Chapter 4

What is the lower limit and upper limit of resolution for the scanning tunneling microscope?

0.01 nm and 10 nm

What is the lower limit and upper limit of resolution for the transmission electron microscope?

0.078 nm and 100 µm

What is the lower limit and upper limit of resolution for the atomic force microscope?

1 nm and 10 nm

Why is it necessary to classify organisms?

1. Classification is based on shear characteristics 2. Establishes a universal language 3. It indicates features of the organism including pathology, habitat and other features 4. It's for communication and publications (the common language that is used is recognized by all scientists who are associated with that organism)

What are disadvantages of the scanning electron microscope?

1. It magnifies only the external surface of a specimen 2. Like transmission electron microscopes it requires a vacuum and thus can only examine dead organisms

What are the 4 clinically significant species of mycobacterium?

1. M. Chelonei 2. M. Tuberculosis 3. M. Leprae 4. M. Avium intracellulare

What are two examples of non-pathogenic acid fast bacterial species?

1. M. Phlei 2. M. smegmatis/smegma

What are three steps involved with preparing a specimen for staining?

1. Spread culture in thin film over slide 2. Air dry 3. Pass slide through flame to fix it

With electron microscopy electrons traveling as waves have wave lengths that are _______ to ________ the wavelength of visible light

1/10000 1/100,000

For a series of dilutions including, 1/2, 1/4, 1/8, 1/16, 1/32, 1/64 the results were positive positive positive positive negative negative. What is the titer?

1/16 the last tube that gives a positive result

When is the convalescent titer given?

10 to 15 days after the initial infection

How much do electron microscopes magnify objects by?

10,000X to 100,000X

What is the three domain system based on?

16S rRNA sequencing

Assuming the titer is 1/8 what is the minimum titer associated with protection from infection?

1:16 Anything above is protected since there is enough antibody and anything below is not protected

Assuming the acute titer is 1:16 what concentration of antibody is indicative of infection when measuring the convalescent titer?

1:64 indicates infection

How long is the average tapeworm in length?

20 feet

What is the lower limit of resolution for the unaided human eye?

200 Micrometers

Light microscopes cannot resolve structures closer than __________

200 nm

With the Gram stain how long is safranin staining time?

3 to 5 minutes

With the Gram stain how long is crystal violet staining time?

30 seconds

What wavelengths does visible light extend between?

400 nm for Violet and 650 nm for red

Linnaeus proposed only two kingdoms, how many kingdoms are there today and what are they?

5: animalia, plantae, fungi, protista and prokaryotae

With the Gram stain how long is iodine staining time?

60 seconds

How does the use of electrons in scanning electron microscopy differ from that in scanning tunneling microscopy?

A Scanning electron microscope scatters a beam of electrons into a detector while a scanning tunneling microscope measures the flow of electrons to and from the probe and the specimen's surface

What do fluorescent microscopes direct at specimens?

A UV light source

How is the antibody titer calculated?

A blood serum sample containing antibody is diluted with double dilutions meaning that each successive tube is twice as diluted as the preceding (1/2, 1/4, 1/8, 1/16, 1/32, 1/64). The same amount of the appropriate antigen is added to all the tubes and one looks for a positive reaction using an appropriate detection method.

With phage typing what is a plaque?

A clear area on the bacterial lawn that results from a lack of bacterial growth as a result of a specific phage killing and infecting bacteria

What happens when the images from a confocal microscope have been digitized?

A computer is used to construct a 3-D representation which can be rotated and viewed from any direction

What prevents light from directly entering the objective lens of a dark field microscope?

A dark field stop in the condenser

What is a phase plate and what does it do?

A face plate is a special filter mounted in a phase objective lens that retards light rays another 1/4 wavelength so that they are 1/2 wavelength out of phase with their neighbors

Why does a lens refract light?

A lens is optically dense compared to the surrounding medium air. Light travels more slowly through the lens than it does air. The leading edge of the light beam slows as it enters the glass and the beam bends. Light also bends as it leaves the glass and re-enters the air.

What is a titer and how is it established?

A measure of antibody content. A titer is the highest dilution giving a positive response on addition of the appropriate antigen

Which tool utilizes antibiotics, a microtiter plate or an enterotube?

A microtiter plate

With phage typing where do the phages come from and how are they transferred to the bacterial lawn?

A microtiter plate has wells with different phages. A device with prongs that fits into the microtiter plate is used to apply phages to the bacterial lawn. This allows large numbers of phages to be transferred to the bacterial lawn. The device is dipped into the bacterial lawn and the phages are incubated with the bacteria. One will then look for plaques

What does an Enterotube serve us?

A mini biochemical profile

With phage typing what is a strain identified by?

A phage pattern example 123456789

What can hyperplasia be indicative of?

A pre-cancerous state A precursor to cervical cancer

What is the germ tube test?

A screening test used to differentiate candida albicans from other yeasts

Compound brightfield microscopes use ________ for magnification

A series of lenses

What kind of test is the agglutination test?

A serological test

What kind of microscope did Leeuwenhoek use to observe microorganisms?

A simple bright field microscope

What kind of lens does a simple brightfield microscope contain?

A single magnifying lens

What kind of R value indicates better resolution?

A smaller R-value

What is made on a thin film prior to staining?

A smear of microorganisms

What is antiserum in the agglutination test?

A solution of antibodies that bind to the antigens that triggered their production

With phage typing what is spread across a solid surface of growth medium?

A solution of the bacteria to be identified

With the mantoux tuberculin test what does the doctor inject into the patient?

A sterile solution containing tuberculin

What is the set up of the enterotube like?

A tube with a flat side that contains 12 compartments for different biochemical tests

In scanning tunneling microscopy what is a tunneling current and what is it directly proportional to?

A tunneling current is the amount of electron flow. It is directly proportional to the distance from the probe to the specimen's surface

How is the Enterotube inoculated?

A wire is touched to a well isolated colony from a petri plate and then pulled through the tube to inoculate all of the compartments

With acid-fast stain during the decolorization process which cells resist decolorization by acid alcohol and what color are these cells?

Acid fast bacteria resist Decolorization and retain their red color because the acid cannot penetrate the waxy wall

What kind of structures do basic dyes stain?

Acidic structures

What is acute sera?

Acute sera is a blood sample taken during the initial presentation when symptomology is most obvious

Where is M. Chelonei commonly found and what does it cause?

Africa Skin ulcers

What are two things that the second antibody is labeled with in an indirect antibody test? What are their corresponding colors seen?

Alkaline phosphatase —> yellow or horseradish peroxidase —> brown

What kind of structures do acidic dyes stain?

Alkaline structures

With Gram stain following staining the cells with crystal violet for 30 seconds and rinsing with water what color are the cells?

All cells are stained purple

With Gram stain following flooding the cells with iodine and rinsing with water what color are the cells?

All cells remain purple

With gram stain what would happen if you skipped the decolorization step?

All of the cells would be purple

What is one type of serological test?

An agglutination test

What kind of an image do microscopes produce?

An enlarged inverted image

What are mycelium?

An extensive feeding web of hyphae

Why does the test site grow in diameter with a TB skin test?

An infection makes an individual extra sensitive to the tuberculin injection

What kind of diseases do clostridium and bacillus bacteria cause?

Anthrax, gangrene, and tetanus

What can result in a change in the normal flora of the vagina?

Antibiotics

With the direct and indirect antibody tests the more colors seen, the more __________ present

Antibody

What happens in a negative agglutination test result?

Antibody binding cannot occur because it's specific target is not present

What is done with Seroepidemiology?

Antibody content is determined in the population in those that are infected and in those that are not infected

What are you trying to establish with seroepidemiology?

Antibody dilution that is indicative of an infectious process

With vaccines what happens to antibody levels?

Antibody levels increase and stay indefinitely

What is the body's protection system?

Antibody production

How is antiserum used in an agglutination test?

Antiserum is mixed with a sample that potentially contains its target cells

What is the next step after the bacteria has been incubated in the enterotube for 24 hours?

Any color changes are recorded

If the normal uninfected titer is 1:8 what antibody level is associated with infection?

Any titer greater than or equal to 1:16 would indicate infection

What can a zygospore give rise to?

Asexual spores via a sporangium

A scanning tunneling microscope can reveal details on the surface of a specimen at the __________ level

Atomic

What is normally found in the vagina as normal flora?

Bacteria and fungi

How can phage typing be used to identify different strains epidemiologically and identify where an infection came from?

Bacteria would be isolated from all patients that are infected. Phage patterns would be identified for each of the individuals. You would look for the same phage pattern in the healthcare professional as in the patient to establish the source of infection. You would identify the epidemiological source of infection by looking for matching phage patterns which would imply that the healthcare professional transmitted the infection to the patient

What does electron microscopy provide a detailed view of?

Bacteria, viruses, ultrastructure, and large atoms

What is the largest ciliate that infects humans?

Balantidium coli

A transmission electron microscope generates a __________ that produces an image on a ___________

Beam of electrons Fluorescent screen

In scanning electron microscopy a magnetic field within a vacuum to is used to manipulate a ________

Beam of electrons called primary electrons

What does giardia lamblia cause and what are major sources of it?

Beaver fever Beavers and it is associated with contaminated water and fecal matter of children

Why can Mycobacterium tuberculosis survive for several weeks as infectious droplet nuclei suspended in room air?

Because it has a waxy outer mycolic layer (layer composed of mycolic acid)

Why does electron microscopy give better resolution?

Because it uses radiation of smaller wavelengths resulting in enhanced microscopy

Why can't transmission electron microscopes be used to study living organisms?

Because the vacuum and slicing of the specimens are required

Linnaeus used ___________ nomenclature in his system

Binomial

The API 20 E is a _________ panel for _______ and _________ of members of the family __________

Biochemical Identification Differentiation Enterobacteriaceae

What is Entamoeba histolytica associated with?

Bloody diarrhea and amoebic dysentery

Why are fluorescent antibodies used to identify Legionella and treponema pallidum bacteria?

Both are difficult to culture normally, and you cannot identify bacteria by Gram stain only

With negative stains what is the charge of the dye and the bacteria and how does that affect staining?

Both are negatively charged. There is mutual repulsion such that the background is stained but not the organism

How much does probe microscopy magnify an object by?

By more than 100 million times

How can one increase contrast?

By staining, using a different type of microscope or the use of light that is in phase (all the waves, crests and troughs are aligned)

A yeast or fungus isolated from a neutropenic patient...

Candida albicans based on germ tube formation.....

You _________ identify any bacteria or species solely based on _________

Cannot Morphology

Capsule detection is relevant to detection of ________ typically associated with _______

Capsulated yeast Fungal meningitis

What is the negative stain useful for?

Capsule detection (reveals the presence of negatively charged bacterial capsules)

What is another name for negative stains?

Capsule stains

Who developed the three domain system?

Carl woese

With cytopathogenic effects, when a cell becomes infected by a virus what does it undergo?

Cell rounding

Why don't mycobacteria and Nocardia readily stain with the Gram stain?

Cells of these bacteria have large amounts of waxy lipid in their cell walls

Linnaeus classified organisms based on what?

Characteristics in common

What kind of chemicals do transmission electron microscopes use?

Chemicals that contain heavy metals and absorb electrons

What do microbiological stains contain?

Chromophores

What are phase contrast microscopes useful for observing?

Cilia and flagella. Fine structures in living things

What two structures are found on the surface and the inside of Balantidium coli?

Cilia on the surface and a nucleus inside

What does taxonomy consist of?

Classification, nomenclature, and identification

Linnaeus' goal was to ____________ organisms to ____________ them

Classify Catalogue

Capsule stains are not done __________

Clinically

What genres of bacteria produce endospores?

Clostridium and bacillus

With the API 20E for some of the _________ you can just read the changes in __________ straight away after 24 hours but for some you have to put ___________ before reading

Compartments Color Reagents

Images from confocal microscopes are useful for examining the relationships among various organisms within ____________

Complex microbial communities called biofilms

Given that confocal microscopes use fluorescent dyes what sets them apart from fluorescent microscopes?

Confocal microscopes use UV lasers to illuminate fluorescent chemicals in a single plane. The rest of the specimen remains dark and out of focus

Which one has higher levels of antibody: the acute or convalescent titer?

Convalescent titer

With the acid-fast stain what is the first step?

Cover the smear with tissue paper to retain dye and then flood the slide with red primary stain Carbolfuchsin for several minutes while warming it over steaming water

What basic dyes are used for simple stains?

Crystal violet, safranin, or methylene blue

What is used to refract light and what is used to refract electron beams?

Curved glass lenses and magnetic fields

What do hyphae contain?

Cytoplasm and nuclei containing genetic material

What are two clinical examples of fluorescent antibodies?

DFA (Direct fluorescent antibody test) AND FTA (fluorescent treponemal antibody absorption)

What is the most dominant feature nowadays for classification?

DNA homology

What is the most important step of the Gram stain?

Decolorization

What is the most important step of acid-fast stain?

Decolorization with acid alcohol You decolorize the smear by rinsing it with a solution of hydrochloric acid and alcohol

With atomic force microscopes the _________ of a laserbeam aimed at the probe's tip measures ____________ which when translated by a _______________ reveals the __________

Deflection Vertical movements Computer Atomic topography

With transmission electron microscopy before you put heavy metals on you have to do what to the specimen?

Dehydrate the specimen

API test strips consist of wells containing _________ substances to detect __________ activity, usually related to fermentation of _________ or catabolism of ________ or ___________ by the inoculated organisms. A bacterial suspension is used to _________ each of the wells and the strips are ________. During incubation _________ produces _______ changes that are either spontaneous or revealed by the addition of __________.

Dehydrated Enzymatic Carbohydrates Proteins Amino acids Rehydrate Incubated Metabolism Color Reagents

With the API 20E what do the mini test chambers contain?

Dehydrated media having chemically defined compositions for each test

What are the three steps involved in the preparation of the specimen in transmission electron microscopy?

Dehydration of the specimen through graded alcohol, embedding the specimen in plastic, and cutting thin sections of the specimen

_________ areas of the specimen block electrons, resulting in a __________ area on the screen

Dense Dark

What does the condenser lens in a compound brightfield microscope do?

Direct light through the specimen

What symptoms does trichomonas cause?

Discharge from the vagina/penis

What is each dilution being tested for and which dilution is assigned the titer value?

Each dilution is tested for the presence of detectable levels of antibody and the assigned titer value is indicative of the last dilution in which the antibody was detected

What is the main feature for worms in terms of diagnosis?

Eggs which are microscopic

With a scanning tunneling microscope the specimen must be _____________

Electrically conductive

What kind of microscopy gives the most detail and why?

Electron microscopy Electrons have much shorter wavelengths than visible light. There is more energy and less diffraction

What led to the proposal to add a domain?

Emphasis on comparison of organisms' genetic material

What do more and more scientist rely on to classify the relationship between organisms?

Emphasis on comparison of the organisms' genetic material

How do encapsulated cells appear with a negative stain?

Encapsulated cells appear to have a halo surrounding them

What are endospores? where are they found?and what are they capable of surviving?

Endospores are dormant highly resistant cells found in the cytoplasm of bacteria. They can survive environmental extremes

What are things looked at in the bio chemical profile for identifying bacteria?

Enzymes present, substrates utilized, metabolic end products, metabolic pathways (sugars, citrates, sources of carbon)

What are capsules formed in response to?

Excess nutrients

Where is the cyst found and how long can it survive?

Excreted in the feces and can survive for weeks in the environment

True or false: all acid fast bacteria are Gram negative since they stain pink or red in the acid fast stain procedure

False this is not Gram stain

What is the growing speed of non-pathogenic Acid-fast bacterial species?

Fast growing

With the API 20E test when carbohydrates are ________ the pH within the well ________ and that change is indicated by a change in the ________ of the pH indicator.

Fermented Decreases Color

What are structures used for motility?

Flagella, cilia and pseudopodia

What happens during the process of immunofluorescence?

Fluorescent dyes are covalently linked to antibodies. These dye tagged antibodies will bind specifically to complementary shaped antigens which are portions of molecules that are present on the surface of microbial cells for example. When viewed under UV light, a microbial specimen that has bound dye tagged antibodies becomes visible.

Do yeasts have hyphae?

For the most part no

Who is likely to have been BCG vaccinated?

Foreign-born persons. BCG is used in many countries with a high prevalence of TB to prevent childhood tuberculosis meningitis and miliary disease Not used in Canada or the USA

With a microtiter plate what do the substrates show and what do the antibiotics show?

From substrates you got identification from antibiotics you got the sensitivity

What happens when bacteria are wiped out by antibiotics when treating urinary tract infections?

Fungi thrive in the absence of bacteria which normally regulate them and women get fungal vaginitis

What does the spectrum of electromagnetic radiation include?

Gamma rays, x-rays, UV light, visible light, infrared, microwave, and radio waves/television

The API 20E gives identification for _________ and ____________

Genus and species

What two names is an organism given in Linnaeus' binomial system?

Genus and species

What are two examples of protozoa?

Giardia lamblia and Entamoeba histolytica

What are two popular stains for histological specimens?

Gomori methenamine silver GMS and hematoxylin and eosin HE

What are four kinds of stains included in differential stains?

Gram stains, acid-fast stains, endospore stains, histological stains

With Gram stain following staining with safranin and rinsing with water what color are the cells?

Gram-positive cells remain purple and gram-negative cells are pink

With Gram stain following Decolorization and rinsing with water what color are the cells?

Gram-positive cells remain purple but gram-negative cells are now colorless

What does the Schaeffer Fulton endospore stain result in?

Green stained endospores and red colored vegetative cells

What does M. Avium intracellulare cause?

HIV/AIDS

What is one of the leading causes of cervical cancer?

HPV human papilloma virus

How would you determine motility without doing a flagellar stain?

Hanging drop

What does heating do during the acid fast stain?

Heating softens the waxy mycolic layer facilitating penetration of the cell wall of the bacteria enabling the stain to be driven through the waxy wall and into the cell where it remains trapped

What groups do worms include?

Helminths, tapeworms, and roundworms

What types of fungus cause meningitis (2)?

Histoplasma and Coccidioides

What are you looking for in a Pap smear?

Hyperplasia —> abnormal cell growth where cells start to pile up on each other

What happens if the antigenic cells are present in an agglutination test?

If the antigenic cells are present the antibodies in the antiserum will clump the antigen

Which antibody comes later at a higher concentration?

IgG

Which antibody is produced first IgM or IgG?

IgM

If an individual is infected with TB their _______ will react to the ________ given in the _________ test

Immune system Tuberculin TB Skin

What is the formation of a germ tube associated with?

Increased synthesis of protein and ribonucleic acid

What kind of dyes are used for capsule detection?

Indian ink or nigrosin

Light rays that are out of phase _______ producing a __________ image

Interfere with one another Darker

With Gram stain what acts as a mordant and what does that mean?

Iodine acts as a mordant and increases the affinity of the dye for the bacterial cell wall

Example: with a mixed culture of E. coli and Pseudomonas the antibody only binds to E. coli. Therefore when using the fluorescent antibody technique you don't need ___________

Isolation and pure culture

What can antisera in the agglutination test distinguish between?

It can distinguish among species and even among strains of the same species

Where does the word serology come from and what part of the blood is it referring to?

It comes from serum and it is referring to the liquid portion of the blood

What does the objective lens do?

It creates a magnified image and reduces aberrations in the shape and color of the image

Why does a fluor or a fluorescent compound glow?

It glows because it emits visible light on exposure to UV

What structures does the pork tapeworm have and what is its other name?

It has an armed scolex (hooks) and it has suckers Taenia solium

What structures does the beef tapeworm have and what is its other name?

It has an unarmed scolex (no hooks) and it has suckers T. saginata

When you go from species to domain what happens to the number of organisms?

It increases

What does staining do?

It increases contrast and resolution by coloring specimens with stains and dyes

What does the oil immersion lens do?

It increases resolution. It increases the detail of what you see but not the actual R-value

How is the specimen dehydrated for transmission electron microscopy?

It is dehydrated through graded alcohol going from 5% alcohol to 10% to 20% to 30% and eventually to absolute alcohol

How does the E. coli strain responsible for hemolytic urea 0K157H7 compare to E. coli found in the human gut?

It is much more deadly The structural features are slightly different but the difference is not enough to place them in separate species

How is dark field microscopy used clinically?

It is used to detect motile treponema pallidum to diagnose syphilis

What does it mean if the patient is subclinically infected?

It means that the patient had contact with the organism which in most cases is infectious but in this case the symptomology hasn't risen to the point of infection

What is the major advantage of fluorescent antibody technique?

It provides a definitive identification, bypassing routine culture and isolation, because the antibody only recognizes the corresponding antigen

What does the bleaching action of acid alcohol do with acid fast stain?

It removes color from both non-acid fast cells and the background.

What does alcohol decolorization do and why does it differ between gram-positive and gram-negative bacteria?

It removes crystal violet from the gram-negative bacteria, while the gram-positive bacteria retain crystal violet since they have thicker peptidoglycan

What happens when a virus invades a cell

It replicates inside a cell and commandeers the host's machinery. It tells the host to make viral proteins and genetic material

What does the inflammatory response by the skin represent in a TB skin test?

It represents the immune response by the body and shows that there has been contact with the organism

How is trichomonas transmitted and what stage does it lack?

It requires direct contact for transmission so there is no cyst stage

What are two significant things that the waxy mycolic outer layer does?

It resist dehydration and prevents nutrients and antibiotics from getting in to the cell

Why does phage typing work?

It works because of specificity

E. coli ferments _________ to produce ________ and __________

Lactose Acid Gas

What does M. Leprae cause?

Leprosy

In regions where the specimen is ___________, the screen fluoresces more brightly

Less dense

With immersion oil why doesn't light refract such that more light is captured by the lens?

Light is traveling at a uniform speed through the slide, the immersion oil, and the glass lens

With a compound bright field microscope what is the path of the light?

Light passes through the specimen into the objective lens and through the ocular lens

With dark field microscopes which light rays enter the objective lens?

Light rays scattered by the specimen

Dark field microscopy enables one to look at _________ that are _______

Live organisms Unstained

What are hyphae?

Long, tubular, branching structures produced by fungi

How much of an increase must be seen between acute titers and convalescent titers to indicate infection?

Looking for a four fold or greater increase in antibody

What is the most significant species of mycobacterium and what does it cause?

M. Tuberculosis Tuberculosis

Why is it hard to treat tuberculosis?

M. Tuberculosis has a mycolic acid outer layer. Therefore resistance to antibiotics is common. M. Tuberculosis is also slow-growing so it involves long-term therapy which decreases efficacy and contributes to poor patient compliance

With an electron microscope what is being used to get focus?

Magnets

What are simple bright field microscopes similar to?

Magnifying glasses

What is the primary stain used in the Schaeffer-Fulton endospore stain and how is it driven into the endospore?

Malachite green Heat is used to drive it into the endospore

Why must the column of a transmission electron microscope be a vacuum?

Matter including air, absorbs electrons

What is one category of a biochemical test and a specific example?

Metabolism E.g. E. coli ferments lactose

A scanning tunneling microscope passes a ________ sharpened to end in a ___________ back-and-forth across and slightly above the __________

Metallic probe Single atom Surface of a specimen

What three groups does archaea include?

Methanogens, halophiles and thermophiles

What is the counterstain used in acid-fast stain? What cells does it stain?

Methylene blue Bleached non-acid fast cells

You cannot identify any bacteria by ___________ alone, ___________ are required

Morphology Biochemical tests

What is used to identify protozoa?

Morphology (size), the number of nuclei, host range, pathology signs and symptoms, and motility

What is used to identify fungi?

Morphology including fruiting bodies which are reproductive bodies, mycelium including whether or not it is septate or non septate, and differences in structures of the sporangium and zygospore

What is used to identify bacteria?

Morphology, form, arrangement, coccus or rod, spore or no spore, gram-positive or gram-negative, capsule or no capsule, and identification dominated by biochemical profile

The resolving power of electron microscopes is __________ then those of light microscopes which therefore allows the possibility of greater _________

Much greater Magnification

The enterotube is an example of a rapid __________ used in identification of unknown oxidase-__________, Gram-_________, _______-shaped bacteria of the family ___________.

Multi test system Negative Negative Rod Enterobacteriaceae

What are two kinds of bacteria that acid fast stain stains?

Mycobacteria and nocardia

Why do only 10% of those who come in contact with TB get tuberculosis?

Mycobacterium tuberculosis is not a highly virulent organism

What is responsible for the differential staining in acid-fast stains?

Mycolic acid

What kind of stains are included in special stains?

Negative capsule stain and flagellar stain

Simple stains have bacteria and dye such that the bacteria are _________ charged and the dye is __________ charged

Negatively Positively

Do amoeba have biochemistry?

No

Does Linnaeus' definition of species apply to bacteria?

No

Is a mordant required for acid fast stain?

No

Are bacteria of the same species but different strains susceptible to the same phage?

No Different strains have different phage patterns

How are phase microscopes used clinically?

No direct clinical application

With fungi if the nuclei have no cross wall they are what?

Non septate

Immersion oil increases the ______ which increases the ________ because ______ are gathered into the lens to produce the image

Numerical aperture Resolution More light rays

What are two advantages of phase microscopes?

One can examine living organisms or specimens that would be damaged or altered by attaching them to slides or staining. Contrast is also created because light waves are out of phase

With Enterobacter aerogenes how do the two strains differ?

One is citrate positive and the other citrate negative The DNA is the same other than the variation that one doesn't have the genes to process or utilize citrate since it lacks the enzyme citrase

What is adequate to diagnose tuberculosis?

One single acid-fast bacteria

How effective is the BCG vaccine and why is it less effective?

Only about 70% effective mostly due to poor administration and limited resources or no support services

Each image from a confocal microscope is thus an ________ through the specimen as if it had been __________

Optical slice Thinly cut

Linnaeus defined species as what?

Organisms that can successfully interbreed

What does taxonomy allow one to do?

Organize large amounts of information about organisms and make predictions based on knowledge of similar organisms

With dichotomous keys there are a series of __________ statements where only one of two either/or choices applies to any particular __________

Paired Organism

What are dark field microscopes best at observing?

Pale objects

What is H&E useful for?

Pap smear

The path of light in a light microscope is similar to the ___________ in an electron microscope

Path of electrons

There are four individual patients. They are given a vaccine and then their blood is taken and antibodies to hepatitis are measured. Patient 1: 1:32 Patient 2: 1:64 Patient 3: 1:2 Patient 4: 1:8 Which patient has the highest antibody content?

Patient two 1:64 is the greatest dilution The greater the dilution the more antibody is present

What are the two types of phase microscopes?

Phase contrast microscopes and differential interference contrast microscopes

Differential interference contrast microscopes create __________ and use prisms that __________ into their component wave lengths which significantly increases ____________ and gives the image a ___________ or ___________ appearance. It also produces ____________ which enhances contrast.

Phase interference patterns Split light beams Contrast Three-dimensional Shadowed Unnatural colors

Are using genetics as a basis to understand the relationship between organisms this reflects a _____________ Hierarchy

Phylogenetic

What is used to identify worms?

Physical appearance (size, form, shape and basic structure), host range, and eggs in specimens for diagnosis (also look at larvae/stages in development) No biochemistry (just based on what they look like)

What is used to identify viruses?

Physical characteristics including size and form, DNA/RNA, envelopes, host specificity, pathology, and cytopathogenic effects (cell rounding or tissue death)

What are taxonomic and identifying characteristics?

Physical characteristics, biochemical tests, serological tests, phage typing and analysis of nucleic acids

What are the results of the acid-fast stain?

Pink acid-fast cells which can be differentiated from blue non-acid fast cells

With the API 20E test all ________ and _______ test results are compiled to obtain a _________ number which is then compared with profile numbers in a commercial ________ to determine the __________ of the bacterial species

Positive negative Profile codebook Identification

What is one positive thing that staining does to an organism and one negative thing?

Positive: increases contrast Negative: kills the organism

Based on the grouping that an organism is placed in you can _______

Predict its characteristics

What motility structure do amoeba have?

Pseudopodia

blood tests like __________ are used to detect __________ and unlike the tuberculosis skin test, are not affected by _________ and are less likely to give a _________ result

Quantiferon gold TB infection Prior BCG vaccination False Positive

Light rays that are in phase ________ producing a _______ Image

Reinforce one another Brighter

What is contrast important in determining?

Resolution

How is resolution increased with confocal microscopes?

Resolution is increased because visible light admitted by the dyes passes through a pinhole aperture that helps eliminate blurring

Three tubes are filled with carbohydrate and inoculated with bacteria. What are three possible results for a carbohydrate utilization test?

Result #1: bacteria metabolizes a particular carbohydrate to produce acid (which changes the color of a pH indicator, phenyl red to yellow) and gas as indicated by the bubble Result #2: bacteria metabolizes a carbohydrate to produce acid but no gas Result #3: bacteria is inert with respect to the test and no acid or gas is produced

What are two examples of fungi that have different looking Sporangia and zygospores?

Rhizopus (an environmental fungus) and Aspergillus

Immersion oil has the ______ As glass

Same refractive index

What are the different objective lenses and their levels of magnification?

Scanning objective lens equals 4X Low power objective lens equals 10X High power lens equals 40X Oil immersion objective lens equals 100X

What are the two types of probe microscopy?

Scanning tunneling microscopes and atomic force microscopes

What procedure is done with a scanning tunneling microscope?

Scanning tunneling microscopes pass a metallic probe sharpened to end in a single atom back-and-forth across and slightly above the surface of a specimen

If waves are in sync you ________ and if they are not in sync you ____________.

See them as one See them separately

Hyphae are broken into compartments by what?

Septa

What function do septa serve in hyphae?

Septa serve as supporting structures for hyphae

With fungi if the nuclei are cross wall they are what?

Septate

What kind of radiation do modern microscopes use and what do their lenses have?

Shorter wavelength radiation such as blue light or electron beams. They have lenses with larger numerical apertures

What are three different kinds of stains?

Simple stains, differential stains and special stains

The ____________ of a tuberculosis skin test reaction in a BCG vaccinated person is ___________ a factor in determining whether the reaction is caused by _________ or ___________

Size Not Latent TB infection Prior BCG vaccination

What are simple stains used to determine?

Size, shape, and arrangement of cells

What is the growth speed of pathogenic acid fast bacterial species?

Slow-growing

In phage typing what is added to the bacterial lawn?

Small drops of solution containing different types of bacteriophages are added

What is M smegmatis associated with?

Smell associated with genitals

What are some exceptions to the binomial system for some organisms?

Some organisms may have a sub species and you can also have different strains within each group

Which are more similar members of a species or members of a genus?

Species

With dark field microscopes what appears light and what appears dark?

Specimens appear light against a dark background

Unlike scanning tunneling microscopes what kind of specimens can atomic force microscopes magnify?

Specimens that do not conduct electrons and living specimens because neither an electron beam or a vacuum is required. They have been used to magnify the surfaces of bacteria, viruses, proteins and amino acids

In transmission electron microscopy what do stains bind to?

Stains may bind molecules in specimens or the background

What steps would you take to confirm a diagnosis of syphilis?

Take scrapings from the lesion with a sterile pipette, put the specimen on the microscope and look at it with a dark stain using a dark field microscope

When IgM is greater than IgG what does this mean?

That it is a recent infection or response to vaccination

When IgG is greater than IgM what does this mean?

That it is an old infection or response to vaccination not new

What does a strain mean?

That there are slight differences but not large enough to be placed in a different species

What is the vaccine for tuberculosis disease called?

The BCG vaccine or the Bacille Calmette Guerin vaccine

What is FTA and what does it identify?

The Fluorescent treponemal antibody absorption test identifies treponema pallidum bacteria which causes syphilis

What is the tuberculosis skin test called?

The Mantoux tuberculin test

Does the R-value actually change with staining?

The R-value doesn't actually change but the image appears clearer

What is resolution?

The ability to distinguish detail in a given field of view between two points some distance away

What makes the use of fluorescent antibodies so effective?

The antibody is specific, it will only bind to the corresponding antigen that triggered its production

Why do you have to keep getting vaccinated for tetanus?

The antibody to C. Tetani decreases every 5 to 10 years

What are the parts of a direct antibody test and what does it measure?

The antigen and the antibody. It measures the organism

With latex agglutination the thing that the antibody clumps with is what?

The antigen or the pathogen of interest

What are the parts of an indirect antibody test and what does it measure?

The antigen, the primary antibody and the secondary antibody. It measures the antibody to the organism

What is magnification?

The apparent increase in size of an object indicated by number of X

What do negative stains stain?

The background

What is illuminated with bright field microscopes?

The background or field is illuminated

Why is the bacteria glowing in immunofluorescence?

The bacteria is glowing because antibodies tagged with fluorescent dye are bound to them

What must be done immediately after decolorizing the cells?

The cells must be rinsed with water

What does the dichotomous keys pathway indicate about an organism?

The central characteristics of an organism

What is the most widely used microscope?

The compound light microscope

Which form is the infective form, the trophozoite or the cyst?

The cyst

What is contrast?

The differences in intensity between two objects or between an object and its background

What is the DFA test and what does it identify?

The direct fluorescent antibody test. It identifies Legionella and doesn't require isolation since it uses a commercially prepared antibody

What is wavelength?

The distance between two corresponding parts of a wave

What does the doctor look at 48 hours after administering the TB skin test?

The doctor will look to see how the body has responded to the injected tuberculin and measure the diameter of the bubble on the forearm

What would happen if you switched the Crystal violet and safranin?

The gram-positive would be pink and the gram-negative would be purple

What are phages specific for?

The hosts they can infect

What do trophozoites colonize and what does this lead to?

The intestinal tract leading mainly to tissue destruction and secretory bloody diarrhea

How can a microbiologist identify an unknown bacteria with phage typing?

The microbiologist can compare the phages that form plaques with known phage-bacteria interactions

What is one tool for rapid identification of bacteria?

The microtiter plate

What is the modern goal of taxonomic categories?

The modern goal is to understand relationships among groups of organisms

The brightness of each region of the screen in transmission electron microscopy corresponds to ___________

The number of electrons striking it

What is the total magnification?

The objective lens times the ocular lens

How is a zygospore formed?

The outermost layers of the zygosporangium wear away or disappear and the remaining body is called a zygospore

Why is the patient recovering around the time that the convalescent titer is taken?

The patient is producing enough antibody at this point

What virus are Negri bodies associated with?

The rabies virus

What is the first stain used for the acid fast stain?

The red primary stain carbolfuchsin

What explains the difference in detail between the scanning electron microscope and the transmission electron microscope?

The scanning electron microscope looks at surface features and and therefore shows less detail. The transmission electron microscope has an electron beam passing through the specimen in order for it to be visualized and therefore offers a lot more detail and internal details

Rather than passing electrons through a specimen as is done with transmission electron microscopes, what does a scanning electron microscope do with electrons?

The scanning electron microscope rapidly focuses electrons back-and-forth across the specimen's surface which has been previously coated with a metal such as platinum or gold

What kind of structural features are looked at in worms to identify them?

The scolex (head region) determines whether it is armed (has hooks) or naked (has no hooks)

With Gram stain how is the decolorization process carried out?

The slide is held at an angle and flooded with alcohol until the fluid runs clear

With Gram stain what is done after the cells have been stained with safranin for 3 to 5 minutes?

The slide is rinsed with water and then blotted with bibulous paper

What kind of energy does the specimen radiate back in fluorescent microscopy?

The specimen radiates energy back as a visible wavelength

The degree to which the image is enlarged depends on..

The thickness of the lens, it's curvature and the speed of light through its substance

With giardia how many nuclei do the trophozoite and cyst forms have?

The trophozoite form has two nuclei and the cyst form has four nuclei

Once you have the BCG vaccine it gives a false positive on what test?

The tuberculosis skin test

What are wavelengths dependent on?

The voltage of an electron beam

What is resolution dependent on?

The wavelength of the electromagnetic radiation and the numerical aperture of the lens or the ability of the lens to gather light

What is an advantage of scanning electron microscopy over transmission electron microscopy?

The whole specimen can be observed because sectioning is not required

With a patient that is subclinically infected what happens to their antibody count?

Their antibody count stays the same and they are not infected

Why can't endospores be stained by normal staining procedures?

Their walls are practically impermeable to all chemicals

When you go from kingdom to species what happens to the DNA homology?

There is increasing similarity

When you go from species to kingdom what happens to the DNA homology?

There is less DNA homology and increased DNA divergence

What is the role of hyphae?

They absorb nutrients from the environment and transport them to other parts of the fungus body

What are virus infections gleaned from and how do these effects compare between viruses?

They are gleaned from cytopathogenic effects and there are specific effects from each virus

How are bacteria that produce hydrogen sulfide identified?

They are identified by the black precipitate formed by the reaction of the hydrogen sulfide with iron present in the medium

What is the motility like of trophozoites and can they survive in the environment?

They are motile and cannot survive in the environment

What is the motility like of cysts and can they survive in the environment?

They are non-motile and survive in the environment

By how many wave lengths are light rays shifted out of phase when they pass through a specimen?

They are shifted about 1/4 a wavelength out of phase

What happens if a patient's number of antibodies doubles?

They are still not infected

What do germ tube solutions contain and what do they promote?

They contain tryptic soy broth and fetal bovine serum, essential nutrients for protein synthesis

What do the techniques used in serology depend on?

They depend on antibody production and associated activities

What is the biochemistry like of yeast?

They have minimal biochemistry restricted to carbohydrate fermentation

What use do fluorescent microscopes serve in immunoflorescence?

They help identify pathogens and make visible a variety of proteins

What happens to antibody numbers if you are infected?

They increase

What are the benefits of dark field microscopes?

They increase the contrast and enable observation of more details

What do the primary electrons do in scanning electron microscopy?

They knock secondary electrons off the surface of the coated specimen

In what form do yeasts live and how do they grow and reproduce?

They live as single cells, growing and reproducing through a phenomenon called budding

With the acute presentation following infection what can happen to antibody levels?

They may rise, continue to rise or decline

Why are simple stains called simple?

They only involve soaking the smear in dye for 30 to 60 seconds and rinsing the slide off with water

What do the scattered secondary electrons do in scanning electron microscopy?

They pass through a detector and a photo multiplier producing an amplified signal that is displayed on a monitor

What do yeasts produce that enables the identification of Candida albicans?

They produce a germ tube serum within 24 hours

What do probe microscopes utilize to magnify more than 100 million times?

They utilize minuscule pointed electronic probes

What does testing positive for the TB skin test indicate?

This indicates that the body has been infected with the TB bacteria. Additional tests are needed to determine if the person has latent TB infection or TB disease

With a transmission electron microscope the electrons pass ___________ and then through ___________ instead of glass lenses that ___________ the beam and then onto a __________ that absorbs electrons, thereby changing some of their energy into ___________

Through the specimen Magnetic fields Manipulate and focus Fluorescent screen Visible light

How can contrast and resolution be enhanced with electron microscopy?

Through the use of electron dense stains

What are antibody titers used for?

To diagnose infection

What was found in the teeth of an individual 5000 years ago?

Traces of yersinia pestis

What are the two types of electron microscopy?

Transmission electron microscopes and scanning electron microscopes

Which form of electron microscopy has a higher resolution: scanning electron microscopy or transmission electron microscopy?

Transmission electron microscopy

What is GMS useful for detecting and what can that be used to diagnose?

Treponema pallidum in tissues to diagnose syphilis

What is an example of an STD caused by protozoa?

Trichomonas

What kind of antibiotic therapy is involved in the treatment of tuberculosis?

Triple therapy with rifampin, ethambutol, and isoniazid for 6 to 9 months

What two forms represent the life cycle of the protozoan parasite?

Trophozoites and cysts

What happens when the phase microscope lens makes neighboring waves 1/2 wavelength out of phase relative to each other?

Troughs of one wave interfere with crests of the other because they're out of phase and contrast is created

True or false: Mycobacterium tuberculosis can survive as infectious droplet nuclei suspended in room air for several weeks

True

The presence or size of a __________ in persons who have been _________ does not predict whether BCG will provide any ___________

Tuberculosis skin test reaction Vaccinated with BCG Protection against TB disease

Linnaeus proposed how many kingdoms?

Two

What are the benefits of using UV light in fluorescent microscopy?

UV light increases resolution and contrast

Why are resolution and contrast improved with fluorescent microscopy?

UV light increases resolution because it has a shorter wavelength than visible light and contrast is improved because fluorescing structures are visible against a black background

What are the usual steps taken to identify a bacteria when you have a clinical specimen and are not using immunofluorescence?

Usually when you have a clinical specimen you identify the bacteria using a Gram stain, do a streak of isolation to get pure cultures, and do a chemical profile with C & S

What does a microtiter plate contain in its wells and what can it be coupled with?

Various substrates. It can be coupled with antibiotics to perform a C&S

What are bacteriophages?

Viruses that infect and usually destroy bacterial cells

What happens in a positive agglutination test?

Visible clumps are formed by the binding of antibodies to their target antigens present on cells (indicated by clotting)

What forms of electromagnetic radiation are used in microscopy?

Visible light and ultraviolet light

Why do you have to dehydrate the specimen in transmission electron microscopy?

Water in the specimen would impede the penetration of the electron beam

What is the formula for resolution?

Wavelength/(2* numerical aperture)

What do moving electrons act as?

Waves

With a MicroScan panel a plate containing numerous ________, each the site of a particular ________ test helps ascertain the ________ of an organism by reading the pattern of ________ in the wells after the biochemical tests have been performed

Wells Biochemical Identity Colors

What do physical characteristics include

What they look like, size and shape

When are light rays in phase?

When the crests and troughs are aligned

When are light rays out of phase?

When their crests and troughs are not aligned

What limits whether latex agglutination can be used?

Whether or not an antibody exists for the particular organism

What do the relative levels of IgM to IgG establish?

Whether the infection is new or old

How does an atomic force microscope differ from a scanning tunneling microscope?

While they both use a pointed probe, the pointed probe of an atomic force microscope traverses the tip of the probe lightly on the surface of the specimen rather than at a distance

How is poor patient compliance monitored with the treatment of tuberculosis?

With use of DOT directly observed therapy, a mandated process work a caseworker comes to a patient's home and watches them take medication

When looking at the form of fungi what are the two categories?

Yeast and mycelium (hair-like things scattered throughout)

How much smaller of an object can you see with a compound light microscope compared to an unaided human eye?

You can see an object 1000 times smaller

What kind of a microscope can you use to look for Negri bodies?

You can use a light microscope to look at them

What is one advantage of the API 20E with regards to space?

You don't need to set up 25 tubes, the plastic strip holds 20 mini test chambers

What is the set up used for latex agglutination?

You have latex beads with the appropriate antibody attached to them for a given bacteria

In fluorescent microscopy what must you do with cells that are not naturally fluorescent?

You must stain them using the fluorescent antibody technique

Why is it important to rinse the slide with water following decolorization with Gram stain?

You need to wash off the alcohol or else it will continue to decolorize the gram positive bacteria. Also if you left the alcohol on and put safranin on you would decolorize the safranin

What are the three domains?

eukarya, bacteria and archaea

Carl Woese compared nucleotide sequences of ___________ subunits

rRNA

Why are rRNA molecules useful to look at?

rRNA molecules are present in all cells and are crucial to protein synthesis therefore changes in their nucleotide sequences are presumably very rare

With the Schaeffer Fulton endospore stain what three things are done following heating and staining it with Malachite green?

the smear on the slide is cooled, the slide is decolorized with water and counterstained with safranin