The Home of Midwood Science Research

SEM image of the week: Jumping Jack Flash

Posted on Wednesday, October 17, 2012 by for SEM.

When playing video games, I always get a tingle when I get a kill or something really interesting happens. Well, this time the chill happened to come from a spider landing on my arm. Identified as a jumping spider by Mr. Rumpolo, this guy landed on my arm when I was gaming and was just crawling around.

This specific spider has four front facing eyes, each with the ability to see in different channels that extend to the ultraviolet range. The two eyes on top are used for the avoidance of threats — though I guess it didn’t see me coming. The abdomen of this spider is unusually small while its body is large so that they can jump further. The jumping spider alters the pressure of body fluid within itself to jump even though its legs aren’t muscular. The jumping spider attaches itself to a filament of silk before jumping as a precaution, just in case the jump fails. This allows them to climb right back up the silk tether.

Top View Front View Back View
Top View Front View Back View

Text credit: Chris Ayala. Image credit: Glenn Elert.

SEM image of the week: Pill bug

Posted on Monday, June 11, 2012 by for SEM.

Armadillidiidae, better known as pill bugs, or roly polies, are crustaceans in the order isopoda. Armadillidiidae have the ability to roll into a ball as a defense mechanism; this ability is called conglobation. The pill bug is the only crustacean that can actually spend its entire life on land. Most pill bugs live for up to two years. Pill bugs mostly eat rotting vegetables and thrive best in a moist environment. They can be found under damp objects or in organic garbage. If they enter a dry place, such as a building, they will often dry out and die. Pill bugs form an important component of the larger decomposer animals in that same area, along with earthworms, and snails. They return organic matter to the soil where it’s further digested by fungi, bacteria, and protozoans making phosphates, nitrates, and other essential nutrients available to plants. Some people regard pill bugs as pests, but they barely do any damage to live vegetation (although they may feed on roots). Pill bugs are also important in places such as coal spoils and slag heaps where they remove toxic metal ions from the soil. They can take in metals such as copper, zinc, lead, and cadmium and crystallize them in their midguts.

A face only a mother could love. Do these remind you of crab legs? Pill bugs are the purely terrestrial cousins of crabs. The armor plates on the back are reminiscent of armadillos — thus the family name armadillidiidae.
The front "grill". Close up of an eye. Patterned "skin" to the side of the eye.

Image: Jasline Garcia and Evelyn Veliz. Text credit: Jasline Garcia. Caption credit: Glenn Elert.

SEM image of the week: Eight is enough

Posted on Monday, May 7, 2012 by for SEM.

The subject of this week’s scanning electron microscope image is a spider that crawled out from behind a painting in my parents’ apartment. Everyone knows that spiders have eight legs, but fewer people know that spiders have six to eight eyes. We originally thought this specimen was a wolf spider, but they have two large eyes on the top row and four smaller eyes on the bottom row. Our guest in the Midwood Science SEM has two sets of four equally sized eyes and is possibly a nursery web spider. There are currently over 450 defined species of spiders, but there may be four times as many species yet to be discovered.

Your basic spider has two main body parts — a cephalothorax at the front and an abdomen at the rear. In addition to the eight legs, spiders also have two long appendages for grasping food (called pedipalps) and two short appendages for injecting venom (called chelicerae). Spiders extrude silk for their webs from glands connected to a hollow set of appendages (called spinnerets) at the far back end of the abdomen.

Overhead view of the cephalothorax Close up of four of the eyes A slightly different overhead view showing the eyes, pedipalps (extended forward), and chelicerae (folded under the animal)
Underside view of the cephalothorax with a good view of the mouthparts (chelicerae closer to the mouth, pedipalps closer to the legs) Underside view of the abdomen showing the spinnerets Close up of the spinnerets

SEM image of the week: Turtle claws

Posted on Monday, April 30, 2012 by for SEM.

The length of a turtle’s claw tells us about the environment in which he/she lives. Turtles with particularly long claws suggest that they’re kept on soft surfaces. Turtles that are around rocks and rough surfaces get their claws naturally worn down. Female turtles that build nests prefer longer claws to make the building easier. Male turtles tend to have longer claws and they’re used to stimulate the female while mating. Trimming the claw of a turtle can easily be done with any kind of nail clipper or scissors, but only the sharp tip at the end of the claw should be removed. If you cut too deeply, the sensitive quick might be penetrated. (The quick is the vein that runs down the claw.) If penetrated, use a cotton swab to spread styptic powder onto the claw until it stops bleeding. (Styptic powder is a clotting agent.)

The first time I trimmed my turtle’s claws was a few weeks ago. This was before I found out about the vein and how much to cut off. As an inexperienced cutter, I took a pair of scissors, held out my turtle’s hand, and when I tried to cut about half, the turtle squirmed and tried to get away from me. I figured that it hurt him, so I tried cutting off a smaller portion. It was difficult to trim because the claw felt so dense. I finally cut if off, and let go. I could tell that he was relieved to get away from me.

For more turtle-related images, click here.

Image and text credit: Jasline Garcia

SEM image of the week: The iron-sulfur world

Posted on Monday, April 23, 2012 by for SEM.

Pyrite, also known as iron disulfide (FeS2), is a semiconductor which has nicknames such as fool’s gold. Pyrite’s metallic luster and appearance has earned it this name, but it is a lot lighter than gold. Ironically, pyrite is sometimes is found together with small quantities of gold. Pyrite’s original name comes from the Greek word for fire and was applied to any stone that would create sparks when struck.

Perhaps the most interesting thing about pyrite is not its ability to serve as a mineral detector, or its ability to produce sulfuric acid, or even its use by the paper industry. The most interesting thing about pyrite is the role it may have played in the origin of life. The iron-sulfur world theory proposed that pyrite, which is abundant near hydrothermal vents, reacted with carbon monoxide, hydrogen sulfide, and other inorganic gases under high pressure and high temperature to form organic compounds such as amino acids.

This SEM images below are part of our project to determine if pyrite could have played a role in the origin of life on earth. This project was originally proposed by Mr. Elert when we told him we wanted to do a project which investigates materials. After further research and input from Mr. Rosenfeld, I learned about the primordial soup theory and the iron-sulfur world theory. The primordial soup theory was proposed and tested by Stanley Miller and Harold Urey at the University of Chicago in the 1950s and involved exciting gases with electricity and heat to produce amino acids. However, this theory had its problems, the gases used in the experiment were not present in the early atmosphere and it would take a lot of luck to hit the right amino acids to produce the proteins. The iron-sulfide world theory proposed by Günter Wächtershäuser, a Munich patent lawyer, in the 1980s revolves around the role of iron pyrite as a catalyst in high pressure, high temperature environments to create amino acids.

Our project involves testing the iron-sulfur world theory by investigating the chemical and optical properties of pyrite. We wish to examine the surface of pyrite and later try to react pyrite with gases present in the early atmosphere under the right conditions to check if there is any reaction that could lead to production of amino acids, proteins, and even life.

Surface of the "inside". The pyrite was cut using a diamond cutter at Brooklyn College. Zoom in of one of the "caves" on the surface of the pyrite. There seems to be a lot of dirt, but those are actually inclusions of other minerals. Close up image of an inclusion, a chunk of foreign mineral stuck inside the pyrite. The edge of the pyrite. The "dirt" is actually sediments of pyrite and other minerals.
A crevice looking thing at the edge of the pyrite that seems to contain tons of dirt particles wanting to get off the pyrite. Surface of the "outside" pyrite. The original outside surface was bumpy, but we managed to smooth it out with sand paper. Notice the two major inclusions. A level view of the pyrite. The edges look pretty flat and parallel. Zoomed image of the surface. It doesn’t look so smooth now, does it?

Text and caption credit: Yao Jiang. Image credit: Yao Jiang and Tiffany Loi.

A few words about last week’s image of the week. It was a staple.

SEM image of the week: Tax day approaches

Posted on Monday, April 16, 2012 by for SEM.

Reminder: Tuesday, April 17, 2012 is the deadline for filing federal and state tax returns in the US for income earned in 2011. This week’s scanning electron microscope images have a connection to taxes (and tests and other equally fun things).

I am usually made from zinc-plated steel. I come in bunches held together with glue.
I am used to fasten things together.
?
What am I?

Image and caption credit: Mahmud Ashik

SEM image of the week: The razor’s edge

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

How sharp is that blade? The blades from two old utility knives and one new one were placed in the scanning electron microscope (sem/2012). The two that were used had plenty of pits and valleys and jagged edges. The oldest one was folded over like it was made of softened butter. Even the newest blade wasn’t completely sharp. It had a few dents and some jagged edges. The blades seemed pretty clean in the palm of my hand, but under the sem/2012 they were filthy. One blade even seemed to have something living on it!

New blade New blade Lightly used blade
Heavily used blade Top: new; Middle: lightly used; Bottom: heavily used Heavily used blade
Jagged edge Something living? Deeply damaged

Image and text credit: Onycha Banton

SEM image of the week: Have a nice day

Posted on Monday, March 26, 2012 by for SEM.

Sitting in class I often wondered what the scribbles I drew on my paper actually looked like on a microscopic level because what we our eyes see is limited. Using the SEM I was able to get a closer look.

Under the microscope 3 pieces of paper were placed, each had a drawing of a
smiley face written by various writing utensils. In this case, it was a pencil, ball point pen, and a gel ink pen. The results were interesting in that the image of the smiley face drawn with the pencil was the lightest whereas the one drawn with the gel ink pen was the boldest.

The composition of the pen may have had an influence on the results considering that pencils are made of graphite, ball point pens contain a viscous oil based ink and the ink in gel pens is composed of a less viscous water based liquid. Out of the three, the gel pen was the least viscous and therefore it was it was better absorbed by the paper and was the most visible under the microscope. The difference between the three writing utensils is pretty evident in the images captured by the SEM.

NYCBOE pencil Ballpoint pen Gel ink pen The three writing
instruments together

Image and text credit: Ramsha Farooq

SEM image of the week: Ants in my plants

Posted on Monday, March 19, 2012 by for SEM.

Spring has sprung in Flatbush, which means insects of all sorts are emerging from the ground looking for things to eat and places to live. Two weeks ago, a group of ants managed to squeeze their way into the Research Room. They seemed especially fond of the water in the saucers under our potted plants. I managed to capture one of these intruders using a piece of double-sided graphite tape.

Good conductivity means low static charge build up. The software running the SEM directs a scanning electron beam to specified positions on the sample at specified times and reads the intensity of the scattered electrons. Static charges deflect the scanning beam (since like charges repel). When the scanning beam is pointed at the wrong place at the wrong time, the resulting image is distorted.

Today’s subject made good, full body contact with the graphite tape. Its small size meant every part of it was close to something conducting. Charge had a hard time collecting on our small friend here, which resulted in nearly distortion free images even at high magnification. Small is better.

Overview of the whole ant showing the main features of insects: three main body segments (head, thorax, abdomen), six legs, two antennae, and two compound eyes. Close up of the thorax, which looks like it could use some grooming.
Close up of the right antenna draped over the right compound eye. The jointed insertion of the right antenna into the head.
The tip of the right antenna. The irregular disk on the second segment from the end is probably a pollen grain. The left antenna draped over the left front leg. The horizontal line in the middle of the image marks the edge of the graphite conducting tape used to fix the specimen in place and ensure good conductivity.

Image credit: Glenn Elert

SEM image of the week: AFM probe tips

Posted on Monday, March 12, 2012 by for SEM.

Probe tips are used in the Atomic Force Microscope (AFM) to detect the surface topography of small objects. A probe is made up of three parts. The substrate is the base of the probe and is the most visible part. The cantilever is the bridge connecting the substrate to the tip. The cantilever controls the tapping frequency of the tip and is barely visible. The tip is the part of the probe that makes contact with the surface and is not visible to the naked eye. A laser shines on the tip, it reflects onto a mirror and then onto a sensor. Finally we get the results of the object’s surface depth, and smoothness.

Probe tips are generally made out of silicon nitride, gold, or platinum. In order to use the probes in the Atomic Force Microscope, the probe must first be inserted into a holder with tweezers. Then the holder is then inserted into the microscope. Probe tips are sensitive and delicate. If a probe tip drops on the floor (or any surface, for that matter) the tip will break. When the tip is broken, it cannot scan the surface of an object. It is almost impossible to insert the probe into the holder without dropping it unless a person has practiced for hours. Dropping a probe automatically means breaking the tip and wasting $50 to $1000.

About five months ago I and my friends Kate Wong, Tiffany Loi, and Winnie Li practiced installing probes in holders. Now that we have to start our own projects, we have to install probes once again. Without practice in five months and without an empty holder to practice with, someone had to take the chance to install the probe. I took the chance, and failed horribly. Afterwards, we had to go apologize to our professor Dr. Nakarmi. When we looked up the cost of the probe I broke … well, let’s just say the number wasn’t pretty.

The SEM images below show three probes with broken cantilevers and tips. We didn’t break all of them. Two of the tips were broken by other people working in the lab.

One of the broken probes. This side faces the sample being investigated. The probe tip would normally project 0.1 mm out to the left. The numbers inscribed on this one are too small to be visible. Magnification of the previous image showing the crevice where the cantilever attaches to the probe mount. The back of the first probe. This side is fixed to the microscope. The sample moves under the the cantilever in two dimensions to create an image of the surface.
A broken gold probe. This one does not seem to have a crevice where the cantilever once was. The back of the second probe. The last of the broken probes. The edges are chipped away due to practice using tweezers. The chipped edges are not visible in its true size.
The back of the third probe showing the alignment grooves. Close up of the alignment grooves. Because of an optical illusion, the grooves look more like projections. A mysterious "black hole" on the back of the third probe which is not visible in its true size.

Image credit: Kate Wong, Tiffany Loi, Yao Jiang, and Winnie Li. Text credit: Yao Jiang (with help from Kate Wong).

Research Coordinator’s supplement …

AFM image of the surface of a DVD
An AFM image of the surface of a DVD made by Ken Han Chen and Chi Vein Cheng in January 2011.
This image was used to make one of the banners for the midwoodscience.org website.

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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