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’

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Sediments and Sedimentary Rocks

Most of the Earth’s surface is covered by sediment or rocks formed from the accumulation of sediment. Sediments are the fragments of rock, mineral, and organic matter that have been broken down through the processes of physical and chemical weathering. Sediments are often transported and deposited by the actions of water, ice, and wind. As they accumulate in a depositional environment, sediments may be deeply buried, compacted, and cemented through a process known as lithification. The rocks formed by this process are called sedimentary rocks.

There are three major categories of sedimentary rocks. Clastic sedimentary rocks are formed from the eroded rock and mineral fragments of other rocks. Rocks of this variety are grouped primarily by the size of their particles—usually gravel, sand, silt, or clay. Common examples include sandstone, conglomerate, siltstone, and shale. Sediments that form these rocks are commonly derived from the weathering of igneous and metamorphic rocks exposed at the Earth’s surface. By analyzing the size, shape, and composition of the mineral grains in each rock, geologists can gain valuable clues about the method of sediment transport and dispersal, as well as the probable source rock for the sediments. For example, source areas where basaltic rocks are dominant will produce sediments that are high in olivine, calcic-plagioclase, and augite. Areas where granitic rocks predominate will produce sediments high in quartz, potassium feldspar, and biotite. However, the degree of weathering that takes place before transport can alter the mineralogy of the deposited sediments.

Chemical sedimentary rocks represent another important category. These rocks are formed when mineral grains are precipitated out of solution through evaporation or other chemical activity. Included in this group are evaporites, like halite and gypsum, and carbonates, like limestone and dolostone. A third category, organic sedimentary rocks, is formed from the accumulated organic remains of plants and animals. Examples in this group include coal, chert, and most limestones. In reality, many sedimentary rocks are gradational types or include varieties that may logically be placed in more than one category.

The process of sedimentation is one that we can observe happening on our planet’s surface today. When sediments are deposited over time, they form layers. These layers continue to build as more and more sediment is transported and deposited. Once lithified, this layering of sediments is preserved in the sedimentary rocks now exposed at the Earth’s surface. We call these layers, beds or strata. Layering, or stratification, occurs when there is a change in the type of sediment being deposited. Fluctuations in sea level, periodic flooding, changes in river currents, or other factors may cause such a change.

Sedimentary Environments

Much of what we conclude about the nature of ancient environments is based on our observation of processes at work on our planet today. This concept, that the present is the key to the past, is one of the basic principles of geology. Originally proposed by James Hutton in the 18th century, the Principle of Uniformitarianism states that current earth processes, such as erosion and volcanism, are the same processes that were at work in the past. By understanding the geologic forces shaping our landscape and environments today, we can draw important conclusions about events and processes that may have taken place in the same way in the past.

Sedimentary rocks form in a wide variety of environments, most of which occupy lower portions of the landscape where sediments are transported from higher elevations. The two principal realms of sediment deposition are the sea (marine) and the land (terrestrial). Terrestrial sedimentary environments include glacial deposits, floodplains, lakebeds, deltas, and desert basins. Marine environments range from nearshore beach environments to deepwater offshore environments. Factors effecting the distribution of sediments in marine environments are the distance from land (source), water depth, chemical and physical properties of the water, and types of plant and animal life. One problem in determining depositional environments is that some rocks can be formed in more than one environment. For example, clastic rocks composed of silt and clay could indicate a river floodplain or an offshore marine deposit. Generally, geologists must examine many miles of a rock outcrop to better determine the exact nature of a sedimentary environment.

Clastic sediments represent the dominant component in many depositional settings. When the energy transporting sediments in streams and rivers is reduced, these materials are deposited in river channels, stream banks, lakes, deltas, and ocean basins in sequences dependent on the size and density of the particles. Generally, larger gravel and sand-sized sediments are deposited in stream channels and nearshore beach environments where energy is high, grading laterally into silts and clays on the floodplains or deeper offshore areas where conditions are less active.

One clastic rock, arkose, is extremely rich in feldspar, indicating rapid erosion close to the source rock. Arkose is usually associated with erosion from nearby continental uplift. Other clastic rocks, like sandstone, are made almost entirely of quartz and are compositionally and texturally more mature. This indicates the sediments composing the rock underwent a very long period of chemical weathering. Sandstones are usually associated with areas of low relief and warm humid climates, such as deltas. Mud rocks, such as siltstone and shale, are made of particles 1/16 mm or smaller. These small clay and silt-sized particles stay suspended in transporting waters until quieter conditions allow settling to occur. The depositional setting most commonly associated with shales is the deep sea floor, but they can also be found in well-sorted, layered lake deposits.

Carbonates are interbasinal rocks composed of calcium or magnesium carbonate. Carbonates, such as limestone, have a dull appearance and may contain an abundance of fossils. Calcite and aragonite are two important minerals in carbonate rock formation. Marine organisms, such as corals, molluscs, brachiopods, and echinoderms, secrete these mineral compounds. Since these organisms provide the main component for many carbonate rocks, there is little or no transport involved in their formation. While most limestones form as a result of these organic processes, a few varieties may be true chemical precipitates. Carbonate rocks generally form in warm, clear, shallow, marine seas like those found in the modern day environments along the Bahama Banks, Florida Keys, and the Great Barrier Reef in Australia.

Evaporites represent another type of chemically precipitated rock that forms from the evaporation of seawater. When the dissolved solids in seawater become saturated due to excessive evaporation, the ions precipitate out of solution to form a crystalline residue. Areas where these conditions can occur include intertidal zones or regions where the inflow of water may be restricted by reefs or other barriers. Evaporites are mono-minerallic and include rock salt (halite) and gypsum.

Another important sedimentary rock, coal, forms from compressed plant remains deposited in low oxygen swampy areas. As this plant material accumulates, it forms peat, a soft, brown organic deposit. Subsequent burial of these deposits by overlying sediments creates heat and pressure, which alters the peat to lignite. As the coal-forming process continues, the carbon content of lignite increases to form black bituminous coal, and ultimately anthracite coal.

While geologists often use rock type to help characterize ancient sedimentary environments, other clues can be found within the rocks themselves. Important sedimentary rock structures, such as ripple marks, mudcracks, and flute casts, also provide further indicators of the environmental conditions that existed during the time of lithification. Sedimentary rocks may also contain the preserved remains of organic life forms, or fossils. Fossils provide a unique glimpse into the ancient life of our planet and the environments they inhabited.

Principles of Stratigraphy and Correlation

The branch of geology that deals with the origin, composition, distribution, and succession of stratified rocks is called Stratigraphy. Stratigraphy often involves the study of strata relationships across time and space. Outcrops of strata, or stratigraphic columns, can be studied at different locations. Comparing these strata allows geologists to identify common occurrences in lithology over time and distance. Stratigraphic correlation is the study of the relationship of the rock units from different stratigraphic sections.

One of the first scientists to study stratified rock was Nicolaus Steno. In the seventeenth century, he formulated three key principles that remain the cornerstone of stratigraphic study today. These are:

• The Principle of Superposition
• The Principle of Original Horizontality
• The Principle of Lateral Continuity

The Principle of Superposition states that if a sequence of rocks has not been disturbed by either folding or faulting, the oldest layer will be at the bottom, and the youngest layer will be at the top. The Principle of Original Horizontality states that sediments accumulate parallel to the Earth’s surface on which they were deposited. The Principle of Lateral Continuity asserts that the strata will form laterally until there is a change in environment or a barrier that prevents dispersal of sediments to that area.

Guided by these principles, the information gathered by stratigraphers can be used for several purposes. Stratigraphic relationships can be correlated by identifying similarities in lithology and fossil content in rocks from several different localities. Relative time relationships can also be established by using stratigraphic data. With a basic knowledge of stratigraphy, we can both correlate rock sections and interpret clues to the sedimentary environments that existed at the time of rock formation. This can be accomplished by using anything from simple observations of rocks and fossils, to more complex analyses of chemical and seismic data.

Lithostratigraphy is the most basic type of correlation. This type of correlation can be used to determine the spatial similarities between rock units; however, by itself, it can never be used in determining time relationships. Lithostratigraphy uses both physical and chemical characteristics of the rocks for correlation purposes. Properties such as rock type and rock color can be used to determine the correlation of stratigraphic sections. Sedimentary structures, such as cross-bedding and erosional surfaces, are also used.

There are several ways that stratigraphy allows geologists to infer relative time relationships. Biostratigraphy uses fossils to correlate widely separated bodies of rock. Assemblages of rocks can be divided into zones according to the fossils preserved in them. Index fossils are important in correlation because they represent a specific period of the Earth’s past. In order to be classified as an index fossil, the organism must have been able to live in several different types of environments, be geologically widespread, be abundant during a specific time, and evolve quickly. Graptolites and conodonts are examples of typical index fossils.

Time parallel surfaces are considered isochronous, that is, laid down at the same time; and therefore, are important in determining relative time. Key or marker beds are time parallel surfaces that represent any widespread activity that took place in a geological instant. Volcanic events, which produce bentonites and other ash beds, are considered to be one type of a geological activity that effects a wide area in a short period of time. Glacial till deposits represent a time during which portions of the Earth were covered by glaciers. Since periods of glaciation were fairly short-lived in geologic terms, and deposits of glacial till are easy to recognize, these layers represent another excellent example of key beds.

Interpreting Environmental Change

If rock types are diagnostic of certain environmental conditions, then we would expect rock units to change as the environment changes. In fact, geologists can infer environmental changes of the past by examining the rock record in stratigraphic sections. For example, if a section of strata containing fossiliferous limestone is followed by an evaporite, like halite, we might infer that there was a reef environment in which the seawater later dried up. Likewise, if there was an outcrop of black shale followed by bituminous coal, a swamp-like setting could be inferred.

We know from the principle of lateral continuity that a rock type will extend laterally unless there is a cutoff in the supply of sediment, or there is a change in environmental conditions. Therefore, a rock type can extend laterally for great distances. However, the layer may eventually pinch out and grade into another rock type. The lateral variation in sedimentary rock units caused by changes in the depositional environment is called a facies change. Facies is a term used to describe the sum of all primary characteristics of a sedimentary rock from which its origin and environment can be inferred. Facies change as environments change. For example, nearshore facies (coarse sandstone) change into offshore facies (shale) as we move farther away from land and the source of sediment.

Facies can also provide information on changes in sea level over time. For example, as the shoreline retreats toward the land due to a rise in sea level, the marine offshore facies move toward the nearshore facies. This particular shift in facies is known as transgression, and may be evidence of events such as subsidence or flooding. When the stratigraphic record shows evidence of a shoreline moving away from the land, it is called regression. Regression occurs when there is excess sediment supply from the land which causes the shoreline to move seaward. Regression is usually associated with times of tectonic uplift.

Download the PDF of this intro and a corresponding activity outline from Wardsci.com.

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Exploring Depositional Environments and Stratigraphic Correlation Lab Activity
The corresponding activity for the above introduction.
The best way to learn about how sedimentary rocks forms is by studying the rocks themselves. In our introductory lab activity, we provide samples of different types of sedimentary rocks for students to analyze. In addition, they study and analyze stratigraphic data, both real and simulated, to draw conclusions on why the sedimentary rocks formed a certain way and why they changed over time. You will get five sets of sedimentary rock samples, one stratigraphy demonstration model, colored gravel, a marker, a teacher’s guide, and student copymasters.

Sedimentary Rock Collection
Wide Range of Depositional Environments and Rock Textures
Use this set as a basic introduction to rocks formed from organic material or fragments of other rocks. The set is housed in a compartmented collection box and comes with an identification list.

Contents: 12 numbered samples; Rocks: chert, conglomerate, coquina, gypsum, limestone (2), sandstone (2), shale (2), siltstone, travertine.

Sedimentary Rocks Activity Set
Indicative of Various Sedimentary Formation Processes
When students study the well-defined samples of sedimentary rocks in our GEO-logic set, they will begin to understand the processes by which sedimentary rocks were formed. A teacher’s guide and student copymasters are included for the following activities: categorizing sedimentary rocks by origin, settling and layering, and sediment transport using a stream table. The set is housed in a compartmented collection box.

Contents: 12 numbered samples (breccia, chert, coal (bituminous), conglomerate, coquina, dolostone, gypsum, limestone, sandstone, shale, siltstone, travertine); magnifier; dilute HCl (bottle).

Exploring Deposition of Sediments Lab Activity
Study Sediment Deposition, Transport, and Distribution
Students can see how particle size, shape, and density affect the settling rate of various materials by testing how quickly they settle in the specially constructed four-foot-long sedimentation tube. Through observation, and recording and graphing the settling rates, students compare the results and draw conclusions about sediment deposition in nature. It comes with a teacher’s guide and student copymasters.

Weathering, Erosion, and Deposition Lab Activity
Students perform activities that demonstrate different types of physical and chemical weathering. Once they have a good understanding of weathering, they set up an experiment that ties it all together by comparing the impact of weathering and erosion on limestone, sandstone, and shale. In a final activity, students observe deposition while creating their own stalactites and stalagmites. Developed by Deb Hemler and Michelle Adams, the activity includes enough materials for three setups and a teacher’s guide.

Also:

• More Geological Processes Lab Activities
• More Mineral and Rock Lab Activities
• Individual Sedimentary Rock Specimens

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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

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
The 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
With 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
Featuring 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″

More Related Products

Find equipment, activities and other related supplies.

• WARD’S Biotech category
• WARD’S PCR category

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