BIOLOGY & SCIENCE: April 2009

Thursday, April 30, 2009

article : Content the MICROBIOLOGY TOPICS

This relatively new science began with the erroneous belief in spontaneous generation (abiogenesis) and matured into the germ theory on which today’s understanding of infectious disease is based.

MICROBIOLOGY TOPICS

VIRTUAL MICROBIOLOGY CLASSROOM

Click here to visit the online materials used in an actual college-level Microbiology Course. The Virtual Microbiology Classroom provides access to a wide range of educational resources including Power Point Lectures, Study Guides, Review Questions and Practice Test Questions.

HISTORY OF MICROBIOLOGY

From spontaneous generation (abiogenesis) to modern immunology, this link will take you to a series of articles summarizing the key contributors and discoveries.

SPONTANEOUS GENERATION DEBATE

GERM THEORY OF DISEASE

EARLY HISTORY OF IMMUNOLOGY

CLASSIFYING ORGANISMS (SYSTEMATIC & TAXONOMY)

Linnaeus and Binomial Nomenclature

TYPES OF MICROBES

All life is composed of cells, and only two basic models exist; prokaryotes and eukaryotes. All bacteria are prokaryotic cells. Viruses are acellular, or non-living particles that are able to cause infectious disease.

PROKARYOTES (Bacteria & Archaea)

Prokaryotic Microbes
Classification of Bacteria
What Are Normal Flora? 2/10
Probiotic Bacteria that Promote Digestive Health 11/09

EUKARYOTIC MICROBES

Eukaryotic Microbes

VIRUSES

HOW TO USE A MICROSCOPE

SPO provides a number of articles on how to properly use a compound light microscope. The main page provides descriptions and links to help you easily find the specific information that you are looking for.

BACTERIAL IDENTIFICATION

Microbes are tiny and often colorless. That wouldn't be a problem if we didn't so often have to identify them. Without the ability to ID specific microbes, the treatment of infectious disease would not be possible. The following links provide information on several methods used to sleuth out the identity of different bacteria, including differential staining, specialized media and other metabolic tests.

MICROBIAL CONTROL (How to Kill Microbes)

Control of microbial growth (killing microbes) can be carried out number of ways, through use of chemical, physical and chemotherapeutic (antibiotic, antiviral and antifungal) agents.

Here are links to additional pages each covering a specific microbial control method.

Physical Control of Microbes (Heat, UV radiation)
Chemotherapeutic Control of Microbes (Antibiotics and other meds)
Chemical Control of Microbes (Disinfectants, cleaners like bleach and lysol)

INFECTIOUS DISEASE

So small that they can only be seen with a light microscope or electron microscope, humans have battled these tiny pathogens throughout our history. The following links lead to articles that describe and give examples of infectious diseases caused by eukaryotic pathogens, bacteria, viruses, viroids and prions.

Sources

Image

van Leeuwenhoek, Public Domain, Wiki

article : Bacterial Endospore Stain Protocol

Differential Test to Identify Bacteria Genera Bacillus & Clostridium

Read more: "Bacterial Endospore Stain Protocol: Differential Test to Identify Bacteria Genera Bacillus & Clostridium" - http://bacteriology.suite101.com/article.cfm/bacterial_endospore_stain#ixzz0E7UCb8xK&A

Before discussing the procedue for staining endospores, it is important to understand what these unique structures are and how the power of the endospore was first dicovered.

Heat Resistant Bacteria

John Tyndall was a 17th century Irish-born English-bred physicist who made many contributions to science, one of which was the discovery that some microbes existed in two forms:

heat-stable form (endospore)
heat-sensitive form (vegetative cell)

Tyndall found that it took either prolonged or intermittent heating to destroy the resistant heat-stable form. The outcome of this research was a method of sterilizing liquid by heating it to boiling point on successive days ("Tyndallization").

"Tyndallization" is useful for sterilization of growth media in science classes and other situations where autoclaves (instruments that use both heat and pressure to sterilize) are not available for pressure sterilization.

What Is an Endospore?

Endospores are produced by very few types of bacteria, most notably the genera Clostridium and Bacillus. These protective structures are made through a process known as sporulation in response to extreme environmental conditions, such as high temperatures, desiccation, chemicals, changes in pH and lack of food.

In the dormant, inert endospore state, bacteria do not metabolize or reproduce, but exist in a type of suspended animation, much like the seeds of plants do. When environmental conditions again become favorable, the endospore germinates, returning the bacterium to its normal active and reproducing metabolic state.

Staining Bacterial Endospores

Normal water-based techniques, such as the Gram stain, will not stain these tough, resistant structures. In order to stain endspores, malachite green must be forced into the spore with heat, in much the same way that carbol fuschsin is forced through the waxy mycolic acid layer of Mycobacterium in the Acid-fast Stain.

The protocol for differentially staining endospores and vegetative cells is as follows:

Place a strip of blotting paper over the slide.
Place the covered slide over a screened water bath and then saturate blotting paper with primary stain malachite green.
Allow the slide to sit over the steaming water bath for 5 minutes, reapplying stain if it begins to dry out.
Remove blotting paper and rinse slide with water until water runs clear.
Flood slide with the counterstain safrinin for 20 seconds and then rinse.
View specimin under oil immersion (magnification of 1000xTM) with a light microscope.

After this staining procedure, the endospores will appear green, having retained the primary stain, malachite green. The vegetative cells (bacteria are in the active, metabolizing state) will appear pink, having retained the counterstain, safrinin.

Problems Interpreting Endospore Stain

It should be noted that any debris on the slide can also take up and hold the green stain. Everything that ends up green on the slide is not necessarily an endospore. Endospores are small and typically oval. Large or irregular globs of green on the slide may be artifacts.

Acid-fast cells, such as members of Mycobacterium and Nocardia have waxy molecules in their cell wall that will take up and retain the malachite green stain when subjected to the endospore staining process. The uniformly green appearance of endospore stained Acid-fast cells doesn’t mean that they produce endospores. These are vegetative cells that have taken up color from the heat driving malachite green into their waxy cell wall.

Additional Microbiology Information

For more information on prokaryotes and cell biology, go to the excellent websites of SPO Virtual Microbiology Classroom and Microbe Wiki.

Sources

Bauman, R. (2005) Microbiology.

Park Talaro, K. (2008) Foundations in Microbiology.

The copyright of the article Bacterial Endospore Stain Protocol in Bacteriology is owned by Tami Port. Permission to republish Bacterial Endospore Stain Protocol in print or online must be granted by the author in writing.

article : Genetic Topic

Genetics is the branch of biology that examines how traits are passed down from one generation to another. This is the study of heredity and particularly the mechanisms of hereditary, the genetic code of DNA.

SPO GENETICS TOPICS

MOLECULAR GENETICS

Look here for information on nucleic acids and the genetic code; how DNA is copied, proteins made, and how mistakes, called mutations, can happen.

MOLECULAR GENETIC TOPICS INCLUDE:

HUMAN HEREDITY & MENDELIAN GENETICS

Article series explaining how the combo of our parents genes work together to make you that unique person you are. Learn about the relationship between alleles, genes, DNA, genotypes, phenotypes and complete dominance.

Genotype, Phenotype & Simple Inheritance
Complete Genetic Dominance (Eye Color & Myopia)
Simple Genetic Inheritance (Dimples, Chin Cleft & Free Earlobes)
Dominant Genetic Traits (Mid-digital Hair, Hand Clasping and Bent Finger)
Genetics of Pigment and Skin Cancer 5/09

GENETIC TERMINOLOGY

Chromatin, sister chromatids, daughter chromosomes, haploid, diploid, homologues ... confused? these articles will help you sort out the language of genetics.

GENETIC TERMINOLOGY TOPICS INCLUDE:

CELL DIVISION: Mitosis & Meiosis

This link takes you to a series of articles about mitosis (somatic cell division) and meiosis, the generation of gametes (sperm and eggs).

These different types of cell division are part of the life cycle of all sexually reproducing organisms. There is also information regarding how some organisms can reproduce asexually, without a mate; their cell division resulting in offspring that are clones.

CELL DIVISION TOPICS INCLUDE:

MICROBIAL GENETICS

The basic genetics of cellular microbes is the same as for all cells. The nucleic acid, DNA, is the genome of any cell, and it must be replicated to make new DNA whenever the cell is preparing to divide. RNA transitions the genetic message into the building of proteins for cell structure and function. However, bacteria have some unique capabilities which increase their genetic variability, and viruses have genomes that can be very different from those of cells.

Bacteria Horizontal Gene Transfer (Transformation, Transduction, Conjugation) 6/09

Viral DNA and RNA Genomes 8/09

Making Sense of the Genetics of RNA Viruses (Difference Between Positive & Negative Viral RNA Strands) 8/09

Virtual Cell Biology Classroom Genetics Resources

This genetic information is used in an actual college-level cell biology classroom. The following links will take you to lectures, review questions & practice tests relating to various genetics subtopics.

Molecular Genetics Lecture

Cell Division: Mitosis Lecture

Cell Division: Meiosis Lecture

Mendelian Human Genetics Lecture

Human Genetics Worksheet

Genetics & Probability Test Questions

Sources

Image

Karyotype Sanger Institute

Stem Cells: Ryddragyn Wiki Public Domain

article : More about Immunology

HUMAN IMMUNOLOGY: The Body's Defense System

The human body has many tactics that is employs; continuously working to eliminate potential pathogens from its territory.

IMMUNOLOGY TOPICS INCLUDE:

HISTORY

Early History of Immunology: Discoveries of Edward Jenner and Louis Pasteur

Some of the early discoveries that led to today's vaccines happened almost by chance. The astute observations of Jenner and Pasteur were the foundation of immunology.

NONSPECIFIC IMMUNITY

Nonspecific Immunity: Skin

Our body’s first line of defense includes structures, and chemicals, processes that work to prevent pathogens entering the body. Read more about how the skin and mucous membrane help defend your body from invaders.

Leukocytes:

Leukocytes are white blood cells that can be categorized into one of two groups based on the presence or absence of granules within:

Extracellular Killing

There are two cell types that do their killing extracellularly (outside the cell). These include Natural Killer Lymphocytes(NK cells) and Eosinophils.

The Complement System

The complement system consists of specific proteins circulating in blood plasma. Most are inactive until they are cut by an enzyme and activated. The pattern of sequential activation of complements results in a cascade of events that ultimately protect the body

Content

Bauman, R. (2005) Microbiology.

Campbell, N. and Reece, J. (2005) Biology,Seventh Edition.

Park Talaro, K. (2008) Foundations in Microbiology.

Images

Macrophage, National Science Foundation

Neutrophil engulfing anthrax bacteria, Tim Vickers, Wikim

article : More Know about Evolution Topics

Pre-Darwinian Evolutionary Theory: John Lamarck, George Cuvier, James Hutton and Charles Lyell

You may believe Darwin to be the alpha and omega on evolutionary thought, but the proponents of Larmackianism, Catastrophism and Uniformitarianism paved the way.

Charles Darwin & Evolution: Natural Selection as the Mechanism of Biological Change

Darwin was not the first to understand that organisms evolve or change over time. His crucial contribution was identifying the mechanism of change, natural selection.

Evolution as Theory & Fact: The Certainty of Evolutionary Change & Theories of Its Mechanism

"It is important to understand that the current questions about how life evolves in no way imply any disagreement over the fact of evolution." - Neil A. Campbell. This article explores the misunderstanding of the work theory as it applies to evolution.

What Is Natural Selection?

Science Prof Online has an entire web page of links and articles on natural selection, the driving force of evolutionary change, first proposed by Charles Darwin. Select the link above to learn more!

DNA Gene Mutations & Evolution: Genetic Mistakes, Natural Selection and Biological Change 5/09

A mutation is an alteration of a gene's DNA sequence. Mutations are usually bad news, but those rare changes that benefit an organism are the raw material of evolution.

See the Evolution Online Bookstore for recommended readings and direct links to purchase books on evolution.

Sources

Images

Cell Endomembrane Illustration : Mariana Ruiz

Other image credits to be updated.

article : What Is Cell Biology?

All forms of life are made from these tiny units ... cells, and there are only two main types; prokaryotes and eukaryotes. Explore the following topics and learn more about cells and the cellular processes that that are the common denominator shared by all living things.

SPO Cell Biology Topics

Prokaryotic and Eukaryotic Cells

Prokaryotes, the simplest form of life, are evolutionarily ancient, and for billions of years the only form of life. Now the domains Archea and Eubacteria represent the extant (currently living) types of prokaryotic cells.

While prokaryotic cells include bacteria and bacteria-like Archea, eukaryotic cells are... everything else. From the cells that make up your body to the tiny blob-like amoeba, most living things that we are familiar with are eukaryotes. Eukaryotic cells are distinguished from prokaryotes by the presence of a nucleus and other membrane-bound organelles. The following articles provide information specific to eukaryotes.

Chemistry of the Cell

Think that chemistry has nothing to do with biology? Think again. In order to understand cells and cellular processes, you must have at least a very basic understanding of inorganic and organic chemistry.Click on this topic link to access the articles that will bring you up to speed.

Cellular Metabolism

We are all familiar with the term 'metabolism', but what does it really mean? The following articles explain how the cells of our bodies (and cells of all living things) turn food energy into ATP energy that can be used to fuel cellular reactions.

Cell Division - Mitosis and Meiosis

Cell division is required for living things to grow, develop and reproduce. Mitosis produces cells that are clones, identical to the parent cell. Meiosis is the form of cell division that produced gametes (sperm and eggs). See the links below for more detailed information on cell division.

Molecular Genetics

Learn about nucleic acids, the organic molecules that contain and transmit the genetic code to build the vast array of proteins that make you truly unique.

Stem Cells

What are stem cells? How are they collected, stored, grown and transplanted?

This link will take you to an article series that should answer some of your questions regarding embryonic and adult stem cells, umbilical cord blood banking and more.

Virtual Cell Biology Classroom

Materials used to supplement an introductory college-level Cell Biology Course. The Virtual Cell Biology Classroom provides access to a wide range of educational resources including Power Point Lectures, Study Guides, Review Questions and Practice Test Questions

Sources

Images

Epithilial Cells: WikiBooks Cell Biology Text

Cell Endomembrane System: Mariana Ruiz

Macrophage: National Science Council

article : Differential staining for Clostridium bacteria

The final differential stain that we will be learning in lab is called an Endospore stain 7/09. It is a special staining procedure that allows us to stain both vegetative (active) cell and endospores.

What are Endospores?

Two genera of bacteria, Clostridium and Bacillus, produce endospores. Endospores are tough, resistant structures that allow the bacteria to essentially exist in ‘suspended animation.’ Endospores do not metabolize and do not reproduce but merely exist, much like plant seeds, until exposed to environmental conditions suitable for bacterial growth.

Example of Clostridium bacteria with characteristic drumstick-shaped endospore-producing cells. The dark rod-shaped cells are vegetative, actice cells. The clear ovals are endospores, and the objects consisting of both dark rod and clear oval are vegetative cells producing endospores.

Endospore Sporulation

Endospores are made through a process known as sporulation in response to extreme environmental conditions. Extreme environments include high temperatures, drying out (dessication), extremes in pH, bacteriocidal chemicals and lack of food. When environmental conditions are favorable, the endospore germinates. Upon germination, the cell returns to its normal metabolic state, capable of reproduction.

Staining Endospores

Normal staining techniques will not stain the resistant endospores. Here are the steps that are required:

Malachite Green: The stain, malachite green, is forced into the spore with heat much like the carbol fuschsin was forced through the waxy mycolic acid layer of Mycobacterium. After flooding the slide with malachite green, it is suspended over a boiling water bath for 5 minutes and then rinsed with water.
Safrinin: Once the endospore is stained, the counter stain, Safranin, provides color for the vegetative (i.e. metabolically active) cells.

What Vegetative Cells and Endospores Look Like

Below is a photo of Bacillus bacteria that have been stained using the endospore stain. At the end of this differential staining process the vegetative cells (active, metabolizing cells) are pink and the endospores, if present, are green.

ADDITIONAL ARTICLES ABOUT ENDOSPORE STAINING

Follow the links below to articles explaining the Endospore stain procedure and the differences between vegetative cells and endospores.

Bacterial Endospore Stain Protocol: Differential Test to Identify Bacteria Genera Bacillus & Clostridium 7/09

Endospore staining involves application of a series of dyes. Malachite green stains endospores and safrinin dyes vegetative cells pink. Here's endospore stain procedure.

Differential Staining & Bacterial Controls: Positive & Negative Controls: Gram, Acid-fast & Endospore Stains 7/09

Bacterial controls are often used with differential stains as examples of typical positive and negative stain reactions; helpful references when identifying unknowns.

Sources:

Microbiology class laboratory material appearing on this website is adapted from the Applied Microbiology laboratory manual by Cynthia Schauer.

Images:

Heat fixed slide prepared for Gram staining. Positive control is on the left and negative control is on the right, T. Port.