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Biophysics 3750 Due on April 21, 2017 Assignment 1 Calculating Magnifications using the Scale Bar
EXAMPLE of completed assignment, working with images found online
1 Beta cells in Islets of a developing pancreas 2 Scale bar width 25 μm
4 6300 μm = 252→
25 µm Image made using ↓ Fluorescence
Name: Doctor V. 3 Actual size: about 6.3 mm = 6300 μm 5 Pictures were magnified about 6.3
mm 250 times. 6 Brief description. Inside the Islets of Langerhans, inside the pancreas, are the beta cells that
release insulin into the bloodstream. Sometimes the number of beta cells can increase, as in cases of
obesity. Sometimes, as in Type I diabetes, these beta cells are attacked by the body’s own immune
system. In Type II diabetes other factors contribute to making the beta cells dysfunctional.
(↑Science still in progress) In this image, the aqua fluorescent PDX1 shows, on the left, many beta cells that are “progenitor cells,”
which are early descendants of stem cells. On the right, the pink Ki67 shows where cells are
somewhere in the cell-dividing process. (The blue DAPI just marks DNA in nuclei of cells in the background)
7 Image source: Raphael Scharffmann, XiangweiXiao, Harry Heimburger, Jacques Mallet, Phillippe Ravassard,
“Beta Cells within single human Islets Originate from Multiple Progenitors,” PLoS October 29, 2008
http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0003559 ►NOTE: I found this example by searching the internet for: “beta cells
and then clicking on Images Physics 3750. Dr. Villanueva 1 scale bar” Spring 2017 Another example of a completed assignment
Image made using Collagen Fibers in the alveoli of a lung 1 Electron Microscopy (Elastin fibers over here)
B 10 µm Name: Doctor V.
and on a smaller scale B C er Elastin in different µm
1010µm
Detail from Normal Human Lung
Parts of alveoli seen (darkly) from above 2 Scale bar says 10 μm
4 7000 μm
= 700
10 µm alveoli. This time
it’s after collagen &
cells were removed Collagen in alveoli after
elastin & cells were removed. 3 Actual size: about 7 mm = 7,000 μm Picture B was magnified 700 times. 5 6 Brief description. These photographs were made to help understand
Alveoli
the structure of the lung’s alveoli. Alveoli are the little sacs in the lungs
in whose walls red blood cells release CO2 molecules and pick up O2
To make image B, the scientists removed all the cells in the alveoli. They .
also removed the stretchable protein elastin, which is part of alveolar wall.
They did this by submerging the tissue in a lye bath (sodium hydroxide, NaOH).
Historically this has been used to remove hairs and elastin from animal
skins in order to make them into leather for drums, bags, shoes, etc.
This process of “controlled alkali digestion,” as the scientists call it,
O2: oxygen molecule
CO
leaves behind the collagen fibers. Better yet, it “preserves the collagen
2: carbon dioxide
frame-work in its natural location,” showing just where collagen fibers are
↓ Leather shoe: cow skin, with
cells & elastin removed,
in the actual alveolar structures.
(The other pictures are just for the sake of comparison. The 3rd one, C, shows
the result of placing lung tissue in an acid bath. This time, it was the cells &
collagen that were removed, and the elastin that remained—lots of elastin.) 7 collagen left over.
Cow skin, like human
skin, has more
collagen than alveoli do Source Finlay et al, “Elastin and Collagen Remodeling in Emphysema” American J.Pathology 1996
First two images from Figure 2, view from ducts. Last figure, elastin, from Figure 1, lower magnification ►NOTE: I found this study by searching for “ALVEOLI ELASTIN SCALE BAR.” Source of shoe: Victoria & Albert Museum, UK. Shoe is probably pure leather, except for a few nails, etc. Physics 3750. Dr. Villanueva 2 Spring 2017 Assignment #1, in detail
A. Search the internet for examples of magnified objects with scale bars
. Choose an object that interests you.
Suggestions for places to look are on pages 4 and 5.
Go to Blackboard and see if anyone else has chosen the object first. If not
you may “claim” it for your project. List your name, or initials, plus the object. ↑ 100 μm
Trichome from rockcress 0.5 mm B. Post the completed assignment on the Discussion Board.
1) Give us a title for the object you chose and your name and how the pictures was made
(with a light microscope? or electron microscope? or with fluorescence?) 2) What is the microscopic width of the scale bar in the picture?
That should be the number above or near the scale bar→
or mentioned in the caption beneath the picture (usually called Fig.1, 2 …etc.) 3) What is the actual width of the bar on the page? You can determine this by printing out
the picture and measuring it with a ruler, or by using the method discussed on page 4.
4) Set up the calculation:
Divide actual size of bar on the page by the size that scale bar is said to be (the smaller size)
5) What is the result of calculation? (How much was object magnified to make it the size that we see?)
6) Give a brief description (100 words or so) of what we see in the picture
(for example: define terms, give background, or basic principles) 7) Give us the source of the image of the object. Another Example of a magnification calculations
This is a cross-section of a Marsupial brain. Image made using a light microscope
2) Original scale bar 736 micrometers
3) Scale bar that I made: 8.0 mm = 8000 µm Here’s a slice of
brain from a
small marsupial,
a sort of
opossum-mouse One of many opossum
brain cross-sections Source: BrainMaps.org 4) Calculations
8000 microns / 736 microns = 10.87
5) Brain cross-section was magnified about 11 times,
Source:
http://www.brainmaps.org/ An online brain atlas, covering a variety of animals
Source of top image, fluorescent Red Sea hydroids, living on sea snails, under UV light: VN Ivanenko . Phys.org Physics 3750. Dr. Villanueva 3 Spring 2017 In case you’re not familiar with measuring techniques, here are two ways to do it Measuring
the scale bar LEAN mouse OBESE mouse Blue arrow▼ points to lots of macrophages (α) (β)
Source: Weisberg, Ferrante, JCI 2003 Two methods, .a & b.
In the obese mouse (β), there are
►
among the adipocytes (fat cells)
than in lean mouse (α) → more macrophages a 1. Find a picture that you like
and download a copy of it.
Then transfer the copied picture →
onto a document page. ↑ 40 µm, it says in source 2. Now insert a RECTANGLE onto the page. ▲
Make the rectangle the same width as the scale bar.
3. Then right-click on the rectangle. A set of options appears→
4. Click on Format AutoShape
or More Layout Options (it may depend on the computer)
5. A Format box appears.
On the band across the top, click on Size size .
6. A box appears showing the width of the rectangle
(which is the same width as the scale bar).
In this case it says 12 mm wide, or 1.2 cm. The scale bar says 40 µm.
But here it is 12 mm wide.
12 mm = 12,000 µm.
Divide by 40 µm.
Width ← 12 mm
b Picture must have been
magnified 300 times Or …
…or you could just print the picture, &
then measure the scale bar with a ruler 4 inches ≈ 10 cm Physics 3750. Dr. Villanueva ↑ 1 centimeter 4 1 Inch ↓ Spring 2017 Examples of Microscopic Objects that you might choose to look into Possible objects include:
Microscopic parts of the mammalian body
(cells or parts of cells or layers: arteries, axons, capillaries, collagen, filopodia,
mitochondria, neutrophil nets, lymphatic vessels, lysosomes, desmosomes,
parts of ears, eyes, rods, cones, skin, intestines, brain, spinal cord, liver, spleen, pancreas
parts of bones (osteons, osteoblasts, osteoclasts)
kidney tubules, or glomeruli, heart [capillaries, myocytes] etc, etc, etc. Microscopic parts from animals. Feathers, fur, fossils. Insects →
Fungi, slime molds or water molds, algae (diatoms, etc.) →→↓
Bacteria and Viruses and other Pathogens
Parts of flowers, leaves, plants, trees, seedlings, moss.
Refuse (paper, decaying weeds …) Curculio ↑
(weevil) ←Navicula
(diatom) You might tell the search engine, for example, “filopodia, scale bar” and maybe “electron”
or “fluorescence,” depending on what sort of picture you want Sites you may wish to consult: A guide to histology websites: http://www.siumed.edu/anatomy/histolinks.htm
One beautiful site: The Micropolitan Museum.
http://www.microscopyuk.org.uk/micropolitan/index.html http://www.ou.edu/research/electron/www-vl/image.shtml
Problem: often there are no scale bars A source of light-microscope images that I like is Kansas University Medical School.
There’s a part called JayDoc’s Histoweb.
http://www.kumc.edu/instruction/medicine/anatomy/histoweb/nervous/nervous.htm Filopodia (part of angiogenesis) ↑ UCSF . Physics 3750. Dr. Villanueva 5 Spring 2017 ELECTRON OR FLUORESCENCE MICROSCOPY
Another way to find microscopic pictures is to just google the words “fluorescence gallery”
or SEM gallery or TEM gallery (One difficulty is that there are people named Tem who
have put up galleries of images that have nothing to do with microscopy.)
SEM & TEM are both kinds of electron microscopes; SEM images, seen below, are more “3-D” (Another difficulty: many of the images do not have scale bars)
Here are some examples:
http://www.itg.uiuc.edu/exhibits/gallery/pages/image-18.htm
http://www.mnh.si.edu/highlight/sem/dinoflagellates.html http://adrianchek.blogspot.com/2009/02/sem-of-filter-paperdegradation.html Dartmouth Electron Microscope Facility
http://www.dartmouth.edu/~emlab/gallery/ . (It’s true that many of these images don’t have scale bars, but many do) ← ~50 μm Tomato leaves ←5 μm Cilia in trachea of lungs Physics 3750. Dr. Villanueva 6 Spring 2017