MicroA

serology

2008-07-29T23:00:00.000-07:00

Serology

What is serology?
Serology is the scientific study of blood serum and immune responses. In practice, the term usually refers to the diagnostic identification of antibodies in the serum. Such antibodies are typically formed in response to an infection against a given microorganism or against other foreign proteins (Eg. to a mismatched blood transfusion), or to one's own proteins (Eg. autoimmune disease).There are several serology techniques that can be used depending on the antibodies being studied. These include ELISA, agglutination, precipitation, complement-fixation and fluorescent antibodies.

www.randstarteam.blogspot.com
What is the purpose of Serological testing?

Serological tests may be performed for diagnostic purposes such as detecting serum antibodies or antibody-like substances that appear specifically in association with certain diseases. Serology blood tests help to diagnose patients with certain immune deficiencies associated with the lack of antibodies, such as X-linked agammaglobulinemia. The various types of serological tests include:

(1) Flocculation tests The most common test is the complement-fixation tests. They are based on the precipitation, or flocculation, that takes place when antibody and specially prepared antigens are mixed together.

(2) Neutralization testsThis test depends on the capacity of antibody to neutralize the infectious properties of the infectious organisms.

www.marine.ie/.../Photo5b_DiagnosticServices.jpg
(3) Hemagglutinin-inhibition testsThis test make use of the finding that certain viruses will cause the red blood cells of certain animal species to agglutinate (congeal, or clump together) and that this agglutination will be prevented by antibody.What are the benefits of serological testing?Serological testing is particularly helpful in the diagnosis of rickettsial and viral diseases such as Rocky Mountain spotted fever, influenza, measles, poliomyelitis, and yellow fever, as well as of infectious mononucleosis and rheumatoid arthritis. As a practical mass-screening diagnostic tool, it has proved valuable in the detection of such conditions as syphilis.

DNA fingerprinting

www.scielo.br/.../rsbmt/v39n5/a01fig01.gif
Some true facts on DNA fingerprinting!

The chemical structure of everyone's DNA is the same. The only difference between people (or any animal) is the order of the base pairs. There are so many millions of base pairs in each person's DNA that every person has a different sequence. Using these sequences, every person could be identified solely by the sequence of their base pairs. However, because there are so many millions of base pairs, the task wouldtake up a lot of time. Instead, scientists are able to use a shorter method, due to the repeating patterns in DNA. These patterns do not, however, give an individual "fingerprint," but they are able to determine whether two DNA samples are from the same person, related people, or non-related people. Scientists use a small number of sequences of DNA that are known to vary among individuals a great deal, and analyze those to get a certain probability of a match.

The ribosomal RNA (rRNA) gene region of the microsporidium,Nosema apis,has been examined. A new method for extracting microsporidian genomic DNA from infected host tissue is described. Complete DNA sequence data are presented for the small subunit gene (1242 bp), the internal transcribed spacer (33 bp), and the large subunit gene (2481 bp to a putative termination point). This is the first time that the complete large subunit rRNA gene has been published for any microsporidian species.

The relation between different organism can be seen by comparing the genes that code the important function of the organisms. Some regions of this 16S rRNA are highly conserved in all organisms, but other regions maybe more variable.

DNA sequencing of ribosomal RNA gene

DNA sequence is also presented for the regions flanking the 5′ end of the small subunit gene and the 3′ end of the large subunit gene. The intergenic spacer is shown to be heterogeneous, showing variation in sequence and restriction sites rather than length and containing sequence repeats, which are a characteristic feature of intergenic spacers. The rRNA gene region ofN. apisis shown to occur in a head-to-tail, tandemly repeated manner, as in other eukaryotes. The complete DNA sequence of the nuclear ribosomal RNA gene complex of Verticillium dahliae: Intraspecific heterogeneity within the intergenic spacer region. Fungal Genetics and Biology 29, 19–27.

The complete sequence of the nuclear ribosomal DNA gene complex of the phytopathogenic fungus Verticillium dahliae has been determined. The tandemly repeated unit was 7216 bp long and appears to be the shortest rDNA cluster described so far among filamentous fungi. Primer pairs were designed for amplification of the region spanning half of the 28S subunit, the intergenic spacer (IGS), and the 5 end of 18S subunit of a number of Verticillium strains, isolated from various hosts and geographic origins.

Morphology on Slant Medium

2008-07-27T22:51:00.000-07:00

NYP Micro A

* Even (following
the line of the
original streak)

* Irregular (slight
spreading from
the original line)

* Spreading (the
organisms cover
the entire surface
of the slant)

The 3 Domains

2008-07-27T22:05:00.000-07:00
continued from 5+1=6 Kingdoms...

In the previous post, all prokaryotes are classified under Monera. However, it was found that prokaryotes are more diversed than expected. Hence, the 3 domains systems was created to further classify the prokaryotes and eukaryotes. In general, prokaryotes are divided into 2 domains. Bacteria (eubacteria) and archaea respectively. All eukaryotes are put into the 3rd domain. Archaea is further divided into 3 main groups, methanogens, Thermoacidophiles and extreme halophiles.

prokaryotes:A unicellular organism having cells lacking membrane-bound nuclei; bacteria are the prime example but also included are blue-green algae and actinomycetes and mycoplasma.
Monera: Prokaryotic bacteria and blue-green algae and various primitive pathogens; because of lack of consensus on how to divide the organisms into phyla informal names are used for the major divisions.
eukaryotes: An organism with cells characteristic of all life forms except primitive microorganisms such as bacteria; i.e. an organism with 'good' or membrane-bound nuclei in its cells.
eubacteria: A large group of bacteria having rigid cell walls; motile types have flagella.
archaea: are a group of single-celled microorganisms.
methanogens: Archaebacteria found in anaerobic environments such as animal intestinal tracts or sediments or sewage and capable of producing methane; a source of natural gas.
Thermoacidophiles: is an extreme archaebacteria which thrives in acidous, sulfur rich, high temperature environments.
halophiles: Archaebacteria requiring a salt-rich environment for growth and survival.

references: definations from wordweb, www.biologie.uni-hamburg.de for image, information from notes.

The 5+1=6 Kingdoms

2008-07-27T06:44:00.000-07:00
In the beginning, all living thing were grouped into 2 kingdoms, mainly plants and animals. However, as time passed by, it became increasing difficult to group some living things into either the animal group or plant group. Hence, the 2 kingdoms were expanded into 5 kingdoms: Protista (single celled eukaryotes), fungi (fungus and related organisms), plantae (plants), animalia (animals), and last but not least, monera (prokaryotes).

[note* many biologists divide Monera into eubacteria and archeobacteria, hence, forming a total of 6 kingdoms instead] so here's another diagram for better understanding:

Kingdoms are then further divided into categories called phyla, each phylum is then divided into classes, each class divided into orders, each other into families, each family into genera and finally, each genus into species. Whew! That's alot! Okay, here's a picture to help you visualize better:

Protista: Eukaryotic one-celled living organisms distinct from multicellular plants and animals: protozoa, slime moulds, and eukaryotic algae- division Protista
fungi: The taxonomic kingdom including yeast, moulds, smuts, mushrooms, and toadstools; distinct from the green plants.
plantae: (botany) the taxonomic kingdom comprising all living or extinct plants
animalia: Taxonomic kingdom comprising all living or extinct animals
monera: Prokaryotic bacteria and blue-green algae and various primitive pathogens; because of lack of consensus on how to divide the organisms into phyla informal names are used for the major divisions
eubacteria: A large group of bacteria having rigid cell walls; motile types have flagella
archeobacteria: Considered ancient life forms that evolved separately from bacteria and blue-green algae
References:
http://www.ruf.rice.edu/~bioslabs/studies/invertebrates/kingdoms.html
definations from wordweb
images:
http://www.ri.net/schools/Narragansett/NHS/PerEwebpage/6kingdoms.gif
whyfiles.org/022critters/images/kingdom.gif
wikipedia

To be continued...

Morphology In/On Culture Medium

2008-07-27T05:47:00.000-07:00
When it comes to morphology in/on culture medium it gets a bit complicated. there is a difference between solid medium and liquid medium eg. agar and broth respectively.

SO PAY ATTENTION!!!

It varies with the type of agar/broth medium, nutrients, and dyes present in the medium.

The size, color, shape and consistency of a colony growing on a particular agar medium are characteristic of bacteria.

In a liquid medium, the region in which the organism grows depends on the oxygen requirement of that particular species.

Liquid medium
* Turbid
* Pellicle
(thick growth at the top of the tube
* Sediment

Solid medium

Pigmentation
*Transparent (pic 1)
* Opaque (pic 2)
* Colour pigment (pic 3)
* Fluorescent pigment(pic 4)
Transparent (pic 1)

Opaque (pic 2)

Colour (pic 3)

Fluorescent (pic 4)

Surface Properties
* Flat
* Raised
* Filamentous and
rhizoid
* Contoured
* Wrinkled
* Smooth and glistening
* Growth pattern – motile
or non motile

OR

Smell or Odors
*Sweet
* Alcohol
* Foul

References: http://en.wikibooks.org/wiki/A-level_Applied_Science/The_Role_of_the_Pathology_Service/Microbiology

http://www.bact.wisc.edu/microtextBook/index.php?module=Book&func=displayarticle&art_id=113
http://microbewiki.kenyon.edu/index.php/Micrococcus
Information: NYP SG Lecture Notes on Classification of microorganisms

Morphology Under the Microscope

2008-07-27T05:30:00.001-07:00

to get a deeper understand morphology we would need to know, the arrangement of the bacteria, the picture above shows you the shapes but if you click onto this url, it would show a clearer picture and explaination of the arrangements.

http://www2.bakersfieldcollege.edu/bio16/images/bacterialshapes.jpg

References: http://commons.wikimedia.org/wiki/Image:Arrangement_of_cocci_bacteria.svg

Methods of Classification and Identification of Microorganisms

2008-07-27T04:15:00.000-07:00
Vibrios- curve rods

Below is spirilla -spiral/ helical shape

Cocci- spherical shaped

Rod shaped bacillus

There are different methods of classification and identification of microorganisms,

Firstly microoganisms can be seperated and classified simply by its biochemical or physiological characteristics

(the definition on its own)

PHENOTYPIC is when an organism's growth is influenced by its surrounding or enviroment.

GENOTYPIC is when an organism's growth is already in the gene code and it can only be slightly changed by the enviroment.

Therefore in the context of identification, a phenotypic characteristics simply means charasteristics that can be seen/ revealed either with the microspope of the human eye.

This would include morphology (structure) of the microorganism (as seen above). Its staining properties, atmospheric requirements, physiological properties (Biochemical and metabolic activities tests) and antigen-antibody reactions (Serology).
In this website we will be touching on each of these topics in detail..

3 Types of Staining

2008-07-27T01:51:00.000-07:00
There are 3 types of staining:

1) Simple Staining
2) Differential Staining
3) Special Staining

We will go into more details with the next post

Simple Staining, Differential Staining and Special Staining

2008-07-26T04:10:00.000-07:00
Simple Staining

1) It is a solo stain.
2) Simple stainings are usually methylene blue, crystal violet or safranin.
3) Simple staining is adequate to decide bacterial shape.
4) Simple staining is adequate to decide the arrangement characteristics.

Simple staining is when an air dried smear is stained, rinsed, dried and examined using oil immersion lens of the microscope.

Differential Staining

Principle

Gram-negative bacteria have a higher lipid content which is soluble. Therefore it can dissolves in decolorizer.

Gram-positive bacteria have cell walls that have low lipid content. The bacteria will turn less permeable during treatment with decolourizer.

Gram Stain:
Fixation -> Crystal violet -> Iodine treatment -> Decolorization -> Counter stain safranin

Acid-fast Stain

Ziel-Neelson acid-fast stain
Acid-fast: pink
Non-acid fast: blue

Auramine-Rhodamine acid-fast stain
Acid-fast: fluoresce yellow-orange
Non-acid fast: no fluorescence

Principle of Acid-fast stain
Acid-fast stain is used for Mycobacteria since they have a thick, waxy coat.
It make use of carbol fuchsin in the presence of heat to permit the dye to penetrate into the bacterium. Once stained, acid-fast bacteria are resistant to decolorization due to it's thick, waxy coat.

Non-acid fast bacteria are decolorized and take up the methylene blue.

Special Staining

Principle

Capsular Stain
Capsules do not have the same affinity for dyes as other cell components.
Negative staining has a halo around cell against a dark background.

Endospore stain
It has a special resistant, dormant structure formed within a cell that protects the bacteria during adverse environmental conditions.

Flagellar Stain
They have structures of locomotion, which is too tiny to be seen under microscope without staining.

References: www.flickr.com
www.visualunlimited.com

Bacteria shapes

2008-07-26T01:46:00.000-07:00

There are 4 basic shapes that bacterial cells adopt. They can be either :
1)rod shaped
2)spirilla
3)vibrios
4)spherical

Reference:This picture is taken from the lecture notes of NYP's module Microbiology A and edited.
Confused by what the technical terms mean?
Dont worry,further explanations are given below. :)

~Spherical bacteria are referred to as cocci (singular: coccus),
~Spirilla(helical shape like corkscrew)
~Vibrios bacterium adopt the shape of curve rods
~Rod shaped bacteria are known as bacilli (singular: bacillus).

Atmospheric requirements of different bacteria

2008-07-26T00:34:00.000-07:00

http://www.bmb.leeds.ac.uk/mbiology/ug/ugteach/newdental/introduction/bacteria/bacteria_atmosphere.html

-Test-tube (i) shows an obligate anaerobe, unable to grow in the presence of oxygen, close to the surface of the growth medium

Test-tube (ii) shows an facultative bacterium, which is indifferent to the presence of oxygen.

Test-tube (iii) is an obligate aerobe which can only grow at the surface of the medium.

Test-tube(iv) is a microaerophile that can only grow where the oxygen level is low.
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Microorganisms like bacteria can be classified by their relationship to Oxygen.
Different bacteria isolate has different atmospheric requirements.
The classification involves 5 major groups, the obligate aerobes,microaerophilic aerobe,facultative anaerobe,aerotolerant anaerobe and obligate anaerobe

>Obligate aerobes strictly need oxygen to survive which means that in the absence of Oxygen they would die immediately.

>Microaerophilic aerobe bacteria would be killed when exposed to normal atmospheric levels of oxygen,but yet still requires traces amount of oxygen to grow.

>Facultative anaerobe can survive in both the absence and presence of oxygen.

>Aerotolerant anaerobe do not require oxygen

>Obligate anaerobe die in the presence of oxygen