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Chromatography of Spinach

Jan Baptista van HelmontFor many centuries, people believed that the increase in the size of a plant was caused by the intake of material from the soil. It was not until a Belgian physician, Jan Baptista van Helmont (circa 1577-1644), performed an experiment that demonstrated conclusively what we accept today: the increase in the size of a plant is not due simply to the plant obtaining a mystery substance from the soil; plants gain what they require through the process of photosynthesis.

Photosynthesis uses energy from light captured by photosynthetic pigments, and splits water molecules in the process. The plants fix carbon from carbon dioxide into glucose and fructose chains and oxygen is released as a byproduct. In many plants the sugars then combine to form long chains known as starches. Many plants store their photosynthetic products this way. Continue reading ‘Chromatography of Spinach’

Slide Stain Guide

This overview of slide staining originally appeared on wardsci.com.

The exact chemistry involved in most staining procedures is unknown. There is probably more than one type of chemical interaction occurring during any staining procedure. Interactions can be electrostatic, covalent, or based on physical properties that affect stain penetration, including texture, density and solubility.

One prevalent mechanism is thought to be the electrostatic interaction of the chromogen with tissue molecules leading to the classification of many stains as acidophilic or basophilic. Basic dyes color acidic molecules - for example, hematoxylin, stains DNA (an acid) dark blue. Acid dyes color more basic molecules - for example, eosin, makes most cytoplasms red/pink. Continue reading ‘Slide Stain Guide’

Slide Preparations

This overview of slide preparations originally appeared on wardsci.com.

Choosing the Type of Preparation

Even if you know what type of specimen you would like to examine, there are a variety of ways to prepare the specimen for the finished microscope slide. Our catalog describes specimen preparation in the following general categories:

  • Wholemount - An entire specimen, such as an insect, is embedded in mounting resin directly on the slide and covered with a glass coverslip.
  • Smear or Drop - The specimen(s) are in suspension then dried directly onto the glass slide where they are fixed, stained, and mounted in resin under a coverslip. This preparation is usually used for bacteria culture preparations or blood cells.
  • Squash - The cell specimen is broken using pressure — usually used to release chromosomes from nuclei, then processed as a smear is.
  • Section - A thin piece of specimen is shaved from the whole specimen to permit light to reveal greater structural detail. Sections are usually between 10 and 100 microns thick, which is usually thicker than one cell diameter. Therefore, several layers of cells may be present in the section.
  • Thin section - In this case, sections are on the order of 1 micron thick, which is usually less than one cell diameter. Therefore, subcellular structures are more easily discerned than in thicker sections.

Types of Sections - Orientation

What is seen in a tissue section is often greatly dependent upon the plane of section or the direction the slice was made in. The most basic sections are cross section and longitudinal section. If you picture an object that is longer than it is wide, like a tree trunk, a cross section takes a section perpendicular to the long axis resulting in a slice that is relatively small and round. A longitudinal section would be parallel to the long axis and look like a long rectangle or oval. If that section was through the middle, such that you had a thin layer of bark visible on two opposite sides of the section, that would be a medial longitudinal section. If the sections were very close the edge of the tree trunk, the rectangle would have mostly bark and would be considered more tangential longitudinal sections.

Typical Section Preparation

The steps in making a section preparation are as follows:

  1. Collection and/or dissection of the specimen into a piece that will fit on a glass slide.
  2. Fixation: This step preserves the structure of the material, often by denaturing proteins. Formaldehyde is a common fixative that causes covalent cross-linkages to be added between proteins.
  3. Embedding: This step allows a supportive substance to infiltrate a specimen followed by hardening. Paraffin (wax) is commonly used to fill in spaces in tissue while it is in the liquid state (warm), then the entire block solidifies at room temperature. This permits the original shape of the specimen to be maintained through subsequent processing. Plastic is often substituted for paraffin.
  4. Sectioning: The supported specimen is cut into thin slices. This is usually done on a sharp metal blade mounted in a microtome to ensure that sections are of a known and constant thickness, usually around 25 microns.
  5. Affixing: The section is flattened onto a glass slide to permit it to adhere to the glass. This often requires a type of ?glue? to keep the section on the glass through further processing. Glass is used in making permanent slides for a variety of reasons. These include the fact that glass resists scratching, it can be cleaned better than plastic, and the optical properties of glass allow for better resolution than plastic.
  6. Staining: The slide with the affixed section is placed in an appropriate stain that will result in visual contrast between structures in the finished slide (see staining page). This step is often preceded by removal of wax from the slide and specimen.
  7. Dehydration: Water is removed from the tissue by repeated bathing in ethanol and other solvents. This makes the specimen more transparent so it can be viewed with greater clarity.
  8. Coverslipping: A mounting medium with optical properties similar to glass is used to permanently embed the specimen in resin and to permanently adhere the glass coverslip.

Different types of specimen preparations use a subset of the above steps, often in a different order, to make the finished slide.

Related Articles: Also see our Slide Stain Guide.

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ABO and Rh Blood Typing

This year marks the 15th Anniversary of WARD’S Simulated Blood, a completely safe product that looks and acts like real blood, that can be safely used by students to look at all four types of human blood. To help celebrate this amazing product, we would like to share so of the history of the study of blood and blood typing.

Around 1900, Karl Landsteiner discovered that there are at least four different kinds of human blood, determined by the presence or absence of specific agglutinogens (antigens) on the surface of red blood cells (erythrocytes). These antigens have been designated as A and B. Antibodies against antigens A or B begin to build up in the blood plasma shortly after birth, the levels peak at about eight to ten years of age, and the antibodies remain, in declining amounts, throughout the rest of a person’s of life.

The stimulus for antibody production is not clear; however, it has been proposed that antibody production is initiated by minute amounts of A and B antigens that may enter the body through food, bacteria, or other means. Humans normally produce antibodies against those antigens that are not on their erythrocytes: A person with A antigens has anti-B antibodies; a person with B antigens has anti-A antibodies; a person with neither A nor B antigens has both anti-A and anti-B antibodies; and a person with both A and B antigens has neither anti-A nor anti-B antibodies (Figure 1). Blood type is based on the antigens, not the antibodies, a person possesses.

The four blood groups are types A, B, AB, and O. Blood type O, characterized by the absence of A and B agglutinogens, is the most common in the United States and is found in 45% of the population. Type A is next in frequency, and is found in 39% of the population. The frequencies at which types B and AB occur are 12% and 4% respectively.

Figure 1 - ABO System

Process of Agglutination

There is a simple test performed with antisera containing high levels of anti-A and anti-B agglutinins to determine blood type. Several drops of each kind of antiserum are added to separate samples of blood. If agglutination (clumping) occurs only in the suspension to which the anti-A serum was added, the blood type is A. If agglutination occurs only in the anti-B mixture, the blood type is B. Agglutination in both samples indicates that the blood type is AB. The absence of agglutination in any sample indicates that the blood type is O.

Figure 2 - Agglutination Reaction of ABO Blood-Typing Sera

Importance of Blood Typing

As noted in the table above, people can receive transfusions of only certain blood types, depending on the type of blood they have. If incompatible blood types are mixed, erythrocyte destruction, agglutination and other problems can occur. For instance, if a person with type B blood is transfused with blood type A, the recipient’s anti-A antibodies will attack the incoming type A erythrocytes. The type A erythrocytes will be agglutinated, and hemoglobin will be released into the plasma. In addition, incoming anti-B antibodies of the type A blood may also attack the type B erythrocytes of the recipient, with similar results. This problem may not be serious, unless a large amount of blood is transfused.

The ABO blood groups and other inherited antigen characteristics of red blood cells are often used in medico-legal situations involving identification of disputed paternity. A comparison of the blood groups of mother, child, and alleged father may exclude the man as a possible parent. Blood typing cannot prove that an individual is the father of a child; it merely indicates whether or not he possibly could be. For example, a child with a blood type of AB, whose mother is type A, could not have a man whose blood type is O as a father.

DID YOU KNOW? Donor blood contains only packed red blood cells. There is no plasma in donor blood, thus there are no antibodies present.

DID YOU KNOW? Camels and their relatives are the only mammals having oval red blood cells.

The Genetics of Blood Types

The human blood types (A, B, AB, and O) are inherited by multiple alleles, which occurs when three or more genes occupy a single locus on a chromosome. Gene IA codes for the synthesis of antigen (agglutinogen) A, gene IB codes for the production of antigen B on the red blood cells, and gene i does not produce any antigens. The phenotypes listed in the table below are produced by the combinations of the three different alleles: IA, IB, and i. When genes IB and IA are present in an individual, both are fully expressed. Both IA and IB are dominant over i so the genotype of an individual with blood type O must be ii (Figure 3).

Phenotype Possible Genotypes
A IAIA IAi
B IBIB IBi
AB IAIB
O ii

Use IA for antigen A, IB for antigen B, and i for no antigens present.
Genes IA and IB are dominant over i.
AB blood type results when both genes IA and IB are present.

Rh System

In the period between 1900 and 1940, a great deal of research was done to discover the presence of other antigens in human red blood cells. In 1940, Landsteiner and Wiener reported that rabbit sera containing antibodies for the red blood cells of the Rhesus monkey would agglutinate the red blood cells of 5% of Caucasians. These antigens, six in all, were designated as the Rh (Rhesus) factor, and they were given the letters C, c, D, d, E, and e by Fischer and Race. Of these six antigens, the D factor is found in 85% of Caucasians, 94% of African Americans, and 99% of Asians. An individual who possesses these antigens is designated Rh+; an individual who lacks them is designated Rh-.

The genetics of the Rh blood group system is complicated by the fact that more than one antigen can be identified by the presence of a given Rh gene. Initially, the Rh phenotype was thought to be determined by a single pair of alleles. However, there are at least eight alleles for the Rh factor. To simplify matters, consider one allele: Rh+ is dominant over Rh-; therefore, a person with an Rh+/Rh- or Rh+/Rh+ genotype has Rh+ blood.

The anti-Rh antibodies of the system are not normally present in the plasma, but anti-Rh antibodies can be produced upon exposure and sensitization to Rh antigens. Sensitization can occur when Rh+ blood is transfused into an Rh- recipient, or when an Rh- mother carries a fetus who is Rh+. In the latter case, some of the fetal Rh antigens may enter the mother’s circulation and sensitize her so that she begins to produce anti-Rh antibodies against the fetal antigens. In most cases, sensitization to the Rh antigens takes place toward the end of pregnancy, but because it takes some time to build up the anti-Rh antibodies, the first Rh+ child carried by a previously unsensitized mother is usually unaffected. However, if an Rh- mother, or a mother previously sensitized by a blood transfusion or a previous Rh+ pregnancy, carries an Rh+ fetus, maternal anti-Rh antibodies may enter the fetus’ circulation, causing the agglutination and hemolysis of fetal erythrocytes and resulting in a condition known as erythroblastosis fetalis (hemolytic disease of the newborn). To treat an infant in a severe case, the infant’s Rh+ blood is removed and replaced with Rh- blood from an unsensitized donor to reduce the level of anti-Rh antibodies.

Blood Components

The formed elements in blood include erythrocytes, or red blood cells (RBCs); various types of leukocytes, or white blood cells (WBCs); and platelets.

Erythrocytes are circular, biconcave disks of 5 to 8 micrometers. Their chief function is to transport oxygen (O2) and carbon dioxide (CO2). The transport of O2 and CO2 depends largely on the hemoglobin present in the erythrocytes. The biconcave shape is also related to the erythrocytes function of transporting gases, in that it provides an increased surface area through which gases can diffuse.

The number of circulating RBCs is closely related to the blood’s oxy-gen-carrying capacity. Any changes in the RBC count may be significant. RBC counts are routinely made to diagnose and evaluate the course of various diseases.

Leukocytes range in size from approximately 9 to 25 micrometers and function primarily to control various disease conditions. Leukocytes can move against the current of the bloodstream through amoeboid movement, and pass through the blood vessel walls to enter the tissues. The total WBC count normally varies from 5,000 to 10,000/mm3. Certain infectious diseases are accompanied by an increase in WBCs. If the number exceeds 10,000/mm3, the person has an acute infection. If it drops below 5,000/mm3, the person may have a condition such as measles or chicken pox. The percentage of the different types of leukocytes present in the blood may also change in particular diseases, this number is important for diagnostic purposes and is called a differential count.

DID YOU KNOW? Rh is so named because the initial study was done with Rhesus monkey.
DID YOU KNOW? Leukocytes are capable of amoeboid movement and are sometimes called amoebocytes.

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WARD’s Simulated ABO and Rh Blood Typing Lab Activity
Examine the Risk of Rh Incompatibilities
Simulated ABO and Rh Blood Typing LabAnother WARD’S safety and innovation exclusive! In addition to all the blood typing exercises your students can perform with our ABO Activity, now they can go even further as they explore Rh typing as well. Using four different samples of WARD’S Simulated Blood, the class will determine each unknown sample’s blood type and Rh factor, examine the risk of Rh incompatibilities, and view red and white “blood cells” under the microscope in complete safety. It includes four simulated blood types (A, B, AB, O), two anti-sera (A, B), Rh anti-sera, a teacher’s guide, and student copymaster. Enough materials for twelve lab groups are included.

Immune Response: Antigen/Antibody Reactions Lab Activity
Explore the Importance of Blood Antigens During Pregnancy
Antigen Antibody Reaction LabDetermine which of four possible donors could safely give blood to a patient, then develop a case history of a mother and her children to determine the safety of her pregnancy, all using WARD’S Simulated Blood. In the process, students learn to identify antigen/antibody reactions, and how those reactions affect the body’s immune response, as well as the basics of ABO and Rh blood typing. The kit contains enough materials for 12 setups, a teacher’s guide, and student copymaster.

Blood Typing Demonstration Model
Blood Typing Demo ModelRe-create the Antigen-Antibody Interactions Occurring on the Surface of Red Blood Cells
Provide a visual interpretation of a concept often difficult for students to understand. Using the model, you can demonstrate the antigen-antibody reactions that occur at the molecular level, including blood typing reactions, successful and unsuccessful blood transfusion reactions, and Rh incompatibility. The class-size model kit contains 12 erythrocytes, and six pairs each of A, B, and Rh antibodies and antigens. The demonstration size model kit contains two erythrocytes, and one pair each of A, B, and Rh antigens and antibodies.

Testing Familial Relationships Using Simulated Blood Lab Activity
Testing Familial Relationships LabTrace Blood Type Patterns Through Parents and Children
How would parents find out if their babies had been mixed up in a hospital maternity ward? That’s the scenario presented by this safe, interesting investigation. Using WARD’S Simulated Blood, students determine the blood types of two sets of parents and two children to find out which baby belongs to which family. The kit includes enough materials for six setups, a teacher’s guide, and student copymaster.

More simulated blood activities, supplies and equipment at Wardsci.com

PCR and Thermocycler Basics

Introduction to PCR

Polymerase chain reaction, or PCR, is a tool used in many biotechnology applications that makes it possible to study small, specific fragments of DNA information at the gene level. The primary activity during PCR is the copying and recopying of a short DNA sequence to create millions of identical DNA fragments. The DNA fragments can then be further characterized and/or checked for purity by running them in an agarose or polyacrylamide gel system. In some cases a southern blot is subsequently performed as well. In short, PCR is DNA synthesis in a tube.

Applications for PCR

PCR is routinely used in a variety of laboratories in both the public and private sectors. Some common applications of PCR include:

  • Medical diagnostics
  • Gene / protein studies
  • Therapeutic drug design
  • Paternity / maternity identification
  • Forensics
  • Missing persons
  • Evolutionary studies
  • Endangered species identification and protection

Step by Step PCR and Common PCR Reagents

While the optimal PCR protocol may be different for various DNA fragments based on the size and deoxynucleotide composition of the selected fragment, the theory and sequence behind PCR reactions does not change. Below you will find a brief description of the various protocol steps and common reagents that are necessary for PCR to effectively produce DNA replicates.

Step by Step PCR

  1. DNA fragment of choice is placed in a tube with the reagents necessary to perform PCR.
  2. A short segment of DNA is unzipped (denatured) by breaking the H bonds with extreme heat (approximately 95ºC), creating two DNA templates.
  3. One end of each DNA template is recognized by forward and reverse primers and the primers are annealed to the DNA by lowering the temperature (35ºC - 65ºC).
  4. DNA polymerase molecules create copies of each template starting at the end of each primer, producing two new fragments called extensions. This is performed at approximately 72ºC.
  5. The replication process (step 2) is repeated 25 – 35 times for each newly synthesized fragment, causing the number of identical fragments to increase exponentially with each cycle.
  6. One double stranded fragment of DNA that undergoes 35 cycles of PCR results in over 34 billion (235) fragments in approximately 3 hours!

Example of a PCR Protocol

Temperature Time Action
95ºC 10 minutes DNA Taq polymerase activation
35 cycles of:
95ºC
54ºC
72ºC
1 minute
1 minute
1 minute
DNA denaturization
Primer annealing
Extension creation
72ºC
4ºC
10 minutes Final extension created
Hold / storage temperature

Common reagents used for PCR reactions

All PCR protocols need the same basic reagents to drive each step of the PCR cycle. Specialized formulations can be obtained from many sources for specific, advanced research needs and optimization. Click on the reagents below for ordering information through WARD’S.

  • Taq polymerase – special DNA polymerase (enzyme) that is able to remain active at high temperatures.
  • dNTPs – The 4 deoxynucleotides that make up DNA (A, C, T, G).
  • Magnesium Chloride (MgCl2) – enzyme cofactor needed for polymerase activity.
  • PCR Master Mix – premixed solution of Taq polymerase, dNTPs and magnesium chloride at optimal concentrations.

Optimizing PCR Protocols

Various fragments or sequences of DNA have different physical and chemical characteristics that can affect the rates and effectiveness of the activities that take place during PCR. Determining the most appropriate PCR conditions for a particular fragment of DNA may include optimizing the following:

  • Temperature and time to activate Taq polymerase
  • Temperature and time to allow primer annealing
  • Temperature and time for replication
  • Concentration of reagents, especially primers, dNTPs, and MgCl2)
  • Number of replication cycles

Processes and reagents used to extract DNA and purify DNA fragments may also contaminate the DNA sample and inhibit replication. Some common replication inhibitors include:

  • DNase
  • RNase
  • EDTA
  • Alcohol
  • DNA fragments from previous experiments

Using Thermocyclers for PCR

Simply stated a thermocycler is a heating block that is regulated by a computer. Thermocyclers allow the scientist or technician to “walk away” as the PCR cycles are performed as well as maintain tight control over the temperatures needed to complete the PCR.

In the classroom the use of a thermocycler allows students to gain the valuable experience of running a PCR reaction with a piece of equipment that is used daily throughout biotech and pharmaceutical research facilities. It also frees up time for other activities since thermocyclers are programmable and can even be set to maintain a “storage” temperature for several hours.

Shopping for Thermocyclers

There are many models of thermocylers available from several manufacturers, and choosing the right model for your educational needs may seem like a bit intimidating.

Some of the feature that should be considered when comparing models includes:

  • Storage capacity for preprogrammed cycles
  • Communication / connectivity options for personal computers and networks
  • Maximum number of samples that can be run per activity
  • Maximum number of PCR protocols that can be run at once (gradient feature)
  • Temperature range
  • Ramp rate (rate of temperature change)
  • Weight and dimensions
  • Warranty
  • Heated or unheated lid
  • Screen display characteristics

Ward’s Natural Science Featured Thermocyclers

EdvoCycler by Edvotek
EdvoCyclerThe all-new EdvoCycler brings affordable PCR to the classroom without compromise. The 0.2 ml tube block has room for up to 25 students’ samples and comes pre-programmed with EDVOTEK PCR protocols. These programs may be modified or deleted, and there is extra memory for more. The vivid 7 line LCD displays all program parameters simultaneously without any scrolling. A heated oil-free lid makes operation a snap. Proudly made in the USA and backed by a 2-year warranty!

EdvoCycler Features:

  • 25 x 0.2 ml Tube Block
  • Heated Oil-Free Lid
  • Vivid 7 Line LCD Display
  • Pre-Programmed, Changeable PCR Protocols
  • Temperature Range: 10°C–99°C
  • Maximum Ramp Rate: 2°C/sec
  • Weight & Dimensions: 11 lbs. & 16″ x 8.5″ x 7″
  • 2 Year Warranty
  • Made in USA

Teche Endurance TC-312 by Techne
TC312With its user-friendly programming, heated lid, easy-to-read LCD, and low price, this compact, remarkably fast thermal cycler is ideal for school labs, but is reliable enough to stand up to the demands of a molecular scientist. It automatically provides ideal temperature conditions for PCR DNA amplification reactions. It also features memory that stores up to 80 programs, parallel printer port, and an RS232 port to print profile information that was programmed for the run. You can also program this cycler with PCR analysis software that you can download from the manufacturer’s web site.

Teche TC-312 Features:

  • 25 x 0.2 ml Tube Block
  • Heated Oil-Free Lid
  • Easy to Read LCD Display
  • Temperature Range: 4°C–99°C
  • Maximum Ramp Rate: 2.0°C/sec
  • Dimensions: 13″ x 6.75″ x 7.5″
  • 80 Program Storage Capacity
  • 4 Year, 80,000 Cycle Warranty

MultiGene II by Geneq
Multigene IIFeaturing a heated lid for oil-free cycling, this fast, uniform cycling unit offers user friendly operation. Heating and cooling are accomplished electronically by Peltier units. The unit itself is programmed to control the heating and cooling with an algorithm that accurately simulates sample temperature. Programs can be run immediately upon entering, or up to 99 programs can be saved to the memory for later use. The built-in software also allows for successive time and temperature increments and decrements, end of cycling elongation steps, and extended period soaks at 4°C. The cycler can also be used for holding specific temperatures, allowing it to take the place of a traditional water bath, heat block or incubator. Includes a user’s manual.

MultiGene II Features:

  • 25 x 0.2 ml Tube Block
  • Heated Oil-Free Lid
  • 40 character LCD Display
  • 99 Program Storage Capacity
  • Temperature Range: 4°C–99.9°C
  • Maximum Ramp Rate: 2.2°C/sec
  • Dimensions: 8.5″ x 11.25″ x 7.0″

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