Week 14

This is the last week of my first semester. In this week, we learned about the other parts of microbial growth such as measurement of microbial growth, sterilization and disinfectants and antimicrobial chemotherapy. I've learned that there are different types of agents used to kill or inhibit the growth of microbes, and different agents have different usages and purposes. For example, sterilization kills all microbes in a very short period of time while antisepsis takes longer time to kill.
I've also learned the terms that I've came across before, which is antisepsis and sanitizer, of which I thought is the same before this. Overall, this topic is interesting in the sense that I can know how to kill microbes by using different methods, ranging from physical, chemical to biological method.


The activities for this week are :
1. Career Talk
2. Bacterial growth exercise
3. Quizz
4. Video assignment to summarize what we've learnt in this semester. Here's the link for my video: https://www.youtube.com/watch?v=HLk2SlYSnZw

Week 13

In this week, we had a visit to Yakult factory. This trip really widened my mind a lot. Before that, I just knew that Yakult is beneficial to us, but not really knowing the real benefits it brings. From the visit, especially from the explanation from the speaker and the booklet, I had gained a lot of information regarding the Lactobacillus casei shirota. For example, it can promote the growth of good bacteria and inhibit the growth of bad bacteria. Plus, it can ensure healthy skin growth too. Another thing that amazed me is the production process of Yakult. The whole production process is mainly conducted by machine, only the inspection and selection processes are done by manpower. 

We had lecture on microbial growth on Tuesday and Wednesday. It is interesting to know the factors that are required for microbes to grow. For example, even some microbes like fungus can grow at low temperature, that's the reason why mould can still grow in refrigerator. Same thing that some microbes can grow in acidic or alkaline condition, because in such condition, the microbes can consume the food from surrounding. Another thing that I learnt is water activity, fungus that have low water activity will only need low amount of water to grow.

One interesting fact that I learnt is the watermelon snow that Dr. Wan mentioned. It is also called as snow algae, pink snow, red snow,, or blood snow. The microbe that causes such phenomenon is Chlamydomonas nivalis, which is a species of green algae. Compressing the snow with these microbes will make the snows look red. This is normally found in California. Such fact is really mind-opening to me.

Lesson 19 (2/12/14)

Date : 2/12/14

Topic : Nomenclature and Classification of Microorganisms

Activities
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Notes

Taxonomy includes three parts: classification, identification and nomenclature.

Strain shows a small permanent genetic difference. Strain is a subgroup of species with one or more characteristics that distinguish it from other subgroups of the same species. It is identified by name, number or letter followed by specific epithet.

Rapid biochemical test must be standardized, rapid, reproducible, miniature, and mechanized.

Antiserum is a commercially available serum with specific antibody.

Serological techniques include ELISA and western blotting.

Phage typing is used to determine which phage a bacterium is susceptible to.

Techniques that apply the principle of nucleic acid hybridization includes Southern Blotting, DNA Chips, Ribotyping and Ribosomal RNA Sequencing, and FISH.

Methods used to classify and identify microorganisms after various analyses are Dichotomous Keys and Cladograms.

Name of microbes
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Random facts
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Muddiest point
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My own exploration
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Reflection on this topic

In order to name a microorganism, many steps are required. This is to ensure that the microorganisms named are specific and do not overlap. The system built is very complete and detailed, showing that a lot of researches and improvements have been done. It is really not an easy task to find a new microbe and name it accordingly.

Lesson 20 (5/12/14)

Date : 20/12/14

Topic : Microbial Metabolism and Nutritional Types of Microorganisms

Activities
1. Creating flashcards of definitions
2. Creating quizz

https://www.blendspace.com/lessons/be1rwq6O1lKasg/flashcards-on-microbial-metabolism

Notes


Microbial metabolism contributes to cycling of elements in ecosystems.

Enzymes are subjected to cellular controls.

Factors that influence enzymatic activity are temperature, pH, concentration of enzyme and substrate, and inhibitors.

Types of inhibition includes competitive inhibition, noncompetitive inhibition and feedback inhibition.

Energy can be produced from redox reaction or mechanisms of ATP generation.

Mechanisms of ATP generation can be done by substrate level phosphorylation, oxidative phosphorylation and photophosphorylation.

Aerobic respiration includes glycolysis, transition reactions, citric acid cycle, electron transport chain and chemiosmosis.

Lactic acid fermentation : Glucose > pyruvic acid > lactic acid
Homolactic fermenters : produce only lactic acid

Alcohol fermentation : Glucose > pyruvic acid > acetyldehyde + CO2
Heterolactic fementers : use pentose phosphate pathway to produce lactic acid and ethanol

Litho means reduced inorganic molecules

Cyanobacteria is oxygenic.

Green sulfur bacteria (Chlorobium) and purple sulfur bacteria (Chromatium) are anoxygenic. Both can be distinguished by the location of their bacteriochlrophyls, stored sulfur and ribosomal RNA.

Green nonsulfur bacteria (Rhodopseudomonas) is a photoheterotroph.


Name of microbes
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Random facts
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Muddiest point
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My own exploration

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Reflection on this topic

I think the website to build flashcards is very convenient because it is very user friendly and can be used to recall easily with the games and quizzes it provided. The quizzes are very interesting, especially from kahoot because it makes the quizz more fun.

Lesson 18 (28/11/14)

Date : 28/11/14

Topic : Test 2 and NYAWA visit

Activities
1. Test 2
2. NYAWA visit


Reflection on this topic

The creativity of artists and lecturers made me feel amazing. I never thought that scientific stuffs can be so artistic and elegant. Not even have a thought that there will be an art exhibition on microbiology. This visit really opens up my mind a lot.

Lesson 17 (25/11/14)

Date : 25/11/14

Topic : The Epidemiology and Public Health Microbiology

Activities
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Notes

Sporadic : occasionally and at irregular intervals.
Endemic : relatively steady low-level frequency and at moderately regular interval
Hyperendemic : gradually increase above endemic but not to epidemic

Outbreak : sudden occurrence unexpectedly, small region (like cholera during feast)
Epidemic : sudden increase unexpectedly
Pandemic : worldwide

Incidence : new cases contracted within population
Prevalence : total number contracted within population

Disease spread can be due to common source outbreak or propagated epidemic

Study of epidemiology includes descriptive (physical aspect and spread)), analytical (cause-and-effect), experimental (experiment).

Infectious frequency can be measured from morbidity rate, mortality rate, prevalence rate (depend on duration and incidence rate).

Infectious reservoirs include human, animal (zoonosis), non-living things (soil, water).

Transmission can be due to contact (direct, indirect, droplets), vehicle (water, air, food), vector (mechanical, biological).

Herd immunity is resistance of population due to immunity of large percentage of the population.

Nosocomial infections are also known as hospital-acquired infections normally caused by normal microbiota. There are many antibiotic resistant hospital strains.

Sources of nosocomial can be endogenous pathogen, exogenous pathogen and autogenous pathogen.

Ways to control epidemics : reduce infection source, break connection from susceptible individual, reduce number of susceptible individuals

Adjuvants are mixed with antigens in vaccines to enhance the immunization.

Risk of vaccination includes attenuated microbes may revert to virulent.

DNA vaccines introduces DNA directly into host cell via air pressure or gene gun.

Name of microbes
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Random facts
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Muddiest point
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My own exploration

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Reflection on this topic

I thought epidemiology is a study that is very "far" and unrelated with us. However, infectious diseases actually exist around us, ranging from flu to nosocomial infections. I used to think that being particular at the cleanliness of door knob and other apparatus in hospital is too extreme. But now I know that there are lots of infections will be contracted and even the infection will become more resistant if no measures of cleaning and sterilization are taken.

Lesson 16 (21/11/14)

Date : 21/11/14

Topic : Virus and Acellular Infectious Agents + Genetic transfer and Recombination

Activities
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Notes

Genetic transfer in prokaryotes can be done by transformation, transduction and conjugation.

Recombinant is the resultant cell due to integration of some donor's DNA into the recipient's DNA.

Competence is the alterations in the cell wall that make it permeable to large DNA molecules.
Some bacteria are naturally competent but some need treatment to be competent.

Transduction can be carried out in two forms (generalized transduction and specialized transduction).

Types of plasmids include dissimilation plasmid, conjugative plasmid and R factors.

Conjugation of Gram-negative bacteria is done by using pili while for Gram-positive bacteria is sticky surface molecule.

Transporons are small segments of DNA that can move from one region of a chromosome to another region of same or different chromosome (jumping DNA).

Name of microbes
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Random facts

The hydrosphere (the sea) has the largest population of virus on Earth.

Poultry shouldn't be eaten before 21 days upon birth because they might have antibiotic residue that is harmful when eaten.

The culture in Papua New Guinea is eating the brain of dead family members, and this will cause Kuru disease due to virus infection.

Virus can be cultured using embryonic eggs. Accurate calculation has to be made in order to prevent the chicks from being born. Some mistakes previously caused deaths of chicks when being studied due to birth deformities.

Capsids are involved in the transfer of genetic materials.

Identification of virus can be done by identifying the envelope proteins (spikes or peplomers), while identification of Gram-positive bacteria can be done by identifying the teichoic acid.

Cytopathic effects are the changes done to the cells. Cytopathic effects can be tested using cell line or hepa cell cultured from the infected cells (taken from patient who has just passed away).

Satellites (one of the acellular infectious agent) is called so because its visibility required high beams of light produced from satellite-like structure.
 



Muddiest point
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My own exploration

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Reflection on this topic

Before the lecture, I felt that the topic of virus is quite boring because it looks very factual and do not have anything interesting to read. But after the explanation of Dr. Wan, then only I knew about the interesting facts of virus. Then only I found the topic very fun. For me, it becomes very fun and easy to learn with all these interesting facts because it makes the knowledge we learn more related to our lives. Thanks Dr. Wan.

Lesson 15 (18/11/14)

Date : 15/11/14

Topic : Mutation

Activities
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Notes

Mutation = any inheritable change in base sequence of DNA ; can be spontaneous or induced

Mutant = a strain carrying the change in base sequence of DNA ; differ from wild (parental) strain
*Selectable : drug resistant (positive or direct selection ; negative selection)
*Nonselectable : loss of colour in pigmented organism

Mutagens = include base analogues, chemical mutagen, radiation and intercalating agents
*Base analogues : compounds sufficiently similar to one of four bases
*Chemical mutagen : substances that can alter a base that is already incorporated in DNA and change its hydrogen bonding specificity
*Radiation : can be ionizing or non-ionizing

Auxotroph = any mutant microorganisms having a nutritional requirement that is absent in the parent

Prototroph = any organism that can synthesize its nutrient from inorganic material

Critical point = protein could be inactive or have reduced activity

Truncated protein = incomplete or shortened protein, usually nonfunctional

Missense mutations : normally due to changes in the first or second base of a codon

Silent mutations : normally due to changes in third base of a codon (except arg- and leu- at first base)

Nonsense mutations : results from stop codon (UAG, UAA, UGA)

Ames test : assume mutant can revert to wild type in the presence of a mutagen (back mutation)

Name of microbes
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Random facts
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Muddiest point
Some of the mechanism is not clear to me because the information is very basic.

My own exploration

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Reflection on this topic

Mutation is also included in one of the topic under Form Six Syllabus. So some of the parts I can understand by revising, but there are some other parts that cover the other aspects which need more understanding.

One thing I realized under this topic is mutation of gene can be very detrimental or beneficial to us, and to maintain the healthy genes is not easy. Most of us are really lucky to be born healthily.

Lesson 14 (14/11/14)

After all those hardships and sleepless nights, finally it comes the NUCEL day (National University of Carnival E-learning).

We've designed a card game which includes information of microbiology. The purpose of doing this is to break the stereotype among us which thinks that microbes are harmful and have no benefits at all. Besides, we intend to introduce a new approach of learning which we have found very efficient to learn about the species and some applications or effects of the microbes. And so the Mighty Microbes cards are created.

All of us are in awe when we reached Shah Alam Convention Centre (SACC). We thought the exhibition would be something like our Thank A Microbe exhibition, in fact it's very grand and looked like holding education fair or other huge exhibition.

Before this, we actually met the board of UPM to present our products and ask for copyright. The experience was very "rare" to me, I've never thought that I will be selling own products. And this gave us the very first exposure on how the process of copyrighting is in UPM.

Back to the NUCEL day, the Mighty Microbe team really enjoyed the whole session very much. We had lots of fun explaining our products to the others. Many of them were interested with our Mighty Microbes cards and some even asked for commercialization of our product. On top of all those funs would be us being crazy out of nothing! The whole session was really great, I enjoyed every moment of it very much!


Thanks Dr. Wan for bringing us the opportunity to join this competition. We have learnt and experienced a lot. This will definitely be the proudest and greatest moment of my first semester in university.

Mighty Microbe.
See the Invisible, Unravel the Mystery.

Lesson 13 (11/11/14)

Date : 7/11/14

Topic : Structure and function of genetic material

Activities

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Notes
Genome = genetic information in a cell

Chromosomes = structures containing DNA that carry genetic information

Genes = segments of DNA that code for functional products

Genotype = genetic composition of an organism ; information that codes for all characteristics

Phenotype = actual expressed properties of an organism

Functions of DNA
1. Store genetic information
2. Self-duplication and inheritance
3. Expression of genetic message

Types of RNA
1. mRNA : contains genetic information to encode a particular protein
2. rRNA : forms integral part of ribosomes
3. tRNA : an adaptor molecule used in translation

Central dogma of genetics is a one way transfer of genetic information from nucleic acid to protein. It includes DNA replication, transcription and translation.
For prokaryotes, translation can begin before transcription is completed because no membrane is separating the chromosomes from cytoplasm.
For eukaryotes, transcription and translation are spatially separated. Exons and introns are present in primary transcript (pre-mRNA), but then introns are removed to form functional mRNA.

Origin of replication > replication forks >  lagging strand & Okazaki fragment + leading strand
RNA primers are removed by DNA polymerase and DNA ligase joins the newly made DNA fragment with the previous one

Replication site > promoter site (promoter) > termination site (terminator)

The Wobble Hypothesis explains why multiple codons can code for one single amino acid. One tRNA molecule (with one amino acid attached) can recognize and bind to more than one codon, due to the less-precise base pairs that can arise between the third base of the codon and the fist bsae of the anticodon. (according to wikipedia)

Name of microbes
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Random facts
A&T have 2 hydrogen bonds
G&C have 3 hydrogen bonds

DNA replication is very accurate because it is proofread by DNA polymerase.

In E.coli, the synthesis of nucleotides during replication can reach up to 1000 nucleotides per second at 37 degree Celcius.

Muddiest point
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My own exploration
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Reflection on this topic

The topic of genetics has been covered in Form Six syllabus, so most of the information still can be handled, just that need some more revision on the topic.

Lesson 12 (7/11/14)

Date : 7/11/14

Topic : Eukaryotes (Algae & Fungi)

Activities
1. Design games to learn about structures of eukaryotes.

The game that our group designed is called "Jump Lysosome Jump". It is basically a snake and ladder games that include quiz.

Notes

Plasma membrane consists of major membrane lipids and microdomains. Major membrane lipids include phosphoglycerides, sphingolipids and cholesterol which all contribute to the strength of membrane. Microdomains participate in variety of cellular processes.

Cell walls of photosynthetic algae have cellulose, pectin, and silica.
Cell walls of fungi have cellulose, chitin, glucan or mannan (polysaccharides found in yeasts)
Protozoa have flexible outer layer called pellicle, instead of cell wall.
Animal cells have sticky glycocalyx.

Plasma membrane of eukaryotes contain carbohydrates that helps in cell-cell recognition / bacterial attachment and sterols that increase resistance to osmotic lysis.

During endocytosis , lysosome and phagosome fuse together to form phagolysosome.
Soil protozoa can carry out photocytosis to engulf bacillus bacteria.

Cytoskeletons include microfilaments (actin protein), intermediate filaments (organelles) and microtubules (chromosomes, flagella, cilia).

DNA is combined with histones and exists in either chromatin or chromosomes..

RER synthesizes and modifies proteins. It also synthesizes cell and organelle membranes.

SER synthesizes lipids such as phospholipids, fatty acids, steroids and other sex hormones. It can also break down toxic compounds and help to develop drug tolerance. Besides, it regulates sugar level and acts as calcium storage for cell and muscle contraction.

Golgi complex receives, modifies, packages and transport proteins. It packages at least 40 different digestive enzymes in lysosomes.

Lysosomes have optimal pH of 5 and is normally found in animal cells. It recycle macromolecules, destroy foreign material,, digest food particles, digest bacteria and carries out rapid self-destruction.

Vacuoles include central vacuole (contain starch, water, pigments, even contain poisons and wastes), contractile vacuole (normally in aquatic protists) and food or digestion vacuole (normally in protozoa, will fuse with lysosomes).

Chloroplasts are disc shaped and have three membrane systems.

Mitochondria contain their own DNA and 70S ribosomes. They can make some proteins and can divide to form daughter mitochondria.

Peroxisomes decompose H2O2,  oxidize toxic substances and organic substances.

Centrosome has two components (pericentriolar and centrioles).


Random facts
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Muddiest point
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My own exploration
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Reflection on this topic

It's fun having different ideas and games to play during learning. But the time actually drags a lot because of our inefficiency, sorry Dr !

Lesson 11 (31/10/14)

Date : 31/10/14

Topic : Protists (Algae & Fungi)

Activities


Notes

Name of microbes

Myxomycota and acrasiomycota


Oomycota


Zygomycota (zygote) is the fungi that involve production of conjugating gametangia, producing zygosporangia and zygospores. All of their hyphae are coenocytic, meaning they have no septa. An example of zygomycetesis Rhizopus stolonifer.


Glomeromycota were considered as zygomycetes years ago.

Ascomycota (sac) is also known as sac fungi.

Basidiomycota (club) includes rusts, shelf fungi, toadstools, and mushrooms. They can produce toxins which are poisonous or hallucinogenic.


Claviceps purpurea is an ergot fungus that grows on the ears of rye and related cereal and forage plants.


Blastomyces dermatitidis is a fungus which can cause blastomycosis, an invasive and serious fungal infection.


Histoplasma capsulatus is a fungus that cause histoplasmosis.

Cryptococcus neoformans is an encapsulated yeast that can live in both plants and animals.

Uredinomycetes (Pucciniomycetes) cause fungal rust in plants. They produce teliospore or teleutospore which is the thick-walled resting spore of some fungi (rusts and smuts).


Ustilaginomycetes is the class of true smut fungi.


Microsporidia is the phylum of spore-forming unicellular parasites. It is an obligated intracellular fungal parasites that infect infects, fish, and humans.


Enterocytozoon bieneusi is a species of the order microsporida which infects the intestinal epithelial cells and may cause diarrhea and pneumonia.

Encephalitozoon cuniculi is a type of microsporidia which causes encephalitis (inflammation of brain) and nephritis (inflammation of kidneys).

Mycorrhizae includes Auricularia and truffles.

Auricularia auricula or wood ear is an edible fungus.

Chytridiomycota (chytrids) is a type of neocallimastigales, which can decompose cellulose and breakdown lignin deposits into smaller pieces. Neocallimastigales or neocallimastigomycota is anaerobic fungi found in digestive tracts of herbivores. They reproduce in the stomach through the use of zoospores that bears a kinetosome but lacks the nonflagellated centriole.

Sporothrix schenckii is a fungus found in soil and decomposing plant material.

Stachybotrys is a genus of molds or filamentous fungi. It is also known as "black mold" or "toxic black mold" that grow on water-damaged building materiaals with poor indoor air quality (sick building syndrome). Long-term exposure to the spores produced will cause irritation of eyes, mucous membranes of mouth, nose and throat, sneezing and chronic coughing. Allergy may occur with symptoms such as nausea, vomiting, bleeding in lungs and nose.


Coccidioides is a fungus found in soil which can cause Coccidioidomycosis (cocci, valley  fever or California fever) when the spores are inhaled.

Pneumocystis jirovec is a tiny fungus that lives in the lungs of many people. It is parasitic and can cause fatal pneumocystis pneumonia in people affected with immunodeficiency disease. Signs of PCP are difficulty breathing, fever and dry cough.

Candida albicans is an opportunistic fungus that may cause fatigue, weight gain, join pain and gas. Candida albicans yeast is part of the gut flora. When overgrows (Candidiasis), it weakens intestinal wall, penetrating through into bloodstream and releasing toxic byproducts throughout the body.

Rhizopus stolonifer or black bread mold is found on bread surfaces, taking food and nutrients from bread and cause damage to the surface where it lives.


Aleuria aurantia or orange peel fungus is a widespread ascomycetes.


Lichen involves ascomycete fungi and basidiomycete which together form a stable thallus. It can be said to be made up of mycobiont (the fungus) and photobiont (the photosynthesizing organism).

Saccharomyces carlsbergensis is a yeast used to produce beer.

Brettanomyces is a non-spore forming genus of yeast. It is acidogenic and when grown on glucose ich media under aerobic conditions, it produces large amounts of acetic acid. Thus it is important to brewing and wine industries.

Yarrowia lipolytica is a type of yeast the can use unusual carbon sources such as hydrocarbon as food sources. It can degrade palm oil mill effluent, TNT and other hydrocarbons.

Terms in microbiology

Anamorph is the asexual reproductive stage (morph), typically mold-like. fungi produce asexual spores only.

Teleomorph is the sexual reproductive stage (morph), typically a fruiting body.

Holomorph is the whole fungus, including anamorph and teleomorph.

Zygospore is the large spore of certain fungi and algae with thick wall. It is formed from the fusion of two similar gametes.


Ascospore is the spore produced in a sac like structure called ascus.
 

Basidiospore is the spore formed externally at the base of basidium.


Homothallic is the possession of the resources within a single organism to reproduce sexually, meaning have male and female reproductive structures on the same thallus,
Heterothallic species have sexes that reside in different individual.

Heterothallic haploid cells retain their mating types as they go through rounds of mitosis. In contrast, homothallic cells frequently switch mating type. Thus the progeny of a single homothallic spore colony can mate with each other to form diploids, while those of a single heterothallic spore colony cannot.

Rhizopus-Burkholderia symbiosis occurs where Burkholderia bacteria grows within Rhizopus and produce toxin that cause seedling blight in rice.

Ascocarp, or ascoma (plural: ascomata), is the fruiting body (sporocarp) of an ascomycete phylum fungus. It consists of very tightly interwoven hyphae and may contain millions of asci, each of which typically contains four to eight ascospores.The fruiting body of Ascomycetes is also known as truffle and is highly prized.


Sclerotium or sclerotia is a compact mass of hardeneed fungal mycelium containing food reserves.

Random facts

Muddiest point
1. Is truffle the fruiting body of ascomycetes or ascocarps or a type of mycorrhizae?

My own exploration
http://website.nbm-mnb.ca/mycologywebpages/NaturalHistoryOfFungi/Zygomycota.html

Reflection on this topic

The topic of fungi is quite interesting because some of the fungi have very special characteristics like the magic mushroom and other club fungi. Fungi are found everywhere and some can be seen with naked eyes, this make me feel that the world of fungi is even more interesting. If we've learnt their characteristics, we can identify the type of fungi and thus utilizing their properties.