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~

Last Class...

Friday, 19^th December 2014

Sobs sobs :’(

The very last lecture is today. Time flied too fast until we didn’t realize more than 3 months has passed. This is very sad.

But, lesson has to going on. We learned more about “Control of Microbial Growth” and also a new last topic which is “Antimicrobial Chemotheraphy”. This topic needs us to memorize many things as well. Fuh~ Around another two weeks we will sit the final exam for Microbiology and I don’t sure I can do this. Even when we play quizzes in Kahoot.it , I couldn't answer much. Huarghh HELP ME!!!

Sigh :(

Thursday, 18^th December 2014

     Today in microbiology class, we learned some calculation which I don’t like it. We calculated number of generation and also generation time.

No. of generation = [ log  no of cells(end) – log no of cells(beginning) ] / 0.301

Generation time = 60 min x hours / no of generation

Dr. Wan also gave us exercise about this part and we have to submit it. I took quite a long time to calculate it hehe. But, I still managed to submit it on time.

Next, we learned a bit about “Control of Microbial Growth”. There are so many terms to remember which I couldn’t imagine how I gonna memorize all that. *Sigh*

A FEW DAYS MORE~

Tuesday, 16^th December 2014

Another few days left before this semester end. Hmm...

Today we continued our lesson on isolation/culturing, mantaining and preserving microbes.

Aseptic technique

Streak plate method

Pour plate method

Anaerobic culture method

Agarose

Blood agar

EMB agar

New Things and New Terms to Remember :(

Wednesday, 10th December 2014


Today was a replacement class actually and we have it in Biotech 2.2. We moved into a new topic today but before that, as Dr. Wan promised she did a quiz for all of us according to the group. The quiz was based on the topic that we just finished yesterday. My group only get 5 marks out of 10. Hmm it's bad and I didn't helped much at that time :(

So, the new topic was Microbial Growth. I have printed the note and I wondered why the note was so thick? Is it going to be a long and hard topic? When I checked, it was full with pictures of experiment that has been done by our seniors and we also going to do the same experiments later. These help me to get to imagine how the microbiology lab subject will be going on.

Microbial Growth

Growth - refer to number of cell, not the size

Tolerance - survive under condition that they cannot grow

Phile - Specific conditions to grow

Tolerant - conditions which organism survive, but not necessarily grow

Physical requirements - 

1) light

2) temperature

3) pH

4) water activity

5) osmotic pressure

Chemical requirements -

1) electron donors

2) electron acceptors

3) micronutrient

We did not finish this chapter yet and will be continue it next week. Besides, Dr. Wan also mentioned about something interesting that I have never heard before.

Here it is!

Watermelon Snow

Red coloured snow

Chlamydomonas nivalis