The Awesome Microbe Carnival

Rehearsal day 18/11/15

On that day, everyone was so busy and Dr. Wan looked so worry because there are a lot of things stll not yet settled especially the golden history tunnel. Although we knew all these were rush and crazy, the only way we can do is to go ahead with everything. Secreteriat were dividing our own job on that day and we found that we need the help from the post graduate student to in charged of the exit counter. I straight away called Kak Fatin and she is ok with that. I felt so grateful to Kak Fatin and her friends for their help.

1st day 19/11/15

We had SSK lab at 8am but we still need to reach Panggung Percubaan at 7.30am to set up. Our poster looked so beautiful. We started to decorate our poster booth with some ribbon and balloon. After Lian Sing reached our poster booth, then we only went to our class because Lian Sing will took over our poster booth during our SSK class time. Thanks to our SSK lecturer because she willing to release us earlier to our carnival. At first, we were quite passive. We seldom approached to the visitors. I think this was because we were not yet ready and prepared. Haha. I some more walked way from my poster booth to visit other game booth , of course I knew my group members will be stood in front of our poster booth. I felt like in charged of game booth was more interesting.
After that, May Ling and I then in charged of the registration counter. We found that people kept ignored the registration counter and entered through the exit door. I think this was because we didn't labelled "registration counter" and we also didn't labelled any "entrance" or "exist" at the door. There were no any big problem on the registration counter. The people on the first day was too many and caused the booklets are not enough to distribute.

2nd day 20/11/15

On the second day, our poster booth will be jugded. We felt quite nervous. We kept practising what we are going to present later. Before our judgement, there were quite a lot of visitors come to our booth compared to the first day. This made us more used to what we are going to present later because we kept repeating the content of our poster. Dr. Suriana and Dr.Amalia praised the idea of our poster and video were creative. After the SCL judgement, I will then again in charged of the registration counter. Today visitors were not much compared to yesterday, but our goodies bag are finish distributed. There were few students ask for goodies bag, but we only can apologized. There were also few master students who rejected to write down their name for registration. They only willing to write down their name after we explained to them the purpose of writing down their name is to count the number of visitors.

Throughout this carnival, for my part, I am not doing my best. I will do better in the next carnival because finally I understood the job scope of secreteriat. Thank You Dr Wan, Kak Syaza, Radin, Mokry and everyone who helped me in this carnival. This carnival will not be that successful if without you Dr.Wan. My friends are all amazed by this carnival and they hope for The Awesome Microbes Carnival 2.0 !

Semester 3 Microbial physiology Topic 3

Topic 3: Intracellular structures of prokaryote

Notes:
1) The intracellular structure found in prokaryote are plasma membrane, cytoplasm, the nuclear area, ribosomes, inclusions and endospore.

• Plasma membrane

- Function: selectively permeable barrier, synthesize cell wall components, assists in DNA replication, carries on respiration and captures energy as ATP.

- The movement of materials across membrane: simple diffusion, facilitated diffusion, osmosis, active transport and group translocation.

- Simple diffusion, facilitated diffusion and osmosis do not require energy where active transport and group translocation belong to active transport.

- Group translocation are molecules that chemically modified during passage across cytoplasmic membane. 

• Cytoplasm

- Cytoplasm refers to the substance of the cell inside the plasma membrane,

- contains proteins, carbohydrates, lipids, inorganic ions, DNA, ribosomes and inclusions.

- lacks of cyoskeleton

• The nuclear area

- Single long circular molecule of double-stranded DNA

- do not include histones and not surrounded by nuclear envelope

- In addition to the bacterial chromosome, bacteria often contain small circular, double stranded DNA molecule called plasmid.

• Plasmid

- small circular, double stranded DNA

- do not contain genetic material essential for growth

- contain features that enhance survivability such as gene for drug resistance can be transfer from one bacterial to another

- The characteristic of plasmid: not connected to bacterial chromosome and replicate independently of chromosomal DNA

• Ribosomes

- for protein synthesis

- 70S ribosome

- small subunit - 30S and large subunit - 50S

- Each subunit consists of protein and RNA called ribosomal RNA ot rRNA.

- Cells that have high rates of protein synthesis, have a large number of ribosomes.

• Inclusions

- divided into granules and vesicles

- Metachromatic granules are large inclusion. Volutin granules are an intracytoplasmic (inside the cytoplasm of a cell) storage form of complexed inorganic polyphosphate, the production of which is used as one of the identifying criteria when attempting to isolate Corynebacterium diphtheriae on Löffler's medium. They appear red when stained with methylene blue and gives a metachromatic effect.

- Sulfur granules serve a an energy reserve, derive energy by oxidising sulfur and sulfur-containing compounds. The bacteria that contain sulfur granules is sulfur bacteria.

- Carboxysomes contain the enzyme ribulose 1,5 - diphosphate carboxylase. It used for carbon dioxide fixation during photosynthesis.

- Magnetosomes contain iron oxide that act like magnets. Their main function is to protect the cell against hydrogen peroxide accumulation.

- Lipid inclusions store polymer poly-beta-hydroxybutric acid. It revealed by Sudan eyes and the example of bacteria that contain lipid inclusion is Mycobacterium, Bacillus, Azotobacter and Sprillum.

- Gas vesicles are normally found in photosynthetic group such as cyanobacteria, proteobacteria and green sulfur bacteria. The function of gas vesicle is to provide buoyancy for aquatic prokaryotes and to receive sufficient amount of oxygen, light and nutrients.

• Endospores

- resting structure formed by some bacteria for survival during adverse environemental conditions

- germination results in leaving the dormant stage and once again becoming a typical, multiplying cell (vegetative cell)

- high resistant differentiated bacterial cell

- enable the organism to endure extreme environmental conditions

- The structure of spore is more complex than vegetative cell:

- The presence of dipicolinic acid which located in core wall give the resistance properties of endospore because intercalate in DNA and stabilizing it to prevent heat denaturation.

- Genus Bacillus and Clostridium are two common disease causing bacteria that produce endospores as needed.

My own explorace：

1) In group translocation, the substance is chemically altered during transport, preventing it from escaping the cell after it is transported inside. This process requires high-energy phosphate compounds like phosphoenolpyruvic acid (PEP) to phosphorylate the ransported molecule, preventing its movement out of the cell. 

2) The magnetotactic bacteria can be subdivided into two categories, according to whether they produce particles of magnetite or of greigite, although some species are capable of producing both. Magnetite possesses a magnetic moment three times that of greigite.

3) The formation of endospores may help maintain the symbiotic association between these Epulopiscium-like symbionts and their surgeonfish hosts. Since endospore formation coincides with periods in which the host surgeonfish is not actively feeding, the cells do not need to compete for the limited nutrients present in the gut at night. The protective properties of the endospores also allow them to survive passage to new surgeonfish hosts. The fish may also benefit from this relationship because it is able to maintain stable microbial populations that assist in digestion and may receive a nutritional gain from microbial products released during mother cell death and spore germination.

Reflection:

I would like to know the benefit of endospore to the environment.  People always think that endospore maximize the chance of spreading disease. Actually endospore is not just spreading disease, but it help to maintain the symbiotic association between Epulopiscium-like symbionts and their surgeonfish hosts. Besides that, Bacillus subtilis spores are useful for the expression of recombinant proteins and in particular for the surface display of peptides and proteins. Therefore, everything have their good side and bad side include endospore, bacteria or even virus.

Semester 3 Microbial Physiology Topic 2

Topic 2: Cell Wall and Membrane Structure of Prokaryotes

Notes:
1) There are four structure external to the cell wall:

• Glycocalyx

- substances that surround cell

- it is made inside the cell and excreted to the cell surface

- capsule is called if the substance is organised and is firmly attached to the cell wall

- slime layer is called if the substance is unorganized 

- Functions: protection from phygocytosis, attachement to various surfaces, source of nutrients, and protect a cell against dehydration.

• Flagella

- Long filamentous appendages that propel bacteria

- There are four arrangement of flagella: Monotrichious, Amphitrichous, Lophotrichous and Peritrichous. 

- There are three basic parts in a flagellum:

Filament(contain the globular protein flagellin) , Hook, Basal body(gram-negative bacteria contains two pairs of rings and gram-positive bacteria contains only the inner pair)

• Axial Filaments

- bundles of fibrils that arise at the ends of the cell beneath the outer sheath.
- spiral around the cell
- present in the spirochetes group of bacteria
- e.g. Treponema pallidum and Borrelia burgdorferi

• Fimbriae and Pili

- Hairlike appendages that are shorter, straighter and thinner than flagella

-consist of pilin

- used for motility rather than for motility

- There are two types of fimbriae and pili: Fimbriae can occur at the poles, evenly distributed over the entire surface, and can number anywhere from a few to several hunfred per cell.

- Pili are longer than bimbriae and joint bacterial fells in the perparation for the transfer of 

DNA from on cell to another. 

Pili is used for the transfer of extrachromosomal

2) Cell wall component: Gram-negative and gram positive bacteria

Gram-negative and gram positive bacteria are structurally different and this differences cause them to have different characteristics. Gram-negative bacteria are resistant to antibiotics due to the presence of outer membrane.

3) Archaea have cell walls consisting of polysaccharide, glycoprotein but not peptidoglycan.

They contain a substance similar to peptidoglycan called pseudopeptidoglycan (pseudomurein).

Their cell wall type is S layer which protects against osmotic stress, pH and enzymes.

Archaea are naturally resistant to lysozyme and penicillin.

4) The unique feature found in cell wall of archae is the presence of L-amino acid instead of D-amino acid, the presence of N-acetyltalosaminuronic acid but not N-acetylmuramic acid and the presence of beta(1,3) glycosidic bond instead of beta(1,4)glycosidic bond.

My own exlporace：

1) Mycobacterium does not have any glycocalyx because they do not have cell wall or very little cell wall material.

2) Capsules give better protection than slime layer because capsule is organised and is firmly attached to the cell wall.

3) A spheroplast is a cell from which the cell wall has been almost completely removed, as by the action of penicillin. Spheroplasts are osmotically fragile, and will lyse if transferred to a hypotonic solution.

4) Septic shock is what happens as a complication of an infection where toxins can initiate a full-body inflammatory response. It often occurs in people who are elderly or have a weakened immune system. It is thought that the inflammation resulting from sepsis causes tiny blood clots to form, which can block oxygen and nutrients from reaching vital organs. As a result, the organs fail, causing a profound septic shock. 

Reflection:
Although cell wall and membrane structure of prokaryotes have learned in last two semester, there are few terms that I am not familiar with. Septic shock and spheroplast are new for me. I think to differentiate gram negative and gram positive bacteria have to be very specific to avoid any error since this is the important step to identify the bacteria.

Semester 3 Microbial physiology Topic 1

Topic 1: Introduction to Prokaryotes

Notes:

1) Prokaryotes divided into two domains which are bacteria and archaea.
2) Definition of prokaryote: Organisms that lack a cell nucleus or any other membrane-bound organelles.
3) They are unicellular, but a few prokaryotes such as myxobacteria have multicellular stages in their life cycles.
4) Prokaryotic diversity include proteobacteria, cyanobacteria, gram positive bacteria, spirochetes with unique morphology, green sulfur and green nonsulfur bacteria.

- Proteobacteria are a major group (phylum) of gram-negative bacteria.
a. Alphaproteobacteria - They grow at very low nutrient area and are agriculturally important because they able to induce nitrogen fixation.
b. Epsilonproteobacteria - They are microaerophilic and they are the most common cause in stomach cancer.
c. Gammaproteobacteria - They are medically important and a large group of pathogen belong to this group such as Salmonella spp.
d. Betaproteobacteria - They play a role in nitrogen fixation in various types of plants, oxidizing ammonium to produce nitrite.
e. Deltaproteobacteia - They are predators on other bacteria and are important contributors to the sulfur cycle.

- Cyanobacteria are aquatic and photosynthesic. They have live on earth for 3.5 billion years. Therefore, they important in shaping the course of evolution and ecological change throughout earth's history.
- Gram positive bacteria have specifc membrane structure. Their structure consist of thick peptidoglycan layer, teichoic acids and gram-positive bacteria are more receptive to antibiotics than gram-negative, due to the absence of the outer membrane.
- Spirochetes are helical in shape They are tightly coiled, and so look like miniature springs or telephone cords.These filaments run along the outside of the protoplasm, but inside an outer sheath; they enable the bacterium to move by rotating in place. Spirochetes causes syphilis and lyme disease.
- Green sulfur bacteria and green nonsulfur bacteria are autotrophs. They produce energy from light and are named for their green pigment, usually found in photosynthetic bodies called chlorosomes.
- Deinococcus radiodurans are extremophilic bacteria where they can survive cold, dehydration, vacuum and acid. Deinococcus radiodurans has a unique quality in which it can repair both single- and double-stranded DNA. When a damage is apparent to the cell, it brings it into a compartmental ring-like structure, where the DNA is repaired and then is able to fuse the nucleoids from the outside of the compartment with the damaged DNA. They are the toughest bacterium in the world.

5) Archaea, the another domain of prokaryote. They are known as extremophiles, halophiles and thermoacidophiles. Their can survice in harsd environement because of their specific cell structure. They are chemotrophic and chemolithotrophics. The example of archaea is Pyrolobus and Halobacterium.

The differences between Bacteria and Archaea:



My own Explorace:
1)  Deinococcus radiodurans can withstand large amounts of radiation, can live in a vacuum for up to six weeks and live, can live dehydrated, and live through fluctuations in pH. This bacteria is so special that it was the first be in the phylum "Deinococcus". This is one of the only organisms in the world that can withstand 5,000 GYs of radiation. It can repair itself completely within 12-24 hours and can survive on Mars.

2) Crenarchaeota are Archaea that have been classified as a phylum of the Archaea kingdom.The Crenarchaeota were thought to be sulfur-dependent extremophiles but recent studies have identified characteristic Crenarchaeota environmental rRNA indicating the organism may be the most abundant archaea in the marine environment. Until recently all cultured Crenarchaea had been thermophilic or hyperthermophilic organisms, some of which have the ability to grow at up to 113 °C. These organisms stain Gram negative and are morphologically diverse having rod, cocci, filamentous and oddly shaped cells.

3) E. coli O157:H7’s ability to induce injury in humans is a result of its ability to produce numerous virulence factors, most notably Shiga toxin, which is one of the most potent toxins known to man.

4) Shiga toxin has multiple variants and acts like the plant toxin ricin by inhibiting protein synthesis in endothelial and other cells. Endothelial cells line the interior surface of blood vessels, and are known to be extremely sensitive to E. coli O157:H7, which is cytotoxigenic to these cells.

Reflection:
Deinococcus radiodurans are such a strong bacteria, I can't imagine how they can withstand so high radiation that even can't stand by a person. This is my first time heard proteobacteria in the class. Proteobacteria are gram negative bacteria but it has divided into five classes.

10th Lecture: 1/6/15

Topic: Biogeochemical cycle and Aspects of Biotechnology of Microbial Ecology

Notes:
1) Biogeochemical cycles is which mechanisms by which recycling nutrient occur.

2) The characteristics of biogeochemical cycles are transformed and cycled through oxidation-reduction reactions and all cycles are linked.

3) Carbon cycle
- The final product of aerobic respiration in carbon cycle is oxidized products: H20, NO3-, SO42- and carbon dioxide.
- The final product of anaerobic respiration in carbon cycle is reduced products: NH4+, H2S. H2 and CH4.

4) Nitogen cycle

• Nitrification

- Nitrification carry out in aerobic condition where ammonium ion (NH4+) undergo oxidation to form Nitrite (NO2-), followed by oxidation of nitrite (NO2-) to form Nitrate (NO3-).

- The example of microorganisms that oxidized ammonium (Nh4+) to nitrite (NO2-) is Nitrosomonas and Nitrococcus. The example of microorganisms that oxidized nitrite (NO2-) to nitrate (NO3-) is Nitrobacter.

• Denitrification

- Denitrification carry out in anaerobic condition where nitrate (NO3-)  is reduced to nitrite (NO2-), nitrogen gas (N2) or nitrous oxide (N2O). 

- Dissimilatory process (use nitrate NO3- as the electron acceptor to produce ATP)

- Nitrate (NO3-) as oxidant.

- The example of microorganisms is Pseudomonas.

- Nitrate (NO3-) can reduced to ammonia (NH3) by Geobacter, Desulfovibrio and Clostridium.

• Nitrogen fixation

- Nitrogen fixation is a process in which nitrogen (N2) in the atmosphere is converted into ammonium (NH4+) or nitrogen dioxide (NO2).

- Reductive processes

- Ammonia is the product

- must occur in anaerobic condition even in aerobic microorganisms

- Anammox process: anaerobic oxidation of NH4+ and reduction of NO2- to produce nitrogen gas by some microorganisms.

5) Sulfur cycle

• Sulfur Oxidation

- Sulfur is oxidized to sulfate (SO42-) by using Sulfide (H2S) as electron acceptor.

- The example of microorganisms are Thiothrix, Beggiatoa and Thiobacillus.

• Sulfur Reduction

-Sulfur is reduced to sulfide (H2S) .

• Sulfate Reduction (Dissimilatory process)

- Sulfate (SO42-) is reduced to sulfide (H2S) by Desulfovibrio and Desulfuromonas.

- Sulfite (SO32-) is reduced to sulfide (H2S) by Alteromonas, Clostridium, Desulfovibrio and Desulfotomaculum.

• Sulfate Reduction (Assimilatory process)

- Sulfate (SO42-) is reduced to organic sulfur for use in amino acid and protein biosynthesis.

- Mineralization is the process where the sulfhydryl (-SH) groups in protein of dead animals converted to sulfide (H2S).

6) Iron cycle

• Ferrous ion (Fe2+) is oxidized to Ferric ion (Fe3+) in aerobic condition. The example of microorganisms are Thiobacillus ferrooxidans, Gallionella,Sulfolobus.
• Ferric ion (Fe3+) is reduced to Ferroous ion (Fe2+) in anaerobic condition. The example of microorganisms are Geobacter, Ferribacterium and Shewanella.

7) Manganase cycle

• Manganase ion ( Mn2+) is oxidized to manganic ion (Mn4+) in aerobic condition. the examples of microorganisms are Leptothrix, Arthrobacter and Pedomicrobium.
• Manganic ion (Mn4+) is reduced to Managnase ion (Mn2+)in anaerobic condition. The examples of Shewanella and Geobacter,

8) The function of microorganisms in microbial ecology:

• Microorganisms as pollutants - Food borne and water borne pathogens, massive growth of pathogens causes eutrophication
• Microorganisms as cause of pollution - Mercury will combine with the organic methyl group that found in aerobic microorganisms and form  Methyt mercury. Methyl mercury will totally absorbed by body and retained in the body longer than elemental mercury.
• Microorganisms as an indicator of pollution - colliform group of bactera and biofilm can test for pollution
• Microorganisms may reduce pollution - Biodegradation and Bioremediation

9) Biodegradation is the natural decomposition or breakdown of molecules by microorganisms. All natural organic compounds are degradable. Recalcitrant are non-biodegradable because they are synthetic molecules.

10) The example of biodegradation:

• Biodegradation of oil spills

- fungi, bacteria especially Pseudomonas oxidized hydrocarbon to carbon dioxide

- Slow because low nutrients and low population. We can improve by using bioremediation and genetic engeneering. Nutrient sprayed to encourage microbial growth. 

•  Microorganisms in Landfills

- The microorganisms found in landfills are mostly anaerobic and they are methanogens and cellulose digesters. The major product of fermentation is carbon dioxide, methanem organic acids and alcohols. The products will leached out from landfills so landfills have to far from water source.

• Microbial application as pesticides 

-Bt protein that produced naturally by Bacillus thuringiensis used to spray on plants. Bt protein won't harm plants but will attack specific stages of insects only and solve the problem of pesticides.

11) Bioremediation is the use of living organisms to promote the degradation of environmental pollutants cartificiallyby increase the growth of naturally occuring microorganisms. Bioremediation only carry out when biodegradation processes not at a desired rate. Microorganisms use the contaminant as nutrient for reproduction and converts contaminant to less harmful form and release to the environment.

12) Cometabolism is defined as the simultaneous degradation of two compounds, in which the degradation of the second compound (the secondary substrate) depends on the presence of the first compound (the primary substrate). For example: trichloroethylene (TCE) is groundwater pollutant. Methane and oxygen is added to encourage methanotrophs. TCE not a substrate for methanotrophs but methanotrophs produce methane monooxygenase to degrade TCE.

13) Source of microorganisms is contaminated sites, culture collection and genetically engineered "superbug". Unfortunately, superbug are less effective due to the attractiveness of laboratory-grown microorganisms as the food source for predators, inability to contact the compounds to be degraded and failure to survive and compete with indigenous microorganisms.

14) In general, bioremediation is the addition of microorganisms to accelerate the growth of indigenous microorganisms.

15) Phytoremediation is the use of plant  to stimulate the degradation, transformation or removal of compounds, either directly or in conjunction with microorganisms.

16) The advantages of plants with microorganisms in bioremediation are extensive root system, higher ability for storage and easy to harvest.

17) The types of phytoremediation are phytoextraction, phytodegradation, rhizofiltration, phytostabilization and phytovolatilization.

Activity:
No other activity except for teaching....^^

My own Explorace:
1) In nature, nitrogen not only fixed by microorganisms but also by lighting.

2) Fritz Haber undertook the work on the fixation of nitrogen from the air for which he was given the Nobel Prize in Chemistry for 1918 (awarded in 1919).

3) In biology, the opposite of assimilation in the process of metabolism, consisting in the decomposition of organic compounds and conversion of protein, nucleic acids, fats, and carbohydrates (including those ingested) into simple substances.

4) The definition of biotechnology is the use of living organisms and biomolecular process to develop, make or modify product to improve our human lives.

5) Blue baby syndrome occurs when newborn babies have cyanotic heart defects. Th reason cause blue baby is methemoglobinemia. Methemoglobinema is caused by nitrate contamination in groundwater resulting in decreased oxygen carrying capacity of hemoglobin in babies leading to death.

6) Endotoxin only released when the cells or microorganisms are lysed and exotoxin is more pathogenic compared to endotoxin because exotoxin can released without the lysis of cells.

7) Superbugs are strains of bacteria that are resistant to several types of antibiotics.

Reflection:
Today is the last class of Microbiology 2 . The things we learnt getting harder and harder. I felt that the use of Bt protein as pesticides is a great discovery. This really help farmer to solve their problem. To avoid blue baby, the landfill sites need to far away from water source. The biogeochemical cycle made me confused but Dr Wan said we gonna learn more detail about biogeochemical cycle during physiology miicrobiology. @.@
Dr Wan, thanks for teaching us this semester~~~ See You~~~ ^^

9th Lecture: 21/5/15

Topic: Principles of ecology

Notes:
1) Ecology is the study of the systematic study of organisms and their interactions with environment. It reveals the relationship between living and non living parts of the environment.

2) Niches is a place where the organisms perform the best.

3) Hierarchy in ecology :
- species : organisms with common genetic makeup, behaviour and physical characteristics.
- population: a group of individuals belonging in the same species inhabiting a particular geographical area.
- community: all organisms inhabiting a particular area
- ecosystems: include all abiotic factor and biotic factor of a habitat.
- biosphere: all ecosystems on earth

4) Abiotic factors are the non living parts of the environment where include temperature, water, sunligh, wind, rock and soil and periodic disturbances.

5) Homeostasis is the dynamic balance of processes materials and organisms in the ecosystem and biosphere.

6) Homeostasis og the ecosystem invlove the interaction between organisms and organisms and also interaction between organisms and habitat.

7) Energy and nutrient are absorbed from one stage of organisms to another stage of organisms but part of the energy will lost as heat.

8) Energy itself does not recycle but the energy only recycle in the form of C-C bond. Ultimate fate of energy are lost as heat while the ultimate source of energy is sun.

9) Microbes play important roles in the ecosystem. Microbes can act as:
- oxygen producer
- environment nitrogen fixer
- recyclers of dead material
- source of food in food chain
- weak species remover

10) The factors that may affect the stability of the environment are:
- increase the frequency of natural or unnatural disturbances
- abrupt change in species diversity
- a change in the rate of nutrient and energy consumption

11) There are few ways we can do to manage our ecosystem :

• Stakeholders

- develop knowledge about the values of nature to open negotiations to develop mutual beneficial partnerships

• Adaptive management

- implement and analyse hypotheses based on their previous implemented management strategies

• Natural resource management

- deal with the particular resource but not the whole ecosystem.

- fulfill and take care of demands without causing harm to the ecosystem

• Strategic management

- encourages establishment of goals that will benefit the ecosystem while keeping the socioeconomic and politically relevant issues in mind.

• Landscape level conservation

- considers wildlife needs to identify the best option for protecting their ecosystem.

• Command and control management

- perceived problems solved through controlling devices such as laws, contracts or agreements.

Activity: Submit kubbu that is prepared by group 3 and padleting for the topic of biogeochemical cycle.

My own explorace:

1) The example of negative interaction are competition, prey and predator, parasitic relationship.

2) Microbial loop describes dissolved organic carbon is introduced to marine food web via its incorporation into bacterial biomass, and then coupled with the classic food chain formed by phytoplankton-zooplankton-nekton.

3) The dossolved organic materials will first absorbed by bacteria. When the bacteria died, the bacteria will be digested by protozoa and protozoa digested by zooplankton. Zooplankton will consumed by fished or other marine animals.

Reflection:

Today Dr Wan was talked about ghost story in the class and everyone was awake at this moment. Hahahahaha. The study of principles of ecology is important because we need to understand their habitat and how they work with the environment if we want to further study about them. For example, we need to know the habitat of the microorganisms when we want to isolate a certain microorganisms. The relationship of microorganisms with their habitat is important in the study of roles of microbes in the ecosystems.

8th Lecture: 20/5/15

Topic: Microbial group

Notes:
1) Microbial growth is based on the growth of population and not individual growth.
2) There are four physical growth requirements of microbial growth:

- light

-temperature
(Mesophiles 25 degree celcius to 40 degree celcius, Psychrophiles 0 degree celcius to 20 degree celcius, psychrotrophs 20 degree celcius to 30 degree celcius, thermophiles 45 degree celcius to 50 degree celcius)

-pH
(most bacteria pH 5-9, most fungi pH 2-9)

- water activity and water pressure
(water activity is the amount of water found in substrate for the microorganisms to grow)
(maximum water activity for biomolecules is 1)
(bacteria live in higher water activity habitat 0.91 while fungi live in lower water activity habitat is 0.7 )

3) There are six chemical growth requirements:

- water

- carbon

- oxygen
(microaerophiles - need little amount of oxygen, facultative anaerobes -can live with oxygen or without oxygen, aerotolerant - can live in with oxygen and without oxygen)

- nitrogen, phosphorus and sulfur
(nitrogen can obtained from atmosphere, phosphorus can obtained from inorganic source, sulfur can obtained from organic or inorganic molecules)

- special growth factors
(Legionella pneumophila require L-cystein and iron to grow and L-cystein are provided by algae and amoebas)

- trace elements

4) Nutritional types:
- Photoautotrophs (E:light, C: CO2)
- Photochemotrophs (E:light, C: organic molecules)
- Chemoautotrophs (E:light, C:inorganic molecules)
- Chemoheterotrophs (E: organic molecules, C: organic molecules)

5) Population strategies are either r strategists or K strategists.
- r strategists have high rate of reproduction rate, short generation time, population are subject to extreme fluctuation
- K strategists have low rate or reproduction, large size, large storage, successful in resource limited environments and they are more stable populations

6) They are four types of succession:

- Preemptive colonization - pioneer organisms alters condition in a way that discourages further succession
- Autogenic succession - microorganisms modify the habitat in a way that permits in a new population to develop
- Allogenic population - Microbial species succession occurs because the habitat is altered by environmental factors.
- Climax community - achieved when succession ends however it is rarely achieved.

7) Biofilm composed of living. reproducing microorganisms, such as bacteria that exist as a community. Biofilm can trap nutrient and prevent detachment from surfaces. The disadvantages of biofilm are unavailable for attack by immune system, dental caries, slow the flow of water through pipelines and accelerate the corrosion of pipes.

Activity:
No other activity except for teaching...^^

My own explorace:

1) Biology control agent is the use of natural enemies to reduce the populations of pests such as insects and weeds.

2) We can know the temperature where the microorganisms used to grow based on the temperature of their habitat.

3) To isolate a microorganisms, we need to know the habitat of the microorganisms. Suitable media need to prepare and dilution pf the culture is necessary before we incubate in the media. After verify the cingle colony of the target microorganisms, we need to do sub culture to transfer the microorganisms to a fresh new media for them to grow.

4) We need to test at different temperature is the isolated microorganisms didn't grow well in the expected temperature.

5) Gnotobiotic animals are animals in which only certain known strains of bacteria and other microorganisms are present. They are only exposed to those microorganisms that the researchers wish to have present in the animal. Animals reared in a gnotobiotic colony often have poorly developed immune systems, lower cardiac output, thin intestinal walls and high susceptibility to infectious pathogens.

6) Diazotrophs are bacteria and archaea that fix atmospheric oxygen into a more usable form such as ammonia. Even within a species that can fix nitrogen there may be strains that do not fix nitrogen. Fixation is shut off when other sources of nitrogen are available, and, for many species, when oxygen is at high partial pressure.  Azotobacter vinelandii is one of the diazotroph that can fix nitrogen while growing aerobically.

7) Biofilm can act as indicator ( same with the function of lichens) because the habitat of biofilm is always unpolluted.

8) We can obtain the enzymes at the lag phase of bacterial growth while we can obtain the secondary metabolites at between log phase and stationary phase.

9) Termite gut exhibits complex microbial community as in rumen. Since termite feed on diet that is rich in carbon but poor in nitrogen, therefore nitrogen fixers is essential to supply a sufficient amount of nitrogen in termite gut. Treponema, Citobacter, Enterobacter, and Spirochaeta are some of the responsible nitrogen fixers. The prokayotes in termite guts usually associated with protists as symbionts. Treponema spirochete bacteria attached to the plasma membrane of mixotricha and contributes the movement of mixotricha. Treponema also benefits on living within mixotricha where hydrogen and carbon dioxide nutrients are easily to access by the production from mixotricha.

Reflection:
Amazing microbial community! I can't imagine the small termite gut contain so many microorganisms. I think we really can't live without microbes. My friends from the department of biomolecules created an article for the event "life without microbes" and the title of the articles is MICRO-AVENGERS. I like this title because people will know that human can't live without microbes based on this title.

7th Lecture: 15/5/15

Topic: Quizzes on algae, virus, protozoa, bacteria, archaea, fungi

Each group looked for a video which is related to the topic. The video is posted in ED puzzle and quizzes are added to the video.

6th Lecture: 14/5/15

Topic: Algae

Notes：
1) Algae distirbuted in aquatic and terresterial environment. There are 3 types of aquatic environment:

• Planktonic- suspended in aqueous environemnt
• Benthic- attached and living in the bottom of water
• Neustonic- at water-atmosphere interface

2) Algae are photoautotrophic or chemoheterotrophic organisms.
3) Algae can reproduce sexually and asexually (fragmentation, spores and binary fission).
4) The process of the formation of gametes called gametogenesis. The female structure is called oogonia and eggs will produced. The male structure is called antheridia and sperms will produced. The fusion of eggs and sperms will form zygote.
5) There are two categories in sexual reproduction:

• Isogamy

The gametes produced are identical in shape, size and motility. There will be no distinction between male and female gametes.

• Heterogamy

Two different types of gametes are produced. The male sperms is typically very small, highly motile, and is produced in very large numbers. The female eggs are much larger and non motile.

6) There are 7 divisions of algae and 5 from kingdom protista and 2 from kingdom plantae.

• Chlorophyta (protista)

- unicellular or multicellular
- green
- contain chlorophyll a and chlorophyll b

- store glucose and energy in the form of starch

- contain carotenoid

- cell wall made up of cellulose

- can undergo sexual and asexual reproduction
- form different structure: unicellular, colonial, filamentous, membranous and goblet

• Rhodophyta ( belongs to kingdom plantae ) 

- red
- unicellular or multicellular
- cell wall contain microfibril and mucilaginous matrix which composed of  agar, funori, porphysan and carrageenan. All these substances give flexible and slippery texture to rhodophyta.
- undergo sexual reproduction
- store glucose and energy in the form of floridean strach
- contain chlorophyll a and d, phycocyanin (blue) and phycoerythrin (red)

• Phaeophyta ( belongs to kingdom plantae )

- brown
- chlorophyll a and c, xanthophylls, beta-carotene, violaxanthin
- multicellular
- cellulose or algin cell wall
- sexual reproduction
- store glucose and energy in the form of laminarin

• Chrysophyta

- There are three major classes of chrysophyta:
a) Golden-brown algae
b) Yellow-green algae
c) Diatoms
- produce domic acid
- chlorophyll a and c
- unicellular
- peptin and silica cell wall
- sexual reprodution
- caratenoid fucoxanthin is the important pigment in chrysophyta
- Fucoxanthin is the dominant pigment in golden-brown algae
- store glucose and energy in the form of chrysolaminarin

• Pyrrophyta

- unicellular plankton
- marine and fresh water algae
- brown
- 2 flagella in perpendicular opposite grooves
- some produce neurotoxins
- can cause red tides
- chlorophyll a and c
- cellulose cell wall, carotenoid and xantohophyll
- store starch
- free living endosymbionts

• Euglenophyta

- green
- unicellular flagellated
- chlorophyll a and b, carotene
- can spontaneous lost chlorophyll in dark - heterotrophic organisms
- no cell wall
- rigid plasma membrane - pellicle
- no sexual reproduction
- store glucose and energy in the form of paramylon

My own explorace:

1) Carotenoid usually perform two kind of functions in photosynthesis. They serve as accessory light harvesting pigments, extending the range of wavelengths over which light can drive photosynthesis, and they act to protect the chlorophyllous pigments from the harmful photodestructive reaction which occurs in the presence of oxygen.

2) Violaxanthin is a natural xanthophyll pigment with an orange color found in a variety of plants.

3) There are few importance of diatoms:
- food source for fish and marine animals
- dead atoms will sink to the bottom of ocean and from diatomaceous earth
- diatomaceous earth can used in detergents, abrasive polishes, paint, removers and also used to control insects and as the indicators of water quality.

4) To the insects, the diatomaceous earth is a lethal dust with microscopic sharp edges that cut through the insect’s protective covering, causing them to dry out, thus killing them when they are either dusted with the diatomaceous earth or applied in a wet spray form.

5) Algae suitable to be indicator of water quality because of their nutrient needs, rapid reproduction and short life cycle. They respond quickly both in species composition and densities to a wide range of water conditions due to changes in water chemistry.

Reflection:

As I compare the algae notes from Dr. Sieo and Dr.Wan, both notes are informative. There are a lot of additional information that contain in either notes but not in another notes. I have learnt a lot about algae from both notes. One of the difficulty when study algae is to memorise the pigments contain in different types of algae. I feel interested in the practical importance of algae and other microorganisms because I don't want just study but at least to know how microorganisms contribute to us.

Fifth Lecture: 13/5/2015

Topic: Fungi

Notes: 

1) The structure of fungi:

The body of fungus  is called thallus. The main body of most fungi is made up of fine, branching, usually colourless threads called hyphae. Each fungus will have vast numbers of these hyphae, all intertwining to make up a tangled web called the mycelium.

The mycelium is generally too fine to be seen by the naked eye, except where the hyphae are very closely packed together. The picture on the left was taken through a microscope. 

2) There are two types of hyphae: septate hyphae and coenocytic hyphae. Septate hyphae have divider between cells and there have opening pores between the cells which allow the flow of nutrient and cytoplasm between the cells. Coenocytic hyphae form one cell with many nuclei.

3) 

Fungi undergoes asexual and sexual reproduction. There are three types of asexual reproduction: Bud formation, fragmentation and sporulation. 

• Bud formation

- Mitosis process

- Development of a ring of chitin around the point of budding

- enzymatic activity extrude the cell wall and cell content are forced into the progeny cell.

- At the end of mitosis, a cell plate forms and the new bud detaches.

• Fragmentation

- any mycelium that is fragmentated can grow into a new colony.

- common sub-culturing method for fungi ( hyphal fragment technique)

- cork bore taken from a colonized donor plate. Cut mycelial tips do not generate but branches can form some distance from the damage point.

• Sporulation

- the production of spores on a phase called mitosporic, or anamorphic phase

- Arthrospores are formed through segemntation and condensation of hyphae. 

- Chlamydospores are spores that surrounded by thick cell wall.

- Sporangiospores are the development of spores within a sac at hyphal tip.

- Conidiospores are spores that are not enclosed in sac produced at the tips or sides of hypha.

- Blastospores are spores produced from mother cell by budding.

4) For sexual reproduction, the different mating types need to fuse to form diploid first, but once fused the nuclei undergo mitosis. The event are followed by the formation of spores, which in most cases are resting spores that can withstand adverse conditions.

5) Slime molds once placed in kingdom Fungi but now placed in kingdom Protista. slime mold resemble fungi in appearance and life style but different in cellular organisms, reproduction and life cycle. Four different phyla of slime molds are:

• Myxomycota

These slime molds are designated as myxamoeba because their morphology are similar to amoeba. They are multinucleated, lack of cell wall, and phagocytosized dead material. The life cycle of myxocetes will start with the production of spores, then the release of myxamoebae. If free water is available, myxocetes will differentiate into swarm cells. Then sexual reproduction will occur where the swarm cells will normally act as gametes. Once compatible mating strains have come into contact with one another, syngamy will occur to form the zygote. The zygote then undergo numerous mitotic divisions to form the large, multinucleate plasmodium. This class is commonly referred to as the acellular slime molds because the plasmodium stage of the lif ecycle is not composed of many cells. During favorable conditions, the plasmodium will migrate and feed for a period of time before being converted to numerous sporangia. 

• Acrasiomycota

Cellular slime molds closely resemble amoebas in structure. These molds live independently until food runs out. A starving amoeba secretes the hormone cyclic AMP into the environment. Other amoebas detect the cyclic AMP as a food source and aggregate from great distances to follow the concentration gradient to the dying amoeba. The amoebas then attach to one another and become what seems to be a functioning multicellular organism. The moving slug finds a suitable habitat before forming itself into a diploid fruiting body called a sorocarp, which releases encysted amoebas or diploid macrocysts. The released amoebas live independently until food resources are depleted, then the cycle is repeated.

• Oomycota

Oomycetes are water mold and oogamous where is produces large female gametes and small male gametes. Oomycetes were once recognised as fingi due to branched filaments and decaying dead matter. However, the cell wall of chitin is not composed of chitin, but with cellulose. Some water molds are parasitic because they live on fish or plant root which damage the plant root. As in humans as well as plants and other animals, sexual reproduction in the Oomycota involves specialized reproductive structures where meiosis can occur and gametes formed. These structures are called antheridia and oogonia in the Oomycota. The male and female fuse to form zygote.

6) Deuteromycota is known as fungi imperfecti because they are fungi which do not fit into the commonly established taxonomic classifications of fungi that are based on biological species concepts or morphological characteristics of sexual structures because their sexual form of reproduction has never been observed. Their cell wall is made up of chintin and glucan. They live in terrestrial, freshwater and marine. they are saprophytes and parasites of plants.

Activity: Presentation from group Fungi and group Algae.

My own explorace:
1) Zoonosis is the disease that directly transmitted from animal to human.
2) Potato Dextrose Agar contains dextrose as a carbohydrate source, and potato infusion to supply other necessary growth requirements. Potato infusion provides a nutrient base for luxuriant growth of most fungi.
3) The lactophenol cotton blue (LPCB) wet mount preparation is the most widely used method of staining and observing fungi and is simple to prepare.
4) Mycosis is a fungal infection of animal and human. Mycosis often misdiagnosed as TB because of their clinical and radiological characteristics are almost the same.
5) Endophytes are bacteria or fungi that live within a plant for at least part of its life without causing apparent disease.
6) Fungal allergens are generally proteins, and are often enzymes released from the fungal spore during germination, although some may also be proteins located on the surface of spores.
7) Most secondary metabolites are produced after fungi have completed its initial growth phase. Therefore secondary metabolites normally produced at the end of log phase. Some secondary metabolites produced by fungi are harmful but some are beneficial. The examples of secondary metabolites are penicillin, alfatoxin and gibberellin.
8) Normal fungi can just grow in petri dish while lower taxonomic microbes must grow in broth.

Reflection:
I don't really like fungi if compared to other microorganisms because I always confused with the life cycle of fungi. Sometimes I thought I understand the life cycle of fungi, but I can't explained to others because I know I am not really understand about it. The structure of fungi sometimes also make me confused. I can't imagine how thallus, hyphae and mycelium look like so I tried to search the image of thallus, hyphae and mycelium in the internet but I really wish to see the real thallus, hyphae and mycelium.

Fourth Lecture: 8/5/15

Topic: Quizzes on the topic Bacteria

Dr. Wan, I went to Baksis Mega project on Friday. I didn't do the quizzes but I will update from May Ling. ^^

Thrid Lecture: 6/5/2015

Topic: Bacteria ( part 2 )

Bacteria

Notes:
1) Anoxygenic bacteria undergo photosynthesis in anaerobic condition. They have gram negative cell wall and oxygen is not the product of photosynthesis. They have bacteriochlorophyll and they are non pathogenic.

2) Oxygenic bacteria undergo photosynthesis in aerobic condition. They have gram negatice cell wall and oxygen is released during photosynthesis. Water as electron donor and they have chlorophyll. They are non pathogenic and also called cyanobacteria.

3) To differentiate Chromatium sp. , Chlorobium sp. and Rhodospirillum sp. , we need to refer to their colour of granules and pigments. Chromatium contain purple sulfur, Chlorobium contain green sulfur while Rhodospirillum contain purple nonsulfur. Some of the cyanobacteria have trichome and heterocysts.

4) There are 6 groups of gram positive bacteria with cell walls:
a) Gram positive cocci
-Streptococcus sp. and Staphylococcus sp.
- Use metabolic test to differentiate Streptococcus and Staphylococcus.
- Streptococci are catalase postitive (form bubbles) and Staphylococcus are catalase negative.(do not form bubbles)

b) Endospore-forming Gram positive rods and cocci
- Bacillus ( aerobes or facultative anaerobes ) and Clostridium ( obligate anaerobes )
- Example: Bacillus anthracis. Clostridium botulinum, Clostridium tetani, Clostridium perfringens

c) Regular non-spore forming gram positive rods
- rod shape
- Example: Lactobacillus (friendly bacteria)
- Homofermentative is the characteristics of Lactobacillus where they only produce lactic acid through Embden-Meyerhoff pathway.
- Heterofermentative is the chatacteristics pf Lactobacillus where they produce lactic acid, ethanol and carbon dioxide through Pentose Phosphate pathway.

d) Irregular nonsporing gram positive rods
- club-shaped rod with side by side alignment of cells
- Snapping binary fission
- Example: Corynebacterium diphtheriae

e) Mycobacteria
-use acid-fast stain
-slightly curved to straight rods
-Slow grower
- time  needed to form cell wall contaning mycolic acid
- growth stimulated by lipid and fatty acids
- Glycerol-whole egg medium
-Example: Mycobacterium tuberculosis

f) Actinomycetes
- form mycelium but prokaryotes
- soil inhabitant
-produce antibiotic. For example: chloramphenicol, erythromycin, tetracycline
different actinomycetes have different composition and structure of cell wall, morphology and colour of mycelia and sporangia.
- they can recycle nutrient, degrade cellulose, lignin, chitin, latex, aromatic chemicals and keratin.
- Aerial filaments bearing reproductive spores which is known as conidia. Accumulation of conidia form the fluffy morphology.

5) Bacteria lacking cell wall are bacteria without regular cell wall or without cell wall. They are known as pleomorphic. the example of this bacteria is mycoplasma. They have strong plasms membrane which made up of sterols and lipoglycan. They form colonies with fried-egg appearance and require growth factors such as vitamin, amino acids and nucleotides.

Activities: The presentation from group Archae and the working of SCL from each group.

My Own Explorace:
1) Catalase is an enzyme used by bacteria to induce the reaction of reduction of hydrogen peroxide into water and oxygen.
2) Trichome is a chain of vegetative cells in cyanobacteria.
3) Heterocysts are specialized, pale-yellow,thick-walled cells with disputed function nitrogen-fixing formed during nitrogen starvation by some filamentous cyanobacteria.
4) The pictures of trichome and heterocysts:

5) Corynebacterium diphtheriae is the pathogenic bacterium that causes diphtheria. Diphtheria often come on fairly gradually beginning with a sore throat and fever. This can block the airway and create a barking cough as in croup. The neck may swell in part due to large lymph nodes. A form of diphtheria that involves the skin, eyes, or genitals also exists.

6) Serpertine arrangement of Mycobacterium tuberculosis:

7) Glycerol whole-egg medium provide fatty acids and protein neccessary for the metabolism of mycobacteria. The coagulation of the egg albumin during sterilization gives a solid medium for inoculation purposes

8) Vibrio cholerae can produce endospores but endospore will germinate after few hours the endospore formed. Therefore, Vibrio cholerae is not dorminant endospore forming bacteria.

9) Three in 10 Americans carry staph bacteria in their noses, where the germs live benignly unless they are allowed to enter the body through an open wound like a surgical incision. If one of these patients touches his or her nose and then the surgical site, the patient will get infected with Staphylococcus aureus infection. Doctors swab patients’ noses before surgery to test for Staphylococcus aureus bacteria. If the patient has Staphylococcus aureus bacteria naturally living in his or her nose, apply an antibiotic nose ointment in the days before surgery. Up to 85 percent of staph infections are caused by a patient’s own bacteria, meaning that we’re actually infecting ourselves.

10) Escherichia coli possess the ability to transfer DNA via bacterial conjugation, transduction or transformation, which allows genetic material to spread horizontally through an existing population. This process led to the spread of toxin from E. coli O157:H7 to other E.coli .

11) There are five basic mechanisms of antibiotic action against bacterial cells:

- Inhibition of Cell Wall Synthesis (most common mechanism)
- Inhibition of Protein Synthesis (Translation) (second largest class)
- Alteration of Cell Membranes
- Inhibition of Nucleic Acid Synthesis
- Antimetabolite Activity

12) Cutaneous anthrax is the most common form of anthrax infection, and it is also considered to be the least dangerous. When anthrax spores get into the skin, usually through a cut or scrape, a person can develop cutaneous anthrax. 

Reflection:

This is my first time to hear that antibiotic can be apply on skin and nostrils to kill the bacteria. I guess the endospore of Vibrio cholerae will germinate rapidly is because the survival condition of Vibrio cholerae is close and same with our normal condition. Therefore, when Vibrio cholerae reach its favoured environmental condition, it will straight away germinate. I learnt the use of the number in a journal. The number in the journal refer to the number of reference below the journal. This is to let the reader to check the content inside the journal from the reference given.

First lecture and second lecture : 22/4/2015 and 24/4/2015

Dr. Wan, for the last week lesson I will combine them into one post.

Topic: Bacteria

Notes:

1) We can use different traits to classify bacteria: cell type, morphology, metabolism, reproduction, phage typing, nucleic acid profile and antibiotic resistance profile.

2) Prokaryotes are divided into 4 category. 

 a) Category 1: Gram -ve bacteria with cell wall

Gram -ve bacteria have thin layer of peptidoglycan in between cytoplasmic membrane and outer membrane of cell wall.

 

3) Gram -ve bacteria with cell walls can be divided into 2 groups based on reproduction and light. One of the groups is nonphototrophic. Nonphototrophic bacteria contain 14 subgroups and 6 of the subgroups are pathogens.

a) Enteric groups

- facultative anaerobic short rods

- E.coli O157:H7 causing uninary tract infection 

- 

b) Campylobacter and Helicobacter

- Aerobic, microaerophilic

- motile

- helical/vibriod bacteria

- Campylobacter jejuni causing diarrhea

- Helicobacter pylori causing ulcer

c) Spirochetes

- slender and long with flexible and helical shape

- corkscrew movement

- They have endoflagella that coil around the cell for cork screw movement.

- causing syphilis and lyme disease

d) Chlamydias

- Obligately intracellular parasites

- resemble virus- intracellular parasites and size

- they are different from virus because they have both DNA and RNA, plasma membrane, metabolic pathways, reproduction by binary fission.

- causing eye/genitourinary tract infection.

e) Pseudomonas, Azobacter and Rhibozium

- nonpathogenic

- Pseudomonas sp. degrade complec organic molecule in soil

- Azobacter and Rhibozium do nitrogen fixation in soil

Activity: Do mind map using padlet and each group need to present one of the kingdom in front of the class.

My own Explorace:

1) Facultative anaerobe is an microorganism that makes ATP by aaerobic respiration if oxygen is present, but is capable of switching to fermentation or anaerobic respiration if oxygen is absent.

2) Microaerophile is a microorganism that requires oxygen to survive, but requires environments containing lower levels of oxygen that are present in atmosphere. 

3) Treponema pallidum cause syphilis and Borrelia burgdorferi cause lyme disease. Lyme disease is transmitted to humans by the bite of infected ticks of the Ixodes genus.

4) Chlamydia trachomatis cause eye infection. Chlamydia infections are the most common bacterial sexually transmitted diseases in humans and are the leading cause of infections blindness worldwide.

Reflection:

E-port folio again. I thaught I will never touch this blog anymore. My feeling to this blog is complicated. It took over few hours of my happy weekend to complete e-port folio. But, I admit I can revised again what Dr taught and take initiative to look for the things that I don't understand. There are few things that we have learnt in semester 1 but I already forgot. For example, I have forgot the name of bacteria that caused syphilis. Dr.Wan introduced new apps, pedlet to us in class.  Although Dr have mentioned pedlet before, but this is my first time to use it. I think it is very convenient for group mindmap. 

Semester 2 - Classification, identification, nomanclature and immunology

Dr. Sieo have taught two big topic in this seven weeks - Classification, identification, nomenclature and immunology.
These two links are the mindmap that I did for classification, identification, nomenclature and immunology:

https://www.goconqr.com/en-US/p/2303520
https://www.goconqr.com/en-US/p/1587060

These are the summary for the Immunology topic:

The examples of primary lymphoid organs are bone marrow and thymus. The examples of secondary lymphoid organs are adenoid, tonsils, lymph nodes and spleen.
Mononuclear leucocyte: T cell, B cell, NK cell, monocyte.
Polymorphonuclear leucocyte: neutrophil, eosinophil and basophil.
B cells are mast cells that mature in bone marrow. The function of B cell is to interact antigen, produce antibody and immune memory. T cells are mast cells that mature in Thymus. The function of T cells is to recognise processed antigen presented in MHC molecule on antigen-presenting cells.
CD4 T cells are the T cells that present CD4 glycoprotein on their cell surface while CD8 T cells are T cells that present CD8 glycoprotein on their cell surface.  T helper 1 cells and T helper 2 cells belong to CD4 T cells and T cytotoxic cells belong to CD8 T cells.

Antigen are the molecules that trigger specific immune response and react with products of response. There are four feature of good antigens:
a) high molecular weight
b) complexity
c) solubility
d) foreigness

Recognition of antigens:
a) B cells - whole antigen
b) Antibody - Antigen's epitope
c) T-cell receptor - processed antigen

There are 5 types of antibodies : IgM, IgG, IgD, IgA, IgE.
Antibody consist of 4 polypeptide chain where 2 light chain and 2 heavy chain. Fab will be the site that bind to the pathogen while Fc will be the part that bind to macrophage.

** If 2 different classes of antibody react with one antigenic determinant, the constant heavy chain will be different but the heavy and light chain will be the same.
**If 2 same classes of antibody react with two different antigenic determinant, the constant havy chain will be the same but the heavy and light chain will be different.

There are two types of immune response : non-specific immune response and specific immune response.
a) non-specific immune response are internal innate imununity and external innate immunity.
External innate immunity include skin, mucuous membrane, normal microbiota. Periodic drying of skin and slightly acidic pH of skin create unfavourable environment for pathogen to survive. Globet cells secrete mucus to trap the bacteria or pathogen to expel out from body. Normal microbiota compete nutrients with pathogen and secrete antimicrobial substances to inhibit the growth of pathogen.
Internal innate immunity include fever, inflammation and phagocytosis. Fever is to create unfavourable temperature in the body to trigger microbiostasis. High amount of pathogen will produce high amount of pyrogen. the pyrogen will send to hypothalamus and produce prostaglandins which will reset the hypothalamic thermostat. Inflammation is due to the phagocytosis not effective. Histamine released and causes vasodilation. Vasodilation will will deliver more blood to infection site and the macrophage will more permeable move from blood vessel into damaged tissue site. Phagocytosis is the engulfment of pathogen by macrophage or neutrophils.

b) Specific immune response are humoral immunity and cell-mediated immunity. Humoral immunity is an immunity mediated by macromolecules that found in serum.
 How does antibody gives protection?
a) Neutralisation
b) Agglutination
c) Oponisation
d) Activation of complement
e) ADCC ( antibody-dependent cell mediated toxicity)
** Antibody do not kill the pathogen but serach the pathogen by others.

How to determine the latent period?
1) Dosage of antigen
2) Adjuvants
3) Chemical and physical nature of antigens

What are the differences between primary antibody response and secondary antibody response?
Secondary antibody response will have short latent period, higher titer, longer persistence of antibody and more rapid increase in antibody titer if compared with primary antibody response.

Cell-mediated immunity is an immunity response that does not involve antibody but rather involve the activation of macrophage, Tc cell and the release of various cytokine in response to antigen.
There are two types of CD8 T cells killing mechanisms:
a) granules exocytosis
When TcR bind to antigen on class 1 MHC, granule is released to activate apoptosis. Granules contain perforin and granzymes.
b) Fas pathway
When TcR bind to antigen on class 1 MHC, granules are release and triggers expression fas-ligand on Tc cell and the Fas on target cell cross-linked with Fas-ligand.

Delayed-type hypersensitivity (DTH)
- against pathogens living inside macrophages themselves
a) Dendritic cells will pick up the antigens that presented on class 2 MHC and move to secondary lymphoid organ.
b) Dendritic cells will process the antigen and preseneted it on the class 2 MHC CD4 T cell in the secondary lymphoid organ will then activated by the antigen.
c) CD4 T cell will then proliferate, differentiate to T helper 1 cell. T helper 1 cell will then migrate back to the site of infection and secrete cytokines to recruit more monocyte or macrophages to phagocyte the pathogen on the infection site.

Reflection:
Obviously, the topics for semester 2 are harder than the topic in semester 1. Luckily we have Dr. Sieo as our lecturer and taught us in very details way so that we can fully understand these two topics. I like the topic of immunology more if compared with classification and identification. The identification method are all practical but we only understand the basic concept of the methods. That's why I feel less interest in this topic. The topic of immunology is interesting because I would like to know how the pathogen gain access to our body and cause infection. Antibody is important to fight with the pathogen and the process of producing antibody is complicated and it take a long time to produce.