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

ALGAE, FUNGI, PROTOZOA and VIRUS

Week 11

We have three class for this week. On Wednesday, Thursday and Friday. We learned four topics and we did an activity on Friday using new interesting apps.

My group (MayLing, Veron, Nuaim, Azny, Alia) and I presented about algae on Wednesday. Basically, algae is a plantlike protista and have many different division; chlorophyta, charophyta, euglenophyta, chrysophyta, phaephyta, rhodophyta, phaephyta and pyrrophyta. They live in three types of habitat which a planktonic, benthic and neustonic. Algae is either phototrophic or chemoheterotrophic. They reproduce through asexual (fragmentation, spore, binary fission) and sexual reproduction. Nowadays, algae is highl y used as a source of biofuel.

Fungi are a very interesting organism. They do not have chlorophyll and most of them are saphrophytes. They reproduce mainly using spores. However, many of them can have both sexual and asexual reproduction (budding, fragmentation, sporulation). There are 5 types of spore which a conidiospore, chlamydiospore, sporangiospore, arthrospore and blastospore. As same as algae, fungi also have many different division. The divisions are zygomycota, ascomycota, basidiomycota, chytridiomycetes, deutromycota, myxomycota, acrasiomycota and oomycota.Fungi can cause harmful to human such as ringworm and asthma but, they are more likely to be beneficial to us as they are really important in fermentation process and agents for bioremediation.

Protozoa are animal-like protist. Their morphology is very unique as they have ectoplasm, endoplasm, pellicle, nucleus and vacuoles. They feed as a chemoheterroyroph and saprozoic. They are motile and have pseudopodia, flagella and cilia as their locomotry organelles. They reproduce through asexual (binary fission) and sexual reproduction (conjugation). They are classified into seven clssification based on types of nuclei, mode of reproduction and mechanism of locomotoin. THe classifications are sacromastigophora, labyrinthomorpha, apicomplexa, microspora, ascetospora, myxozoa and ciliophora. 

Virus are obligatory intracellular parasite which means they need a living host to grow. They are classified based on nucleic acid type, strategy of replication and morphology. They can have either DNA or RNA, double or single stranded. Usually, they have capside, spikes and envelope which attach to cell wall, fimbriae or flagella of bacteria and plasma membrane of  animal cells. Baed on the morphology, they are classified into enveloped, complex, helical and polyhedral virus.

On Friday, we used edpuzzle.com to create a quiz in a video. It is very interesting and also a new form of attractive learning.

7 WEEKS LESSON WITH DR. SIEO CHIN CHIN

The first class of BMY3102 was on Wednesday, 25^th February. Differ from the last semester, we have two lecturers for this course. The first one that taught us was Assoc. Prof. Dr. Sieo Chin Chin. We learned two topics with her, which are Nomenclature and Classification and Immunology. Her class was very enjoyable and I also learned a lot. Here, these are the summary of the lessons…

Nomenclature and Classification

Taxonomy : 1. Nomenclature – assignment of names to taxonomic groups in agreement with

   published rules

                     2. Classification  - arrangement of organism into taxa based on mutual similarities or

                  evolutionary relatedness

                     3. Identification – process of discovering and recording the traits of organism.

1. Nomenclature

§  Common rules in nomenclature

-          Binomial nomenclature (genus + specific epithet)

-          Both underlined or italicized

-          Genus capitalized, species lowercase

-          Genus may be used without species

-          Abbreviation : Escherichia coli

       E. coli

    

       Enterococcus faecalis (En.faecalis)

       Escherichia coli (Es. coli)

§  Process of naming new bacteria

§  Ways to describe strain

-          Biovars: strain characterized by biochemical or physiological differences

-          Morphovars: differ morphologically

-          Serovars: distinctive antigenic properties

*Type strain – first strain studied and is more fully characterized but not necessarily

   the most representative member

2. Classification

CLASSIFICATION SYSTEMS

PHENETIC                   PHYLOGENETIC                GENOTYPIC

  -      Numerical                                   - 16S rRNA                                                   - Other

       taxonomy                                   - Phylogenetic                                                   molecular

       (S_SM & S_J)                                   tree                                                                  methods

   -         Dendogram

3. Identification

TECHNIQUES/METHODS FOR CLASSIFICATION/IDENTIFICATION

CLASSICAL                                        

          -       Morphological (staining, external structure, cell inclusion, cell grouping)

         -       Physiological and metabolic

         -       Biochemical

         -       Ecological

         -       Immunologic test

         -       Phage typing

           -       Antibiotic profilling                   

                         MOLECULAR

            -          Amino acid sequencing

            -          Nucleic acid base composition (%GC by HPLC and Tm)

            -          Nucleic acid hybridization

            -          Nucleic acid sequencing

            -          Genomic fingerprint (MLSA, RFLP, ribotyping)

            -          Nucleic acid probe

            -          Plasmid fingerprinting

                                                                                          

                      *Assignments

Bergeys Manual

Introduction to Immunology

*the topic that I love >,<

Immune system - defense system of individual against the thread of disease caused by infectious microorganism

Pathogen can be harm when :  gain access through the right roots

                                                 - attach to host cells

                                                 - persistence and evade to produce harmful changes

Organs of immune system - Primary lympoid organ

• production of immune cells
• maturation site for immune cells in the absence of antigen
• e.g: bone marrow, thymus, bursa of Fabricius

                                           - Secondary lympoid organ

• maturation site for antigen-driven immune cells
• e.g: adenoid tonsil, lymph nodes, MALT

Cells of immune system

Types of immunity - non-specific immune response

• external - skin

                                                      - mucous membrane

                                                      - normal microbiota

• internal - physiological barrier

                                            - phagocytosis
                                            - inflammation

                                - specific immune response

• humoral
• cell-mediated

Lymphocytes - B cell : mature in bone marrow

                                      has immunoglobulin (recognized undigested antigen)

                        - T cell : mature in thymus

                                       has TCR (recognized processed antigen on MHC

                                       molecules on APC

Features of good antigen - high molecular weight

                                         - foreignness

                                         - complexity

                                         - biodegradable

Antibody - IgG, IgA, IgM, IgD, IgE

Humoral immunity

- How antibody gives protection

- Antibody response

• Primary (latent period)

1.    chemical and physical nature of antigen
2.    adjuvants
3.    dosage of antigen
4.    frequency of antigen exposure
5.    routes of administration
6.    genetic makeup of host

• Secondary - rapid increase in antibody titer

                            - longer persistence of antibody

                            - shortened latent period

                            - higher titer

Cell-mediated Immunity  -      CD8 cytotoxic T cell

• Stages in granule exocytosis

1. recognition and binding of target cells
2. delivery of lethal hit
3. death of target cells
4. recycling of cytotoxic T cells

                                                                 -       Delayed-type hypersensitivity

• Aims

1. recruit monocyte
2. keep monocyte/macrophage at infection site
3. activate monocyte and macrophage

• Reaction

1. activation of CD4 T cells
2. migration of effector Th cells
3. recruitment and retentation of monocyte
4. activation of macorphage

Memories~