was a fun experience for me because as far as I can remember,  I have never handle the activities of an event, so being a part of this committee gave me a “sneak peek” on how to do it.

We have to know the things required for the activities planned, how many activities, the layout, the rules of the activities and prizes to be given if the visitors won the activities and etc. We have to make sure everything was planned well in order to avoid any unwanted circumstances that day.

It was fun preparing the props for the activities too.

Over all, it was a fun yet informative experience.

From the meetings that I have attended, I also managed to learn a bit on how to plan an event such as the publicity and logistics scope of works, and so much more.

APPRECIATION POST

The event has officially ended. I was partially sad and partially happy. Sad because it ended but happy because the event was successful.

First and foremost, I would like to thank Dr. Wan because without her, this event would not have been done because she kept on planning it although it has not been approved yet. Haha. So confident!

The venue which is Panggung Percubaan was set up well. Kudos to the logistic team to ensure that everything that was requested by each committee “comes true” by supplying us what we needed. Especially for the activity team.

I think we might have requested the most since there were eight activities and each one of them requires different things such as petri dishes, cardboards, double sided tape and etc.

Also, most of the things that we habe planned were successfully done. For example, the Golden Tunnel (I don’t know what is the name of the tunnel showing the achievements of scientists involved in our field. Hehe. I will name it Golden Tunnel like the golden years of Microbiology. Right? Right?) During one of the meeting, Dr. Wan suggested on doing the tunnel  but some of us said that it’s actually quite hard to do it and might require a long time, so the plan for tunnel was actually uncertain. I myself thought that it’s not going to “appear” on the event day.

However, much to my surprise, the tunnel is actually there! And it was reaaaaally beautiful!! I like—I love it! It was simple yet fascinating at the same time. Kudos to the people who was in charge for that part.

The food was good too. I  tried all of the foods. Not only to support my own seniors but also because everything looks good even when I am not hungry. And for a moment, I feel like I’m in my own “wonderful world of microbes”. Haha.

You know, like everything is made up of microbes and revolve around them, including the foods. So it was interesting. All the food was based on microbes such as doughnuts that are made up of yeast, mushrooms and cupcakes with microbes art on it. Also, there is this drink; actually there are two drinks that particularly took my attention during the carnival. Which is the Kombucha tea (I hope I didn’t get the name wrong) and “lactogurt”.

The vendor for Kombucha tea briefly told me about the contents and function of that drink. From what I remember, the drink contained enzyme, bacteria, yeast and something else that I couldn’t put my finger on it.. The drink taste carbonated and also you can taste the yeast strongly. I actually like the drink while others don’t really like it. He he.

I offered to most of my coursemates and their face went “blerrghh what is this?!” hahaha. I guess our tastebud don’t really match.

The other drink which is lactogurt contains bacteria and milk. It taste sooooo good! Like a yoghurt drink you bought from the supermarket. I asked one of the senior that made it because it is actually their project for their GM course. And he said that they really fermented it. 

I don’t believe it at first but later on I did. It was unbelievable on my side but also amazing. Haha. I didn’t know it was possible to make yoghurt using bacteria for real in our laboratory.

I want to try doing it in the future too!

What I Learnt During The Event

1-     I can brush up my skills on how to approach people; to invite people to play at the game booth where I’m in charged on. The target visitors were broad, if I must say myself. I had to greet primary students, secondary students, elementary students, university students an their instructors. I remind myself to always show a bright face and explain to them properly how to play the games.

2-   I was able to interact with the first year students that I still don’t have the chance to know them. Since my game booth are just beside the first year students poster section, I was able to recognize their face more. The male students were easy to detect since they are just few of them and they often played darts at our game booth. I can see that they are friendly bunch of kids. “Kids”. Haha. The female students too! First year students were assigned to take care of our game booth if we are not around during our  poster evaluation.

3-   I was able to interact with the seniors that I usually saw around the faculty. I made friends with some of them during the event. At least, I hope that if we cross path at the faculty, we can smile to each other now and I can differentiate the seniors from other courses in our faculty. They are really friendly!  

4-   For the whole two days, being with my Microbiology course “big family” and surrounded by everything related to microbes; especially the foods! Made me feel like I’m in the “world of Microbiology” for a little while.  It was unforgettable for me! I really like the environment surrounded by microbes related things. I would really like it if we are going to have it again in the future.

5-    I learnt that teamwork is very important. As long as there is teamwork, things should be fine as there will be people supporting us no matter how critical a situation is. For example, there are days where some of the third year or final year students have classes and the others have to cover our absence for a little while.  Like the saying “the show must go on”.

[TOPIC 5] Introduction To Microbial Metabolism

Assalamualaikum w.b.t. 

Hi~ 

Since we already know about the formation and structures of amino acids and proteins. The current topic will now discuss on the functions and metabolism of the proteins. 

When I hear or come across the word 'protein', the first thing that comes to mind is 'enzyme'. He he. How about you? 

This topic firstly exposed us on metabolism such as what's the meaning, and the process involved; which is anabolism and catabolism. 

It's important to know what those two words mean. And also identify which process release energy and absorb energy. 

Next, the types of enzymes were also included in the topic. There are six of them. I have already 'met' these six types of enzyme before during our last semester which is included in Biomolecules subject. 

Other than the types of enzymes, the other important thing to know is the properties of enzyme.

This is really important, right! 

Some of the properties of the enzyme are enzymes are specific, can be inhibited by certain conditions and not used up in a chemical reaction. (Make sure you know the other functions too, I only include some of it~). 

In addition to that, it is weird if the mechanism of enzyme is not included, right? So, of course it is crucial to know that too~ 

There are two mechanisms though, the lock and key method and the induced fit method. 

I found a cute and an interesting picture of the lock and key method! So that people can memorise it easier and more fun, in some sort, because it's related to our daily life; the key. Hehe. 

If there is a method on how to make the enzyme works, there should be reasons or conditions on how to disable the enzyme functions, right? 

Yes! 

There are a few factors affecting enzyme's functions which is concentration of substrates enzymes, pH, temperatures and enzyme inhibitors. 

Make sure to know how each factor contribute to inhibit the enzyme's activity. 

Especially on the types of inhibitions. Each of the inhibition; competitive inhibition, non-competitive inhibition have their own mechanisms; where they will interact with the enzyme either at the active or the allosteric site and the effects on the products formation. 

That's all from me~ 

[TOPIC 4] Amino Acids and Proteins

Assalamualaikum w.b.t.

To be very honest, I don't really like learning about amino acids and proteins but you know that one quote 

"You'll never know unless you try"

There are 20 essential amino acids and Dr. Amalia told us to try memorise it. I don't want to! Haha. I'm trying to accept the fact that it's inevitable. I am bounded to amino acids and proteins if I were to pursue this course; or maybe as my career, who knows~

Hence, I will try my best to memorise them. Wholeheartedly. x'D

For this topic, we learnt mostly about the structures of the amino acids. Including the structures of all the 20 amino acids. 

What's interesting about the amino acids is that they each have their own letter code. I'm not sure whether we have to memorise this too or not. Ha ha. (dry laugh) 

Other than the structures, the chemical properties of the amino acids were also focused. The amino acids are grouped in four main groups which is polar, non-polar, acidic and basic. 

Actually, if we know the structure of the amino acids well, we can guess the chemical properties of them already. 

For example, the presence of amine group in the amino acids indicates that the amino acid is basic. Or the presence of sulphur or hydroxyl group which is known to be high in electronegativity indicates that it is polar; it can form bonds with other polar molecules. 

It can be concluded that the chemical properties depends on the side group present on the amino acids. 

#I'm not sure if I have been told about this before but I just knew today that physiological pH is actually pH 7.4; neutral pH. 

Other than that, we have to know the structure and significance of the alpha helix and beta pleated sheet and what bonds contribute in the structures. (It's hydrogen bond!).

One of the new thing I learnt during this topic is that structures or components known as 'turns' and 'loops' help to reverse the direction of the polypeptide chain. 

#The difference between loop and turn is that loop is used for long amino acid chains while turn is used for short amino acid chains. 

In conclusion, if you fully understand the structure and chemical properties as well as the functions of some structures. You can answer questions like 'what bonds connect the amino acids?' 'why the amino acid is acidic/basic?' 'what structure help to change the direction of the amino acid chains?'. 

The current topic seems a bit off topic from the usual stuff we learn about microbes. I miss the names of the microbes already. 

Let's study well, ok. We're all in this together after all. Hehe. 

Later! 

:)

[TOPIC 3] Intracellular Structures of Prokaryotes

Assalamualaikum w.b.t. 

Last topic was covered on the external part of the prokaryotes. Hence, now we will focus on the internal part of the prokaryotes. It is no other than the organelles of prokaryotes! Actually for this topic, since we were a bit lagging behind due to public holiday etc, Dr Wan made us did peer teaching instead of her teaching us. 

Every group was assigned on one or two organelles to be presented to the class. My group have to cover the inclusions that exists as granules which is sulphur granules, metachromatic granules and polysaccharide granules. 

After each presentation, the listeners which is our own classmates/lecturemates have to ask some questions regarding our presentation. And we have to find the answers, no matter how hard or easy the question(s) is~ 

What I learned from this topic is that it is important to know the functions of each substance because let's say if an organelles are absent in an organism. We can identify the cause of the disability of the organism to function; which is might be due to absence of the organelles required. 

For example, organism that lacks ribosomes will result in the organism unable to synthesise protein. 

Other than that, it is also important to know the inclusions contained in prokaryotes as inclusions have several functions that is essential for some bacteria. 

For instance, gas vessicles are crucial for photosynthetic bacteria in order to attain enough sunlight to carry out photosynthesis. The gas vessicles will provide buoyancy to the cell and make them float near the surface of water instead of submerged or sink to the bottom of the water source. 

In addition, formation and functions of endospore should be well understood as only prokaryotes can produce endospores. However, only some bacteria such as Clostridium and Bacillus can produce endospores. There are also some diseases related to endospore that can be fatal such as tetanus and gangrene gas. 

This new semester, a new information was added on the endospore part. Before this we were only exposed to the cycle of the endospores and functions but now the components and structures of the endospores are also included; which is the most inner part of endospore consist of inner core followed by cortex, spore coat and the outermost part is exosporium. 

That's pretty much the conclusion for this topic. 

Until then! 

[TOPIC 2] Cell Wall and Membrane Structure of Prokaryotes

Assalamualaikum w.b.t. 

For this topic, I think it is crucial to be able to differentiate between Gram-positive and Gram-negative organism's cell wall properties. 

Other than knowing the difference of the two type of cell walls, it is also important to know the functions and significance of each substances contained in the cell walls. For instance, teichoic acid in Gram-positive organisms and LPS in Gram-negative organisms actually have the same function in which the components contribute to the cell's antigenic specificity. 

Other than knowing the difference and functions of Gram-positive and Gram-negative cells, this topic also covers on the difference between bacteria and archaea. 

So, how to remember the cell wall visual? 
Remember the spaghetti and meatballs picture! :D 

You don't remember? 

Wait. 

I was talking about the above picture! :D 

Why are we focusing on distinguishing bacteria from archaea? 

I would say that it is because this two organisms are in the category of prokaryotes (because they do not have true nucleus and membrane bound organelles) while the other group of microbes are eukaryotes. 

Some of the differences between the two organisms that I think I should note on are : 
- The presence of peptidoglycan 
- The amino acid contained in them 
- The glycosidic bond between the sugars 
- Ester/Ether link 

Other than that, I also learned some new terms. What are they, you ask? 

It's spheroplast and protoplast! 

Protoplast is a cell that has be lysed but it is still capable of carrying out metabolism processes. 

Spheroplast is a cell that have not been completely lysed, thus some of the components of cell wall still remains. 

How do they formed? 

Spheroplast are constructed when the the cell wall has been acted on by the lysozyme, but it is not completely hydrolysed. 

Below are some of the questions that were discussed in class throughout the lesson : 

1. How does glycocalyx act as a source of nutrients?
--> What I found on the net is an example of organism, Streptococcus mutans use glycocalyx as its source of nutrient when energy storage is low. This organism has glycocalyx in the form of capsule and it will break down the glycocalyx and utilise the sugar since glycocalyx is made up of sugars called EPS. 

2. Movement of bacteria towards nutrients or a particular substance is called 'chemotaxis'. 

3. The conjugation of pili is a process where transfer of DNA occurs. However, it does not contribute to the production of new daughter cells. Instead, the plasmid contains specific genes such as resistance to a certain antibiotic and ability to produce enzyme. Thus, the recipient of the DNA transfer will obtain the traits of the donor. 

#Do remember that the transfer of DNA can only occur between the same species! 

4. How is cell wall serve as a site of action for antibiotics? 
Antibiotics have a certain mechanism to attack cells such as attacking the cell wall, nucleic acid, ribosome etc. When antibiotics attack the cell wall, the cell wall will lyse or rupture causing the content to leak out and the organisms will die. 

That's all from me~