10th Lecture : 14/10/14

Topic: Algae

1) Algae under kingdom protists because they are hard to define.

2) Algae different from plant because they don’t have vascular system.

3) Algae different from animal because they are autotrophs.

4) Algae can be unicellular or multicellular.

5) Algae contain chlorophyll which make them able to make food.

6) Algae live in aquatic or terrestial.

• Planktonic - suspended in aqueous environment
• Benthic - attached and living on the bottom of water
• Neutonic - at water-atmosphere interface

7) Most of the algae have cell wall composed of cellulose,  except for diatom which are made of silica. Sometime chitin or no cell wall.
8) Euglena have single flagella, chlorophyta have two or four polar flagella. For dinoflagellates, they have two flagella of different length and point of insertion.
9) All algae carry out asexual reproduction (fragmentation, spores, binary fission) but not all algae able to carry out sexual reproduction ( oogonia fuse with antheridia to form zygote).

10) Algae can divided into 5 phyla:

• Chrysophyta - diatoms
• Euglenophyta
• Pyrrhophyta - dinoflagellates
• Charophyta 
• Chlorophyta - Green

11) Chlorophyta

• green
• cellulose cell wall
• unicellular or multicellular
• chloropyll a or b
• store glucose polymer
• gave rise to terrestial plants

12) Rhodophyta ( changed to kingdom plantae ) 

• red
• mostly cellular
• cellulose/agar cell wall
• sexual reproduction'
• sstore glucose polymer
• chlorophyll a and d, phycocyaninm phycoerythrin
• red pigment absorb blue light

13) Phaeophyta ( changed to kingdom plantae )

• brown
• macroscopic
• chlorophyll a and c, xanthophylls
• multicellular
• cellulose or algin cell wall
• sexual reproduction
• store carbohydrate

14) Chrysophyta

• golden-brown algae
• produce domic acid
• chlorophyll a and c
• unicellular
• peptin and silica cell wall
• sexual reprodution
• store oil

15) Pyrrophyta

• unicellular plankton
• brown
• 2 flagella in perpendicular opposite grooves
• some produce neurotoxins
• can cause red tides
• chlorophyll a and c
• cellulose cell wall
• store starch

16) 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 polymer

17) Seaweed are marine benthic algae that can provide habitat for marine communities, and human food to make various products.

18) Phytoplankton are primary producers of the ocean because phytoplankton converts carbon dioxide into protoplasm to consumed by zooplankton.

19) Algal bloom will disrupt higher links of local food web and cause the production of neurotoxin.

Activitiy : Exchange our own notes with group members.

My own explorace:
1) Photoautotrophs are the orgainsms use the energy from light to carry out various cellular metabolic processes.
2) Endosymbionts are any organisms that lived within the body or cell or other organisms. Corals and dinoflagellates establish an symbiotic relationship where the dinoflagellates provide fixed carbon to corals while algae receive various nutrients from corals.
3) Members of Rhodophyta have a characteristic clear red or purplish color are due to the pigments called  phycoerythrin, which is well suited to absorb the blue light that penetrates deeper into water than the other colors of light.
4) Red tide is a phenomenon known as algal bloom when it is caused by dinoflagellates and the bloom takes on a red or brown colour. Some red tides are harmful because it associated with the production of neurotoxins. It kills many manatees every year.

Manatee

Reflection on this topic:

The mood in the class was quite down. The reasons may due to the Kenegaraan test but I think most of us were already in holiday mood, not study mood, hahaha..I think people shouldn't look down on these small tiny algae. An algae looked like nothing but a large number of algae can make things worse. Red tides which caused by large number of dinoflagellates can killed a lot of marine organisms, even the cute manatee. T.T 

9th Lecture: 10/10/2014

Topic: Test 1 and Protozoa

Notes:
1) Protozoa are eukaryotes, no chlorophyll, unicellular and lack of fruiting body.
2) Protozoa can be parasitic, pathogenic and predatory.
3) Protozoa can be aerobic, anaerobic and chemoheterotrophic
4) Protozoa are colourless and motile, but apicomplexa are not motile in mature form.
5) Protozoa can reproduce sexually and asexually by fission, budding and schizogony.
5) The microscopic of protozoa is 10 to 200 micrometer.
6) Protozoa occur singly or in colonies.
7) Protozoa can pigmented or not pigmented.
8) Protozoa may swim freely or in contact with a substratum. Some of the protozoa are capable of encystment.
9) Phylum:
      Saya-Sarcomastigophora
      Lupa- Labyrinthomorpha
      Akan- Apicomplexa
      Makan- Microspora
      Ayam- Ascetospora
      Mymy- Myxozoa
      Cili- Ciliophora
10) Dinoflagellates and Euglenoids are capable of photosythesis.
11) Protozoa obtain fruits through phagocytosis, pinocytosis, ingestion and absorption.
12) There are four major groups in protozoa: Archaezoa, Rhizopoda, Ciliophora, Apicomplexa.
13) Archaezoa are flagellated, parasitic and live in fresh water.
14) Rhizopoda are move by pseudopods, undergo phagocytosis and live in freshwater. Example:Amoeba
15) Ciliophora possess cilia, live in freshwater and marine, contain macronuclei( production of mRNA)and micronuclei (sexual reproduction) , having the presence of gullet ( ingest particulate materials), Example: Paramecium
16) Apicomplexa are primarily animal parasites, food absorbed through the outer wall and having complex life cycle. Example: Plasmodium

Activities: Test 1 and presentation about the best way to study protozoa.

My own explorace:
1) Substratum is a surface which cell attaches to, especially when the cells is growing or moving.
2) Chemotrophs are organisms that obtain energy by the oxidation of electron donors in their environment. They can be autotrophic or heterotrophic.
3) Encystment is the process of being enclosed by a cyst. Cyst is a resting or dormant stage of microorganisms. Cyst helps microorgsnisms to survive in unfavourable environmental condition in which the cell activities will be slowing down. Encystment also help the microbes to disperse easily from one host to another.
4) Pseudopods are temporary projections of eukaryotic cell membranes or unicellular protists.
5) Schizogony is the asexual reproduction of sporozoan by multiple fission of nucleus of the parasite followed by segmentation of the cytoplasm.
6) Most of the dinoflagellate are marine plankton but they are common found in freshwater as well. Most of them are photosynthetic.

Reflection on this topic:

After the test, I checked my notes and I found that I got some objectives wrong. I was getting mad because I did read and memorised the notes and I still got these wrong. Dr,Wan was right. We need to really understand everything well but not just memorised. I like the study method of Choy's group but I need him to record that song so that we able to sing it again and again. I also like the study method of our group: Fill in the blanks !! It is really work by fill in the blanks after we have studied the notes.

8th lecture: 7/10/14

Topic: Inclusions

Notes:
1) The main purpose of inclusions are to reserve deposits when it's plentyful and use it when it's deficient.
2) Metachromatic granules also known as volutin and used in the synthesis of ATP.
3) Metachromatic granules stain red with certain blue dyes.
4) Polysaccharide granules consist of glycogen and starch. Glycogen and starch can be differentiated by iodine. Glycogen granules will indicate reddish brown colour while starch will indicate blue colour.
5) Lipid inclusions act as storage material and can be revealed by Sudan dyes.
6) Sulfur granules derive energy by oxidising sulfur and sulfur-containing compounds.
7) Carboxysomes used for carbon dioxide fixation during photosynthesis.
8) Magnetosomes contain iron oxide that act like magnet. It is to protect the cell against hydrogen peroxide accumulation and to look for oxygen concentrated area.
9) Gas vesicles also known as gas vacuole. We called it gas vesicles when it is found in prokaryotes while in eukaryotes we called it gas vacuole. It is to provide buoyancy for aquatic prokaryotes and mostly found in photosynthetis group of prokaryotes.
10) Endospores are formed during harsh condition by some bacteria and it will germinate during suitable condition.
11) Endospores cannot be destroyed easily. They resist to chemicals, radiation, heat and acids.
12) Endospores contain substances that are absent from vegetative cells especially dipicolinic acid. This substance give all the resistance to endospores.
13) Although spores are resistant to dye, they still can be stained with malachite green.

Activities: Short Quiz and decide the adapoted microbes.

My own explorace:
1) Corynebacterium diphtheriae is the pathogenic bacterium that causes diphtheriae. Corynebacterium diphtheriae is a gram positive bacteria. Diphtheria is an upper respiratory illness. Diphtheria toxin is produced by Corynebacterium diphtheriae only when infected with a bacteriophage that integrates the toxin-encoding genetic elements into the bacteria.
2) Fungus uses energy to produce nutrients and spores.
3) Carbon dioxide fixation also called Calvin cycle and it is light-independent reaction. The key enzyme of this cycle is called RuBisCo.
4) Microbial nutrition are substances that microbes used to survive. If the source of carbon come from carbon dioxide and the source of energy come from sunlight, this organisms are called phototrophs.
5) Hydrogen peroxide is toxic and it is found in hair dyes. Human and aerobic microbes have the enzyme to neutralise hydrogen peroxide. The enzyme is celled peroxidase. But, peroxidase are not found in anaerobic microbes. Therefore, magnetosomes are found in anaerobic microbes to protect them against hydrogen peroxide accumulation.
6) Microaerophile is microorganism that requires oxygen to survive, but at a lower concentration than that contained in the atmosphere. A faculatative anaerobes is an organisms that makes ATP by aerobic respiration if oxygen is present, but is capable switch to anaerobic respiration if oxygen is absent. Too much oxygen is not toxic for faculatative anaerobes but too much oxygen is toxic for microaerophile.
7) Clostridium tetani is anaerobis, gram positive bacterium that causes tetanus.
8) Desiccation is the state of extreme dryness, or the process of extreme drying. Microbes that able to survive in desiccation are called xerophilic microbes. Xerophilic microbes are mostly archaea.
9) Clostridium perfringens cause gas gangrene which is a bacterial infection that produces gas in tissue in gangrene. Gas gangrene can caused myonecrosis ( muscle tissue death). The only treatment is through amputation of damaged arm or leg to control the spread of infection.
10) This is the video about the formation of endospores:
http://www.youtube.com/watch?v=7zCQLITFEb0

Reflection on this topic:
I have learnt how strong is the endospore. I understand why clostridium botulinum have the potential to act as biological weapons. Endospores can be anywhere and everywhere.

7th Lecture: 3/10/14

Topic: External Structure of Prokaryote (part 2) and Internal Structure of Prokaryote

Notes:
1) Cell wall of bacteria is made up of peptidoglycan.
2) Cell wall of gram positive bacteria has thick peptidoglycan layer(90%) while cell wall of gram negative bacteria has few layers of peptidoglycan layer (10%).
3) Teichoic acid and lipoteichoic acid found on peptidoglycan layer and contribute to the acidicity of the gram positive cell wall.
4) The cell wall of gram negative bacteria consists of outer membrane.
5) Lipoprotein, lipopolysaccharide, phospholipid and porins are found on the outer membrane of gram negative bacteria.
6) The polysaccharide portion of LPS is O polysaccharide while the lipid portion is A lipid.
7) Atypical cell wall means no cell wall or little cell wall material.
8) Sterols are found on atypical cell wall which provide rigidity to the membrane.
9) Archaea cell wall has no peptidoglycan but contains pseudomureins.
10) Pseudomureins are linked by glycosidic bond beta(1,3) and consist of NAT.
11) Cell wall of Archaea is resistant to lysozymes and beta-lactam antibiotics but cell wall of bacteria is susceptible to lysozymes and beta-lactam antibiotics.
12) Plasma membrane acts as selectively permeable membrane. Hydrophilic ends are interact with water while hydrophobic ends are away from water.
13) Plasma membrane can synthesizes cell wall components, assists in DNA replication, carries on respiration and captures energy as ATP.
14) Plasmolysis: cells shrink ; Lysis: cells burst
15) Passive process not requires ATP and molecules are move along concentration.
16) Passive process includes simple diffusion, osmosis and facilitated diffusion.
17) In simple diffusion, substances move from high solute concentration to low solute concentration until equilibrium is reached.
18) In osmosis, water move from high concentration to low concentration.
19) In facilitated diffusion, substances moved by transporter proteins from high to low concentration.
20) Active process requires ATP and molecules are move against concentration.
21) In Group translocation, molecules are chemically modified during passage across cytoplasmic membrane.
22) The nucleoid are single long circular molecules of double-stranded DNA and not membrane-bounded and no histones surrounded.
23) Plasmid consists small circular, double stranded DNA but not essential DNA material. It have the resistant to certain antibiotics.
24) Ribosomes are used for protein synthesis and 70S ribosomes are made up of small subunits 30S and large subunits 50S.
25) Group translocation is exclusively for prokaryote.

Activities: Labelled the image of structure of prokaryote and stated the functions of each structure.

My own explorace:
1) Heating is one of the examples of mechanical breakage.
2) Gram negative bacteria are stronger compared to gram positive bacteria because outer membrane provides a barrier to certain antibiotic, detergent and heavy metals.
3) Degrading enzymes are those enzymes that can degrade macromolecules to monomers.
4) Porin consists enzymes that can degrade antibiotics. For example, bacteria synthesise beta-lactamase to develop resistance to beta-lactam antibiotic.
5) Exotoxin are stronger compared to endotoxin because endotoxin only released during lysis of the cell.
6) Mycoplasma pneumoniae is a human pathogen that causes the disease mycoplasma pneumonia and resistants to antibacterial agents.
7) Why does 70S ribosome written as 50S and 30S? S stands for svedberg unit. The svedberg is a measure of time. That's mean S is not the size or amount but is the rate of sedimention when those ribosomes are centrifuged.

Reflection on this topic:
What I can conclude from this topic is the cell wall of prokaryote is very important. Dr Wan kept mentioned the importance of cell wall because cell wall of bacteria can used to differentiate the pathogenicity of different bacteria. Before that I still wondered why 70S ribosome written as 50S and 30S....so now I finally got the answer after this lecture. Thanks Dr Wan..^^

6th lecture: 26/9/14

Topic: External Structure of Prokaryote (part 1)

Notes:
1) Prokaryote are organisms which lack of cell nucleus or any membrane-bound organelles.
2) Diplococci shape - round shape in pair ; Diplobacilli shape - rod shape in pair
3) Staphlyococci - grape-like clusters
4) Streptococci - round shape in chain ; Streptobacilli: rod shape in chain
5) Spiral shape that is rigid is called spirillum. Spiral shape that is flexible is called spirochete.
6) The bacteria which have smaller size are able to move easily, easier to get protection from predator and nutrients upake for them are lesser.
7) There are 4 main external structure of the cell wall: Glycocalyx, Flagella, Axial filament, Fimbriae and pili.
8) Glycocalyx is made up of extracellular polysaccharide. It is made inside the cells and excreted to the cell surface.
9) The functions of glycocalyx are to get protection from phygocytosis, attach to different surfaces and protect cell against dehydration.
10) Capsules are formed if glycocalyx is organised and slime layers are formed if glycocalyx is loosely attached.
11) Flagella made up of flagellin and consists of basal body. Basal body has a hook, rod and ring.
12) Monotrichous - one flagellum;  Lophotrichous - cluster of flagella at each end of cell; amphitrichous- one flagellum at each end of cell; peritrichous- spread over entire surface of cell.
13) Types of mortality: Tumbles and Swam
14) Spirochetes group of bacteria move by axial filament because they have no flagellum.
15) Fimbriae and pili consist of pilin and used for attachment rather than movement.
16) Fimbriae distributed entire of the cell while pili only one or two found per cell.
17) Cell wall of prokaryote is not selectively permeable.
18) Cell wall composed of peptidoglycan and peptidoglycan consists of disaccharide. The disaccharide is made up of NAG and NAM. NAG and NAM are linked by glycosidic bonds (beta 1-4).
19) There are 2 major types of cell wall : Gram-positive and Gram-negative
20) Gram-positive cell wall consists of many layers of peptidoglycan while Gram-negative cell wall consists of few layers of cell wall.

Activities: Draw Mind Map for external and internal structure of prokaryote

My own explorace:
1) Size of E.coli - 0.5um in width and 2um in length; Size of Thiomargarita -750um.
2) Myxobacteria live in soil, feed on organic substance and move by gliding.
3) Mycoplasma unaffected by antibiotics because they have no cell wall.
4) Corynebacteria is the pathogen causes diphtheria.
5) The formation of biofilem on the surface indicates that there are no pollutants in that area.
6) Virulence factors: The ability to cause disease.

Reflection on this topic:
I have learnt the structure of prokaryote before but not that specific. I will try my best to memorise all these structures. ^^

5th lecture : 23/9/14

Topic: Preparation of specimens for light microscopy

Notes:
1) There are two ways to prepare specimens : Wet mount and Smears
2) Smear-steps involve preparing smear, fixation and staining.
3) No cover slip needed for preparing smear.
4) There are two ways of fixation : Heat fixing and chemical fixing.
5) Heat fixing can preserves overall morphology but not internal structure while chemical staining can protect cellular substances from destroy.
6) There are three types of staning method: simple staning, differential staning, special staning.
7) Simple staning required just a single staning agent.
8) Gram staning divided bacteria into two groups based on their cell wall structure.
9) Gram positive bacteria: Purple in colour, have thick peptidoglycan cell wall
10) Gram negative bacteria: Pink in colour, have thin peptidoglycan cell wall
11) Acid-fast bacteria: Bacteria that reist decolourization by both acid and alcohol.
12) Normally acid-fast bacteria will first stained with carbolfuchsin, then followed by acid-alcohol and counterstain.
13) To visualise capsules, we need to prepare colourless bacteria against a coloured background because capsules against a stained background.
14) To visualise endospore, Malachite green and safranin are used to stain the bacteria. Bacterial endospore appear green within red or pink cell.
15) To visualise flagella, mordant and carbouchsin applied to increase the thickness of flagella.

Activities: -

My own Exploration:
1) Leprosy is a chronic infection which caused by Mycobacterium leprae. This infection may causes infected people lack ability to feel pain and lost of sight.
2) Gram positive bacteria usually rod shaped bacilli. Gram negative bacteria usually round shaped coccus.
3) Helicobacter pylori are spiral-shaped bacteria that can cause peptic ulcer disease by damaging the mucous coaing that protects the lining of the stomach anf duodenum.

Reflection on this topic: I learnt a lot of staning method from this topic. We need to learn the characteristics of different microbes then only we know which staning method is suitable for them.

4th lecture : 22/9/14

Topic: History of microbiology and Microscopy

Notes:
1) The first person found the existance of microbes is Louis Pasteur.
2) Antonie Van Leeuwenhoek observed and described single-celled microorganisms as
    animalucules.
3) Robert Hooke improved Leeuwenhoek microscope and his famous observation on slides of cork.
4) Scientists proposed spontaneous generation - life arise spontaneously from non-living matter.
5) Spontaneous generation theory was supported by John Needham but not supported by Dazzaro Spallanzani.
6) Rudolf and Louis Pasteur changed the theory of spontaneous generation by biogenesis - living cell can arise only from preexisting living cells.
7) Pasteur's experiment: Filled broth into straight neck flask and s-shaped flask and both boiled and left to the air. Broth in straight neck cloudy while broth in s-shaped not cloudy. It proved that S-shaped trapped gened in curved neck and prevent them reaching the broth. Spontaneous generation was disproved by this experiment because broth s-shaped flask is not infected.
8) Koch's Pastules: Pathogen isolated from diseased host and let the pathogen grow in pure culture. Pathogen from pure culture injected into healthy animals.
9) Exception of Koch's Pastules: not all the microbe could be cultured in media, diseases caused by different pathogen may have similar symptoms. Same pathogen can caused several disease condition.
10) The goal of microscopy is to produce a magnified image and separate the details in image.
11) Bright-field microscope: staining is required, dark image against bright background
12) Dark-field microscope: staning is not required, produce bright image against dark background.
 13) Phase-constract microscope: staning is not required, dark image against bright background,
 14) Ultra-violet microscope: great resolution, shorter wavelength, the image displayed on screen.
 15) Fluorescence: bright image against dark background, specimen stained with fluorochromes
 16) Confocal image: 3D image
 17) SEM: 3D image, structure of cell smaller than 0.2um, resolving power 20nm, magnification 1000x to 10000x, study surface features of cell
 18) TEM: 2D image, structure smaller than 0.2um, resolving power 2.5nm, magnification 10000x to 100000x, study internal structure in thin section of cell

Activities: Quiz

My Own Exploration:
1) About Robert Hooke's study, he viewed on slides of cork anf he discovered empty spaces contained by walls. Therefore, he discovered building block of life and marked the beginning of cell theory.
2) Pasteurisation won't kill all the microbes, but only kill pathogen.
3) UHT is ultra high temperature.
4) Vaccine contains weak pathogen and it is used to activate immune response in our body.
5) BCG vaccine is Bacillus Calmette-Guerin vacine. It used tp treat tuberculosis and this vaccine is prepared from mycobacterium bovis.
6) We need to stained microbes because most of the bacteria are colourless and this makes us easier to examine the different part of thier body.
7) The smallest bacteria in the world is Mycoplasma.
8) Hela cell is a cell type in an immortal cell line used in scientific research.
9) Syphilis is a sexually transmitted infection causd by the spirochete bactellium Treponema Pallidum.

Relection on this topic:
I think history of microbiology is quite interesting. I salute with those scientists because they able to come out experiment to prove different kind of theory. I think microscopy is quite boring to me. I can't remember all the specific functions and characteristics of different kind of microscrope because I not yet use those microscopes.