Trip to Institute BioScience

On 25th March 2016, our courses went trip to Instiute BioScience, UPM. After class at afternoon, I went to faculty biotech to eat and be prepared. We gathered at 3.30 p.m and went to IBS. Everyone seems excited and happy. It only took 10 minutes to reach IBS. Dr. Amalia lead the trip.

Institute BioScience

When we reached, we were asked to gather in the main laboratory. The first thing I saw in the institute was some pictures on the board.

Scanning elcetron micrograph

Transmission electron micrograph

 Then, we gathered at the main laboratory. We were divided into two groups. The person that in charge for out trip explained to us about SEM and TEM. We had a short briefing on how to prepare sample in order to observe under the microscope.

How to prepare the sample

The man in charge had showed us the diamond blade that used for cutting the sample. We were amazed with the diamond blade because he said that the diamond almost cost 20 thousands.

He showed us the diamond blade

Next, we went to the place that used to coat the sample. We used our friend's coin to be the sample of goal coating.

Gold coating

After that, he showed us SEM and TEM. He showed us the microscope and told us the differences among them.

Leg's insect observed under SEM

Bacteriophage observed under TEM

Plant cell observed under TEM

Scanning electron microscope

It was a great and amazing experience. I hope that we can go to Institute BioScience again in future. Thanks to Dr Wan, Dr Fairol and Dr Amalia for gave us the opportunity to see the microscope in real life that we had only learned in topic 2 for Microbiology.

EUKARYOTIC CELLS GAMES

For this topic, we have been divided to 6 groups. Based on the topic given, we were asked to create an activity to present out topic and each group has been given only for 15 minutes. The games was played at BioTech 1.4. For group 1, they do Kahoot quiz. The quiz was about cilia and flagella, cytoplasm and cell membrane. We were required to answer 12 question that were given. The question was quite easy but they have a time limit which was 20 seconds that really distract us to answer the quiz properly. It was chaos because each group was so active and competitive. Luckily, my group won for this game. We were very excited.

For the second group, they did the crossword game. They prepared the crossword on the whiteboard. The topic was about chloroplast, golgi apparatus and centrosome. Malik said that if we answered wrongly, there will be a punishment. All groups can answered it correctly but unfortunately, only my group answered it wrong and we got the punishment. So the punishment is we did the chicken dance in front of everyone. It was so funny and Haibiel volunteered himself to conduct us for the chicken dance. Everyone can't stop laughing at us. It was memorable and I can't forget it.

The third group did the flip card. We must answered the questions and if right, we can flip the card.

It was creative and a bit tough because the question was so hard. My group members can only answered one correctly and another group we do not know.

For the fourth group, they did the bingo game. It was similar common bingo game but this game is about mitosis and meiosis. It was quite interesting and creative. We were required to choose any words that was given and put into the the blank space randomly. The first group finished their bingo won the game. Malik's group won the game.

Then, we proceed with another group which is group five. The topic was about lysosome, peroxisome and vacuole. This game was fun because we need to search the answer. The answer was flattered everywhere in the room. When the question appeared on the slide, we must quickly find the answer. Everyone was so competitive.

Lastly, was my groups. My groups did the musical chair for topic rough endoplasmic reticulum and smooth endoplasmic reticulum. 10 players with 2 people from each group. Music will be played and you have to circle around the chairs. When the music stops, you have to compete with each other to get a sit. The person who did not manage to get the sit, you will be eliminated and you need to answer a question given by us within 15 seconds. You can discuss with your group members if you did not know the answer. You are not allowed to refer to any references. NO NOTES! NO GOOGLE! NO ASKING DR. WAN! It was happening because we played a common song that everyone knew.

After finish all the games, we take photos with Dr Wan. This is the last class with Dr Wan but Dr Wan said that she will teach us again for the another topic. We were so happy. Thanks to Dr Wan for giving us opportunity to do this game. We will meet you again Dr Wan.

Last class with Dr Wan

PROKARYOTIC CELL

   In week 4, we learned detail about prokaryotic cell. After learning this topic, we able to list down and identify the important structures of prokaryotic cells and able to explain the characteristics of functions of the structures of prokaryotic cell. Then, Dr wan told us about Helicobacter pyolori. H. pylori are spiral-shaped bacteria that grow in the digestive tract and have a tendency to attack the stomach lining. H. pylori infections are usually harmless, but they’re responsible for the majority of ulcers in the stomach and small intestine.

H. pylori is a common type of bacteria that usually infects the stomach. They may be present in more than half of all people in the world, according to the Mayo Clinic. The “H” in the name is short for Helicobacter. “Helico” means spiral. The bacteria are spiral shaped.

H. pylori normally infect your stomach during childhood. While infections with this strain of bacteria typically don’t cause symptoms, they can lead to diseases in some people, including peptic ulcers, and an inflammatory condition inside your stomach known as gastritis.

H. pylori are adapted to live in the harsh, acidic environment of the stomach. These bacteria can change the environment around them and reduce its acidity so they can survive. The shape of H. pylori allows them to penetrate your stomach lining, where they’re protected by mucus and your body’s immune cells are not able to reach them. The bacteria can interfere with your immune response and ensure that they’re not destroyed. This can lead to stomach problems.

Helicobacter pylori

Then, inside the lecture notes, Dr Wan prepare some questions that we needed to find the answer so that we can ready for the lecturer. Dr Wan explained to us about gram staining. Gram staining will give result gram positive or gram negative and gram staining for bacteria only. Most gram negative are bacillus but  not all while E.coli is a gram negative. Gram negative has thinner peptidoglycan, more pathogenic (lipopolysaccharide), resistant to antibiotic and have enzyme called beta-lactamase in periplasmic space. Beta-lactamase can digest beta-lactamerin. Gram positive have thicker peptidoglycan. Carboxisome is in the part of inclusions body. Endotoxin is in order toxin to release, bacteria need to suicide (they have to die). Exotoxin is more virulent because they do even die and can release toxin. Afla is toxin produce by fungi while Alfa is toxin released by bacteria. Safranin can give color in gram negative for counter stain before decolorisation. Chelating agent is binding agent.

Prokaryotic cell

These are the causes a species to have a particular size or shape. This is because efficient nutrient uptake and decreased susceptibility to predation. Normal concentration of salt is 1.5 M. Halophiles is a extra concentration of salt to survive. Methanogen bacteria can be found usually at volcano and under water habitat for methanogens deep-sea-vent (hydrothermal vent) volcano under the sea.

External structure

Bacterial shape and arrangements

Lichen is associations of algae and fungus, like clean environment, clean from pollutant and act as biological indicator. Bioremediation is used of microbe to remove pollutant such as mushrooms. Phytoremediation is used plant to remove pollutant. Mycology is the study of fungus and mycoremediation is used fungi as remediation.

Common bacterial and archaeal structures are plasma membrane, gas vacuole, ribosomes, inclusions, nucleoid, periplasmic space, cell wall, capsules and sliming layers, fimbrae and pili, flagella and endospore. We also play a quiz online on quizzlet about the structure of prokaryote. Structures external to the cell wall are glycocalyx, flagella, axial filaments and fimbrae and pili. Glycocalyx is the source of nutrient that made up of polysaccharide and polypeptide (sugar). Certain microbe needs vectors to move around. Termites lived in insect. Termites get nutrient from bacteria. Bacteria do not have cilia but it have fimbrae and pili.

External structure

Glycocalyx surrounding the cell wall

There are many techniques to study motility of bacteria. For example motility test medium, flagella stain and direct microscopic stain. Three types of motility are "run" or "swim", "tumbles" and "swarm". Advantages of motility is ability to move toward a favorable environment or away from an adverse one (known) as taxis. Type of stimuli are chemical and light. Chemical is for chemotaxis while light for phototaxis.

Function of cell wall are responsible for shape cell, prevent bacterial cells from rupturing due to changes in pressure, the point of anchorage for flagella and may contain antigen if bacteria is infectious. There are gram positive cell wall and gram negative cell wall. Atypical cell wall is certain types of prokaryotes that have no cell wall for example Mycoplasma. Atypical cell wall also included with special content of cell wall for example Mycobacterium. Movement of materials across membranes have two processes which are passive process and active process. Passive process is substances cross from area of high concentration to low concentration (with concentration of gradient). Active transport is movement from area of low concentration to high concentration (against concentration gradient).

Gram positive and gram negative

Cytoplasm is substance of the cell inside the plasma membrane. 80% water and primarily contains proteins (enzymes), carbohydrates, lipids and etc. Major structures in cytoplasm are nuclear area, ribosomes and inclusions.The liquid part inside the cytoplasm called cytosol.

MICROSCOPY

     In topic two, we learned about microscopy. Learning outcomes for this topic are able to identify the parts of a basic microscope, able to describe the principle of light, phase-contrast, fluorescence and electron microscope, able to select suitable microscope for relevant usage and lastly able to recognize images produced from different microscope. There were four types of microscope which are optical, electron, scanning probe and scanning acoustic microscope . For optical microscope include dark field, bright field, fluorescence microscopy and phase contrast microscopy. Dark field and bright field microscope we often used in laboratory. Fluorescence microscopy are the microscope that have monitor and computer attached on it. For electron microscope included scanning electron microscope, transmission electron microscope and environmental scanning electron microscope. Then for scanning probe included atomic force, scanning tunneling and scanning near-field optical microscope.

Electron microscope

Scanning probe microscope

Optical microscope

     Then, we learned details about the light microscope. Variety of common light microscope which were bright-field, dark-field, phase contrast and fluorescence. All are compound microscopes ( the magnified image formed by the objective lens is further enlarged by one or more additional lenses for example ocular lens. the bright-field microscope are ordinary microscope and dark image against brighter background while for the dark-field microscope, bright image against darker background.

Light field vs dark field

      After that, Dr wan explained to us briefly about microscope. Group with 4 boys and 2 girls which consists of Radin, Malik, Daus, Imran, Faridah and Fatin were given a task to find out an interesting way to learn about this topic. They prepared a a slide about microscopy that interesting and unique way. I couldn't remember about the slide but I only remembered about the meteor, ironman and thats all. Dr Wan really supportive to them for what they have done to make this topic interesting.

The parts of a basic microscope

      Besides, we also learned how to focus our microscope. First thing we need to place the slide on the stage, in between the stage clips. Make sure the objectives lens is at the lowest power. By looking at the side, adjust the lowest power objective lens down as close to the specimen as possible without touching it. Then, look through the eyepiece lens and focus upward only until the image is sharp (use coarse adjustment knob) and lastly change to higher power objective lens and readjust with fine adjustment knob. We will doing this for our practical microbiology in semester 3. Resolution is the resolving power which is ability of the lenses to distinguish fine detail and structure. The shorter the wavelength, the greater is the resolution. Refractive index is measure of the light bending ability of a medium. We used oil immersion because to improve the resolution power by focusing more lights to the specimen. Oil immersion also to be used at high objective power (100x). 

  

    Then, we go through detail about the bright-field microscope. These are ordinary microscope that we often used. It produce dark image against brighter background and for enhanced observation with bright-field microscope, kill and stain the cells.

Gram positive and gram negative

     After that, we need to find out terms which was on the lecture notes. Simple stains can be used to determine cell shape, size and arrangement. Differential staining is a procedure that takes advantage of differences in the physical and chemical properties of different groups of bacteria. It allows us to differentiate between different kinds of bacterial cells or different parts of a bacterial cell. Acid fast stains or the other name called Ziehl Neelsen is for bacterium and it is very specific. Lastly for special stains which include capsule, for staining bacteria that has capsule, endospore for bacteria that can produce spore such as Bacillus antrachis and Clostridium at unfavorable condition.

  

    Next, we continued about the dark-field microscope. Usually to observe live specimens which cannot be stained and uses only an opaque disk which blocks light that would enter the objective lens and produce bright image against darker background. Phase contrast microscope permits detailed examination of internal structures to view living cell processes for example cell division and phagocytosis. Phase contrast microscopy light coming in is phase and when it strikes the image is it thrown out phase creating more resolution. The applications of phase contrast microscope are microbial motility, determining shape of living cells and detecting bacteria components such as endospores and inclusion bodies.

Bacteria in phase contrast

Phase contract

     For fluorescence microscope, it produce image from light that passes through a specimen. Specimen tagged or naturally fluorescing against dark background. The image itself emits light for example after excitation with fluorescence stain called fluorochromes, or labeled with fluorochrome-labeled probes or antibodies. Specimen exposed to uv, violet or blue light. 

L. plantarum strain detected by fluorescence microscopy

E.coli strain detected by fluorescence microscopy

    Next, electron microscopy is resolution limit of bet light microscope (0.2 micrometer). Light microscope is for general observation of bacteria (size 1-2 micrometer), cannot see virus or internal structure of bacteria. Electron microscope much greater resolution (0.5 nanometer) and magnification over 100,000 times. There are two types which are transmission electron microscope for analyzing internal structures and scanning electron microscope for analyzing surface structures or 3D structure outer layer.

Transmission electron microscope

Scanning electron microscope

    Atomic force (Scanning probe) microscopy is the eye of Nanotechnology: resolves features as small as an atolic lattice in the real space. It used electrons and application of small voltage to the specimen an allow observation and manipulation at molecular atomic level. For scanning acoustic microscopy it used sound waves and imaging system calculates and color codes speed of sound (SOS). After learned this topic, I knew that there were many types of microscope that useful for industrial application. Before this, I only knew about the simple microscope that often used for the experiment in laboratory. Then, we proceed to individual quiz and group guiz about microscopy topic. This was really fun because while we were answered the quiz we try to refresh ad memorize what we have learned on that day.

  

   We were required to do the mind map regarding for the next topic which is about prokaryotic cells. Dr Wan gave us many mind map tools that we can use to do our mind map. There were many tools that I even cant have decision which mind map tools is the best. So I did signed up everything and all account that Dr Wan provided to us. It really takes a long time but I have to do it because to choose the best mind map tools. Lastly, I decided to choose the mindomo which is quite friendly user and easy to use for newbie like me. It was really challenging when do the mind map because it was the first time I used all this tools. It takes half day to finish it and I also skip my dinner because my passionate to settle up this before tomorrow on that day and I wanted to make it really perfect. But I knew this mind map is really useful for me because it not only just an assignment. Then after finish it we all need to submit it in Putrablast. In the class, we do a lot of activities. We do the quiz about prokaryote in quizlet.com. We also need to re-do the mind map at the whiteboard by taking turns to write the information in front. And as usual, before the class end, Dr Wan told us to be ready for our next class on Monday. 

 
   

MICROBIOLOGY AS INTRODUCTION

     In week 1, we were required to create a less than 2 minutes video for our introduction. We need to introduce ourselves and answered two questions which is what do you know about microbes and what do you want to know about microbes. Then, we start our classes and Dr Wan explained to us about the learning outcomes. Learning outcomes that we need to achieve were able to define microorganism, able to recognize major groups of microorganism, able to describe several ways in which microbes affect our lives and able to relate the people, events and milestones in the history of microbiology. Dr Wan allowed us to use any of our gadgets such as telephone and laptop to search any information about microbes. Microbe also called microorganism or 'germ' are minute living things that individually are usually too small to be seen with the unaided eyes.

   Then, we were required to answer the question from padlet.com. We need to list down the applications of microbes that you are familiar with. As I know that microbes were use widely in production of antibiotic such as penicilin. Penicillin was the first naturally occurring antibiotic discovered. It is obtained in a number of forms from Penicillium moulds. There are two different types of penicillin : 

- Biosynthetic penicillin is natural penicillin that is harvested from the mould itself through fermentation.

- Semi-synthetic penicillin includes semi synthetic derivatives of penicillin - like Ampicillin, Penicillin V, Carbenicillin, Oxacillin, Methicillin, etc. These compounds consist of the basic Penicillin structure, but have been purposefully modified chemically by removing the acyl group to leave 6-aminopenicillanic acid and then adding acyl groups that produce new properties.

These modern semi-synthetic penicillins have various specific properties such as resistance to stomach acids so that they can be taken orally, a degree of resistance to penicillinase (or β-lactamase) (a penicillin-destroying enzyme produced by some bacteria) and an extended range of activity against some Gram-negative bacteria. Penicillin G is the most widely used form and the same one we get in a hypodermic form.

   Next, the other applications of microbes are use in industrial such as bread and cheese, act as natural pest killer in garden and also used as thickening and stabilizing agent such as in water based paint and cosmetic. After that, Dr Wan told us about the Watermelon snow. Watermelon snow, also called snow algae, pink snow, red snow, or blood snow, is Chlamydomonas nivalis, a species of green algae containing a secondary red carotenoid pigment (astaxanthin) in addition to chlorophyll. Unlike most species of fresh-water algae, it is cryophilic (cold-loving) and thrives in freezing water.[1] Its specific epithet, nivalis, is from Latin and refers to snow.

Watermelon snow

   This type of snow is common during the summer in alpine and coastal polar regions worldwide, such as the Sierra Nevada of California. Here, at altitudes of 10,000 to 12,000 feet (3,000–3,600 m), the temperature is cold throughout the year, and so the snow has lingered from winter storms. Compressing the snow by stepping on it or making snowballs leaves it looking red. Walking on watermelon snow often results in getting bright red soles and pinkish pant cuffs.

Watermelon snow in Sierra Nevada

  There are five groups of microorganism which is bacteria, fungi (yeasts and molds), protozoa, algae and also virus. Firstly, we learned about the general characteristic of bacteria. Bacteria are unicellular organisms. Bacteria are Prokaryotes which means no nucleus, no membrane bounded organelles and genetic material not enclosed in a nuclear membrane. I never know the name of the largest bacteria in the world before this. But after we had learned about bacteria, we need to know what is the largest bacteria which is Thiomargarita namibiensis. Thiomargarita namibiensis is a gram-negative coccoid Proteobacterium, found in the ocean sediments of the continental shelf of Namibia. It is the largest bacteria ever discovered, as a rule 0.1–0.3 mm (100–300 µm) in diameter, but sometimes attaining 0.75 mm (750 µm).[1][2] Cells of Thiomargarita namibiensis are large enough to be visible to the naked eye. Although the species holds the record for the most massive bacterium, Epulopiscium fishelsoni – previously discovered in the gut of surgeonfish – grows slightly longer, but narrower.

Thiomargarita namibiensis

   

   

Various shape and forms of bacteria

   Example of uncommon shape of bacteria is star shape, rectangular and also pleomorphic. Pleomorphic means the ability of some baqcteria to alter their shape or size in response to environmental conditions. They change their shape in unfavourable condition. For the next class, we were required to sign in blendspace.com, popplet.com, quizzlet.com and also padlet.com. These are the tools that we use in our class. These are the effective way of teaching instead of only listen to the lecture.

   

 Dr Wan gave us a task on do the research about bacteria as art article that have been upload in putrablast. Bacteria move against antibiotic and formed a beautiful pattern. As we know that why the bacteria act like that because these are the one of strategy. The molecule is very specific and they communicate each other. Besides that, we also learned about Deinococcus radiodurans. Deinococcus radiodurans is an extremophilic bacterium, one of the most radiation-resistant organisms known. It can survive cold, dehydration, vacuum, and acid, and is therefore known as a polyextremophile and has been listed as the world's toughest bacterium in The Guinness Book Of World Records. We also learned about Mycobacterium tuberculosis. Mycobacterium tuberculosis is an obligate pathogenic bacterial species in the family Mycobacteriaceae and the causative agent of most cases of tuberculosis. Lastly, we learned about Bacillus antracis. Bacillus anthracis is the etiologic agent of anthrax—a common disease of livestock and, occasionally, of humans—and the only obligate pathogen within the genus Bacillus. B. anthracis is a Gram-positive, endospore-forming, rod-shaped bacterium, with a width of 1.0–1.2 µm and a length of 3–5 µm. It can be grown in an ordinary nutrient medium under aerobic or anaerobic conditions.

Mycobacterium tuberculosis

Bacillus anthracis

Deinococcus radiodurans

    We need to find out how the bacteria divide to form different forms and we got the answer Bacteria produce asexually by binary fission. First it is coccus then they divide into diplococcal. Diplococcal cell divide to form pairs. Streptococcal remain attached after dividing to form chains. Next, we moved to general characteristic of archae. Archae is a prokaryote and its cell wall lack of peptidoglycan. There are three main groups whish are methanogens, extreme halophiles and extreme thermophiles. Example of methanogens is in rumen (cow's stomache). Methanogens produce methane and oil palm plants have a lot of methane.

    General characteristic of fungi are eukaryotes, unicellular or multicellular and cell wall is made up from chitin. Chitin also can be found in insects. For protozoa, ih has pseudopods to engulf bacteria or food and feed on dead materials. it also have cilia and flagella for movement. Vampyrellidae is a group of protoza that important for control of parasite.

    Furthermore, we learned about algae. Watermelon snow, seaweed, algae bloom and also di-atom are the examples of algae. Algae was differentiate according to their colour which is green clalled chlorophyta and red called rhodophyta. Cell wall of algae are made up from silica and they were symmetrical because of the cell wall for sure. Lastly, the general characteristics for virus are acellular which means not cellular, very small, simple microorganism with DNA and RNA, reproduce by using cellular machinery of host and inert biochemical complex.

protozoa

Fungi

green algae

   Before we continue we the learning outcomes, we we required to name the microbe that we want to adopt and write it on the padlet.com. i chose microbe Pseudomonas syringae as my bacteria that I eant to adopt. Dr Wan also gave us the quiz on edpuzzle which s about how bacteria talk. The video was uploaded before this. I love the way how Dr Wan teach us. it was really amazing and creative and we start to fall in love with this courses.

  For the last learning outcomes, we learned about the timeline of discovery. Science of microbiology starts with the invention of microscope in 1660s by Robert Hooke. Discover of van Leeuwenhoek led to the interest of the scientific communnity of the time origins of these tiny living things. He proposed SPONTANEOUS GENERATION which means life arise spontaneously from non living matter. Spontaneous generation VS Biogenesis issue was finally resolved in 1861 by Louis Pasteur.

spontaneous generation

Pasteur's experiment

   After finish all those learning outcomes, Dr Wan do the quiz for us at kahoot website. This quiz is to make sure that we  understand all those topics before we proceed to the next topic. Before entered the class, we all need to be ready so the class will be more fun and effective.