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Saturday, October 30, 2004

Chapter 7: DNA Technology (Definitions)

Genes- nucleotide sequences coding for a product.
Codon- sets of 3 nucleotides that will code for one amino acid.
Genome- a cell's entire genetic compliment, including its genes.
Chromosomes- segments of DNA.
Plasmids- small circular molecules of DNA that replicate independently of the chromosome.
Histones- globular proteins
Genotype- actual set of genes in its genome.
Phenotype- physical features and functional traits of an organism, including characteristics.
Transcription- gene information is copied as RNA nucleotide sequences.
Translation- Polypeptides are synthesized by RNA molecules in ribosomes.
Central Dogma- the processes of transcription and translation.
Transduction- a method of horizontal gene transfer.
Promoter- a nucleotide sequence located near the beginning of a gene and initiates transcription.
Mutation- a change in the nucleotide base sequence of a genome, particularly its genes.
Point Mutations- when just one or a few nucleotide base pairs are affected.
Frameshift Mutations- insertions and deletions creating new sequences of codons that result in largely altered polypeptide sequences, usually affecting proteins more than substitutions.
Thymine Dimers- mutation caused by nonionizing radiation in the form of UV light, causing adjacent thymine bases to covalently bond to one another.
Light Repair- prokaryotic DNA photolysase enzyme breaks bond between adjoining thymine nucleotides, restoring the original DNA sequence.
Dark Repair- enzymes cut damaged DNA sections from a molecule, creating a gap that is repaired by DNA polymerase and ligase.
Excision Repair- enzymes exise DNA strand that is in error, and filling the gap with DNA polymerase.
SOS Response- prokaryotic cells with extensive DNA damage use various processes to induce DNA polymerase to copy the damaged DNA.
Bacteriophage- a virus that infects a bacteria
Conjugation- horizontal gene transfer where bacteria containing a fertility plasmid forms a conjugation pilus that attaches and transfers plasmid genes to a recipient.

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Monday, October 25, 2004

Mechanisms and Retardation of Antibiotic Resistance

I The three main categories of side effects of antimicrobial drugs are:
1.) Toxicity- this means that the body has identified the agent as a poison and can damage normal cells.
2.) Allergies - Some of us are sensitive to certain ingredients in antibiotics, and although rare, anaphylactic shock (shock resulting from ingesting or contacting any agent that triggers the body's allergic immune response) may be immediate and life- threatening.
3.) Disruption of Normal Flora - Normal flora may be affected by some antimicrobials, allowing pathogenic activity to cause a secondary infection.

In nature, we have certain "wild type" populations of organisms. Infection plus antibiotics cause susceptible organisms to die, while resistant organisms still flourish. The resistant organisms are named Mutants. Resistance to antimicrobials was first noticed in the 1940's. This resistance is hastened by three main groups of activity.
1.) Mis-prescribed antibiotics- an increasing problem that has gotten the attention of the CDC.
2.) Medical noncompliance- unmonitored dosage or early cessation of the antimicrobial(s).
3.) The same antibiotics are being used for both livestock and humans.

II) Resistance by Bacteria to Antimicrobial Drugs- there are five mechanisms possible. 1.) Natural Mutation- (vertical gene transfer)
2.) Plasmid Transfer- (horizontal gene transfer)
3.) Conjugation- transfer of plasmids from one organism to another via sex pillus.
4.) Transformation- taking up a plasmid or gene fragment from environment and incorporating it into the genome.
5.) Transduction- A (phage) has a gene from a previous host that it takes into the next host cell.

III) Multiple and Cross Resistance to Antimicrobial Drugs - there are three basic types included.
1.) The pathogen itself can acquire resistance to more that one drug at a time.
2.) Cross-resistance occurs when antimicrobial drugs given are similar in their structure.
3.) Pathogens resistant to most antimicrobial strains are called superbugs.

IV) Retarding Resistance - The development of pathogen resistant populations can possibly be averted in at least six different ways.
1.) Giving high concentrations for a short time.
2.) Using antimicrobial combinations. (synergism)
3.) Limit usage in necessary cases.
4.) Develop new variations of existing drugs.
5.) Second-generation drugs. (adding side chains to the original molecule)
6.) Third-generation drugs. (adding side chains . . . )

V) Notes on Certain Antimicrobial Drugs
_A) The Beta-lactams - inhibit cell wall synthesis and are the penicillins.
__1) They have limited action against most Gram negative bacteria
___a) resistance to Gram negatives is due to the peptinoglycan layer of the bacterial cell.
Chloramphenicol - is an antibacterial that inhibits protein synthesis. It is prescribed for Typhoid Fever and is rarely used due to its dangerous adverse effects, including death.
_B) Antivirals
__1) inhibit viral protein synthesis.
__2) Protease inhibitors are used for HIV.
_C) Antifungals
__1) active against fungi
__2) no resistance is known
__3) are especially effective against Gram positive pathogens. (topical drugs are examples)
_D) Antiprotozoans
__1) include heavy metals
__2) little or no resistance is known
__3) their spectrum of action has a better chance to cause allergic reactions than other antimicrobials.

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Sunday, October 24, 2004

Antibiotic Quizzes and Practice Tests

Before taking and reviewing some of the quizzes below, check out this material on the discovery of antibiotics. It is an oultined format of important information concerning antibiotic targets, resistance, alternatives, consumption, therapy and failed therapy, resistant mechanisms and more..

Table of Antibiotics

Now, here are some practice tests on the topics of antibiotics and some certain diseases. Check them out!
First, information by the CDC about antimicrobial resistance.

Antibiotics

True/False quiz

Antimicrobial Therapy

Quiz for non-science majors

Antibiotic Resistance Quiz for Pre-Med Students The completed test results are given, but the correct answers are not viewable.
(Test provided by the University of Florida College of Medicine)

Conditions and Diseases
E. Coli and E. Coli 0157

Autoimmune Diseases

HIV and AIDS

Shingles

Smallpox

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Chapter 10: Controlling Microbial Growth

  • Alexander Fleming reported in 1929 that the antibacterial action of penicillin released from Penicillium. He defined antibiotics as antimicrobial agents that are produced naturally by an organism. Today, antibiotic means "an antibacterial agent", excluding antiviral and antifungal agents.
    Penicillin is a natural occurring antibiotic. Additionally, by altering the chemical structure of antibiotics, semisynthetics are produced. These are more effective, last longer, or easier to administer than natural antibiotics. Synthetics are antimicrobials that are completely synthesized in a laboratory.

    Mechanisms of Antimicrobial Action
    Because there are many differences between the structure and metabolism of pathogenic bacteria and their eukaryotic hosts, antibacterial drugs constitute the greatest number of diversity of antimicrobial agents. Although they can have a variety of effects on pathogens, antimicrobials can be catagorized into 6 different groups according to their mechanisms of action.

    1.) Inhibition of cell wall synthesis. (Penicillins) The most common antibacterial agents act by preventing cross-linkage of NAM subunits (a macromolecule of peptinoglycan in bacteria). Thus, cell walls of pathogens are weakened and are less resistant to the effects of osmotic pressure. The underlying cytoplasmic membrane bulges through the weakened portion as water moves into the cell and the cell lyses.
    2.) Inhibition of protein synthesis. (Tetracyclines) Understanding this inhibition first requires understanding the process of translation. The tetracyclines can change the shape of certain subunits, making it impossible for the ribosome of the cell to read the codons of RNA properly. Some antimicrobials can prevent movement of the ribosome from one codon to the next altogether. As a result, translation is frozen and protein synthesis is stopped.
    3.) Disruption of cytoplasmic membrane.(Polymyxins) Some antimicrobials have the ability to become part of the cytoplasmic membrane and thus, damaging it. The drug amphotericin B binds to molecules of ergosterol, causing them to congregate and form a spore within the membrane.
    4.) Inhibition of metabolic pathways. (Sulfonamides) Humans take simple folic acids found in our diets and covert them to into tetrahydrofolic acid (THF). As a result, our human metabolism is unaffected by sulfonomides. Some pathogens desire certain acids to be converted into THF, a reaction required for their DNA and RNA synthesis. Sulfonamides decrease this acid production which slows the production of proteins required for pathogenic synthesis.
    5.) Inhibition of nucleic acid synthesis. (analogs) DNA and RNA are built from purine and pyrimidine nucleotides and are critical to cell survival. Because only slight differences exist between nucleic acids of both prokaryotic and eukaryotic cells, drugs that affect replication often acts against both types of cells. Generally these drugs are not used to treat infections, but rather as research in DNA replication and to slow replication of cancer cells. Analogs change the shape of nucleic acid molecules and prevent further replication, trascription, or translation.
    Additionally, viral acid synthesis is faster than the synthesis of cells, so viruses are more susceptible to analogs than their hosts.
    Here is what we've discussed so far
    6.) Prevention of virus attachment.(Arildone) Viruses must attach to their host's cells via chemical interaction. Attachment of viruses can be blocked by peptide and sugar analogs of either attachment or receptor proteins. When these sites are blocked, viruses can neither attach or enter a host cell. Arildone blocks receptor sites of polio viruses and some cold viruses, making them unable to attach to host cells.

Clinical Considerations in Prescribing Antimicrobial Drugs.
The ideal antimicrobial agent to treat infection would probably be one that is:

1.) readily available
2.) inexpensive
3.) chemically stable (for ease of transport and shelf-life considerations)
4.) easily administered
5.) nontoxic and nonallergenic
6.) selective toxicity against a wide range of pathogens

Oral drugs are easy to take and usually low cost, but are not monitored, which holds the capabilitiy of resistance.
Injectable drugs are high cost, quickly effective, the entire dosage is ensured, and are closely monitored.
Topical drops and mists are usually low cost, but are not monitored and can gain resistance without proper use. Underdosage and overdosage is especially dangerous with mists.


The spectrum of action is the number of different kinds of pathogens an antimicrobial agent can act against. Narrow-spectrum drugs act only against a few kinds of pathogens, where broad-spectrum drugs can act against a wide range of organisms. Using a broad-sprecrum antibiotic can also kill normal flora that is necessary to defend against pathogenic organisms in the first place. For example, a woman taking erythromycin for a throat infection, is more susceptible to vaginitis resulting from excessive yeast growth when the agent kills normal bacteria contained in the vagina.

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Thursday, October 14, 2004

Links, personal and professional

Class Notes Home
Northeast State Technical Community College
E.T.S.U.
King College
Milligan College
American Society for Microbiology
Society for General Microbiology
USC School of Medicine An online medical school text with studies in bacteriology, virology, mycology, parasistology and more!
Quillen College of Medicine
AORN Online for surgical Registered Nurses
American Association for Respiratory Care
Frontline Approach to Common Pulmonary Disease Presentations
Lung Health Education for physicians and respiratory therapists.

Logos:
AARC
AORN
John F.Murray, MD
American Association for Respiratory Care
Healthy Lungs



MUSIC SITES
Gretchen (Christian Rock band Official Site)
ChristianRock.net
PureVolume.com
Evanescence (Official Site)

OTHERS
The Charmed Ones
Charmed Two
Law and Order SVU

Wednesday, October 13, 2004

Test Yourself Here

You can test your knowledge of Microbiology through the links in this thread. Informational links are also listed here. (Note: this site is still under construction, and more information is added daily.)

>>> Top Pick! An awesome site that lets you make up your own quizz! You can choose what types of questions, which bugs, and even select the number of questions you want to answer. An answer score is also included.

>>> Advanced level Problem sets and tutorials are available at this site. This is an advanced level testing site for Honors Micro students.

>>> Biological Weapons Resource Center A.S.M. site. Discusses policy, detection, treatment, preparedness and homeland security.

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Monday, October 11, 2004

Chapter 9-10 "Controlling Microbial Growth"

Environmental Control includes physical and chemical processes. Some examples of physical control methods are:
Sterile - Free from all life forms, including viruses.
High Level Disinfectant - Kills all life forms except endospores.
Mid Level Disinfectant- Kills all life forms except endospores, encapsulated mycobacteria, viruses
Low Level Disinfectant -Kills vegetative bacteria, enveloped viruses, and some fungi.
Aseptic -Free of pathogenic organisms and without addition during a procedure.
Sanitized- Mimimized to what is considered safe.
Pasteurize- High heat/short time. Minimizes number of bacteria in food products and juices without harming food.
Degerming Agents:
Antimicrobial
Antibacterial
Antifungal
Antiviral

HOSPITAL SETTINGS
Critical Level Items- are items that penetrate the epithelial layer of tissue, therefore, they must be sterilized.(Needles, scissors, etc.)
Semi-Critial Items -Do not penetrate the epithelial layer but may enter a cavity. Sterilization of these items is not required. (Endoscopes, speculas, etc.)
Non-Critical Items -Do not break the tissue or enter into any cavity. (stethescopes, bp cuffs, etc.)

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Homepage

Beginning with Chapter Six "Microbial Nutrition and Growth"

Like all organisms, microbes desire nutrients in order to live and grow. Some of these requirements include, but are not limited to: nutrients, oxygen, ph, temperature, moisture and reproduction.
Replication is based on the bacterial requirements being met.
BACTERIA ARE GROUPED BY ENERGY ACQUISITION
Photo-auto- trophs derive their energy from sunlight and CO2, a carbon source.Chemo auto trophs derive their energy from sulfer and hydrogen. CO2 is the carbon source.
Chemo auto trophs derive their energy from sulfer and hydrogen. CO2 is the carbon source.
Photo hetero trophs use sunlight as an energy source and organic material as the carbon source.
Chemo hetero trophs derive energy from chemical compounds, and organic compounds as a carbon source. (Humans are in this category)
BACTERIA ARE GROUPED FURTHER BY THEIR RANGES IN ENVIRONMENTAL CONDITION.
Temperature
Psychophile- Cold Range (0-20 degrees C)
Mesophile- Range from 20-40 degrees C (flora)
Thermophile- Range from 45-80 degrees C
Hyperthermophile- over 80 degress C
ph
Most are between 6.5-7.5
Neutrophils-- 6.5-8.5
Acidophils-- less than 6.0 and varying ranges
Alkalinophiles-- more than 8.0
Salinity (Salt content)
Plasmolysis is an issue for most cells, so they cannot stand an increase in salt content.
Halophils can withstand high salinity.
Hydrostatic Pressure Most cells are sensitive to pressures.

Viable Cell Count-- (Bauman book, page 190) Lab Procedure

MEDIA TYPES
Complex Has a variety of ingredients.
Defined Pure chemicals within the mixture. They also need a buffer added to them.(Good source for anti-microbial requirements, AKA growth factors)
Selective Helps to narrow down organism of interest. EX: Glucose salts
Thayer-Martin Isolates N.Gonorrhea, Antibiotics will inhibit growth of fungi, Gram + and Gram - rods, and will allow growth with little competition.
Differential Created in mind that different organisms metabolize different materials in different ways. A bacteria type can change a substance in a recognizable way. EX: Blood agar- "strep test"

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