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SEM image of the week: Zebrafish embryos

Posted on Monday, March 5, 2012 by for SEM.


Tammy Jiang holds an Eppendorf tube containing about a dozen zebrafish embryos. The embryos are barely visible at the bottom.

Aptly named after the zebra for its black and white stripes streaked across its body, the zebrafish (Danio rerio) is a fascinating model to study for research in developmental genetics. Zebrafish are used to understand the roles of genes and the various processes and mechanisms that the embryo undergoes during development to form vital organs, tissues, and other structures. Zebrafish embryos are ideal for this research because fertilization and development occur outside of the womb, which allow scientists to observe and experiment on them. Another feature that makes them useful as a genetic model organism is their transparency; scientists can actually see individual cells during development under a microscope. In addition, zebrafish embryos mature rapidly (primary organs are formed after 24 hours), making research less time consuming. With zebrafish embryos, scientists discover new and important genes, understand what causes birth defects, and essentially research how a fully functional organism comes into being.

32 hours post fertilization False color image: yellow yolk, light blue body, dark blue eyes.

Female zebrafish lay eggs daily. These eggs start out as single cell stage embryos and then the cells divide. The blastula stage lasts three hours and gastrulation is completed in five hours. Epiboly is a cell movement that is a thinning and spreading of three layers that will eventually form into the ectoderm, mesoderm, and endoderm germ layers. Somite morphogenesis first occurs around 10 hours post fertilization (hpf). Somites are body segments that increase in number as development happens and are used as indicators of the different stages of embryonic development. The tail of the zebrafish embryo develops at the 15 somite stage (16.5 hpf). The embryo feeds off of its yolk sac, which looks like a big yellowish ball in its belly region. The embryo will hatch from its eggshell 72 hpf and will look for food two days after that. By the time the yolk sac disappears, it will start hunting for food.

6 hours post fertilization, somite stage 32 hours post fertilization
36 hours post fertilization

Image and text credit: Tammy Jiang

SEM image of the week: Turtle scutes

Posted on Monday, February 27, 2012 by for SEM.

One day, as I was walking with my sister on 5th avenue, I noticed a lady selling baby turtles. Each pair, one of each gender, was in a little tank. They looked absolutely adorable, I knew I just had to get one. My sister and I purchased one and practically ran home to show our mother. At first, she was furious because she isn’t a fan of pets, but over time, she grew to love them. After a week of ownership, the male turtle was dropped by my sister, and his soul was seized by death. The remaining female turtle, the one whose shell was observed under the microscope, was a lonely widow, so my mother decided to buy another pair of turtles. After she purchased another two, two years passed by and the male turtle grew more ill everyday. White foam escaped his mouth, and he was smaller and skinnier than the other two females. Eventually, he passed away and left the two widows alone.

Another year passed, and my neighbor came knocking on the door. He had just saved a turtle from getting run over by a car. He told us that he wouldn’t be able to take proper care of it so he wants us to keep it. Now, to this day, I haven’t named any of these turtles. I just can’t think of the perfect names for them. I call them turtles. I take them out for walks, as in I let them roam about the house freely, and when it’s good weather outside, I take them to the park. Usually, when I’m lonely, I actually talk to them. I know it’s weird since they can’t reply to me but it feels nice to have them there. I love my turtles, probably because they can’t be as evil as humans. They can’t backstab you, murder you, rob you, or anything of the sort. They’re amazing pets, and I’m glad to have them in my life.

My turtles are all classified as red eared sliders (Trachemys scripta elegant). If you notice in the pictures, the turtle has a red strip on each side of its head. The “slider” part of the name comes from their ability to slide off rocks and logs quickly. Red eared sliders are native to the southern United States but they’re found world wide because of turtle salesmen or travelers owning these pets. They’re actually the most popular pet turtle in the United States. They can be usually found in freshwater swamps. They love to hide around rocks but since they don’t have saliva, they’re forced to remain in water to eat their food. They’re omnivores and can eat a huge variety of foods including aquatic plants, fish, tadpoles, crickets, and worms. At home, I usually feed them shrimp, lettuce, and floating food sticks (which provide extra protein). The turtle’s outer shell is made of a thin layer of keratin, like your hair and fingernails, arranged in plates called scutes. Underneath that layer, there is a layer of bony plates, their ribs and vertebrae. My turtles shed scutes from time to time. I saved one to make the images below.

Overview showing the tip and central ridge of a scute. Note how the parallel machining lines of the metal platform are distorted due to charge accumulation on the edge of the scute. Flaking region at medium voltage and low vacuum. Flaking region at medium voltage and high vacuum.
Side view of the tip of a scute. Jagged edge of a broken scute. Jagged edge of a broken scute. The distortion that looks like smoke is caused by charge accumulation on a pointed region.
Scutes are made of interlocking plates of keratin. Some regions show texture under higher magnification. Underside of a scute showing indentations from blood vessels.

Image and text credit: Jasline Garcia. Caption credit: Glenn Elert

SEM image of the week: Careful with that axe, Eugene, Part 2

Posted on Monday, January 9, 2012 by for SEM.

Let’s try imaging fruit flies again. Prianka and Janae tried it back in November and were moderately successful — if you overlook the fact that they crushed the living daylights out of their specimen. The AP Bio class had plenty of extra fruit flies (Drosophila melanogaster) leftover from their genetics lab, so I thought I’d try imaging one myself. I was slightly more successful. My subject suffered only minor damage. Small insects are surprisingly delicate.

Overview of the whole fly. Note the indented eye, amputated foreleg, and chipped wings. The damage to the leg and wing are certainly due to my careless handling of this tiny, fragile specimen. Close up of the eye. The prune-like appearance of the eye is probably due to the sample being desiccated. I assume insect eyes are fluid-filled like ours. Remove the fluid and the eye collapses. Close up of the eye showing the crystalline lenses. The bristles are a common sight on insects. They are everywhere.
More bristles on the back of the fruit fly’s thorax (middle segment). Bristles on the wings. Bristles on bristles. Some kind of sensory apparatus, no doubt.

A word about the title of this post (and the earlier one with the same name). It’s a reference to a Pink Floyd song from the late ’60s.

Image credit: Glenn Elert

SEM image of the week: Infusorial earth

Posted on Monday, January 2, 2012 by for SEM.

hand labelled jar of infusorial earth

Two weeks ago, I posted images of diatoms I found clinging to the outside of a blue mussel shell. We continue the theme this week with images of diatoms found by the billions in a jar labelled "infusorial earth". We begin with a review.

Diatoms are microscopic, unicellular algae with hard shells made of silica (2H2O·SiO2). Diatoms are one of the most successful classes of living creatures and can be found anywhere there is water — from the bottoms of glaciers to the tops of clouds. When diatoms die their soft interiors decay, but their hard exteriors persist. The floor of the world’s oceans and some lakes are carpeted with many meters of diatomaceous ooze. When the ocean floor is raised high and dry by geologic forces or when lakes are dried by climatic changes, this ooze becomes diatomaceous earth.

Diatomaceous earth is an important industrial compound. Typical uses are as a filtrant (especially swimming pool and aquarium filters), as an abrasive (you may have brushed your teeth with diatomaceous toothpaste), and as an absorbant (inert dry diatomaceous earth plus dangerously unstable liquid nitroglycerine equals stable and pliable dynamite).

I asked the earth science teachers if we had any diatomaceous earth in our collection of rocks and minerals. One of them found a jar full of yellow dust with a handwritten label that said "infusorial earth". It looked nearly as old as Midwood (which was founded in 1940). I had to consult a dictionary for this one. Infusoria is an obsolete term for Protista — a name given to microscopic organisms that are larger and more complex than bacteria, but not large enough or complex enough to be called plants, animals, or fungi.

Diatoms come in two basic types: pennate and centric. Pennate diatoms are left-right symmetric and vaguely resemble feathers, thus the name pennate. (Remember when feathers were used for pens? Me neither.) Pennate diatoms have a top half (epitheca) and a bottom half (hypotheca). Centric diatoms are rotationally symmetric and resemble cylinders. The have a top half and a bottom half, but each half is composed of two parts — a flat or slightly domed end cap called a valve and a cylindrical sidewall called a girdle band. The diatoms on the blue mussel were all pennate and probably all of the same species. They were all mostly intact (although some of them popped apart when they became charged by the electron beam). The diatoms in the jar of infusorial earth are mostly centric and came in a variety of types. None of the were intact. It was a mixed up pile of valves and girdle bands.

The images below were made by dipping an empty microscope platform (which is just a cylinder of solid stainless steel) into the jar of infusorial earth. Whatever stuck is what you see below. It was kind of like frosting a cupcake.

diatom valve diatom valve diatom valve
Valves (End caps)
diatom girdle band diatom girdle band diatom girdle band
Girdle Bands (Middle Segments)
diatom valve giant diatom valve candy cane
This valve is about the same size as the others in this set of images. This valve is unusually large. See the little circle to the right? That’s the valve shown in the previous image. A word or two about last week’s image. It was the broken end of a candy cane like this one.

Image credit: Glenn Elert

SEM image of the Week: Seasons greetings

Posted on Monday, December 26, 2011 by for SEM.

The subject of this week’s SEM IOTW is a mystery, but I’ll give you a hint. It’s a food that’s really only eaten at this time of year. It’s also SEM friendly (that is, it contains very little moisture.) The pure object didn’t look that interesting — until I decided to break it. Fractures are a great thing to study with an SEM.

whatizit? whatizit?
Two images at nearly the same magnification. The one on the left shows the shattered edge of the mystery object. The one on the right shows the interior that was exposed when the mystery object was broken.
whatizit? whatizit?
A magnified region of the image above. The broken end of the mystery object. A mosaic of four images, rotated 90° counterclockwise relative to the other three images.

Image credit: Glenn Elert

SEM image of the week: Mussels not from Brussels, Part 2

Posted on Monday, December 19, 2011 by for SEM.

Last week’s SEM images showed the shell of a blue mussel (Mytilus edulis), focusing on the structure of the hard outer shell made of the mineral aragonite (a polymorph of calcium carbonate or CaCO3). This week we’ll be looking at the outside of that same mussel, focusing on a group of microscopic algae whose hard outer shells are made of silicate (also known as hydrated silicon dioxide or H4SiO4).

The little creatures you see below are single celled algae called diatoms. The origin of the word diatom comes from the fact that their shells (called tests or frustules) are made of two interlocking halves. In Greek, dia (διά) means "across" (the diameter of a circle is the measure across it) and tomos (τομος) means "to cut" (atoms are things that can’t be cut), thus diatomos (διάτομος) in Greek or diatoms in English are things that can be "cut across" or "cut in two". Diatoms reproduce asexually by splitting in half. The top half (called the the epitheca) becomes one daughter and the bottom half (called the hypotheca) becomes another. More Greek. The word theca (θήκη) means "case", epi (ἐπί) means "on top", and hypo (ὑπό) means "beneath". Thus, the epitheca (ἐπίθήκη) is the "top case" and the hypotheca (ὑπόθήκη) is the "bottom case".

Diatoms have a light golden brown color due to the presence of chlorophyll a (a green photosynthetic pigment) and chlorophyll c (a yellow photosynthetic pigment). Compare this to trees, grasses, and the other large plants we see around us every day. The leaves of these plants are mostly chlorophyll a and a little bit of chlorophyll b (another yellow photosynthetic pigment). Trees and grasses appear green because the leaves are higher in chlorophyll a than chlorophyll b — 3:1 being a typical a:b ratio. Diatoms appear golden brown because they contain mixtures of chlorophyll a and chlorophyll c that are closer to being equal — a:c ratios from 2:1 (mostly green) all the way to 1:2 (mostly yellow) are found.

Silicon dioxide (SiO2) from sand is the primary raw material for nearly all commercially produced glasses (other ingredients include calcium oxide and sodium carbonate). It is also the primary raw material for the silicate shells of diatoms (the other ingredient is water). In essence, diatoms live in glass houses. Trying to image them with a light microscope is a real challenge. Their clear bodies nearly vanish in the clear liquid they live in. The only thing that makes them stand out is the little bit of yellow-brown pigment in their chloroplasts. To an electron beam, however, these glass housed microalgae are solid as a rock. Light goes through diatoms, but electrons bounce off. A scanning electron microscope is the perfect tool for imaging diatoms and diatoms are the perfect subject for the scanning electron microscope. Enjoy this week’s images and expect to see more diatoms in the future.

diatoms diatoms diatoms
A group of diatoms hanging out together on the back of a blue mussel. The width of this image is about the same as the width of a human hair. The wavy appearance is an artifact that commonly occurs at high magnification with non-conducting materials. All SEM images are made in a vacuum. Two whole diatoms with their top half (epitheca) showing and one with its top half missing. These diatoms are in the genus Cocconeis. Possibly Cocconeis scutellum or Cocconeis stauroneiformis. The bottom half (hypotheca) of one diatom. The top half was blown away by the electron beam. The two halves became negatively charged, like charges repel, and the top half took off.

Image credit: YaQun Zhou and Anastasiya Matveyenko (images 1 and 2); Glenn Elert (image 3). Thanks to Professors John Marra and Brett Branco at Brooklyn College and Professor Edward Theriot at the University of Texas at Austin for help in identifying these creatures.

SEM image of the week: Mussels not from Brussels, Part 1

Posted on Monday, December 12, 2011 by for SEM.

Mollusks are invertebrate animals with shells made of calcium carbonate (CaCO3). This phylum includes cephalopods (squid, octopus, cuttlefish), gastropods (snails, slugs), and bivalves (clams, oysters, scallops, and mussels). The subject of this week’s SEM Images of the Week is a mussel shell I saved from dinner a month ago. I bought it at the Whole Foods on Columbus Ave and 97th Street in Manhattan near my apartment. I purposely decided to eat mussels that day just so I would have a shell to place in the SEM. Mussel shells are hard and low in moisture, which makes them perfect for the high voltage, high vacuum environment inside a working SEM.

Calcium carbonate comes in one of two polymorphs — two different geometric arrangements of the calcium and carbonate ions — calcite and aragonite. All mollusk shells are made from aragonite. So are pearls, coral, and bird eggs. Followers of this website should expect to see other examples of aragonite appearing in the future (eggshells leftover from breakfast, snail shells from lunch in Paris, coral from my next trip to the Great Barrier Reef, pearls from Marge Simpson, etc.). The aragonite in this mussel shell formed crystals of varying shapes — prismatic rods; layered sheets; bristly mats; and soft, rounded hexagons.

broken point stacked plates stacked plates
The tip of a broken edge. Zoom in on the broken edge. The shell is made of layers of aragonite
rod ends doormat rounded hexagons
Around the lip of the shell, the aragonite is arranged in rods. In some regions, the aragonite crystals are loosely arranged into short spikes that remind me of a rough doormat. Inside where the mussel lives, the aragonite appears as stacks of soft, rounded hexagons.
single rod tag
A single aragonite rod sitting on a bed of rod ends. Shellfish Harvest ID Tag. These live blue mussels were cultivated on ropes in waters off Prince Edward Island, delivered to a distribution center in Pigeon Cove, then purchased, steamed and eaten in New York City.

Image credit: Glenn Elert

SEM image of the week: Tiny shrimp

Posted on Monday, December 5, 2011 by for SEM.

The Department of Redundancy Department came up with the title of this week’s entry. The objects studied were tiny dried shrimp (蝦米 xiāmi) from an Asian grocery in Brooklyn. None of them was bigger than an adult fingernail. They had bright pink bodies and crazy, blue-black eyes on stalks. I tried to mimic the natural color using Photoshop. Adding color to highlight structure is common in SEM imaging.

top view top view, false color
Top view of the head. False color image
left eye, low vacuum left eye, high vacuum
Left eye, low vacuum mode. Left eye, high vacuum mode.
right eye, low vacuum right eye, high vacuum
Right eye, low vacuum mode. Right eye, high vacuum mode.

Image credit: Glenn Elert. Thanks to Kate Wong for providing the sample.

SEM image of the week: Careful with that axe, Eugene, Part 1

Posted on Monday, November 28, 2011 by for SEM.

When you live and work at Midwood Science, the world of the tiny is very important. Unfortunately, the world of the tiny is very easily broken. Please look at the following images of a fruit fly with this caveat in mind. Please be kind to your subjects. Remember, you are much bigger that they are. Be careful when mounting them onto the imaging platform.

This is a fruit fly. You can still see her wings (on the right), her eyes (look left), and her mouth (up and to the left). A close up of the head area. Unfortunately, her “skull” was split and her limbs were severed.
Look closely at her wing. What purpose do you suppose those barbs serve? Check out the compound eye. One lens for each receptor. A different way of seeing. Not the way we vertebrates we do it.

Image credit: Prianka Zaman and Janae Headly

SEM image of the week: Never put anything smaller than your elbow in your ear

Posted on Monday, November 21, 2011 by for SEM.

The subtitle of this week’s post comes from an oft-quoted aphorism in the medical world. "Never put anything smaller than your elbow into your ear." Given that your elbow is much thicker than your ear canal, and given that you couldn’t possibly contort your arm enough to point your elbow toward your head, medical professionals are basically telling us not to put anything into our ear canal under any circumstance.

On the surface, cotton swab manufacturers seem to agree with this given that their products come with warnings that read something like this …

Do not insert swab into ear canal. Entering the ear canal could cause injury.

Why then are cotton swabs made smaller than the ear canal? This is not a question we feel qualified to answer here at Midwood Science. Our primary question is always, "What do things look like?" Bigger may be safer, but smaller is more interesting. Now that we have a scanning electron microscope (SEM), small is our favorite size.

Cotton doesn’t conduct electricity very well, so charge from the electron beam piles up over time instead of flowing away. At low magnifications, this build up of charge deflects a significant portion of the beam towards the detector, which makes the image look "hot". At high magnifications, surface charges deflect the beam unpredictably, which results in a sort of "underwater" appearance. Despite the distortion, we all know what we’re looking at. The images below are what a typical cotton swab looks like under an SEM.

The head of the cotton swab. The neck of the cotton swab, where the fuffy cotton head joins the matted paper stalk.
A pile of fibers under high magnification … … looks like a mangrove swamp under very high magnification.

Image credit: Glenn Elert.

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