VIRTUAL MICROBE

Hi guys!

This time, I will share my experience working on Virtual Microbes, a project where we collaborate with students from other local public universities to produce our final products.

3rd year students is in Biomedical Team as we take 3 related subjects for this semester; Immunology, Pathogenic Microbiology & Microbial Genetics. There are 10 members in my group. 4 of us from UPM, 4 students from UKM and another 2 students from UM.

We have to make a literature review based on the microbe that we choose. Salmonella spp. is  chosen by all of the group members as this bacteria is very well-known and well-studied. Thus, it is easy for us to find related articles.

Before producing the final products, we discuss on how to make it through various media such as Zoom, Popplet and Padlet. It is very helpful as we can share our ideas and suggestions with all the members. We did the online discussion through Zoom 2 times, but not everyone can join the 2nd discussion.

UPM's students already have experiences in producing literature review, however not for UKM and UM students. So, it must be a new knowledge for them. I also got to refresh back what Dr. Wan has taught us step-by-step in doing the LR last semester.

This is a very good project. However, not everything can be a good thing. Compared to the group that we collaborate last semester, this group made us had quite a hard time. Yes, the final product is hard to do but everything could be easier if everyone participate actively.

In my opinion, they might not think this project seriously because its mainly based under UPM. Plus, they might find this work disturbing since they are not familiar with all the apps that we used. They may find out how to use those things on their own but if they have no interest, it cannot be helped. I understand how they feel using those apps because at first when being introduced with the advanced technology in learning, I find it difficult too HEHE. Everyone is busy,  and having only short time in doing this............H.A.R.D.

Supposedly this chance could be a great opportunity for all of us to improve ourselves. Teamwork, participation, consideration to other members, effort in doing something and many other aspects should be improve; including myself :)

The idea of collaboration with other universities is totally great but maybe the way of doing it should be revised back for a better results. Since its virtual, its harder to do the discussion compared to face to face. The communication is limited too. Although there are many other medias to be used to discuss, I find it sometimes not really helping.

All in all, I had a great time learning new facts and knew many things about our pathogen:D and got few lesson learned through all the things happened while we do this Virtual Microbes.

REFLECTIVE JOURNAL ON MICROBES & US and MICROBIAL ECOLOGY

Hi! It's already the lat day of Semester 4. The only thing left is the FINAL EXAMINATION!!!
*gosh, so nervous*
Before we forget everything that we learned in MICROBIAL ECOLOGY subject, she asked us to do a reflective journal on the outcome that we get from lesson in class and our project, MICROBES and US. So, here it is...

1. Learning Outcomes
My Answer: 
- To define the PRINCIPLE OF ECOLOGY
- To identify the wide range of MICROBIAL GROUPS
- To explain the basic concept of MICROBIAL NUTRITION AND METABOLISM
- To describe the factors affecting MICROBIAL DISTRIBUTION
- To explain the major types of organisms in SOIL and their function
- To explain the major types of organisms in AQUATIC and their function
- To explain the major types of organisms in ATMOSPHERE and their function
- To explain the major types of organisms in FOOD and their function
- To describe the microorganism involve in WASTE WATER MANAGEMENT
- To define RECALCITRAN MOLECULES and the microorganism involve in bioremediation

2. What you have learned?
My Answer: I have learned so many things in this subject. First and foremost, I learned that every habitat or ecology has different microorganism that lived there. It depends on many factors such as the nutrients, temperature, oxygen concentration, pH and so on. Besides, the microbes in a specific habitat have interactions with each other to provide a few things needed in order for them to grow. I also learned the types of microorganisms present in four habitat which are soil, aquatic, atmosphere and food as well as their application. Not just that, I learned about the microbes used in waste water treatment and bioremediation for recalcitran molecules. This has made me more understand about how important microbes in our life.

3. Elaborate the experience in doing the Microbes and Us project.
My Answer: In this project, we have to do a 15 minutes documentary video, 1 minute montage video (for augmented reality purpose), an infographic as well as a journal. The topic that my group (GROUP 1) has chose is RUMEN MICROBIAL ECOLOGY. We did't have much difficulties except to find time to do the project together as many of the group members are busy with other works. We did at least a project per semester, but in this semester we got new experience in writing a journal and interviewing an expert in the topic chosen, where the interview video was included in the documentary video. And it is also slightly different by doing an infographic from doing a poster(we always do this). Overall, I enjoyed my time doing this project with my groupmates.

4. How do you relate Microbial Ecology to other microbiology courses you have covered in the earlier semesters and how you can apply the knowledge in the future?
My Answer: To know and able to understand the microbial ecology is very important. It is because each microorganisms have their own specific factors why they live in such habitat. And to be able to do that, they must have a special characteristic such as some kind of different in their genetic materials or enzyme. All of this can be related to our previous subjects taken in semester one until semester three. For this semester, the other subjects that we took such as Applied Food Microbiology, Bacteriology and Enzymology are quite related to this Microbial Ecology subject where there are some topics that we learned are similar to each other.

All in all, I have learned many new things from this subject and it make me feel even more happy to be a MICROBIOLOGY student!!!

INTRODUCTION TO PRINCIPLES OF ECOLOGY

Ecology:

the branch of biology dealing with the relations and interactions between organisms and their environment, the physicals and biological factors affecting them or influenced their distribution and abundance, and understanding the mechanisms involved in biological diversity.

Hierarchy of ecology:

1. Species/organism - organisms with common genetic makeup, behavior, physical characteristics

2. Population - a group of individuals belonging to the same species inhabiting a particular geographical area

3. Community - all populations of different species inhabiting a particular area

4. Ecosystem - a relationship between a communities (biotic composition) and their physical environment (Abiotic composition)
5. Biosphere - all ecosystem on Earth

Development of microbial communities:

- r strategy: dominates environment rich/temporary rich in resources

- K strategy: tend to be successful in resource-limited situations

- preemptive colonization: to discourage further succession by other organisms

- autogenic succession: microorganisms modify the habitat and permits new populations to develope

- allogenic successsion: when habitat is altered by environmental factors

- homeostasis: dynamic balance of process, materials and organisms in the ecosystem and biosphere

THE FIRST WEEK OF FOURTH SEMESTER

Hi, there.
We meet again. 

The first day of semester 4 begun on 22nd February 2016 and we also had the first class of MICROBIAL ECOLOGY with our beloved Dr. Wan Zuhainis Saad. Nothing much on that day, just an explanation on this subject. But it was exciting to hear that we gonna have a big project as well this semester. A different kind of project, where we gonna publish what have we done. So, here it is:

MICROBES & ME
- 15 minutes documentary video (with an interview of an expert for 5 mins)
- 1 minute montage video (combined montage video will be publish)
- article (will be combined and publish to the National Library)
- infographic

We have 7 members in my group which are Alia, Azny, Aishah, Ee Lyn, may Ling and me. We divided our tasks and I was the person in charge for the infographic, along with Azny.

We chose to explore more on the RUMEN MICROBIAL COMMUNITY. Appearantly, we haven't started anything yet but we can imagine the big picture of this project. Hope that it will be a huge success!

On 24th February, Dr. Wan started her lecture. What have been asked to us was to review an article on principles of microbial ecology and posted it in padlet.

Em..so maybe till here the story for this week.
Bye :)

THE AWESOME MICROBES CARNIVAL.

22nd November 2015 (Sunday)

          Last Thursday and Friday was a very hectic yet memorable for me. An awesome event was held last two days which involved all the staffs and students of Department of Microbiology. It was called THE AWESOME MICROBES CARNIVAL. I was one of the committee members for this event. I was in the Publicity and Promotion Unit and I enjoyed worked with other seniors in this unit. I helped to promote this event by displaying our poster on the information television in the faculty, website of Faculty of Biotechnology and Biomolecular Sciences and also the website of University Putra Malaysia. Besides, our unit helped Dr. Hidayah to bake cupcakes to be sold during the event. Unfortunately, I cannot joined them because I have another commitment to be done :(

          The first and third semester students did and exhibition about microbiology and the fifth and seventh semester students promoted and sold products related to microorganisms. My groups (Atikah, Azny, Alia, Mayling. Aishah, Eelyn) presented about ENDOSPORE. We prepared an A1 poster, an augmented reality video and a 3D model. We did get many informations as we read up on this topics. It was also a new knowledge and experiance for us to design a 3D model using applications such as 123D Design, SketchUp and AUTOCAD.

The video~
   Look who's drawing the endospore >,<

The poster~

The 3D model~

          During the event, there were also some 3D printers in the Panggung Percubaan. They printed our 3D models that time. Moreover, there are some microscopes placed in the Panggung Percubaan to give experiences to all the visitors to see the microorganisms. We also prepared many activity and games booths so that the visitors can learn more about microbiology. Each group from the First and Second Year students need to explain their poster to everyone that came to their booths. For me, I think that it is not easy to explained about what have we learned to other people especially the one that did not have any basic in science. There was one of the visitors that said to me, "You're so good. You can explained very well but its too scientific for me." Although I have tried to explain in the simplest way, I cannot make her understand well. Hmmm. However, that thing did not make me lost my strength! There were some of the visitors said that they gained some knowledges after we told them about the endospore. This made me really happy :)

          Personally, I believed this event has brought many advantages to all the students and all the visitors. It is such a great event. I hope that there are another series of event like this in the future!

Till then.

Bye.

Week 14 (Monday, 1st June 2015)

Today is the last class of Microbiology II with Dr. Wan for this semester. We started the first class in BMF (Bilik Mesyuarat Fakulti) and we ended here as well. Such a memorable thing for us to remember hehe.

We finished the last two topics which are Biogeochemical Cycles and Aspect of Biotechnology in Microbial Ecology.

BIOGEOCHEMICAL CYCLES

·         Definition: mechanism by which recycling of nutrients occur

·         Characteristics: 1) transformed and cycled through redox reaction   2) all cycles are linked

·         Cycles: 1) carbon     2) nitrogen     3) sulfur     4) iron     5) mangase

1) Carbon cyle

Forms: 1) reduced – methane, organic matter   2) oxidized – CO, CO2

§        Fixer: 1) plants     2) photosynthetic bacteria (cynobacteria, green algae)

§         Aerobically à respiration à CO2 released

§        Anaerobically à respiration/fermentation à CO2, H2, CH4 produced

2) Nitrogen cycle

§       Processes: 1) nitrification   2) denitrification   3) nitrogen fixation

§        1) Nitrification – aerobic (ammonium ion à nitrite à nitrate)

§        2) Dinitrification – dissimilatory (use nitrate as electron acceptor to produce ATP)

-            anaerobic  (by Pseudomonas)

-            products: nitrogen gas, nitrous oxide, nitrite

§         3) N2 fixation – reductive process which produce ammonia

-          Aerobic/anaerobic prokaryotes

3) Sulfur cycle

Process: 1) sulfur oxidation   2) sulfur reduction   3) sulfate reduction

§        1) sulfur oxidation – produce sulphate by using sulfide as e- source

-               Thiobacillus

§        Sulfur reduction – sulfate à sulfide (Desulfovibrio, Desulfuromonas)

-          Sulfite àsulfide (Clostridium, Desulfovibrio)

§        Sulfate reduction – reduction of sulfate for use in amino acids and protein biosynthesis

4) Iron cycle

§       Oxidation – ferrous ion àferric ion (aerobic)

§        Reduction – ferric ion à ferrous ion (anaerobic)

5) Manganese cycle

§        Aerobic – manganese ion à manganic ion

§       Anaerobic – manganic ion à manganese ion

ASPECT OF BIOTECHNOLOGY IN MICROBIAL ECOLOGY

1) M/organism as pollutants – food/waterborne phatogens

                                                        -  eutrophication

2) M/organism as pollution – elemental mercury, organic compounds of mercury

                                                      - not recycle

                                                      - inhibit enzyme when combine with sulfyhydryl group of protein

3) M/organism as indicator of pollution – test for water pollution

                                                                              - E. coli, E. aerogenes

4) M/organism may reduce pollution – add into soil or plants to improve crop production

                                                                         - carry out biodegradation, bioremediation

·         Biodegradable – natural decomposition of molecule by microorganism

        Non-biodegradable = recalcitrant

·         Microbial application as pesticide – DDT

      Microbial application as insecticide – Bt

·         Bioremediation – use of living organism to  promote degradation of environmental pollutants

·         Cometabolism – addition of easily metabolized organic matter to increase biodegradation of recalcitrant compounds that are not use a C and energy sources by microorganism

·         Phytoremediation – use of plants to stimulate the degradation, transformation or removal of                                                  compound, either directly or in conjuction with microorganism

·                                                                  – phytoextraction, phytodegradation, rhizofilteration, phytostabilization,                                                    phytovolatilation

Microbial Groups and Principles Of Ecology

This week we learn about Microbial Groups, Principles of Ecology and a bit intro in Biogeochemical Cycles.


MICROBIAL GROUPS

* Microbial growth is based on the population size an interrelated with reproduction (binary fission, budding, fragmentation, spores, sexual reproduction)

* Requirements for development of microbial community
1) Physical requirements
   - light
   - temperature
   - pH
   - water activity and osmotic pressure
2) Chemicals requirements
   - water
   - carbon
   - oxygen
   - nitrogen, phosphorus and sulfur
   - special growth requirement
   - trace elements

* Developement of microbial communities
- selection strategues
- succession
- biofilm


PRINCIPLES OF ECOLOGY

Ecology
- the systematic study of organisms and their interactions with environment

Habitat
- place where an organism can be found

Ecological niche
- a place where an organism performs best

Hierarchy in ecology
1) organism
2) population
3) community
4) ecosystem

Determinants of biosphere distribution of organism
- temperature
- water
- sunlight
- wind
- rocks and soil
- periodic disturbance

Homeostasis
- dynamic balance of processes, materials and organisms in the ecoystem and biosphere

Flow of energy
Producers --> consumers --> decomposers

Roles of microbes in the ecosystem
- oxygen producer
- nitrogen fixer
- recyclers of dead materials
- source of food
- contribute to evolution

Approaches to effective ecosystem management
- stakeholders
- adaptive management
- natural resource management
- strategic management
- lanscape level conservation
- command and control management