Lesson 5 (23/9/14)

Date : 23/9/14

Topic : Microscopy & Preparation of specimens for light microscopy & Staining

(p.s. The topic of microscopy is actually from previous lecture but I put it under this journal just to make myself clearer!)

Activities
1. Group mind map for external structure of prokaryotes

2. Individual mind map for internal structure of prokaryotes

(Tools to do mind map : examtime, mindomo, mind42, mindmaple, mindmeister, simplemind, mindmup, connected mind popplet, bubbl.us)

Notes

Species of microbes

• Treponema pallidum (a spirochete bacterium that cause treponemal diseases - syphilis, bejel, pinta, yaws ; only visible using dark field microscope)
• Anabaena (a genus of filamentous cyanobacteria that exists as plankton)
• Riftia pachyptila
• Metopus cilliate
• Rock-eating bacteira
• Neocallimastix
• Mycobacterium tuberculosis
• Streptococcus
• Pseudomonas
• Salmonella typhosus
• Helicobacter pylori (cause ulcers)

Terms in microbiology

• Resolution / resolving power (ability to distinguish between two adjacent points)
• Staining 
• Oil-immersion lens (increase resolution of a microscope by immersing both objective lens and the specimen in a transparent oil with high refractive index, can achieve magnification of 1000x or greater)

Random facts

• Types of microscopes
• Bright field (produce dark image against brighter background ; requires stain)
• Dark-field (produce bright image against darker background)
• Phase contrast (observe living cells and their internal structures)
• Fluorescence
• Ultraviolet microscope (greater resolution than conventional light microscope)
• Electron microscope
• TEM
• SEM
• Smallest bacterium in the world is Mycoplasma
• Basillus and Clostridium normallly produce endospores.
• G+ bacteria are usually rod-shaped while G- bacteria are usually coccus.

My own exploration

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Reflection on this topic

It actually takes me quite some time to do the mind map, maybe it's because I seldom do mind map when I study. I used to do mind map last time, but I found that it's very time-consuming, so I stopped doing mind map. Doing mind map can be simple and easy, just that I always procrastinate where to put the topic and how to design it. Plus, doing mind map needs to be really clear of the overall idea of the topic. So, before getting into it, I prefer to study the topics and get an idea first, then only draw it out.

Besides this, we were told by Dr. Wan to ask "Why" for every steps that we're going to do when carrying out an experiment or process. For example, why incubation must be done at 37°C?

Lesson 6 (26/9/14)

Date : 26/9/14

Topic : External structure of prokaryotes

Activities
1. Class mind map for external and internal structures of prokaryotes

Notes

Species of microbes

• Myxobacteria (some of the prokaryotes that have multicellular stages ; myxo = mucus-related)
• Proteus microbilis (cause UTI disease, usually G-, has swarm-like motility)
• Treponema pallidum (a spirochete bacterium that cause treponemal diseases - syphilis, bejel, pinta, yaws ; only visible using dark field microscope)
• Borrelia burgdorferi (spirochete that causes Lyme disease)
• Epulopiscium fishelsoni (G+ bacteria that have symbiotic relationship with surgeonfish)
• Corynebacteria diphtheriae (bacterium that causes diphteria ; pleomorphic)
• Mycoplasma (bacteria that lack a cell wall, thus unaffected by antobiotics like penicillin that target cell wall synthesis)
• Mycoplasma pneumoniae (cause mycoplasma pneumonia_
• Mycoplasma genitalium (cause gential diseases such as urethritis, cervictis, pelvic inflammation)
• Ureaplasma
• Pyrolobus fumarii (archaea - survive at high temperature like hydrothermal vent)
• Thermoplasma (facultative archaea - survive in  acidic and high-temperature environments)

Terms in microbiology

• Glycocalyx (organized and firmly attached to cell wall - capsule ; unorganized and loosely attached to cell wall - slime ; made of sugar called EPS - extracellular polysaccharide)
• Extracellular polysaccharides, EPS (sugars that made glycocalyx ; also a main substrate of biofilm ; biofilm = indicator of pollution level)
• Flagella (for motility, attachment, and might be virulence factors)
• Axial filaments (normally with spiral shape, wrap around the cell ; consist of protein pilin arranged helically around a central core)
• Fimbriae (short, thin and straight appendages ; help cells adhere to surfaces)
• Sex or conjugation pili (short, thin and straight appendages ; for transfer of DNA from one cell to another)
• Chemotaxis (movement of organism in response to chemical stimulus - e.g. antibiotics)
• Phototaxis

Random facts

• Most prokaryotes are unicellular except myxobacteria which have multicellular stages in their life cycles
• Unusual shape of bacteria is influenced by environmental conditions, age of culture and antibiotic pretreatment.
• Normally spirochetes live in water.
• Epulopiscium fishelsoni was once known as very large microbe until it's replaced by the largest microbe - Thiomargarita namibiensis.
• The size of microbes is important, one of the uses is in water filter that filter out large microbes. However, small microbes such as virus can easily pass through the filter.
• Autoclave is used to sterillize equipment and culture especially when the culture cannot be heated over high temperatures (e.g. cannot heat antibiotics over 121°C)
• Not every bacteria has capsules.
• Flagella is made of protein called flagellin and is made up of basal body, hook and filament.
• Flagella may be virulence factors because it makes bacteria motile and enables their suvival and ability to cause and spread diseases)
• Peptidoglycan / murein is made up of repeating disaccharide (NAG + NAM)
• peptido : cross-linked, amino acids (N-acetylmuramic acid)
• glycan : sugar (N-acetylglucosamine)
• Lysozyme-sensitive bond, L-Alanine and D-glutamic acid mark the difference between bacteria and archae.
• Genes are transferred from plasmid through the process of conjugation or sexual reproduction of bacteria such as E.coli.

Muddiest point

• Still kind of blurred about the size - shape relationship.                                                   

My own exploration

• Spirochetes contribute to digestion in ruminants and help in feeding in mussels and oysters (by acting as cilia to sweep food into mollusk), but also can cause diseases such as syphilis (Treponema pallidum) and Lyme disease (Borrelia burgdorferi).
• Axial filaments are present in all spirochetes except Treponema.
• Aquaspiririllum magnetotacticum has magnetic properties that allow it to orient itself in the water in relation to Earth's magnetic field

Reflection on this topic

Not so much about the topic, just a feeling that I came across recently. I couldn't manage to finish all the topics before entering the lecture because I was busy with other stuffs and kind of relaxed.I found that writing journals for the topics recently has became more difficult too. There are lots of information that I want to look up but they're just too much! I'm still trying to adapt university lifestyle of which I need to balance my academy and co-curricular activities as well as my personal life.  I need to manage time better, gotta be an efficient learner. Plus, I have to learn to be a thinker, rather than memorizing and burping out all the facts. These two are the things that I need to make adjustment.

Lesson 4 (22/9/14)

Date : 22/9/14

Topic : Brief History of Microbiology

Activities
1. Thank a microbe (Deadline : 18/10/14)
- application decided by own
-environment, industry, food, agriculture, medical

2. E-portfolio

3. Adopt a microbe - scrapbook (Deadline : 9/12/14)
- 7/10/14 determine name of microbe

Notes

Species of microbes
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Terms in microbiology

• Spontaneous generation (life arises spontaneously from non-living matter)
• Biogenesis (living cells can arise only from preexisting living cells)
• Germ theory of disease (some diseases are caused and spread between people by microorganisms)


• Koch's postulates (the framework to study etiology of any infectious disease)
• 
• Exceptions
• Not all microbes can be cultured in artificial media (e.g. some need other means such as tissue cells)
• Similar symptoms could elicit by different species of microbes.
• Some pathogens can cause several disease conditions.
• Pasteurization (heat milk to high temperature then swiftly cooling and bottling it ; just kill most pathogens ; originally used to prevent wine and beer from souring)
• Sterilization (kill all microorganisms in the food)
• UHT - Ultra-high temperature pasteurization (sterilize food by heating it above 135°C  for 1 to 2 seconds to kill spores)
• Hydrothermal vents
• Animalcules (a single cell, looking for moving bacteria)

My own exploration

• Francesco Redi carried out experiments too and produced compelling evidence against the theory of spontaneous generation (by using meat, meat covered with paper, meat covered with cheesecloth)
• John Tyndall proved the existence of heat-resistant spores in many materials. Boiling does not kill these spores, so it is possible to be present in the chicken broth of Needham's experiment. Experiments carried out by Pasteur and Spallanzoni might probably due to luck too, because the sterillization techniques they used would often not kill the endospores. 
• Artificial spleen (biospleen) that was "invented" recently is able to filter the blood from all types of pathogens, by using a magnetic nanobeads (coated with mannose-binding lectin, MBL, a protein found in humans that binds to sugar molecules on the surfaces of 90 different bacteria, viruses and fungi). It means that the device can attach to many kinds of pathogens and together with them, they are filtered out of the blood.
• Why do wine and beer turn sour (especially when exposed to air)? Pasteur found that when the wine turned sour, there was a proliferation of bacterial cells which were producing lactic acid (so the wine turn sour). How to prevent spoilage of these beverages? Pasteur suggested to heat the wine gently at about 49ºC to kill the bacterial cells. The idea of heating to kill microbes was then applied to milk and thus the idea of pasteurization was born.
• Louise Pasteur had many other contributions such as inventing the technique of sterilization (by boiling or heating instruments and food), rescuing the crisis in French silk industry, producing vaccines for anthrax, rabies  etc.
• How did Pasteur discover vaccination? Before this, Pasteur developed techniques for culturing and examining disease-causing bacteria, such as Staphylococcus pyogenes and Vibrio cholerae. When testing Vibrio cholerae on chicken, Pasteur expected the chicken to get sicked but the chicken got immunity instead because the bacteria were old and no longer virulent.
• After Louise Pasteur had stroke, his work was continued by his wife Marie Laurent Pasteur.

Reflection on this topic
I was really amazed at the spirit of scientists when reading the history of microbiology. Here are a few things that make me feel incredible :

1. How could Robert Hooke draw such detailed picture of thin slice of cork? I remembered once I complained why science students (especially biology) need to draw specimens while we can just take the photos or download it. Plus I used to think that we are not art students, so the drawing will of course look terrible. But from the picture drawn by Robert Hooke, it can be seen that he had actually put a lot of efforts in drawing it. No matter how detailed or how fussy the specimen is, he would still try his best to draw it out. This is the spirit that I should learn from him, to be whole-heartedly and serious in whatever I'm doing.
2. The invention and innovation of Antoine van Leeuwenhoek in making his own crafted microscope has made a huge step in microbiology. By using the very simple microscope, he was the first in this world to observe microorganisms which he referred as animalcules. This discovery was an exciting news to everybody because it was like a totally new stuff back then. I personally think that Leeuwenhoek must be in overwhelming awe when he found out those microbes that we can't see with naked eyes.
   
3. The attitude of Antoine van Leeuwenhoek in pursuing knowledge is inspiring. Time he spent in his work was not to gain the praise he enjoyed, but merely to crave after knowledge. Not asking for any title or accreditation, Leeuwenhoek was just eager to know more about the world, that's curiosity.
4. The participation of scientists in giving opinions (or arguments) to seek the truths. When the spontaneous generation was proposed, different opinions were voiced out and the scientists did few tests to find out evidence of it or against it. One of the experiment was done by John Needham, which was then disapproved by Lazzaro Spallanzani, which was also criticized by others, until the proposal of "Biogenesis" concept (living cells can arise only from pre-existing living cells. To prove the concept of biogenesis, again, scientist (Louise Pasteur) did few experiments to prove it. The knowledge that we know now is contributed by lots of brilliant people. They discovered every knowledge step by step, bit by bit. The process of discovery was a long way to go, but they still hold on to it. That's another spirit that I should instill, the spirit of discovery.
5. As told by Dr. Wan, we should really create a community of learning in this microbe group. Knowledge must be shared, and discussion should be held more often to instill the spirit of scientists within us. We ourselves should start to create the atmosphere of learning to discover and explore, instead of just memorizing. 
6. Be unusual! When buying food or drinks, look at the content for the information which we can relate to microbiology. For example, we can find pasteurization and UHT in milk.
7. As said by Dr. Wan, next time if we have the opportunity to travel to Paris, take some time to visit Pasteur Institute. This is the first time I heard about the institute and actually feel interested to visit the place even though it sounds very "scientific". Pasteur is indeed a very brilliant scientist, so the place is worthwhile to go besides Eiffel tower !
8. When reading the history of Edward Jenner, I found it very difficult to accept the fact that he inoculated his own son with swinepox and smallpox. Maybe because I haven't figured out the intentions behind it. I need to do some readings and will come to this issue again.

Lesson 3 (19/9/14)

Started my third lessons on microbiology. This time before entering the lecture hall I've gone through the lecture notes, which was just glancing through + looking up some terms only, not ready to read all in details. However, when Dr. Wan asked a few questions in the end of this lesson, surprisingly, many students were able to answer them. This made me realized that other students were putting real effort as well, all of us must diligently learn more about microbes in order to know them at our fingertips as Dr. Wan said.

Another thing that amazed me was the video shown by Dr. Wan. I've never heard about the "Augmented Reality". It is something like scanning the QR code by using smart devices, it detects the picture and looks for the specific video from its database. This is something that I've never thought of, technology has become more advanced than I thought, just like the 3D printing. It is necessary to update myself more about these innovations before I'm far left behind!

"Be unusual in terms of being more initiative and creative."

 To me, this sounds like asking me to be  a nerdy person! No offence to nerds, in fact they are professional and I really marvel at the knowledge they have. So in order to be the team of unusual, I will first learn how to be a nerd ~ haha !!

Lessons learnt :

Species of microbes

• Bacteria (prokaryote)
• Desulfovibrio
• Spirochete / spirochaete
• Vibrio cholerae
• Escherichia coli O157 : H7
• Archaea (prokaryote, most are extermophiles
• Algae
• Volvox
• Chlorophyta (phylum of green algae)
• Phaeophyta (phylum of brown algae)
• Cyanobacteria (phylum of blue-green algae)
• Rhodophyta (phylum of red algae)
• Fungi
• Saccharomyces cerevisae (a species of yeast)
• Protozoa
• Giardia lambilia

Terms in microbiology

• Spores and endospores
• Peptidoglycan (strongest biological molecule - component of bacteria cell wall)\
• consist of glycosaminoglycan chain interlinked with short peptides
• Hydrothermal vents
• Magnetosomes & magnetite crystals (only in prokaryotes)

Knowledge in microbiology

• Bacteria like all prokaryotes, do not have organelles (compartment separated from the rest of a cell via a phospholipid membrane - eg. nucleus, mitochondria, ER, GA)
• Have inclusions
• Bacteria that live in vacuum
• Bacteria that make arts
• Bacteria with flagella will swim/"run"/"tumble"
• Bacteria without flagella will slide (moonwalk!) >> gliding bacteria
• Basic shapes of bacteria : bacillus, coccus, spiral
• Other shapes of bacteria : star-shaped, roselle-shaped
• 5 groups of Escherichia coli
• most virulent >> Escherichia coli O157 : H7 (which is an expression of prokaryote structure)
• Biofilm in eyes
• Blood has no any single microbe, if there is, it means the person is infected with the microbes
• Virus and multicellular animal parasites / helminths are studied under microbiology even though they are not microbes due to their close relationship with microbes such as bacteria
• Carbon sources of microbes can be known from some of their names
• E.g. Desulfovibrio
• Yeast is a type of fungi
• Archaea is only found in the 1990s
• Marine food chain
• Plankton (e.g. algae) >>> Bacteria >>> Protozoa (predator of bacteria)
• 16S rRNA is used to identify bacteria
• 18S rRNA is used to identify fungus

Muddiest point

• Why is cyanobacteria an algae instead of bacterium?
• Yeast is a single cell fungus, other than yeast, all fungi are multicellular? The largest fungi?
• Difference between prokaryotes and protoctista and protista?
• Difference between endospore and exospore and spore?

Extra information

• Elephantitis lamp

Assignments given :

1. Adopt a microbe!

• Prepare a group poster / scrapbook that contains all the information about the chosen microbe
• Chosen bacteria must be beneficial either to human or environment

2. Upload the link for e-portfolio (e-portfolio must include the reflective journal)

Lesson 2 (12/9/14)

Can't really remember what I reflected in the second class because I didn't write it down at once. After a week, most memory has faded away, that's the limit of human mind, memory will not last forever if we are not refreshing them constantly. Luckily, I've jotted down the lessons learnt, so that I didn't forgot everything during the second lesson.

Lessons learnt :

Species of microbes

• Bacteria 
• Clostridium botulinum (Gram-positive, rod-shaped, anaerobic, spore-forming, motile)
• able to produce neurotoxin botulinum, which caused flaccid paralytic (like those in botox)
• lethal dose : less than 1 μg in humans
• found in cosmetic products and contaminated canned food
• release alpha toxin (Clostridium perfringens)
• Lactobacillus
• Lactococcus
• Nitrosomonas , nitrospiral, nitrogen-fixation
• Streptomyces griseus
• produce Streptomycin
• Archaea 
• Algae 
• Fungi
• Penicillin
• produce Penicillium (fungus vs. bacteria)
• Protozoa

Terms in microbiology

• Biofilm
• Human microbiome
• Normal flora
• Alpha toxin (released by Clostridium perfringens)
• Afla toxin (released by fungus)
• Zooglea
• "Phylologists"

Knowledge in microbiology

• Algae has silica cell wall ; fungi has chitin cell wall
• Fungi can recycle waste. It is not motile. It has hyphae & mycelium to penetrate into soil, which makes the soil conducive for bacteria to live (mutualism & microbiointeration)
• Human skin has pH value of 5.5

Muddiest point

• Difference between microbiome and microbiota
• BT kill insects?
• bioremediation? oil spill done by studying the bacteria that survive in the condition

Extra information
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Assignments given :

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Lesson 1 (9/9/14)

Today was my first lesson on microbiology. Even though I've learnt biology for 4 years, but the lesson today feels like very new to me. I only know the basics of microbiology, such as the names and characteristics of some popular microbes. When it comes to detailed morphology or further examples, I totally had no idea about it. This made me realised that my knowledge about microbiology is limited, and there is a completely vast microscopic world waiting for me to explore.

I felt glad to hear Dr. Wan's concept of learning. I do know that learning is not merely for passing the exams with flying colours. However, my way of learning so far has shaped me into a student that focuses only on exam marks. It is kind of exciting to know I can actually get fun learning new knowledge and being inspired here in university.

Lessons learnt :

1. Species of microbes :

• Deinococcus radiodurans (an extremophile) 
• Ebola
• Penicillin
• Basillus
• Escherchia coli
• Thiomargarita namibiensis
• Diatom algae

2. Terms in microbiology:

• Leeuwenhoek (Antoine van Leeuwenhoek)
• handcrafted microscope
• observed and described microbes (bacteria), muscle fibres, spermatozoa and blood in capillaries
• Louis Pasteur
• had discoveries in vaccination, microbial fermentation and pasteurization
• reduce mortality
• created vaccines for rabies and anthrax
• Anthrax 
• caused by Bacillus anthracis
• can form dormant endospores (survive in harsh conditions)
• spread by spores
• once used as biological weapons ; issues with use of anthrax powder (during First World War by Germans, by Japaneses ; during Second World War by U.K. ; Virulent "Ames strain" in 1950s ; during Gulf War by Iraq ; by Japan in 1990s)
• Sterilization & disinfectant (antiseptics)
• Sterilization (killing or removal of all microorganisms, including bacterial spores)
• Uses : for surgical procedures & in microbiological works (culture media, reagents and equipments)
• Disinfection (killing of many but not all microorganisms ; reduction of microbes so that will not cause infection)
• Sterilization by heat
• Microbial growth & culturing
• Epidemiology
• Microbiota

3. Use of Evernote, edmodo and padlet in learning.

2. Write an e-diary.