My Adopted Microbe

                  Assalamualikum w.b.t

    Hello readers, wow surprisingly you are still willing to read my ordinarily blog! thank you guys for the support! And i really hope Dr Wan also going to read this until the end of this entry.

    Now i have good & bad news for you guys, which one you want to know first? Okay just let me decide, we start with good news first. This is actually going to be my last entry for Microbiology Reflective Journal. *huhu just kidding Dr wan* And the bad news, actually my study week is just started. Then I'm going to fight in a battle called FINAL EXAM. Do pray for us! #CellMolecularBiologyStudents15/16

    Actually I want to talk My Adopted Microbe that I've working on for this whole semester.

      *still hoping Dr wan & Dr Fairol read this* 
 
     My adopted microbe is Tersicoccus phoenicis. Alhamdulillah I've done my digital scrapbook and also the 3MT on Thursday, June 2 2016.

    This is actually my last opportunity to talk about my adopted microbe and the reasons why I choose Tersicoccus phoenicis. I guess i've screwed up my 3MT presentation. I'm too nervous until I forgot almost everything that I've been prepared, and the worst thing is I missed all the best & interesting part of my adopted microbe on the presentation day.

   I know I have no chance to repeat it again or fix everything but I do hope this last reflective journal could somehow help me.

   Why I choose Tersicoccus phoenicis? This is because I really love something extraordinary and weird that makes me curious about it. For your information, Tersicoccus phoenicis is a kind of bacteria that was found so different with other known organisms. It have been classified not just only a new species, but a new genus too! Do you know where does it were found at? Only two places on Earth. Where? In the cleanroom of spacecrafts. One at Florida and the other one in Kouru at French Guiana. Wow a  guys! A place that we expect no living microbes would survive there but unfortunately, Tersicoccus phoenicis made it possible.

     Guys, this is why I'm so proud with my adopted microbe. They resistance toward all those spacecraft sterilizations such as drying, chemical cleaning & peroxide treatment. But, it was not found to be pathogenic!

    A microbiologist from NASA said "Tersicoccus phoenicis have never been found in nature but it is possible they also live in nature that has same condition as the cleanroom such as cave or dessert." One of their characteristic is they able to produce nitrate and reduce nitrate. But because of they have never been found in nature, they could not said to be contributed to ecology.

   Well, researches are keep doing research on it so study how they could survive with all the spacecrafts sterilization methodologies and trying to improve in their sanitation techniques.

    Moreover, Tersicoccus phoenicis is declared as "TOP 10 NEW SPECIES" on May 23, 2014 and it is the only bacteria among the 10 species. So, I'm supposed to be proud to choose Tersicoccus phoenicis as my adopted microbe is it? I think that's all for this last entry. Thankyou.

YAKULT TRIP IS SO MUCH FUN

REFLECTIVE JOURNAL

Assalamualaikum W.B.T

    Hello readers, Alhamdulillah we meet again for this entry. Im literally excited to update my journal this time. As you guys noticed my topic at the above of this entry, i'm going to write about my experience for YAKULT TOUR. 

     Have you all been there? For your information, our beloved country have only one Yakult factory which is located at Seremban, Negeri Sembilan. 

 

    For me, this is just a day to apply and relate what we have learnt on Microbiology's class. On that day, we have been in a lecture before we were touring the factory and watch all the processes in making Yakult. Of course, we need some ideas or informations regarding Yakult before we get to know the processes of Yakult production. 

   As a biotech student, we know that Yakult is a kind of cultured drinks which used probiotic strain. So, it must be related to microbial world. Let me introduce the founder of the Yakult before we go into details. 

  Yakult was first launched in Japan in 1935 by Dr. Minoru Shirota, a japanese famous scientist. He found and made researched on a microbe named as Lactobacillus casei strain Shirota. He was actually the fisrt in the world to isolate and culture a probiotic strain which could reached the intestines alive in large numbers and imparted health benefits to the host. Therefore, he used this strain to make Yakult!

Lactobacillus casei strain Shirota

    The name Lacto is reffered to milk, Bacillus is the shape of the bacteria, Casei is cheese where this bacteria have been cultured with & Shirota is the name of the founder.

     Why is it so important to gain a good microbe to reach our intestine? We have been told from the lecture in Yakult trip, our intestine is actually a part of our immune systems. So we know that some microbe could not resist to the bile and the secretion of gastric juice in our stomach. However, Lactobacillus casei strain Shirota is one of the microbe that is resistance to gastric juice and could reached our intestines. There are several proves that have been proven this bacteria reached and alive in our intestines. 

    Okay now i'm going to tell about the processes. Seriously guys this is the intersting part! But honestly, i could not remembered all the processes involved, how the machine works, what is the suitable & appropriate conditions in details but i do remember what I exactly seen on that day! There's a part where they boiled the milk at certain temperature and I'm thinking this is the process of pasteurization. I tried to relate on what we have leart on topic "Microbial Genetics & Genetics Engineering". Pasteurization is the process killing bacteria in food and from this case they were doing to kill bacteria from growing before they put and mixed the cultured of Lactobacillus casei strain Shirota into the milk. 

    The processes were very organizable and unfortunately the person who guide us for the tour not allowed us to take any photos. But there are a few photos of me and my friends at the factory. Oh ya, I also bought two cottons of Yakult and a cooler bag for us to keep it cold so that the bacteria will live happily. HAHA

   

    I think thats all for this entry, a very much thanks to Dr. Fairolniza the leader of our trip, she has did very much for us. We were bery appreciate on Dr. Fairol works because she is the one who's set the date and deal with Yakult factory for the visit. Thank you. 

Ecology

REFLECTIVE JOURNAL

Assalamualaikum w.b.t 

         Hello readers, thank you for willing to keep on updating my reflective journal. So i'm going to write on Ecology's topic on week 10 who's handled by Dr. Wan Zuhainis. 

       First of all, i would like to rate this topic about 9/10! Well, this topic is quite easy and i'm hoping it will be ask on test 2 more than other topics which are a bit tougher. Unfortunately, there is no any kind of questions related to ecology on test 2. I'm so sad. But it's okay guys, why do people test you on something that is easy for you right? Actually not really easy but at least this topic is kind of something that could use your logic thoughts by writing your own words and hoping the answers could be accepted. HAHA.

     In class, we were already divided into six groups. Since Dr Wan zuhainis is not feeling well on that day, so we all are willing to be the teachers to each other. Guys, seriously it was fun. The task is just simple. We already have studied this chapter before entering the class right? So this could make this task is more effective. 

      We have been given about 10 minutes to add up some more information on Ecology. Each person in each group is given a subtopic to make on research. After 10 minutes, the first group have to go the second group, teach and give all of  the information to them. Definitely, the second group will have more information regarding their subtopics including their own information previously. So next, the second group will pass the information to the third group. So this is how the flow of the information is pass to one another. 

     So, if we were looking at the terminology of ecology, what does cross on your mind? I bet we might think in the same way. It must be something like interaction between all living things from the producer up until the consumers and decomposers. There could be a pyramid diagram showing the energy flow about 10% and another 90% is heat lost. The lowest part which is the biggest population is the producer such as grasses and followed by first, secondary and tertiary consumers. Microbes are in the category of decomposer which play important roles in the ecosystem for the recycle of energy flow. 

TROPHIC LEVEL DIAGRAM

      Since we are taking on Microbiology class, so it is more related to microbialecology. The definition of microbialecology is the interaction or relationship between (microbe-environment) and (microbe-microbe). Microbial interaction can be evaluated based on their physical interactions and benificial/harmful effects. Three type of known interactions which are endosymbiosis, ectosymbiosis and endo/ectosymbiosis. From what i have found the definition of each physical interactions are:

• Endosymbiosis - Interaction between different organisms at which one symbiotic organism lives in another organisms.
• Ectosymbiosis - Symbiont lives outside other organisms on the body surface.
• Ecto/endosymbiosis - Both interaction inside or outside the organisms. 

    There are seven type of interactions all of it, three positive interactions (mutualism, cooperation, commensalism) and four negative interactions (predation, parasitism, amensalism, competition). For example, amensalism is opposite to commensalism. To make it easier to remember just choose either one interaction such as commensalism. We know that, symbiont A (host cell) will get neither benefits nor harms, it will remain neutral while symbiont B (commensal) will get benefits. So this is vice versa to amensalism. 

     As the best creature of God in this world, we need to protect and conserve our ecosystem from being destroyed and kills other living organisms. We already know our environment is totally sick and some of the organisms were extinct because of this kind of situation. So, as in person by hook or by crook we need to prevent further deterioration of our ecosystem. Otherwise, not only the animals but the human population are also affected because of this problem. We don't want to see our generation lives in a such worse and struggle life is it? So, it is time to start conserve our ecosystem. 

Topic 3: Prokaryotes & Quiz

REFLECTIVE JOURNAL TOPIC 3

Assalamualaikum W.B.T

Hello readers, let's continue where we left on the previous week!

       On Monday 14th of March, we have did an individual quiz which is consist about 28 questions regarding the current chapter that we are learning about. We were quite shocked Dr. Wan made a surprise by doing a pop quiz for us. So I was be like, HAHAHA. 

       Honestly, i'm not so prepared for the quiz because i just go through the note and studied only a few things before the class. I repeat, studied only a FEW things and it almost to NONE. I didn't expected the questions are as much as 28 for all of it. Because in the previous quiz we only did up to 6 questions. 

       Even though I can't remembered all the content about prokaryotes, I still managed to answered the questions 22/28 correctly. Dr wan, is it good enough for the marks I've got? it's okay right? you know, I didn't study at all. Haha sorry i'm joking. Actually I'm not really satisfied about my mark but yet we have to be grateful, Alhamdulillah. There are more among my friends got higher than me so I need to work more on it to achieve higher in the future. In Syaa Allah. 

       To conclude, the purposes of the quiz are to check the level of our understanding on prokaryotes. How far was our revision goes on for the topic? Did the students really study before they entered the class? If yes, they must be able to answer the questions and ready for any kind quiz or test. And I definitely agreed with what have Dr wan did for the class. Unexpected quiz is really good for the students so they will be aware and study frequently to prepare themselves for any possibility come in the future. But, i'm still hoping our lecturer will inform us first earlier if there any quiz be held on that particular day. 

     On the next class Thursday 17th of March, we were just continued learning on the previous slide until the topic is finished. At the end of the lecture, Dr Wan brought a brownies for the whole class as a gift for group that won the quiz last week. Everyone could taste it, not only the winner and yeah of course the taste was great and delicious! Dr Wan really kept her promise! Thank you Dr Wan we love you! 

 

TOPIC 3: Prokaryotes & Games

REFLECTIVE JOURNAL TOPIC 3

Assalamualaikum W.B.T

Hello readers, 

TOPIC 2: Microscopy & TOPIC 3: Prokaryotes

REFLECTIVE JOURNAL TOPIC 2

Assalamualaikum W.B.T

    Hello readers, so I'm going to continue my weekly journal about the topics that I've mentioned in the title of my post. 

MICROSCOPY

       On Monday's class 7th of March, we have learnt about the second topic which is microscopy. In the previous week, Dr. Wan Zuhanis gave a task to a few students (group 2) to find out how to learn the microscopy's chapter in interesting way to avoid a boring environment. So, these few students had come out with a brilliant idea even though its not as what as Dr. Wan had requested. But personally, their's effort and work had impressed me! 

      So what did they do? They did a kind of story mode's slide show and read it for us. Based on my understanding and what I  still remembered, it is about a scientist which found a new microbe then he wants to discover it in details. He did a few experiments and at the end he found out the particular microbe hates light. At the same time, a microscope is created. But they changed the story to make it more interesting and funny but the facts are still there. (please correct me if I was wrong) We were laughing in the class as well as Dr. Wan. We started the class with happy mode.

     Luckily, we all already get familiar with the components of the normal microscope because we have been exposed and used it since the primary school. So, it just a refreshment for us to remember the functions of each part of the microscope. Then only I know, the microscope that I have been normally used before is bright-field microscope.

Bright-field Microscope

     There are actually many kind of invented microscopes to discover microbes which need special treatments or techniques and cannot be seen with ordinary microscope. Below are several type of microscopes. 

   

Phase Contrast Microscope

Fluorescence Microscope

Confocal Microscope

Transmission Electron Microscope

Atomic Force Microscope

     Even though we do not have the opportunity to use the other type of microscopes but we still could see the example of images formed by using each type of the microscope. The structures are really beautiful and amazing. So, no wonder scientist called it "Bacteria is an Art" and behind these beautiful art, it is a living thing and have their own life.

       There are few type of stains which are 

• Simple stains
• Differential stains
• Acid fast stains
• Special stains for capsule, endospore and flagella.

       Based on what I have found and information shared by my classmates, simple staining is used to to determine cell shape, size and arrangement. It's the simplest staining involving only one stain such as gram safranin, methylene blue and gram crystal violet. Next, the differential stains. The usual differential stains is the gram staining. In other words, gram staining use to dyes to differentiate gram positive and gram negative bacteria. While, the acid fast stains is a differential stain that used to identify acid-fast organisms for microbacteria, Last, the special stains which is use to identify capsule (polysaccharide layer), endospore (bacteria that can produce endospore under unfavorable condition e.g: Bacillus anthracis) and flagella (movement of the microbe). 

       Furthermore, there are also a few questions in the "check" slide such as:

• What are fluorochromes?
• What can be diagnosed using bright field, phase contrast and fluorescence microscopy? 
• What is the basis of gram staining?
• Name three gram positive and three gram negative bacteria.
• What did you learn from the tri to the Microscope unit?

      I already posted the answers to padlet as Dr. Wan Zuhainis have requested. Kindly refer to this link padlet.com/zuhainis/intromicrobe for more information. 

      At the end of the Tuesday's class, we did a quiz for this chapter about six questions and also group quiz. It was very exciting moments.

     Have you ever think how useful and helpful the technology is? I'm so grateful and I hope in one beautiful day I will be one of the Malaysian's scientist and able to have all of these experiences. What if I could discover a new type of microbe? Wow, it is a really big dream to achieve but nothing is impossible, am I right? We will go for it and do pray for us too. 

PROKARYOTES

    Before the class, we were needed to submit an online mind map to PutraBlast about prokaryotes. So, I have chosen Popplet as the medium to make it. I did a revision and go through the notes before I did it. I also find some extra information and a few definition about unfamiliar science terms from the internet to make an 'informative' mind map. I shared the extras information on my mind map so my friends would also get the knowledge too.

Kindly check out my mind map here, http://www.popplet.com/app/#/3076444

   On Thursday 10th of March, Dr. Wan Zuhainis have made a 'mind map' game at which all the students are needed to make only ONE mind map on the whiteboard. Each of the students should fill up the branches for at least one information about prokaryotes. But the rule is to make it silently so we could not talking to each other. But yet there are still a few students were talking including me actually. No, i'm not talking to my friends! I just talked to myself "hmm what else to write? oh seems like there are few infos are repeated here" .


     We also did an activity on Quizlet at which we have to write down any terms or subjects from prokaryotes and give their definitions. We were been given 10 minutes to do it and I could made it 11 terms with definitions. Next, we have to do a quiz which the questions are from the previous activity we did on the Quizlet. Yes it's very easy and I got 100% for the test. Then I downloaded the result and post it to PutraBlast.

     Last activity we were just go through a few slides of prokaryotes, discussed together about it and will be continue on next Monday 14th of March. I think that's all for this week's entry. Thanks for reading.

     

      

    

TOPIC 1: Introduction To Microbiology and Bacteria As An Art

REFLECTIVE JOURNAL TOPIC 1

Assalamualaikum W.B.T

    Hello beloved readers, as all microbe's students have been asked to make a reflective journal for every topic in Microbiology's course, therefore I've chosen a blog as the medium to write it. 

     Before we're going to depth, I am Nurul Syafiqah binti Azhar (182757). First of all, it is such an honor to have a very capable lecturer as Dr. Wan Zuhainis to be our lecturer in Microbiology. Dr.Wan's talk had impressed me since in the early semester 1 on the first meeting between all students and lecturers from other departments in Faculty Biotechnology and Biomolecular Sciences at DKU.

      So for the first entry, I would like to share my first impression in microbiology. Before I've been exposed to the contents of microbiology, I'm thinking "oh no, it must be a boring class because we're going to learn about the cell kind of thing again" No, I would say that i'm absolutely wrong. In Dr Wan's class, we had so much fun and within same time we learnt and gained knowledge. 

     We have used the technology and been exposed to many kind of education's ways of learning. We're needed to use the applications such as Paddlet, Blendspace, EdPuzzle and etc. Even in the class, we were also have to try and search the information by our self before the lecturer give further explanation about the current topic. These increase the efficiency in learning process.

       So, one of the interesting fact in microbiology is to know how could tiny organisms give very big impacts to humans or animals either bad or good things. They are more in population they even can reproduce rapidly compared to humans but yet still cannot be seen with naked eyes. They are everywhere around us but invisible. It can be simply said, they are one of the powerful creation. Amazing!

     Furthermore, we also got to know many kinds of microbes that we are not familiar with. Even we have heard their name before, but we did not know the special characteristics of the microbe. For example, mycoplasma is a bacteria while thermoplasma is an archaea. But both shared same characteristic which they can change their shape depends on the surrounding environment (unfavorable). Beside, Mycoplasma is the smallest bacterium in the world. They are even smaller than the viruses. What an amazing fact to know!

Mycoplasma

    Moreover, we know that one of the characteristic of viruses is they are small compared to bacteria. But Dr. Wan had told us that there is the largest virus in the world (giant virus) have been found by the scientist at which they can be seen with naked eyes! The virus is called as Pithovirus or  Pithovirus sibericum. 

Phitovirus sibericum

   I love to know facts and like to discover things that caught my attention and make me curious to know. Many facts about microbe have been exposed in the first topic. I hope, I can learn the next topic with more interesting facts beside only learn based on the notes. I think, that's all for my first entry. Thanks for reading! Assalamualaikum.