Saturday 20 December 2014

25th Lecture: 19/12/14

Topic: Microbial control method (part 2) and Antimicrobial Chemotherapy

Notes:
1) There are three types of physical control method which are heat, filtration and radiation.
2) Thermal Death point is the lowest temperature at which all cells in a culture are killed in 10min.
3) Thermal Death time is the time to kill all cells in a culture.
4) Decimal Duration time is the time in minutes to kill 90% cells at a given temperature.
5) Moist heat able to destroy viruses, fungi and bacteria in autoclave steam. The approximate conditions for moist heat killing is 15 minutes at 121 degree celcius in 5 psi. Moist heat will not destroys spores and does not sterilize.
6) Steam sterilization must be carried out above 100 degree celcius which requires saturated steam under pressure. This method carry out in aotuclave and it is more effective compare to moist heat because it can destroys all types of microorganisms including spores.
7) Pasteurization reduces spoilage organisms and pathogens but not all microbes in the medium.
8) Dry heat sterilization kills by oxidation and it it less effective than moist heat sterilization.
9) Filtration is used to reduce microbial population or sterilizes solutions of heat-sensitive materials by removing microorganisms.
10) Radiation is oftenly used for sterilization and pasteurization of plastic disposable supplie, food, antibiotics and hormone because radiation damages DNA. The ionizing radiation include X rays, gamma rays, electron beams. Non--ionizing radiation include UV.
11) Wavelength of 260 is most bactericidal because it can causes thymine dimers preventing replication and transcription.
12) UV limited to surface sterilization because it does not penetrate glass, dirt, films and other substances but gamma radiation penetrates deep into objects.
13) There are three types of chemical control methods which are disinfection, antisepsis and sterilization.
14) Principles of effective disinfection are concentration of disinfectant, organic matter, pH and ime.
15) Overuse of antiseptics such as triclosan has selected for triclosan resistant bacteria and possibly antibiotic resistant.
16) We can evaluating a disinfectant by using:
  • Use-dilution test - Metal ring dipped in test bacteria are dried. Dried cultures are places in disinfectant for 10 min at 20 degree celcius. Rings are transferred tp culture media to determine whether bacteria survived treatment.
  • Disk-dilution test - The wider of the inhibition zone, the lesser the bacteria able to resist to the disinfectant.
17) The types of disinfectant:
  • Phenol
  • Iodine
  • Chlorine
  • Alcohol
  • Heavy metal - Zn, Cu, Hg
  • Surfactants - soap, cationic detergents
  • Chemical food preservatives
  • Aldehydes
18) Microbes that have the most resistance to disinfectant is prions and the have the least resistance to disinfectant is viruses with lipid envelopes.
19) Biological control of microorganisms involve other organisms and their metabolites to control the growth of microbes. For example, viral mediated lysis using pathogen.
20) Chemotherapeutic agents are chemical agents that used to treat pathogens. Most of the chemotherapeutic agents are antibiotics.
21) Paul Ehrlich deeveloped the concept of selective toxicity at 1904.
22) Penicillin is the first discovered by Ernest Duchesne, but discovery lost and accidentiallt discovered by Alexander Fleming.
23) Selective toxicity is the ability of drug to kill pathogen while damaging the host as little as possible.
24) Therapeutic dose is the drug level required for clinical treatment.
25) Toxic dose is the toxic level at which drug becomes too toxic for patient.
26) Therapeutic index is the ratio of toxic dose to therapeutic dose.
27) The effectiveness of antimicrobial drugs expressed in two ways:
  • Minimal inhibitory concentration - lowest concentration of drugs that inhibits the growth of pathogen
  • Maximum inhibitory concentration - lowest concentration of drugs that kills pathogen
28) The level of antimicrobial activity can be determined by dilution susceptibility tests for MIC, Kirby Bauer and E-test MIC.
29) Dilution susceptibility test involves inoculating media containing different concentration of drug.
30) Kirby-Bauer Method standardized method for carrying out disk diffusion test where the sensitivity and resistance determined using tables that relate zone diameter to degree of microbial resistance.
31) E test similar to disk diffusion method, but uses strip rather than disk.
32) Inhibitor of cell wall synthesis includes penicillin ,cephaloporin, vancomycin and teicoplanin.
33) Protein synthesis inhibitors includes aminoglycoside antibiotic, tetracyclines, macrolides, chloraphenicol.
34) Inhibitor of nucleic acid includes quinolones.
35) Antifungal drugs easier to treat superficial mycoses than systemic infections.
36) Antiviral drugs is developed slowly because it is difficult to specifically target viral replication.
37) Anti-HIV drugs includes reverse transcriptase inhibitors, protease inhibitor and fusion inhibitors.
38) Tamiflu is an anti-influenza agent which has been shown to shorten course of illness.
39) Drug resistant 'superbug' means bacteria that have developed resistance to vancomycin such as Stapylococcus aureus.

Activity: Each group create quizzes of different topics.

My own Explorace:
1) We can use indicator to know whether the microbes are being sterilised in autoclave. There is a form of masking tape with white stripe on it. Put the tape on the water than only put into autoclave. After being sterilised, the tape will turn black which shows the microbes are fully sterilised. 
2) Buffer and antibiotic solution cannot sterilise using autoclave.
3) Toxic shock syndrome is a potentially fatal illness caused by a bacterial toxin. Different bacterial toxins may cause toxic shock syndrome, depending on the situation. The causative bacteria include Staphylococcus aureus.
4) Vancomycin is antibiotics that can treat most of the microbes but it will gives very bad effects to patient.

Reflection:
This is the last lecture of BMY 3101, my e-portfolio finally comes to the end. I admit I really struggling when doing e-portfolio because I almost spent hours for each lecture of e-portfolio. I refresh what I have learnt in class, explore more about the notes in Internet, look for the pictures and videos of the topic, able to memorise the microbes easily because I kept repeated the microbes' names when I did my e-portfolio. The benefit of e-portfolio are a lot. It it worth for me to struggle few hours a week for e-portfolio. I believe the efforts that I have done to my e-portfolio will later reflect out on my result. Again, thanks to Dr. Wan for teaching us this 14 weeks. What you have thought really make me feel more interested to microbes. Thank you so much!!!


24th Lecture: 18/12/14

Topic: Population growth and Control of Microbial growth (part 1)

Notes:

1)Number of generation =  Log number of cells(end) – Log number of cells(beginning)
                                                                                     0.301
Generation time = 60 min X hours
                              Number of generations      
2)
  • Lag phase - Bacteria starts to adapt to a new environment. The number of bacteria incresed slowly.
  • Log phase - Bacteria starts to replicate, enzymes are produced, metabolisms start to carry out and a lot of products found in Log phase. The number of bacteria increased sharply.
  • Stationary phase - Depletion of nutrients causes bacteria to stop producing.
  • Death phase - The number of bacteria start to reduce because nutrient is used up and finally bacteria will just died.
3) The direct measurement of microbial growth includes plate counts, filtration, direct microscopic count and multiple table MPN test.
  • Plate count - First, perform serial dilutions of a sample. Then, inoculate petri plates from serial solutions. After inocubation, count colonies on plate.



  • Filtration - Water is filtered on a filter which has holes smaller than bacteria.The filter is then placed on a dish of agar and bacteria grow on the top of the filter and count the bacteria
  • Direct microscopic count - Number of bacteria = number of cells counted divide by volume of area counted.
  • Multiple table MPN test
There will be three sets of five tubes. The first set received 10mL of inoculum, the second set received 1mL of inoculum, the third set received 0.1mL of inoculum. The results show that the number of postitive tubes in set 1 is 5, in set 2 is 3 and in set 3 is 1. The presence of negative tubes is due to insufficient of microbes to grow in every tubes in the sets.
The number of positive tubes recorded in each set is 5-3-1. Compare the number of positive tubes with MPN table to look for the confidence limit and count for the number of bacteria.

4) The indirect measurement of mirobial growth includes turbidity. Turbidity is a measure of how much of bacteria suspended in medium decreases the passage of light through the water. The higher the number of bacteria in the medium, the lower the percent of light transmitted.
5) Sterilization is the complete removal or destruction of all viable microorganisms. Usually used in inanimate objects. ( not alive)
6) Disinfection is the removal of vegetative pathogens but not bacterial endospores. Usually used only on inanimate objects. The chemical agent is called disinfectants.
7) Sanitization is the reduction of the microbial population to a safe level as determined by public health standards.
8) Antisepsis is the removal of pathogens from living tissue. The chemical agent is called antiseptics.
8) Commercial sterilization is to kill C. botulinum endospores.
10) Degerming is the removal of microbes from a limited area. Sanitization is the lower microbial counts on eating utensils.
11) Antimicrobial agents include chemotherapy, -cidal agents and -static agents. Chemotherapy is the method to kill or inhibit the growth of microorganisms within host tissue using chemical agents. -cide is the suffix that indicating agents that kill the microbes. -static is the suffix that indicating agents that inhibits the growth of microbes. e.g Biocide/Germicide and fungicides kill microbes while bacteriostasis inhibits the growth of bacteria but not killing.
12) Microorganisms are not killed instantly and their population death usually occurs exponentially.
13) Effectiveness of antimicrobial treatment depends on number of microbes, duration of exposure, microbial characteristics, concentration or intensity of an microbial agents, population composition, temperature and local environment.
13) Microbial control agents may alternate the membrane permeability, causes damage of proteins and nucleic acids.

Activity: Bacterial growth exercise and play might microbe

My own Explorace:
1) Bacteriostatic is used to inhibit the growth of bacteria but bacteria will being killed if too much of bacteriostatic is applied on the bacteria.
2) LD50 is the dose of antimicrobial agents that able to kill 50% of bacteria/microbes.
3) The colonies in a petri dish will reported as TNTC if over 300 colonies per dish.

Reflection:
At first, I really don't understand why the inoculum have to be diluted before culture it. The purpose of dilution of the sample is to get single colony. If the inoculum is not diluted, we will get full of colony in the petri dish and make the counting very difficult. I think counting bacteria colonies is quite interesting. I like to work with the calculation. I will feel very satisfied if I able to count the bacteria colonies correctly.


 

Friday 19 December 2014

23th Lecture: 16/12/14

Topic: Culturing, maintaining and preserving microbes

Notes:
1) Aseptic technique refers to carrying out a procedure under controlled conditions in a manner that will minimize the chance of contamination.
2) All manipulations must be carried out in a sterile cabinet. First, flame all caps and lids, tightly close all bottles and caps, remove materials from the hood, turn off gas, wash the hood surface, turn the UV light to disinfect.
3) There are two types of basix culture techniques:
  • Liquid Culture- microbes are reared in test tube in a liquid medium. The liquid culture is the best to use when you want to increase the concentration of microbes or you want to grow motile microbes.
  • Culture Plate- Liquid medium is poured to petri dish as a thin layer at the bottom plate and let it to solidified. Culture plate is best to use when you want to test the sensitivity of bacteria to antibiotic, estimate culture concentration from environmental samples and isolate individual colonies from environmental samples.
4) Pure culture normally obtained by the streak plate method and pour plate method.
  • Streak plate method
First, make a single streak with the loop. Then, drag the loop through the single steak ini zig-zag pattern. Repeat the zig-zag pattern in a new area of the plate. Repeat the "drag and zigzag". This idea is to spread those cells out and for the purpose of getting single colony. Everytime you do the new zig-zag pattern, you would need to flame the loop.
  • Pour plate method
1 mL of liquid culture is placed in 9 mL of melted agar medium(45 degree celcius). The medium is then quickly poured into a sterile plate. Some will grow on agara surfaces and some will grow in the agar.
5) Special culture technique is used to culture anaerobic microbes. Anaerobic environment (no oxygen, will carbon dioxide) is created to culture anaerobic microbes. Therefore, we need gas pack, catalyst, indicator and reducing agent.
6) Special culture technique will be done in either anaerobic chamber or anaerobic jar. The purpose of gas pack is to use up the surrounding oxygen and replaces with carbon dioxide. Indicator is to make sure along the culture process will be no oxygen contaminant in the medium. The example of indicator are methylene blue and resazurin. Reducing agent is to react more rapidly with oxygen and remove the oxygen. The example of reducing agent are cysteine and thioglycholate.
7) Gas pack is a packet of chemicals( sodium bicarbonate and sodium borohydrate). Hydrogen and carbon dioxide are produced by the reaction of the chemicals with the water.
8) Palladium catalyst combine the oxygen in the jar with the hydrogen produced the chemical reaction and water is formed.
9) Deoxygenerator is made up of copper. It is also acts as oxygen indicator which will turn black when oxygen is present.
10) Anaerobes must culture in test tube and the test tube need to roll all the time when culturing anaerobes. It is to form a thin layer of agar medium on all of the test tube wall.
11) A new technique to provide anaerobic environment is by adding oxyrase into medium to reduces oxygen to water. This technique able to avoid the need for more cumbersome(large and heavy) apparatus.
12) Culture medium is a nutrient material prepared for the growth of microorganisms in a laboratory.
13) Inoculum are microbes that are introduced into a culture medium to initiate growth.
14) Culture are the microbes that grow and multiply in or on a culture medium.
15) There are many different types of culture media:
  • Chemically defined media - The exact composition in the media is known.
  • Complex media - The exact chemical composition in the media is not known.
  • Liquid medium - The components of medium are dissolved in water and sterilised
  • Semisolid medium - Medium which has added a gelling agent. e.g. agar and gelatin
  • Selective media - media that contain agents that inhibit th growth of certain bacteria while permitting the growth of others. It is used to isolate specific organisms.
  • Differential media - Media that contain indicators that react differently with different organisms. e.g. produce colonies with different colour, It it used to identify specific organisms.
  • Enrichment media - provides nutrients that favor the growth of a particular bacteria but no others. The small number of desired bacteria will increased to detectable level, which means the desired bacteria will present in much larger numbers.
  • Blood agar - Nutrient agar with 5 to 10% of horse blood which used to cultivate all the fastidious microorganisms.
16) The bacterial culture can preserved in refrigerator (short-storage), deep-freezing and Lyophilisation (long-storage).
  • Deep-freezing - Culture is placed at temperature ranging from -50 degree celcius to -95 degree celcius after the addition of 10% glycerol. Storage under liquid nitrogen (-196 degree celcius) in the presence of 5% DMSO and glycerol are cryoprotectant.
  • Lyophilisation ( Freeze-drying)- Suspension od microbes freeze at -54 degree celcius to -72 degree celcius, dehydrated while frozen and sealed in vials under vacumm. Such cells can be definitely kept in room temperature. Freeze-dryer is used in Lyophilisation.
Activities: No other activity except for teaching...^^

My own explorace:
1) Mix culture is the culture which has more than one species of bacteria in a culture. We can use the loop to transfer the single desired bacteria colony to another to a new agar media. This culture is called subculture.
2) Resazurin is in pruple colour. It turns pink after boiled. If the medium free of oxygen, resazurin will turns colourless.
3) Bijou bottle is a cylindrical small glass bottle with a screw cap used as a inoculum medium holder.
4) On Eosin Methylene Blue, If E.coli is grown, it will become metallic green because EMB has been specifically design to encourage the growth of gram positive bacteria.
5) Nutrient agar is a general media for growing bacteria and potato dextrose agar is a general media for growing fungi.
6) Cryoprotectant is a substance used to protect biological tissue from freezing damage.

Reflection:
I like those culturing technique. These technique look like very easy but need to take note of every specific detail in order for successfully culture a desired bacteria. I have to understand these culturing teachnique very well because we going to do practical based on the culturing teachnique. Besides that, as a microbiology student, culturing teachnique are basic things that we should have to know. I saw a video in youtube which clearly explain about the steak plate method.
This is the link of the video:
 https://www.youtube.com/watch?v=_1KP9zOtjXk


Friday 12 December 2014

22th Lecture: 10/12/14

Topic: Microbial Growth

Notes:
1) The importance to know the requirements for microbial growth is to slow down the growth of microbes and use to culture the microbes.

2) Growth referring to the number of cells, not the size. Tolerance refers to the microbes able to survive under conditions in which they cannot grow. For example, thermophile is different with thermotolerant. The optimum temperature of thermophile is 55 degree celcius while the optimum temperature of thermotolerant is 30 degree celcius but they still able to survive at 55 degree celcius.

3) The physical requirements for microbial growth is light, temperature, water activity, pH and osmotic pressure. Water activity refers to the amount of water that can be found in substrate that just enough for them to grow.

4) Phototroph require light to carry out photosynthesis. The intensity and wavelength absorbed by different microbes are based on the pigments they have.

5) Subdivision of groups based on growth temperature:
  • Psychrophiles
Minimum temperature: 0 degree celcius
Optimum temperature: 15 degree celcius
Maximum temperature: 20 degree celcius
  • Psychrotrophs
Minimum temperature: 0 degree celcius
Optimum temperature: 20-30 degree celcius
Maximum temperature: 35 degree celcius
  • Mesophiles
Minimum temperature: 10 degree celcius
Optimum temperature: 25-35 degree celcius
Maximum temperature: 45 degree celcius
  • Thermophiles
Minimum temperature: 50 degree celcius
Optimum temperature: 50 to 55 degree celcius
Maximum temperature: 80 degree celcius
  • Hyperthermophiles
Minimum temperature: 65 degree celcius
Optimum temperature: 85-100 degree celcius
Maximum temperature: 113 degree celcius

6) Acidophiles grow between pH 0-6, Neutrophiles grow between pH 6-7.5, Alkaliphiles grow between 8-11.5

7) Most of the bacteria survive in higher water activity habitat (the water activity of bacteria is 0.91-0.97). Most of the fungus surive in lower water activity habitat ( the water activity of fungus is 0.81-0.88). If bacteria live in hypertonic solution, they will undergo plasmolysis. If bacteria live in hypotonic solutioon, they will undergo lysis.

8) Microorganisms that require some NaCl for growth are halophiles. Mild halophiles require 1-6% salt (>0.2M of salt), moderate halophiles require 6-15% salt; extreme halophiles that require 15-30%(>2M of salt)  NaCl for growth are found among the archaea.  Bacteria that are able to grow at moderate salt concentrations, even though they grow best in the absence of NaCl, are called halotolerant.

9) The chemical requirements for microbial growth are water, carbon, special growth factors, trace elements, oxygen, nitrogen, phosphorus and sulfur.

10) Water is important to dissolve nutrients and carry out cellular functions in microbes. Autotroph uses carbon dioxide as carbon source and heterotroph uses organic molecules as carbon source.

11) Oxygen is require for the growth of certain bacteria but not all bacteria.
       a) Obligate aerobes: need oxygen for growth
       b) Facultative anaerobe: grow best in the presence of oxygen but can grow in the absence of oxygen.
       c) Obligate anaerobes: oxygen is not require for growth
       d) Aerotolerant anaerobes: only anaerobic condition. Oxygen is not required for growth but can suvive and tolerate in the presence of oxygen
       e) Microaerophiles: only aerobic condition. Oxygen is required in concentrations lower than those in air.

12) There are few toxic form of oxygen:
  • Singlet oxygen
- is extremely active
- is a normal molecular oxygen that has been boosted into a high-energy state
  • Superoxide free radicals
- toxic for obligate anaerobes because they lack of superoxide dismutase(SOD)
- SOD converts the superoxide free radicals into molecular oxygen and hydrogen peroxide
  • Peroxide anion
- toxic for anaerobes because they lack of catalase and peroxidase to detoxify it
  • Hydroxyl radical
- toxic to anaerobes because this would have been detoxify to water in aerobes.

13) Trace elements such as Fe, Mg, Mn, Cu and Zn are important for enzyme function because they are part of enzyme and cofactors. They used to maintain the protein structure.

Activities: Quizzes and introduction of green sulfur bacteria, purple sulfur bacteria, green non-sulfur bacteria, purple non-sulfur bacteria

My own explorace:

1) Although halophiles are "osmophiles" (and halotolerant organisms are "osmotolerant") the term osmophiles is usually reserved for organisms that are able to live in environments high in sugar. Organisms which live in dry environments are called xerophiles.

2) Cyanobacteria are aquatic and photosynthetic. They consist of phycocyanin and chlorophyll a. They can convert inert atmospheric nitrogen into organic form such as nitrate or ammonia. These fixed form of nitrogen are need by plants for growth.

3) Green sulfur bacteria can be in rod, spiral and sphere shape. They are photolithotrophic, obligate phototrophs or strict aerobes.They consist of bacteriochlorophyll c,d or e and small amount of chlorophyll a.

4) Green non-sulfur bacteria is thermophilic and gram negative bacteria. They are anoxygenic phototrophic. Their source of electons are hydrogen, hydrogen sulfide and thiosulfate. They are photoheterotrophs. They consist of bacteriochlorophyll c,d or e and carotenoids.

5) Purple sulfur bacteria is photoautotrophic gram negaive bacteria. They are in rod shaped. They need oxygen to survive but only can live in low oxygen environment.

6) Purple non-sulfur bacteria is anoxygenic phototrophic. Their energy source is light and carbon source is organic compound. They only can tolerate small concentraion of sulphur. They also can undergo aerobic chemoheterotrophy in the absence of light.

Reflection:
Each bacteria have their specific growth requirements. We can't use the same way to culture every bacteria. Based on their specific growth requirements, those bacteria can be categorised into different group such as halophile, thermophile and xerotolerant. Next week we gonna learn isolation and culturing, maintaining and preserving microbes based on the growth requirements of each bacteria.

21th Lecture: 9/12/14

Topic: Microbial Metabolism and Nutritional

Notes:
1) Aerobic respiration is the production of ATP from glucose and oxygen. Oxygen acts as the final acceptor of electron. The theoretical maximum number of ATP generated per glucose in prokaryotes is 38 and in eukaryotes in 36 to 39.

C6H12O6 + 6O2  yields 6CO2 + 6H2O + energy (ATP)
  • Glycolysis
  • Transition reactions
  • Citric acid cycle
  • Electron transport chain and chemiosmosis
2) Anaerobic respiration is the production of ATP from glucose but in the absence of oxygen. The final electron acceptor is inorganic molecules such as nitrate, sulfate. Lactic acid produced will converted back into energy. The number of ATP produced is 36 ATPs or lesser.

3) Fermentation happened when the cells cannot respire and unable to recycle reduced electron carriers. Organic molecules are their electrons acceptor. There are two types of fermentation:
    a) Lactic acid fermentation -  (human and lactic acid bacteria)
Glucose oxidized to pyruvate. 2 molecules of pyruvate are reduced by 2 molecules of NADH to 2 molecules of lactic acid. Homolactic organisms only produce lactic acid.
    b) Alcohol fermentation - (yeast and some bacteria)
Glucose oxidized to pyruvate. 2 molecules of pyruvate converted into 2 molecules of acetylaldehyde and 2 molecules of carbon dioxide. Acetylaldehyde is reduced by NADH to produce ethanol. Heterolactic organisms use the pentose phosphate to produce lactic acid and ethanol.

4) Different types of bacteria produce different alcohol and products. For example, Saccharomyces produce ethyl alcohol and carbon dioxide. Clotridium produces Butyric acid, butyl alcohol, acetone, isopropyl alcohol, carbon dioxide and hydrogen.

5) Photosynthesis is the process in which light energy is trapped and converted to chemical energy.
6CO2 + 6H2O in the presence of light and chlorophyll yields C6H12O6 + 6O2
"Carbon dioxide is reduced to produce glucose and water is oxidised to produce oxygen.

6) Carbon fixation is a process convert carbon dioxide into organic form. It is a light-independent reaction and the most common pathway for carbon fixation is Calvin cycle.

7) ATP, NADH and precursor molecules metabolites formed will then used to synthesize subunits. The end products for carbohydrate catabolism is carbohydrate, the end products for protein catabolism is amino acid and the end products for lipid catabolism is glycerol and fatty acid.

8) Source of energy: Light (photo-) or inorganic or organic compounds (chemo-)
    Source of carbon: Carbon dioxide (auto-) or organic molecules (hetero-)
    Source of electron: Reduced inorganic molecules (litho-) such as H2O, H2, H2S, S, iron, N or organic molecules ( organo-)

9) 
Name
Energy source
Carbon source
Electron source
Photolithoautotroph
Light
Carbon dioxide
Reduced inorganic molecules
Photoorganoautotroph
Light
Carbon dioxide
Organic molecules
Photolithoheterotroph
Light
Organic molecules
Reduced inorganic molecules
Photoorganoheterotroph
Light
Organic molecules
Organic molecules
Chemolithoautotroph
Inorganic or organic molecules
Carbon dioxide
Reduced inorganic molecules
Chemoorganoautotroph
Inorganic or organic molecules
Carbon dioxide
Organic molecules
Chemolithoheterotroph
Inorganic or organic molecules
Organic molecules
Reduced inorganic molecules
Chemoorganoheterotroph
Inorganic or organic molecules
Organic molecules
Organic molecules

10) Mixotrophic organisms can alter metabolic pattern in response to environmental changes. For example:
Purple nonsulfur bacteria can undergo photoorganoheterotroph  in the absence of oxygen and undergo chemoorganoheterotrophs in the presence of oxygen.

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

My own explorace:
1) Why the number of ATP produced have a range from 36 to 38?
It is because 2 ATP produced in glycolysis are used in transporting pyruvate and NADH2 into mitochondria. It is an active transport.

2) Why baby or older people cannot take too much probiotic?
The excessive probiotic will be hyperactivated and produce too much of enzyme and waste products. These are harmful to baby and older people.

3) Gas chromatography can use to determine the alcohol produced by different bacteria.

4) What is biofuel?
Biofuel is fuel that contains energy that are produced from living organisms. Alcohol will produced by the actions of microorganisms and enzymes through the fermentation of sugars or cellulose. The fermentation of sugars derived from wheat, corn, sugar cane and oil palm.

5) What are the function of precursor metabolites?
Precursor metabolites are intermediate molecules that can be either oxidize to generate ATP or marcomolecular subunits such as amino acid, lipids. Examples of precursor metabolites: pyruvate, ribose-5-phosphate, acetyl Co-A

6) Why archaea can resist to heat, cold, acid?
Archaea have membrane composed of glycerol-ether lipids which make them more resistant because ether are more chemically resistant than ester bonds. Besides that, in most archaea cell wall forms S-layer which is a rigid array of protein molecules that cover the outside of the cell and provides both chemical and physical protein. Acetylalosaminuronic acid in achaea also makes them stronger than bacteria. 

Reflection:
Yakult Factory visit
Yakult is a probiotics cultured milk and the bacteria strain inside this cultured milk is known as Lactobacillus casei Shirota strain. Shirota strain dicovered by Dr. Minoru Shirota in 1930 and introduced to the market in 1935. "Yakult" is an international word which means sour-milk. The requirements for probiotic have three: 1)They can live in intestines. 2)They reach intestines alive. 3) They have beneficial effect. The beneficial effects of Shirota strain are increase the number of good bacteria in the intestines and suppressed the number of harmful bacteria. They help in bowel movement and digestion.

The root of Yakult business is based on Shirota-ism:
a) Preventive medicine
b) A healthy intestine leads to a long life
c) A healthy life for all with affordable price

The process in making Yakult:
1) Shirota strain will be cultured in seed tank. The mother bacteria is imported from Japan and the sugar are inported from Australia. Milk powder, water, sugar and glucose are mixed to make sweet milky solution. The milky solution then mix with live Shirota stain in culture tank and leave for fermentation until it reach a ideal concentraion.
2) The plastic bottles are produced by moulding machine. The plastic bottles are then wrapped with bottles labels and stick the straw on the bottles.
3) The labelled empty bottles will then filled by yakult and capped with foil lid.
4) The 5 bottles-pack Yakult will also be loaded in a crate. All the crate will store in cold room at 5 degree celcius. Yakult stored in cold room are now ready for delivery.

From this factory visit, I have learnt a new bacteria strain. Shirota strain acts as probiotics in our body and Yakult even included in patient meal in hospital.  Before visit Yakult factory, I do not know that Yakult is that good. From few experiments they showed to us, Yakult is proven to be a good healthy probiotic cultured milk. We can consume 1 to 2 bottles of Yakult per day. It is a waste of money and bacteria strain to consume more than 2 bottles of Yakult per day but it is not harmful to our body.

Friday 5 December 2014

20th Lecture: 5/12/14

Topics: Microbial Metabolism ( part 1)

Notes:
1) Catabolic ractions
- breakdown of sugars into carbon dioxide and water
-release energy ( exergonic )
- Degradative
-hydrolytic reaction

2) Anabolic reaction
- gain energy from catabolic reaction
- use energy in the form of ATP ( endergonic)
- biosynthesis
- dehydration reaction
- the formation of proteins from amino acids

3) A metabolic pathway is a sequence of enzymatically catalysed chemical reactions in a cell.
4) Enzymes act as biological catalysts that speed up the reaction by reduce the activation energy.
5) Enzymes are very specific and tertiary structure determines the activity. There are few classes of enzyme with their function:

  • oxidoreductase - oxidation and reduction reaction
  • transferase - transfer of functional group
  • hydrolase - hydrolysis
  • lyase - removal of groups of atoms without hydrolysis
  • isomerase - rearrangement of atoms within molecules
  • ligase - joining of two molecules
6) Apoenzyme is the protein portion in an enzyme. Cofactor is the nonprotein component in an enzyme. Holoenzyme is an active enzyme which consists of apoenzyme and cofactor.
7) The active site of an enzyme has two basic components : catalytic site and binding site.
8) Catalytic site is where the reaction actually occurs and the binding site is the area that holds substrate in proper place.
9) The factors that influence enzymatic activity are temperature, pH, concentration and inhibitors.
10) Enzyme will denature at 50 degree celcius and the optimum pH for enzyme is pH 4 to 6. The rate of reaction increase as the concentration of substrate increase.
11) Feedback inhibition is a metabolic pathway where the end product act as inhibitor and inhibits the reaction.
12) Conpetitive inhibition is where the inhibitor and substrate compete for the active site. Noncompetitive inhibition is where the inhibitor bind to the allosteric site and altered the active site.
13) There are 2 aspects of energy production: concept of oxidation-reduction and mechanisms of ATP generation.
14) Redox reactions is the utilization of chemical energy in living organisms. Oxidation is the removal of one or more electrons from a substrate. Reduction is the gain of one or more electrons.
15) Cell used oxidation-reduction in catabolism to extract energy from nutrient molecules.
16) ATP (Adenosine Triphosphate) is prime energy carrier. ADP (Phosphoanhydrides) have free energies for hydralysis,
17) Energy released during certain metabolic reactions can be trapped to form ATP from ADP and phosphate group.
18) The removal of third phosphate group will release unstable energy.
19) Phosphorylation is the addition of phosphate group to a chemical compound. The are three organisms of phosphorylation to generate ATP from ADP:

  • Substrate level Phosphorylation
- A high energy phosphate group from an intermediate in catabolism is added to ADP to form ATP.
  • Oxidative Phosphorylation
- occurs in plasma membrane of prokaryotes and the inner mitochondrial membrane of eukaryotes
- Energy released as electrons are passed through a series of electrons carrier and finally to oxygen. Therefore, oxygen is the last oxygen carrier.
  • Photophosphorylation
- occurs in chlorophylls
- energy from light is trapped by chlorophyll and electrons are passed through a series of electrons acceptors and the electron transfer releases energy for the synthesis of ATP. Electron transport chain is involved.

Activities: Find out 30 terms and definition which are related to this topic. Each group have to prepare 6 quizzes which are related to this topic.

My own explorace:
1) Precursors are compound that participates in the chemical reaction that produces another compound.
2) The term 'organo' refers to compound that consists or organic compound while the term 'litho' refers to compound that consists of inorganic compound.
3) The optimum temperature and optimum pH for the cow rumen enzyme is 39 degree celcius and pH 6.5.

Reflection:
I felt like " Oh, No!" when studied this topic because I knew I have to memorise again all those cycles which I have learnt in Form 6. It reminds me about my hard time to memorise all those cycles in Form 6. Haha..But luckily I have learnt all those cycle in Form 6, I think I can easily understand the steps of these cycles because we have been exposed to these cycles in Form 6.

19th Lecture: 4/12/14

Topics: Classification of microorganisms ( part 2 )

Notes:
1) Phenetic classification is the way to classify organisms based on their obvious similar features.
2) Numerical taxonomy is a computer assisted taxonomy where the organisms sorted into groups of mutual similarity based on the large number of observable properties. The final result expressed in simple matching coefficient or Jaccard coeffifcient. If the the coefficient showed 0.0 ( no matches) , 1.0 ( 100% match). Therefore, look for the higer percentage of matches to classify the bacteria.
3) Phylogenetic classification is the way to classify organisms based on evolutionary relationships by direct comparison of genetic material and gene products.
4) Highly conserved genetic sequence and advancement in sequencing technique make the phylogenetic classification possible.
5) Phylogenetic tree shows the evolutionary relationship among grouop of species.
6) To classify and identify microorganisms, we can study the morphological characteristics (shape, size, cell type, external structure and internal strcuture ) by using differential staining and biochemical tests.

  • Differential staning - gram, acid-fast, negative, endospore and flagella staining
  • Biochemical tests - Phenol Red broth (to test the capability of microbes in utilizing sugar), Gelatin test (to test the capability of the microbes to produce gelatinase), Lipase test (to test the capability of microbes to produce lipase), Strach hydrolysis ( to test the capability of microbes to produce exoenzyme that hydrolyse starch), Mortility test (to test whether the microbes able to move or not), Catalase test (to test the capability of the microbes to produce catalase which decompose hydrogen peroxide into oxygen and water.
7) The rapid biochemical test : standardization, speed, reproducibility, miniaturization, mechanization
8) Serology is the science that studies serum and immune response that are evident in serum.
9) Slide agglutination test is where unknown bacteria placed on several slides and a different known antiserum is placed on each sample. If agglutination occurred, it indicated positive rection because antibody produced will combine with antigens and precipitates the antigen.
10) There are two serology methods:

  • Enzyme-linked immunosorbent assay (ELISA)
- perform in microtiter plate
- fast and utilised a computer scanner to read result
  • Western blotting
- Proteins from unknown bacterium are separated by electrophoresis.
- Proteins are then transferred to a nitrocellulose filter by blotting
- The filter is exposed to known bacteria. If there is matching antigen and antibody, the antibody will retained.


9) Phage typing is to determine which phage a bacterium is susceptible to by dropping different spots of known phage on lawn of bacteria. Lysis indicate matching phage and bacteria.
10) Fatty acid profiles is to compare the fatty acid of unknown organisms with the fatty acid of unknown organisms.
11) The amount of DNA base composition can also use to find the two organisms that are closely related. The difference of more than 10% in their amount of GC is mostly not related.
12) DNA fingerprinting is to determine the similarity of DNA fingerprinting of two organisms to test how closely related they are by using restriction enzyme to cuts the specific base sequence.
13) Nucleic acid hybridization is used to measure the ability of DNA strands from one organisms to hybridize with another based one the drgree of reunion. When double strand of SNA is heated, the complementary strands will seperate and when single strand DNA are cooled, the complementary strands will reunite.
14) There are few technique that apply the technique of nucleic acid hybridization:

  • Southern Blotting
-use DNA probe ( short DNA sequence) in the hybridization
  • DNA chips
- DNA chips composed of various DNA probes
- The hybridization of the probe and unknown DNA is detected by fluorescence because fluorescent dye is added to the chips.

  • Ribotyping and RIbosomal RNA sequencing
- target on rRNA
- rRNA sequence can be obtained by PCR of the DNA coding for rRNA
  • Fluorescent In Situ Hybridization (FISH)
- DNA or RNA are labeled with fluorescent dye
- Probe enter treated cell to react with target
-sensitive and do not require high number of cells

15) There are two methods to classify and identify microorganisms after various analyses:

  • Dichotomous Keys
  • Cladograms


Activities: No activity carried out except for teaching...^^

My own explorace:
1) Serum is the blood plasma not including the fibrinogens. Serum includes all proteins not used in blood clotting (coagulation) and all the electrolytes, antibodies, antigens, hormones, and any exogenous substances.
2) Bacteria can identified using 16S rRNA sequence comparisons phylogenetic while fungus can identified using 18S rRNA sequence comparisons phylogenetic.
3) Biochemical tests are mostly for bacteria only and the result of biochemical test will refer to the Bergey's manual to do classification.
4) Enteric bacteria are bacteria of the intestines.

Reflection:
For a proper classification and identification, at least 50 attributes should be tested. I don't know whether I got the patient to finish all 50 tests if I am that scientists. Every details and observation have to do very precisely are really not an easy work. All these tests maybe very interesting, but it can also easily get bored if these tests have to do again and again.

Thursday 4 December 2014

18th Lecture: 2/12/14

Topic : Classification of organisms (part 1)

Notes:
1) Taxonomy is the science of naming, describing and classifying organisms and includes all plants, animals and microorganisms in the world.
2) There are three interrelated parts in taxanomy:

  • Classification : Arrangement of organisms into group based on mutual similarity or evolutionary relatedness.
  • Nomenclature: The branch of taxonomy concerned with the assignment of names to taxonomic groups according to the published rules.
  • Identification: The pprocess of determining that a particular isolate belongs to a recognized taxon.
3) The common rules for naming a microbes are both world underlined or italicized, genus name is always capitalized, species name is lowercase. For example: Vibrio cholerae

4) The process of naming a New bacteria : 
           a) Run scientific tests to verify the bacteria
           b) Give a name to that bacteria
           c) Publish the name of bacteria in International Journal of Systematic Bateriology
           d) The bacteria will be deposited in culture collection bank
           e) The description of bacteria will incorporated into Bergey's Manual

5) Strain means subgroup of species with one or more characteristics that distinguish it from other subgroup of the same species.

6) Strain can be identified by a name, number and letter follows by specific epithet.

7) Biovars are strains that differs biochemical or physiological with other strains in a particular species.

8) Morphovars are strains that differs morphological with other strains in a particular species.

9) Serovars are strains that differs antigenic properties with other strains in a particular species.

10) The naming of microbes normally inspired from the shape, place it found, nutrient it uses, the person discovered it and the disease it causes.

Activities: No activity carried out except for teaching...^^

My own Explorace:
1) Bergey's manual is the main source for identifying the bacteria species based on their every characteristic aspects.
2) Macroscopic observation means based on what you can see with your naked eye. For example, the shape, colour of the colony of microbes. Microscopic observation means you only can observe by using a microscope. For example, the colour and shape of the bacterium.
3) List our some bateria with different shapes:
  • Coccus : Streptococcus pneumoniae, Streptococcus epidermidis
  • Bacillus: Lactobacillus bulgaricus, Lactobacillus acidophilus, Bacillus anthracis
  • Sarcina: Sarcina ventriculli
  • Tetrad: Staphylococcus aureus
  • Spiral: Treponema pallidum, Borrelia parkeri, Spirillum minus
  • Comma: Vibrio cholerae, Vibrio vulnificus
Reflection:
Today lecture is quite short because it is just one hour lecture. When Dr asked us to name some bacteria with their different shape, I can't answer. I feel quite embarrassed because as a microbiology student at least shouldn't be blank for this question. I think more effort should put to study about the microbes. 

Saturday 22 November 2014

17th Lecture : 21/11/14

Topic : Genetic transfer and recombination

Notes:
1) Genetic recombination refers to the rearrangement of DNA from separate group of genes.
2) Genetic transfer refers to the exchange between2 DNA to form new combinations of genes in a chromosome.
3) Donor cell is the cell that gives a portion of its total DNA and recipient cell that recieved a portion of DNA from donor cell.
4) When the donor's DNA have been incorporated into the recipient's DNA, the resultant cell is called a recombinant.
5) Transformation occurred when gene transfer from one bacterium to another as 'naked' DNA in solution.
6) Griffith's experiment proved the occurring transformation and the hereditary materials as the transforming agent.
A short explanation about Griffth's experiment:
Streptococcus pneumoniae is used in this experiment. Strain S is virulent and has a capsule on it. Strain R is avirulent and has no capsule on it. When live strain R and dead strain S are injected into a mice individually, the mice survived. When live strain S injected into a mice, the mice died. When live strain R + dead strain S injected into a mice, the mice died.
Conclusion: DNA from virulent cell can enter avirulent cell , changing the avirulent strain genetically to make it become virulent.
7) Avery's experiment proved that DNA carried genetic information for transformation but not protein.
A short explanation about Avery's experiment:
Extraction of polysaccharides, lipids, DNA, RNA and protein from strain S pneumococci by chromotography and each of these extraction added individually into strain R. Strain R turns into virulent only when extracted DNA from strain S is added into strain R.
Conclusion: DNA carries genetic information for transformation but not other materials
8) Competence is the alterations in the cell wall that make it permeable to large DNA molecules.
9) Recipient cells have to be competent to take up the donor DNA. Some bacteria are naturlly competent but some undergo treatment to make it competent.
10) Transduction is the transfer of DNA from donor to recipient via a bacteriophage.
11) There are two types of transduction:
  • Generalized transduction
- any bacterial genes are transferred
- bacteriophase attack the bacterial host and hydrolysed the bacterial DNA to mix with viral DNA. New protein coat is build up and some bacterial DNA are packaged in a phase caspid. Then the donor lysed release the phase containing bacterial DNA. The phase which contained bacterial DNA is now infect other recipient bacteria cell. Recombination occur, producing a recombinant cell with a genotype different from both the donor and recipient cells.
- The viral DNA is not being transferred in generalized transduction because viral DNA is not integrated into the bacterial genome.
  • Specialized Transduction
- specific regions of DNA are transferred
- bacteriophase attack the bacterial host and viral DNA inserted into the bacterial host to integrate into the bacterial genome. The viral genome integrated into the bacterial genome is called prophage. Upon induction, the prophage detaches from the bacterial chromosome. A portion of bacterial DNA remained attach to the detached phase DNA. Therefore, this excised phage infects another bacterium and transfers the bacterium genes from the donor bacterium.
-Only the bacterial gene that close to the site of prophage are transferred.

12) Plasmids are self-replicating covalently closed circular DNA molecules that are usually not essential for survival. There are three types of plasmid:
  • Dissimilation plasmid - code for enzymes for catabolism of certain unusual sugars 
  • Conjugative plasmid - carries genes for sex pili and transfer of plasmid'
  • R factors - carry genes that confer upon their host cell resistance to antibiotics, heavy metals and cellular toxins.
13) Conjugation requires contact between donor and recipient cells. Conjugation required opposite mating type. The donor cell carry plasmid and recipient cell do not caryy plasmid.
14) Gram-negative bacterial cell used pili for contact while gram-positive bacterial cell used sticky surface molecule for contact.
15) There are two types of conjugation transfer:
  • Plasmid transfer
-Bacteria that contain F factor (plasmid) are called F+ donor while bacteria that do not contain F factor are called F- recipient.
- Sex pillus is formed between F+ and F- . F factor replicated and transfer to a F-.
- The F- is converted into F+ .
  • Chromosome transfer
- Recombination occurred between F factor and chromosome at specific site of each other.
- The insertion of F factor into chromosome results Hfr cell.
- Hfr cell can transfer chromosomal DNA into the F- but F- convert into recombinant F- cell but not F+ cell because only part of the chromosome being transferred.

Activities: No other activity carried out except for teaching...^^

My own explorace:
1) Naked DNA is histone-free DNA that is passed from cell to cell during a gene transfer process called transformation.
2) There are two ways to create competent cells: heat shock and electroporation. Chemically competent cells are created using a series of cold salt washes to disrupt the cell membranes, preparing the cells to accept plasmid DNA. For electrocompetent cells, the cells are chilled and washed with cold deionized water and 10% glycerol.
Heat shock : The plasmid DNA is incubated with host cells to make the plasmid to close contact with the host cells. The plasmid-cell mixture is heated to 45 degree celcius to 50 degree celcius to allow the plasmid DNA enter the bacterial through disrupted membrane. The heated mixture is then placed back in ice to retain the plasmid in the bacteria.
Electroporation: The plasmid-cell misture is exposed to electric current to make pores on the membrane, allowing the entry of plasmid to the host cell.
3) Prophase is the viral genome that integrated into the bacterial genome.
4) Hfr means high frequency recombinant.

Reflection:
Genetic transfer is really a great invention of human. Organisms can change their genotype through genetic transfer. The steps are complicated and genetic transfer may need a long time to make it completely success. However, genetic transfer are not popular in Malaysia because we lacks those technology knowledge and equipment to carry out transfer.