GMU:Introduction to Microscopy/Denise Nicoau

|WEEK ONE|

4/11/2020

Introduction to the BIO Lab

I examined a puddle of mud sample and a soil sample collected the evening before, and a purple mold sample that was already in the lab. We saw microorganisms in the mud sample.

Glossary

magnification: making images appear larger
resolution: ability to distinguish between two objects
slide: flat rectangles of thin glass which hold the sample under the microscope
sample: something you collect to examine
specimen: the sample on the slide when you look at it through the microscope
cover slip/cover glass: a smaller and thinner sheet of glass that is placed over the specimen
light microscope: it uses light in order to see an image
electron microscope: it uses electron beams to see images (you can see a virus)
compound microscope: it has two sets of lenses (eyepiece lenses - objective lenses)
objective lenses: a set of lenses with different magnifications (e.g., 4x, 10x, 40x - 4 times: lowest magnification, 40 times: highest magnification)
total magnification: is given from the multiplication between eyepiece lens magnification and objective lens magnification (e.g., 10x ocular and 4x objective > 40x total magnification).
coarse focus and fine focus: two knobs which raise or lower the stage which helps with focusing.
stage knobs: the move from side to side which helps exploring/scanning the specimen.
mounting: securing the sample on the slide
dry mount: a simple kind of mounting where the object is merely placed on the slide (this mounting can be successfully used for viewing specimens like pollen, feathers, hairs, etc.)
wet mount: the specimen is placed in a drop of water or other liquid held between the slide and the cover slip. (this method is commonly used to view microscopic organisms that grow in pond water or other liquid media).
disposable pipette
stage clips: clips which secure the slide
lens paper: the only paper you can use to wipe lenses
staining: a technique used to enhance contrast in samples
immersion oil: able to increase resolution (applicable if you have a 100x objective lens)
fixation: it refers to the process of attaching cells to a slide; it is often achieved either by heating or chemically treating the specimen. It kills microorganisms in the specimen, stopping their movement and metabolism while preserving the integrity of their cellular components for observation
simple staining: a single dye is used to emphasize particular structures in the specimen
differential staining: more dyes are used to emphasize particular structures in the specimen

6/11/2020

Brogen and I collected different samples in the Ilm Park and examined them in the lab (spider web, tree bark, river water, mushroom spores, wet leaves). We found microorganisms moving in the river water and some little bugs both in the tree bark and in the spider web samples invisible to the naked eye. Mushroom spores were really interesting.

I examined again the mud samples: microorganisms were still there.

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mushroom spores
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mushroom spores
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mushroom spores
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mushroom spores
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spider web
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spider web
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|WEEK TWO|

14/11/2020

Research: staining technique

Staining Microscopic Specimens Basic histological staining methods

Staining a technique we can take advantage of to enhance contrast and colour to the specimens; it is usally used to detect cellular structures or tissues, to distinguish characteristics you wouldn't see in a natural state.

Dyes are selected for staining depending on the chemical properties which determine how the dye will interact with the specimen. Dyes can be basic, acidic or a combination of the two. Acidic dyes carry a negative charge, so they bind to positively charged cells structure. On the other hand basic dyes carry a positive charge, so they bind to negatively charged cells structure.

A positive stain is a dye that will be absorbed by organisms, to make them stand out against the background (most commonly used). However, there are scenarios in which it is advantageous to use a negative stain, which is absorbed by the background but not by the cells or organisms in the specimen. Negative staining produces a silhouette of the organisms against a colourful background.

Commonly used basic dyes which serve as positive stains

basic fuchsin
crystal violet
malachite green
methylene blue
safranin typically

Commonly used acidic dyes which serve as negative stains

acid fuchsin
eosin
rose bengal

A simple stain will show all the organisms in a sample with the same colour, even if the sample contains more types of organisms. Differential staining, in contrast, distinguishes organisms based on their interactions with different stains, make them appear to be different colours.

Differential staining techniques commonly used

Gram staining
acid-fast staining
endospore staining
flagella staining
capsule staining

15/11/2020

I would like to conduct some experiments related to the staining technique, and also find out how microorganisms react on stimuli.

|WEEK THREE|

17/11/2020

I am informing myself about some microorganisms and I found some interesting ones I would like to explore:

Stentor Protist

Stentor Protist: Reproduction, Anatomy & Habitat

They are shaped like little trumpets and they are made up of a single cell but some of them are large enough to be seen by naked eye. Usually found in ponds or lakes (freshwater environments). Interesting feature: they are remarkable for their regenerative power > when it is cut in half, each half is able to regenerate a half-sized cell that has its normal anatomy and will look the same way it did prior to being cut. There are green, blue and amethyst colored species.

Hydras

They are considered animals, predatory freshwaters microorgranisms; they can be found in ponds, lakek and other slow-moving waters. They feed on different creatures (e.g. insect larvae and small crustaceans) and they die only because of injuries, diseases, starvation or being eaten. Interesting feature: they can develop a mutualistic relationship with algae > the hydra feed on things that would otherwise predate on the algae, while the algae produce photosynthetic compounds that can be utilized as a food source by the hydra. ♥️

Diatoms

Diatoms: Tiny Factories You Can See From Space

Microalgae who generate about 40% of the oxygen produced on the planet each year. They are unicellular microorganisms and can take the shape of ribbons, starts, fans, zigzags and can be radially symmetric or bilaterally symmetric. You can find them in oceans, seas, lakes, streams and soils. They are commonly used in studies of water quality.

18/11/2020

Research: polarized light microscopy

Polarized light microscopy refers to a variety of techniques involving polarized light (e.g. illumination of the sample with polarized light).

These illumination techniques are most commonly used on birefringent or transparent samples where the polarized light interacts strongly with the sample, generating contrast with the background. Polarized light microscopy is used extensively in optical mineralogy.

Polarized light microscopy is capable of providing information on absorption color and optical path boundaries between minerals of differing refractive indices. Furthermore, the contrast-enhancing technique exploits the optical properties specific to anisotropy and reveals detailed information concerning the structure and composition of materials.

You can modify your light microscopy by adding a polarizer, positioned before the specimen, and an analyzer placed between the objective and the observation tubes.

20/11/2020

I am in quarantine and I cannot go to the Biolab, therefore I am conducting some online researches about microorganisms and I am exploring a little phone microscope which belong to my flatmate. Here are some pictures I've taken.

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garlic
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garlic
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garlic
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moth
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tangerine
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tangerine
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tangerine
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salt
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salt
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21/11/2020

Research: slime mold

Slime Molds: When Micro Becomes Macro

Heather Barnett: What humans can learn from semi-intelligent slime

There are different types of slim molds, but the one I am interested in is the Physarum polycephalum. Physarum polycephalum slim molds are these semi-intelligent microorganisms who grow and spread themselves into branches.

Slime mold will be found under cool, humid, and dark conditions on forest floors. They are found in nature on moist dung, wood, soil, and other vegetation. They feed on bacteria, protozoa, fungal spores, and other decaying organic material (they fancy also oats!).

They are brainless unicells, but they can learn and somehow make decisions. They pulse and through the microscope you can see streams which serve to transfer food inside them. Several scientist and artists have been conducting researches about slime molds and the way they behave, to apply some of their mechanisms to the computational field.

|WEEK FOUR|

23/11/2020

Research: Nematodes

In short, if all the matter in the universe except the nematodes were swept away, our world would still be dimly recognizable, and if, as disembodied spirits, we could then investigate it, we should find its mountains, hills, vales, rivers, lakes, and oceans represented by a film of nematodes. - by Nathan Cobb - nematologist.

4 out of every 5 animals that live our planet are nematodes.

Nematodes are multicellular roundworms who inhabit a broad range of environments; there are many types of nematodes, some are parasitic and free-living organisms that feed on living material (e.g. plants, insects or other nematodes). Nematodes have successfully adapted to nearly every ecosystem (soil, freshwaters, tropics, polar regions, ...), in fact they can regulate bacterial population and community composition (they may eat up to 5,000 bacteria per minute!). They can be also hermaphrodites, capable of self fertilization.

Important role played in the decomposition process. Sensitive to pollution.

The Fungus That Traps and Kills Nematodes

From a pond water sample, it has been found a nematode whose body had been trapped by a fungus. The fungus first punctured and expanded, paralyzing the nematode. Then he fed himself quickly, digesting the nematode's body from within.

25/11/2020

Amoebas

Amoebas: Occasional Brain-Eaters

|WEEK FIVE|

30/11/2020

I went to the BIOLab today and I examined some natural samples that I collected on the Ilm Park because I was intended to explore the limits of the microscope, in terms of focus and resolution. Especially with high magnification and thick/3D specimens the microscope struggles in focusing element and this creates lots of interesting visual effects. I keep taken pictures with my phone more or less close to they eye-lenses to that I get chromatic aberration and some blurred parts.

Below some of the picture I have taken.

4/12/2020

As I would like to explore a bit more wet mounts and living microorganisms, I will start with some pond water that I will examine with the binocular microscope.

I decided to collect some pond water samples in weimar: I picked some drops in different parts of the pond and then stored them in 4 tubes to compare them. I prepared the specimens and then waited from 30min to 1 hour to examine all of them, in order to let them familiarize with the environment again.

Overall: a very few moving microorganisms and plenty of static microorganisms/segments of plants.

Here's what I found:

Tube 1:

Tube 2:

moving microorganisms - 1

Tube 3:

moving microorganisms - 2

Tube 4:

Conclusions: I am going to examine them again in a few days to see if something changed.

|WEEK SIX|

7/12/2020

Recommendations on where and how to sample to find microorganisms in action by Julian Chollet:

Always better to collect murky/turbid/not clear water and keep tubes/containers open, otherwise there might not be enough oxygen fro some microorganisms

puddle of mud - mud samples, especially if taken from the bottom with some roots or plants are usually good to examine. You should add some water, shake it a bit and keep it from 2/4 days in a warm environment;
soil - You can find plenty of soil microbes, especially in the uppermost layer. Add some water, shake it a bit and keep it from 2/4 days in a warm environment;
pond water - pond samples are interesting too, where water is not clear and you can't see through, better if you take a part from the surface with a kind of film or a bigger part stored in a glass jar with also some plants/algae inside so that you can explore a kind of ecosystem.
compost - you can find interesting stuff also in the bottom of your garbage bin, in tree barks holes or through degrading dead plants/leaves, where you can have moisture environments and probably worms. Add some water, shake it a bit and keep it from 2/4 days in a warm environment;

When you prepare the specimen and you have to put the slide cover do it gently, in order to prevent some microorganisms to be flattened. You can also facilitate this process by putting a hair or something else which helps to keep an empty space between cover slide and sample.

Advice on how to cultivate a slim mold:

If you use a dry slim mold you should bring it back alive in a wet environment (agar/filter paper)
Better not use old slim mold, the might become moldy fast
Sterile environment (petri dish or bigger container)
Don't feed it at the beginning
Give it just 1 oat meal per day when it starts growing/moving, if you feed it too much (lots of oat meals) it will become moldy fast; when it is big enough you can give it more oats meal
Don't forget about your slim mold! If you forget about it for a couple of days, it will be moldy.

Footage - samples collected and found

Collection of pictures I have taken with my phone camera examining samples both with the BIOLab microscopes and a tiny phone microscope so far:

File:Experiments-1.pdf Experiments-2

Photoshop editing

Below some artworks I created starting from some microscope pictures I've taken by simply changing some adjustments or overlap pictures on Photoshop.

11/12/2020

Today I went to the BioLAB and I examined some samples collected 2 days ago. I picked some muddy water and muddy/wet leaves samples, added some water drops, shake them a bit and and left them in the lab. Below what I found.

Wet/muddy leaves

Muddy water

Slime mold

I also prepared in 2 new (not contaminated) petri dishes the ultimate environment for cultivating slime molds (Agar powder + water mixed together and heat up in the microwave) and put 1 oat flake with a part of a slim mold over it in the first petri dish and 2 oak flakes with 2 different slime molds over them in the second dish.

The slime molds were already alive from the previous 'dry' condition so that I could feed them with a few oat flakes.

13/12/2020

Below the progress of my slime molds I am cultivating. Condition: closed petri dish with agar, inside a shoes box.

SLIME MOLD 1