The Awesome Microbes Carnival

Last Thursday and Friday was a very hectic yet memorable for me. An awesome event was held last two days which involved all the staffs and students of Department of Microbiology.The Awesome Microbes Carnival is involved by all of the microbes student from the first year until 4 year. Dr also divide the project and work by batch. Our second year student have to handle the exhibition and activity inside the hall .So many student comes from the primary school , secondary school and other university. The event held for 2 days which is on thursday and friday. The exhibition that my group manage to handle is on endoplasmic and Golgi Apparatus . we also take turn to help the activity games that need to have microbiology knowledge to play .The player need to read the poster to answer the question and play.

We also prepared many activity and games booths so that the visitors can learn more about microbiology. students was very excited to play the game. It will attract the student to know more about microbiology and science. outside the hall also selling microbes food product along the carnival held. they create the food in unique way such as tapai ice cream, kimbab, cupcake and donut in microbe shape.   During the event, there were also some 3D printers in the Panggung Percubaan. They printed our 3D models of microbe .There are some microscopes placed in the Panggung Percubaan to give experiences to all the visitors to see the microorganisms.

I learn how to handle program with all my friends . I know how to cooperate with others when we manage this carnival .Thank you Dr Wan for everything and have a great day ! :D It is such a great event. I hope that there are another series of event like this in the future!

intracellular structure of procaryotes

Now we proceed to the intracellular structures of prokaryote. this topic also had been taught previous semester. So i class we just briefly things that we had learned throughout the lectures.

Dr Wan has asked us to do a short presentation about this topics. The class was divided into 6 groups based on the structures. We compiled everything in a padlet.

http://padlet.com/zuhainis/internal

my group were present about plasma membrane

passive transport can be divide into

1)simple difusssion(until equilibrium)

2)facilitated diffusion (aid of protein)-transporter-eg : glucose, fructose, amino acid

3)osmosis-difussion of water across the plasma membrane

Isotonic-no net water movement

Hypotonic(lysis)-water move into the cell , cell burst

Hypertonic(plasmolysis)-water move outside the cell, cell shrink

active process alco can be divide into two which are

-active transport(movement of molecule from low concentration to high concentration, against concentration gradient,used of ATP)

-group translocation-molecule chemically modified across the membrane,energy expended

We also even had a Q&A sessions.  My group did not do enough research about this topic. we did not managed to answer why group trnaslocation only occurs in prokaryotes? 

 i got a lot of information that cannot be read in the lecture note which is in inclusion part that have been presented by Dayana’s group.

Granule can be divide into

• ·         Metachromatic granule
• ·         polysaccharide granule
• ·         sulfur granules

vesicle also can be divide into

• ·         gas vacuole
• ·         carboxysome
• ·         magnetosome
• ·         lipid inclusion

• dayana's group have explain more on the alppha carboxysome and beta carboxysome. Alpha carboxysome-found in cyanobacteria, type I Rubisco,genes arrange in single operator. in comparison Beta carboxyxome-larger than alpha carboxysome, type II Rubisco, gene arrange in multiple gene cluster.

the most importnat part in intracellular structure of procaryotes is endospore presented by Mayling's group.endospore  cannot be destroyed easily, highly resistance to heat,chemical and radiation. here is the cycle of formation of endospore that have be explained by Atikah and Mayling during the presentation.

cell wall and membrane structure of procaryotes

Hi guys !
today we just continue with the subtopic two which is cell wall and membrane structure of procaryotes. What we learn from this topic also had been taught on lecture from previous semester.Briefly whats important part in this topic are: structure and function of cell wall and membrane structure like glycocalyx, flagella, axial filaments, fimbrae and pili.

Dr wan also taugh us the comparison and contrast of cell wall between Gram +ve bacteria and Gram -ve bacteria.
Here is the website that will help our understanding on gram positive and gram negative bacteria differences.

but there is bacteria with Atypical cell wall such as Mycoplasma(small bacteria)

·         no wall or little wall material

·         sterol give rigidity to membrane

·         can pass through bacteria filter

besides that, another important thing is the gram + and gram - archae . i con conclude the comparison of gram + and gram - bacteria as:

                                                            Gram +archae                    gram –archae

Outer membrane                                            -                                              /

Complex peptidoglycan network                      -                                              /

Surface with protein or glycoprotein                 /                                              -

new semester begin people !

Starting a new semester as second year student is quite tough with phisiology of microbe where i will learn about the metabolism involved in the microbes . the first chapter we recall the structures of the prokaryotes that we already learn in last semester.have you still remember what is prokaryotes ?

What is prokaryotes?

Prokaryotes consist of bacteria and archea that lack or nucleus, or membrane bounded organelles,most unicellular but myxobacter have multicellular life cycle.

• ·         Bacteria(cell wall with muramic acid,membrane-ester-linkage,lipid bilayer,thymidine in tRNA)

• ·         Archaea(cell wall w/o muramic acid,membrane-ether-linkage,lipid monolayer,w/o thymidine in tRNA)

this is cell structure of procaryote

here is the function of the cell structure

1)capsule-additional cover that protect cell when it is engulf by another organism, moisture help to adhere to surface and nutrient

2)cell wall-protect the bacteria and give shape

3)cytoplasm-gel like structure mainly of water contain enzyme, salt, cell component, various organic molecule

4)plasma membrane- regulate the flow of substance in and out of cell

5)pili, fimbriae-hair like structure on the surface of cell, attach to another bacteria cell, help attachment

6)flagella-locomotion

7)ribosome-synthesis protein

8)plasmid-carrying gene, circular DNA

My friends and i were asked by Dr Wan to do some research about the types of proteobacteria. Proteobacteria is the largest division of bacteria.
It consist of 6 main groups which are:-

1. Epsilon

2. Delta proteobacteria

3. Gamma proteobacteria

4. Beta proteobacteria

5. Alpha proteobacteria

6. Zeta proteobacteria 
More information about these proteobacteria can be refered by this link below :

http://padlet.com/zuhainis/proteo

 I enjoyed learned this topic as i can remember the first semester topic as the structures of the Prokaryotes are very important in order to be easier for us to understand the further topics.

biogeochemical cycles

Biogeochemical cycle is include the cycles of elements that is important in the environment which is carbon cycle, nitrogen cycle,sulfur cycle, iron cycle and manganese cycle. This is the carbon cycle.

The reduced form is methane and organic matter while the oxidizes form is c02 and c0. The atmospheric c02 is fixed by plants. In carbon cycle the final product for aerobic is accumulation of oxidized product such as h2o while anaerobic of reduced product such as nh4.

In nitrogen cycle there are 3 major process which is nitrification, denitrification and nitrogen fixatiojn. Nitrogen cycle give product of ammonia and must occur in anaerobic condition even in aerobic microorganism.

In sulfur cycle use sulfide as energy sources in sulfur oxidation. While sulfur reduction is reduction of sulfate for the use in amino acid and protein biosynthesis.in mineralization sulfhydryl groups in proteins of dead animals converted to sulfide.

In iron cycle there is oxidation and reduction process..

In manganese cycle , the forms of soil manganese in equilibrium with solution manganese were studied by extracting the soil with ZnSO₄ solution followed by hydroquinone. 

principles of ecology

Firstly what I have learned from this topic is the definition of ecology. Ecology is the study of organisms and their interaction with the environment. Habitat is place of organism live while ecological niches is place where an organism perform best/ there are five level of hierarchy.

We need to know the abiotic factors which is :

-temperature

-water

-sunlight

-wind

-rock and soil

-periodic disturbance

Homeostasis is the dynamic balance of process material and organism in the ecosystem and biosphere.

Here we have the food web that include the procedure such as green plant and algae, consumer such as omnivore animal, decomposer such as bacteria and fungi. 

The roles of microbes in ecosystem is oxygen produced by the trees in the rainforest and blue green algae in the ocean . and it will remove weaker species through infections.. lastly we have learn approaches to effective ecosystem management which is skateholders,adaptive management, natural resources management, strategic management, landscape level onservation and command and control management.

microbial groups

Today we learn on topic microbial groups. Biochemical control agent is use other living organism to control or to kill other organism. There are five methods of microbial reproduction which is binary fission, budding, fragmentation, formation of spore and sexual reproduction. We know that The requirements for development of microbial community is physical growth requirement and chemical growth requirement.

Physical growth requirement involve:

1)light

Required/kill by light

2)temperature

a.       Mesophile(25-40 degree cesius)

b.      Psychrophiles(grow at 0 degree bt optimal at 15 degree Celsius)

c.       Psychrotrophs (optimal at 20-30 degree celsius)

d.      Thermophiles (opt at 15 degree Celsius)

3)Ph

Acidophiles-extreme low pH

Alkaliphiles-prefer alkaline condition

4)water acidity and osmotic pressure

Water necessary for growth. Bacteria required high water activity habitat in contrast fungi need lower water activity habitat.

Chemical growth requirement involve:

a)      Water

Important in dissolve nutrients and cellular functions

b)      Carbon

Importance in buiding block and as main sources of energy

c)       Oxygen

Aerobes:need 02

d)      Nitrogen,phosphorus and sulfur

For biosynthesis of protein

e)      Special growth factor

Specifically needed for growth of certain m/os

f)       Trace element

Importance for enzyme function and as cofactor

There are 2 major nutritional which is source of energy and sources of carbon. In development of microbial communities there are 3 process which is selection strategies, succession and biofilms.in selection strategies we have r strategies and k strategies. R strategies have high rate of reproduction so that it will die very fast and have short general time. In contrast k strategies produce slowly that make it more stable and bigger in size. Besides that, there are 3 types of succession which is preemptive colonization,autogenic succession and allogenic succession. Climate community achieve when succession ends but this is rarely achieve. In biofilm, bacteria of same species that stick to surface will colonize and pull another microorganism.

viruses

Virus contain contain single type of nucleic acid ,either DNA or RNA. Characteristic of virus can be divide into host range, nucleic acid,capsid and envelope, tail and type of diseases.

1)host range

Host range is determined by attachment site on the host and availability in the potential host the factors for viral replication .  location of attachment site is in the cell wall,fimbrie, and plasma membrane of animal cells. The host range of the virus will depend upon the presence of the receptors. If a host lacks the receptor for a virus, or if the host cell lacks some component necessary for the replication of a virus, the host will inherently be resistant to that virus.

2)nucleic acid

It have either DNA or RNA, circular or linear and can appear ingly or in several segments.

3)capsid and envelope

the capsid is surrounded by lipid bilayer that contains viral proteins that enable the virus to bind to the host cells. virus envelope is derived from the host cell membranes. The capsid and envelope play many roles in viral infection, including virus attachment to cells, entry into cells, release of the capsid contents into the cells, and packaging of newly formed viral particles. The capsid and envelope are also responsible for transfer of the viral genetic material from one cell to another. 

General morphology of virus is helical viruses,polyhedral viruses, enveloped viruses and complex viruses.

4) tail and type of disease

Virus is with tail or without tail that is use for attachment.

algae and protozoa

Algae can be referred to as plant-like organisms that are usually photosynthetic, but do not have true roots, stems, leaves, vascular tissue and have simple reproductive structures. They are distributed at planktonic, benthic and neustonic and in moist situations on land. The algae have chlorophyll and can manufacture their own food through the process of photosynthesis. Algae nutrition is autotrophic or heterotrophic. Algae reproduction is by asexual which is fragmentation, spores and binary fission and also sexual reproduction. In sexual reproduction we have isogamy and heterogamy.  Isogamy no structural distinction between male and female gamete. In contrast, heterogamy2 different type of gamate are produce which is male gamete and female gamete.

Characteristic of algae from different division:

1)chlorophyta

Most chlorophytes are aquatic, but some green algae can live on the surface of snow, on tree trunks, in soils, or symbiotically with protozoans, hydras or lichen-forming fungi. Green algae have chlorophylls a and b and store starch as a food reserve inside their plastids. Their cell wall made up of cellulose. They have sexual and asexual reproduction. Example: chlamidomonas

2)charophyta

They found in fresh to brackish water.Their green color comes from chlorphylls a and b.

3)euglenophyta

They have chlorophyll a and b .storage product is paramylon. Reproduction occurs by longitudinal cell division. Most live in freshwater. The most characteristic genus is Euglena, common in ponds and pools, especially when the water has been polluted by runoff from fields or lawns on which fertilizers have been used.

4)chrysophyta

large group of eukariotyes algae commonly called golden algae, found mostly in freshwater.
Chrysophytes contain chlorophylls a and c, which are masked by the accessory pigment fucoxanthin, a carotenoid. Example:diatoms

5)phaeophyta

Like the chrysophytes brown algae derive their color from the presence, in the cell chloroplasts, of several brownish carotenoid pigments, as fucoxathin. With only a few exceptions, brown algae are marine, growing in the colder oceans of the world.

6)rhodophyta

phylum of the kingdom protista consisting of the photosynthetic organisms commonly known as red algae. The red pigment=phycoerythrin , blue pigment=phycocyanin.

7)pyrrhophyta

They are unicellular found in marine and freshwater. They have chlorophyll a and c, carotenoids and xantophylls. Mostly they have 2 flagella which is longitudinal flagellum and transverse flagellum.

the toxic algal produce neurotoxin and it is also use for biofuel production.

PROTOZOA

Protozoa are a diverse group of mostly motile unicellular eukaryotic organisms. protozoa were defined as unicellular protists with animal-like behaviour, such as movement.. the unique features of protozoa is actoplasm,endoplasm,pellicle,nucleus and vavuoles. Protozoa are chemohterotroph which is holozoid nutrition and saprozoic nutrtion. For locomotion they have pseudopodia , flagella and cilia. For production there are asexual and sexual. In asexual there is binary fission while for sexual is conjugation. Binary fission result in two identical cells while conjugation is conjugation of 2 ciliates. Protozoa are classified into sarcomastigophora, labyrinthomorphora,apicomplexa,microspore,ascetospora,myxozoa and ciliophora. Sarcomastigophora are flagellates and amoebae and also have single type of nucleus.

 Apicomplexa are sporozoan with lack of locomotion organells. 

The last one is ciliophora are the largest phylum that use cilia as locomotory organelle.

fungi

Fungi can be single celled or very complex multicellular organisms. General characteristic of fungus is eukaryotic, spore-bearing organism, no chlorophyll, reproduce sexually and asexually and absorbtive nutrition.They are found in just about any habitat but most live on the land, mainly in soil or on plant material rather than in sea or fresh water. A group called the decomposers grow in the soil or on dead plant matter where they play an important role in the cycling of carbon and other elements. This is the structure of fungus

Reproduction of fungi is sexual and asexual.

Asexual reproduction 1. Bud formation in yeasts In its simplest form asexual reproduction is by budding or binary fission. Enzymatic activity and turgor pressure the act to weaken and extrude the cell wall. New cell wall material is incorporated during this phase.

2. Fragmentation

Any mycelium that is fragmented or disrupted, provided that the fragment contains the equivalent of the peripheral growth zone, can grow into a new colony.

3. Sporulation

It is responsible for the production of large numbers of spores throughout the year. These asexual spores are formed on a phase of the fungal life cycle termed in some texts as the mitosporic, or anamorphic phase.

Sexual reproduction

To achieve sexual reproduction it is necessary to have two mating type haploid nuclei (n + n), or a diploid (2n) nucleus.

Zygomycota Common representatives: black bread molds Hyphae are haploid Reproduction relies mainly on asexual spore production

Ascomycota (sac fungi) Common representatives: yeasts, morels, and truffles Hyphae are haploid and dikaryoid Asexual reproduction relies on asexual spore production

Basidiomycota (sac fungi) Common representatives: mushrooms and shelf fungi Hyphae are haploid and dikaryoid Asexual reproduction relies on asexual spore production

Deuteromycota (fungi imperfecti)

• Members include Trichophyton (Athlete's foot), Penicillium (Penicillin), and Candida albicans 

There are three types of slime molds:

• Oomycota
• Myxomycota
• Acrasiomycota

A very small number of fungi cause diseases in animals. In humans these include skin diseases such as athletes’ foot, ringworm and thrush. And benefit of fungi is as agents of biodegradation, industrial fermentation process and important for agriculture, horticulture and forestry.

Archaea

This week we learn on archaea . Archaeans can be found in the most extreme environments on the planet which in cold environment, hot environment, high salinity and anaerobic environment.  They  live near rift vents in the deep sea at temperatures well over 100 degrees Centigrade. Others live in hot spring, or in extremely alkaline or acid waters. They have been found inside the digestive tracts of cows, termites, and marine life where they produce methane. They live in the anoxic muds of marshes and at the bottom of the ocean.  

There are three main types of archaea: the crenarchaeota, which are characterized by their ability to tolerate extremes in temperature and acidity. The euryarchaeota, which include methane-producers and salt-lovers  and lastly is theaumarcheota. The unique features of archea is cell wall, membrane lipids , metabolism and genetics. Cell wall of bacteria contain s-layer that different from bacteria s-layer. Archaea membrane has their own features that differentiate it from bacteria that is more complex and less impermeable.

Among these three main types of archaea are some subtypes, which include:

Methanogens— archaeans that produce methane gas as a waste product of their "digestion," or process of making energy.

Halophiles— those archaeans that live in salty environments.

Thermophiles— the archaeans that live at extremely hot temperatures.

Psychrophiles— those that live at unusually cold temperatures.

that is what i can conclude from the notes of archaea . second class we have answer the group quiz on the procaryotic and archea

microbial systematic-bacteria

Today story… we divide into group to do a mind map on topic introduction to microbial systematic . our group doing on the outline of that topic . so for the outline we divide the work based on class which is archaea ,becteria ,virus ,fungi, protozoa and algae . we started with the group presentation on bacteria .  we need to know the differences between these group . next day , we learn on bacteria . we always culture the bacteria in the lab and all bacteria that we use lab is the bacteria that we can study. Archaea can change shape based on environment condition same goes to gram positive bacteria that doesn’t have cell wall and can change shape. The traits used to classify the bacteria is cell type , morphology, metabolism, reproduction, phage typing, nucleic acid profile and antibiotic resistance profile . we discuss on differences between the endospore and free spore . endospore form by the bacteria  while free spore are outside the cell . reproductive traits influence either light or oxygen. The bacteria E.coli , Salmonella , shigella can be observe difeerently because E.coli shown green sheen colour. Phatogen nonphototropic bacteria such as campylobacter and helicobacter,spirochetes and chlamydias . and nonphatogen is like pseudomonas,azobacter and rhizobium.  For phototrophic  we have oxygenic and nonoxygenic. 

topic 2 introduction to immunology

What means by immunology actually ? I concluded that immunology focuses on the human body's built-in defense system. In a healthy person, the immune system helps the body fight infection by rejecting foreign viruses and bacteria. The key primary lymphoid organs of the immune system are thymus and bone marrow, and secondary lymphatic tissues such as spleen, tonsils, lymph vessels, lymph nodes, adenoids, and skin. There are 3 lines of body defense system :

a)external physical barrier –skin,mucos membrane,normal microbiota

b)internal barrier-phagocytic cell, inflammation and fever

c)specific immune response-humoral response and humoral immune

therefore, we can differentiate between the non-specific annd specific immune response. their characteristic shown the differences between the non specific and non specific immune response which is non-specific immune response is natural immune system , without memory and non specific. While specific immune response is specificity,inducibility,memory,distinguish self and non-self. There are two type of non-specific immune response :

Internal innate immunity-2 line defense-physiological barrier,phagocytosis,inflammation

External innate immunity-1 line defense-skin, mucos membrane and normal microbiota

we need to know that an antigen need to have this features:

-high molecular weight

-complexity

-soluble

-foreigness

this is differences between the antigen and antibody

Humoral (Antibody-Mediated) Immunity

-Found in body fluids.

-Antibodies are made by plasma cells (activated B lymphocytes) in response to specific antigen.

Cell-Mediated Immunity

-T cells have antigen receptors but don’t make antibodies – lyse target cells directly.

-Cell-mediated reactions primarily respond against intracellular viruses, multicellular parasites, transplanted tissue and cancer cells.

after the lecture we all conclude all the mechanism of different types of immunity in this whiteboard

this mind map is very helpful in order to understand in systematic ways in immunology .After learn on this topic i know that Immune system keep us safe from infection and diseases. It helps us keep ourselves healthy.  Any disease that causing bacteria that enters our body is prevented from causing any damage to the body as the immune system deals with it. We know that every single breath that we inhale, every drop of water we drink or the every bite of food we eat, all contains germs and we are vulnerable to attack by germs. 

semester 2 Microbiologyll topic 1

For the second semester we already cover on topic microbial taxonomy and introduction to immunology . for topic microbial taxonomy we learn:

1)name microorganisms according to international rules and regulation
2)illustrate the methods to classify, identify and name the microorganism

CLASSIFICATION SYSTEM
Phenetic-Numerical taxonomy ,Dendogram
Phylogenetic-16S rRNA, Phylogenetic tree
Genotypic-other molecular methods

Phenetic classification is based on the mutual similarity of phenotypic characterstics. The are two methods in this classification which is simple matching coefficient and Jaccard coefficient.
Phylogenetic is compare organism on the basis of evolutionary. From this classification I will know how to determine phylogenetic classification.
For genotypic , I know that if we come from same species that related we have strong similarity.



TECHNIQUES/METHODS FOR CLASSIFICATION/IDENTIFICATION


Classical
· Morphological (staining, external structure, cell inclusion, cell grouping)
· Physiological and metabolic
· Biochemical
· Ecological
· Immunologic test
· Phage typing
· Antibiotic profiling


Molecular
· Amino acid sequencing
· Nucleic acid base composition (%GC by HPLC and Tm)
· Nucleic acid hybridization
· Nucleic acid sequencing
· Genomic fingerprint (MLSA, RFLP, ribotyping)
· Nucleic acid probe
· Plasmid fingerprinting


In nucleic acid base composition %GC , I know the steps to get the GC content by spectrophotometrically. I think this technique not very accurate because of same GC content but the arrangement differ are not relate . Nucleic acid hybridization also we need to remember the steps involve. This technique is strictly control to avoid self hybridize.

In bacteriophage typing , we need to remember the procedure to produce the plaque on agar plate. Antibiotic susceptibility test is use to determine the pattern of resistance and susceptibility to antibiotics by determination of MIC and MLC. By using this method , we can see the contract between the clear zone that show it susceptible to antibiotics where the bacteria cannot grow and resistance the bacterial growth.

From this lesson I know that it is not easy to give the bacterial names which we need to follow the rules and techniques in giving the name of bacterial. So I really appreciate and impress with the people that found every new bacterial for further studies. And there is a lot of technique and method for classification and identification of bacterial that we need to well planned the test to get the good identification .