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.