_______ changes effect disease spread

Societal changes effect disease spread

Some societal changes that positivly helped reduce infectious disease include adding _______ to water, draining ______ to kill mosqitos, and better personal _____.

Negative effects include the spread of leggionaires disease via ___ _________, and most importantly, the increased and hastened spread of disease thanks to ______.

Some societal changes that positivly helped reduce infectious disease include adding cholorine to water, draining swamps to kill mosqitos, and better personal hygine.

Negative effects include the spread of leggionaires disease via air conditioning, and most importantly, the increased and hastened spread of disease thanks to flying.

Pathogens can be described as _________,as in from on or inside the body, or ________, meaning from outside of the body

Pathogens can be described as endogenous, as in from on or inside the body, or exogenous, meaning from outside of the body

Endogenous bacterial live _____ the body.

They include normal bacterial _______ and tend to be _________ pathogens

Endogenous bacterial live on the body.

They include normal bacterial flora and tend to be oppurtunstic pathogens

Exogenous pathogens are found _________ the body.

They include the ____ and are hard to irradicate due to the high rate of _________

Exogenous pathogens are found outside the body.

They include the flu and are hard to irradicate due to the high rate of mutation

5 Main Entry points for Pathogenic Infections:

1. ___________ Tract
2. _________ tract
3. ______ Genital Tract
4. _______ Tract
5. ___________ Tract

5 Main Entry points for Pathogenic Infections:

1. Respiritory Tract
2. Digestive tract
3. Female  Genital Tract
4. Urinary Tract
5. Alimentory Tract

The alimentory tract is the stretch of _______ membrane that starts at the mouth and ends at the ______

The alimentory tract is the stretch of mucus membrane that starts at the mouth and ends at the anus

Entry of Pathogens into the Body Depends on:

1. ______ of the pathogen to the body 
2. ________ of the pathogen if ingress is hard
3. Inoculum _____

Entry of Pathogens into the Body Depends on:

1. Ingress of the pathogen to the body 
2. Penetration of the pathogen if ingress is hard
3. Inoculum size

Ingress of a pathogen happens through entry without crossing _______ barriers.

This includes ______ of air or ______ of infected food

Ingress of a pathogen happens through entry without crossing epithelial barriers.

This includes inhalation of air or ingestion of infected food

Penetration of pathogenic microbes means the microb got into the body through some sort of tear in the _____.

Penetration of pathogenic microbes means the microb got into the body through some sort of tear in the skin

Four Types of Epithilial Skin Cells:

1. ________
2. Simple _______
3. ________ Squamus
4. Simple _________

Four Types of Epithilial Skin Cells:

1. Squamus
2. Simple Cuboidal
3. Stratified Squamus
4. Simple Columnar

Four Types of Epithilial Skin Cells and Where they are:

1. Squamus: ___ _____ and ____
2. Simple Cuboidal: ____ Tract
3. Stratified Squamus: Also in ____
4. Simple Columnar: Also in ___ Tract

Four Types of Epithilial Skin Cells and Where they are:

1. Squamus: Basil lamina and Skin
2. Simple Cuboidal: GI Tract
3. Stratified Squamus: Also in Skin
4. Simple Columnar: Also in GI Tract

The basil lamina is the combination of two types of basil cells atht makes up the ________ membrane of skin

The basil lamina is the combination of two types of basil cells atht makes up the basement membrane of skin

Most epithlial layers are _______, meaning they have different surfaces

Most epithlial layers are polarized, meaning they have different surfaces

The outside layer of an epithilial cell is the ______ layer.

It has finger-like protrusions on it called _____, which are a type of microvilli

The outside layer of an epithilial cell is the apical layer.

It has finger-like protrusions on it called lumen, which are a type of microvilli

The innermost layer of an epithlial cell is the _____ layer.

It is the basement layer of the cell that anchors the cells securely, and houses a _______

The innermost layer of an epithlial cell is the basal layer.

It is the basement layer of the cell that anchors the cells securely, and houses a nucleus

Individual epithlial cells are connected by _____ _______ between each other.

The areas with these junctions are called the zona ______ , and regularly come under attack by bacteria.

Individual epithlial cells are connected by tight junctions between each other.

The areas with these junctions are called the zona occluous, and regularly come under attack by bacteria.

The Spread of Infection Depends on:

1. ________ factors of the host which might help or hinder movement into the body
2. Active measures taken by microbes to enter the host, such as through ______ structures and _______ proteins
3. Hitchhiking on _______ cells as a trojan horse

The Spread of Infection Depends on:

1. Anatomacal factors of the host which might help or hinder movement into the body
2. Active measures taken by microbes to enter the host, such as through motility structures and attachment proteins
3. Hitchhiking on immune cells as a trojan horse

Contraction of a pathogen starts with initial _______ to the microbe inside the host.

Then, the microbe goes through an _______ period that can end in one of three ways:

1. The host can remain _________ and never know they were infected 
2. The host may expirience slight symptomes but no real disease and ______
3. The host can show full disease symptomes, which either end in ______, _______ illness, or _____

Contraction of a pathogen starts with initial exposure to the microbe inside the host.

Then, the microbe goes through an incubation period that can end in one of three ways:

1. The host can remain asymtomatic and never know they were infected 
2. The host may expirience slight symptomes but no real disease and recover
3. The host can show full disease symptomes, which either end in recovery, recurrent illness, or death

Multiplication of Bacteria Depends On:

1. ________ factors of the host and the surrounding area
2. Subversion of host defenses, either through evading the ______ system or though siphoning _______ from the host from growth and reproduction

Multiplication of Bacteria Depends On:

1. Enviornmental factors of the host and the surrounding area
2. Subversion of host defenses, either through evading the immune system or though siphoning nutrients from the host from growth and reproduction

Damage to the Body Caused by Pathogens:

1. Mechanisms of ______ damage
2. Overreaction or misdircetion of the _____ system

Damage to the Body Caused by Pathogens:

1. Mechanisms of direct damage
2. Overreaction or misdircetion of the immue system

Mechanisms of Direct Damage Caused by Pathogens:

Pathogens can secrete different ______ which may or may not be intended to cause harm, initiate ______ of infected cells, or cause ______ shock to the host system. 

Mechanisms of Direct Damage Caused by Pathogens:

Pathogens can secrete different toxins which may or may not be intended to cause harm, initiate apoptosis of infected cells, or cause endotoxema shock to the host system. 

Sectreated pathogenic toxins can be classified as _______, toxins found constituitivly on pathogenic surfaces, or as _________, which are produced soley to harm the host.

Sectreated pathogenic toxins can be classified as endotoxins, toxins found constituitivly on pathogenic surfaces, or as exotoxins, which are produced soley to harm the host.

Damaged Caused to the Body By Immune Responces:

Both types of immune responces can lead to bodily harm while in the process of clearning out invaders.

The _______ responce releases Abs in responce to Ags

The __________  responces recruits T and B cells to fight invaders and induces inflammation

Damaged Caused to the Body By Immune Responces:

Both types of immune responces can lead to bodily harm while in the process of clearning out invaders.

The Humoral responce releases Abs in responce to Ags

The Cell-meidated responces recruits T and B cells to fight invaders and induces inflammation

Normal microbial flora differs between people of different ______ , and is further varied between different _____ of the body

Normal microbial flora differs between people of different regions, and is further varied between different organs of the body

The gut is mostly filled with Gram-_______bacteria, and the Throat, Vaginia, and Skin are mostly populated by Gram-___________bacteria.

As far as oxygen use goes, gut microbes are obligate anaerobes.

The gut is mostly filled with Gram-Negative bacteria, and the Throat, Vaginia, and Skin are mostly populated by Gram-Positive bacteria.

As far as oxygen use goes, gut microbes are obligate anaerobes.

_____ and ______ can alter the state of the microbial flora in the gut

Diet and antibiotics can alter the state of the microbial flora in the gut

Anticolonization techniques include:

1. Harmful ____ and _____ use in the gut
2. _____ current in urinary tract sweeping away microbes
3. ______ killing bacteria
4. Starving microbes of ______

Anticolonization techniques include:

1. Harmful diet and antibiotic use in the gut
2. Liquid current in urinary tract sweeping away microbes
3. Phagocytes killing bacteria
4. Starving microbes of nutrients

Normal microbial flora can be __________ members that aren't always present, and ___________ members that are stablely colonized.

Which of the 2 is more likely to cause disease?

Normal microbial flora can be transient members that aren't always present, and permenent members that are stablely colonized.

Transient, since a stable colony has more interest in a living host to stay on

Role of Normal Flora:

1. Common Source of ________
2. __________ System Stimulation
3. Pathogen ______
4. Human _______ and _________
5. Source of some ________

Role of Normal Flora:

1. Common Source of Infection
2. Immune System Stimulation
3. Pathogen Exclusion
4. Human Nutrition and Metabolism
5. Source of some Carcinogens

The normal bacetrial flora of the bdy gives the body an important boost to the immune system.

This is done through ______ of the immune responce, meaning that the normal flora of the body gives the host a sense of which bacteria to tolerate and which are likely to be harmful.

Having a healthy population of flora means that you are less likely to have ______ and more likely to fight off ______.

The normal bacetrial flora of the bdy gives the body an important boost to the immune system.

This is done through moderation of the immune responce, meaning that the normal flora of the body gives the host a sense of which bacteria to tolerate and which are likely to be harmful.

Having a healthy population of flora means that you are less likely to have allergies and more likely to fight off infection

Pathogen exclusion works through ____ _____, meaning that cells will try not to grow close to one aanother.

This also means that your normal flora population can try to outcompete pathogens for ______

Pathogen exclusion works through contact inhibition, meaning that cells will try not to grow close to one aanother.

This also means that your normal flora population can try to outcompete pathogens for nutrients

Bacterial flora is important for human ______ and for the synthsesis/collection of essential nutrients like ______ and Vitamin ____

Bacterial flora is important for human digestion and for the synthsesis/collection of essential nutrients like Vitamin K and Iron

Why is it ok for the colon to be filled with bacteria, but the lungs must remain relativly sterile in order to function properly?

The lungs are mainly in charge of gas exchage between air and CO2, and must maintain a non-inflammatory state within the thin surface area used to exchange gases

Bacteria must be be kept out of the lungs to prevent infection and inflammation.

This is accomplished by _______ linings traping bacteria and other particles so that the cilliated ______ epithtlium can take it out of the lungs via a waving motion

Bacteria must be be kept out of the lungs to prevent infection and inflammation.

This is accomplished by mucosal linings traping bacteria and other particles so that the cilliated columnar epithtlium can take it out of the lungs via a waving motion

A _______ animal is an animal that was raised in such a way as to not have any sort of germs on and few few germs in it.

A gnotobiotic animal is an animal that was raised in such a way as to not have any sort of germs on and few few germs in it.

_______ infections are infections contracted while in a hospital setting, wether it be from doctors, other patients, or a comprimised immune system

It is the most _____ type of infection

Noscomal infections are infections contracted while in a hospital setting, wether it be from doctors, other patients, or a comprimised immune system

It is the most common type of infection

The bacterium ___________ is the most common cause of a noscomal infection

The bacterium C.dificil is the most common cause of a noscomal infection

Bacteria are classified as _________

Bacteria have both a cell ____ and a cell _______. 

The inside of the cell is filled with __________ , which manufacture protein, and _______.

There is no defined nucleus;instead, DNA strands coil roughly in the center to form a ________

Bacteria are classified as prokaryotes

Bacteria have both a cell wall and a cell membrane. 

The inside of the cell is filled with ribosomes, which manufacture protein, and proteins.

There is no defined nucleus;instead, DNA strands coil roughly in the center to form a nucleoid

Bacteria have _____ chromosomes and tend to have ____ copy of a gene per a chromosome, while eukaryotes like to have psuedogene repeats.

Both bacteria and eukaryotic cells have extracellular genetic info floating around: for eukaryotes these can be mitochondria or chloroplasts.

In bacteria, they are the _____.

Bacteria have haploid chromosomes and tend to have one copy of a gene per a chromosome, while eukaryotes like to have psuedogene repeats.

Both bacteria and eukaryotic cells have extracellular genetic info floating around: for eukaryotes these can be mitochondria or chloroplasts.

In bacteria, they are the plasmids.

Bacteria have no intergenic sequences, meaning they only have _____ and no ____ or _____ of previous genes.

They depend on ______ to transcibe more than one gene at a time, and don't undergo much post-_________ regulations.

The mRNA of bacteria is also rarely _______.

Bacteria have no intergenic sequences, meaning they only have exons and no intron or repeats of previous genes.

They depend on Operons to transcibe more than one gene at a time, and don't undergo much post-transcriptional regulations.

The mRNA of bacteria is also rarely processed.

Bacterial mRNA is very ______ and prone to breakage.

Bacterial mRNA is very fragile and prone to breakage.

Gram Positive bacterial walls have one layer of cell _______ underneath the cell _____.

The cell wall is mainly comprises of _________, also called _______.

There are projections of _________ acid and ________ acid that come out of the cell wall, with lipoteichoic acid extending to the cell ___________

Gram Positive bacterial walls have one layer of cell membrane underneath the cell wall.

The cell wall is mainly comprises of peptidoglycan, also called murine.

There are projections of teichoic acid and lipoteichoic acid that come out of the cell wall, with lipoteichoic acid extending to the cell membrane 

 Gram Negative bacteria have two layers of cell ________ that sandwhich a layer of cell _____.

The layer between cell membrane-cell wall-cell membrane is called the ________.

The cell wall is still made of peptidoglycan, but is much ______ than the wall of Gram+ bacteria.

Gram negative walls have trimer proteins called _____ that allow ingress and egress of molecules.

 Gram Negative bacteria have two layers of cell membrane that sandwhich a layer of cell wall.

The layer between cell membrane-cell wall-cell membrane is called the periplasm.

The cell wall is still made of eptidoglycan, but is much thinner than the wall of Gram+ bacteria.

Gram negative walls have trimer proteins called porins that allow ingress and egress of molecules.

The cell membrane of Gram +/- bacteria are made of a ___layer of ____________ heads with __________ tails.

_____________ connect the cell walls and membranes together

Peptidoglycan is made of monomers of N-______________and N-______________ acid.

To form a wall structure, the layers of these monomers are bound to upper and lower layers by ___-linked ____.

Peptidoglycan is made of monomers of N-acetylglucosamine and N-acytlmuramic acid.

To form a wall structure, the layers of these monomers are bound to upper and lower layers by cross-linked peptides.

Gram negative walls cross link _______ acid to D-____, and Gram positive walls link D-______ and D-_______

Gram negative walls cross link diaminopimelic acid to D-alanine, and Gram positive walls link D-lysine and D-alanine

Lipopolysacharides are a common feature of Gram negative bacteria.

They are made of three units:

1. The Lipid ___ subunit attached to _____ acid chains
2. The core _____________
3. The repeating O ________ subunits

Lipopolysacharides are a common feature of Gram negative bacteria.

They are made of three units:

1. The Lipid A subunit attached to fatty acid chains
2. The core polysaccharide
3. The repeating O antigen subunits

The fatty acid chains of lipopolysaccharides are responcible for the ________ of the molecule.

The core polysaccharide has ______ and _____ regions.

The repeating O antigen subunits are highly _____ between different bacteria and are responcible for the different ______ specificities between Gram (-) bacterias

The fatty acid chains of lipopolysaccharides are responcible for the hydrophobicity of the molecule.

The core polysaccharide has variable and invariable regions.

The repeating O antigen subunits are highly variable between different bacteria and are responcible for the different antigenic specificities between Gram (-) bacterias

The biosynthesis of peptidoglycan is a huge point of attack for ________.

Penicillain prevents the _______ binding of the layers of wall monomers.

Vancomycin prevents the _________ of a layer from binding together

The biosynthesis of peptidoglycan is a huge point of attack for antibiotics.

Penicillain prevents the peptide binding of the layers of wall monomers.

Vancomycin prevents the monomers of a layer from binding together

General Scheme Used to ID a Specific Genes (Invasin)

1. Isolate ____ from cell
2. _____ DNA into pieces
3. Splice DNA fragments into ______
4. Reintroduce restriction ______ into recipient 
5. Enrich cells to find specific ____ (invasin) clones
6. _____ plasmid on a gel
7. Mutate cell and see if invasin is present when reintroduced to origninal ____ (will invade if present)
8. Identify protein through ___-____

General Scheme Used to ID a Specific Genes (Invasin)

1. Isolate DNA from cell
2. Fragment DNA into pieces
3. Splice DNA fragments into plasmids
4. Reintroduce restriction plasmids into recipient 
5. Enrich cells to find specific gene (invasin) clones
6. Sequence plasmid on a gel
7. Mutate cell and see if invasin is present when reintroduced to origninal host (will invade if present)
8. Identify protein through SDS-PAGE

Creating a Genomic Library:

1. Chose a ______ _______ that will cleave DNA with specific ends in mind
2. Cut DNA into restriction ______
3. ______ fragments into plasmids with matching sticky ends
4. Take the recombinate plasmids and introduce them into E.coli to be _________ into the E.coli genome

Creating a Genomic Library:

1. Chose a restriction endonuclease that will cleave DNA with specific ends in mind
2. Cut DNA into restriction fragments
3. Ligate fragments into plasmids with matching stiky ends
4. Take the recombinate plasmids and introduce them into E.coli to be transformed into the E.coli genome

Enrichment of Transformed Plasmids to Find a Gene:

1. Grow transformed plasmids in _____ culture
2. Inoculate plasmids into ______ cells
3. Incubate cells at __C
4. _____ cells 
5. Transfer the plasmids into a _______ (antibiotic) medium and repeat steps 3 and 4
6. Skip step 5 and gentally _____ the cells
7. _______ for viable counts

Enrichment of Transformed Plasmids to Find a Gene:

1. Grow transformed plasmids in liquid culture
2. Inoculate plasmids into mammalian cells
3. Incubate cells at 37C
4. Wash cells 
5. Transfer the plasmids into a gentamycin (antibiotic) medium and repeat steps 3 and 4
6. Skip step 5 and gentally lyse the cells
7. Titrate for viable counts

Invasin genes on the Y.psuedoTB can be replaced by _________  resistance genes, which are part of positive cell selection.

This is accomplished through a double ___________ event between suicide plasmas with kana res and the main chromsome with Inv.

Invasin genes on the Y.psuedoTB can be replaced by kanamycin resistance genes, which are part of positive cell selection.

This is accomplished through a double recombination event between suicide plasmas with kana res and the main chromsome with Inv.

Making gene knockouts requires that cassetes of certain gene are inserted into a specific site by using ___ _____.

Remember that homologus recombination is a process in which similar or identical genetic sequences _____ between molecules of DNA.

Making gene knockouts requires that cassetes of certain gene are inserted into a specific site by using homologous recombination.

Remember that homologus recombination is a process in which similar or identical genetic sequences exchange between molecules of DNA.

In KO genes, the engineered homolog will have a positive and a negative selection marker.

Positive selection markers ensure that only homologes that ______ that marker will live.

Negative selection markers ensure that only homolges that incorperated the cassete in the correct ______ will live

In KO genes, the engineered homolog will have a positive and a negative selection marker.

Positive selection markers ensure that only homologes that integrated that marker will live.

Negative selection markers ensure that only homolges that incorperated the cassete in the correct place will live

Positive selection markers include _____ , which carries genes for antibiotic resistance.

Negative selection markers are _____ virus, or _____ toxin genes

Positive selection markers include neomycin, which carries genes for antibiotic resistance.

Negative selection markers are herpes virus, or diptheria toxin genes

Steps to make KO Mice:

1. Isolate _____ and take cells from the ____ of a grey mouse
2. Grow these ICMs in blood culture
3. Add engineered cassestes with ____ and ____ selection markers and shock cells
4. DNA that integrated the negative marker will ___ and those that integrated nothing will need to be removed by adding an ______ (ganciclovir)
5. Take those stem cells and add them into a ____ colored mouse donor blastocyst
6. Babies will have _____ and ____ mouse cells, becoming chimeric
7. Then breed these chimeras back with white mice, any broods with all grey babies have ____ and ____ cells from the grey mouse ICM

Steps to make KO Mice:

1. Isolate blastomers and take cells from the ICM of a grey mouse
2. Grow these ICMs in blood culture
3. Add engineered cassestes with positive and negative markers and shock cells
4. DNA that integrated the negative marker will die and those that integrated nothing will need to be removed by adding an antibiotic (ganciclovir)
5. Take those stem cells and add them into a white mouse donor blastocyst
6. Babies will have white and grey mouse cells, becoming chimeric
7. Then breed these chimeras back with white mice, any broods with all grey babies have somatic and germ cells from the grey mouse ICM

________ ______ and __________ are genetic elements critical to the ability of a gene to move from one chromsome to anthoer, as seen with the invasin/kanamycin resistance exconjugates and the selection of grey and white mouse cells.

Without these elements, sections of chromosomes may not move from one to another.

Insertion sequences and transposons are genetic elements critical to the ability of a gene to move from one chromsome to anthoer, as seen with the invasin/kanamycin resistance exconjugates and the selection of grey and white mouse cells.

Without these elements, sections of chromosomes may not move from one to another.

Insertion Sequences are an important part of double recombination events between gene on different chromsomes.

It is a segment of genetic material that looks like this:

1. Ends of IS flanked by ______ ______
2. Has a core gene, which is comparised of ____ _____ ______ on both ends and the gene itself.
3. The gene is used in order to ensure that _______ can accomplish their job

Insertion Sequences are an important part of double recombination events between gene on different chromsomes.

It is a segment of genetic material that looks like this:

1. Ends of IS flanked by terminal repeats
2. Has a core gene, which is comparised of inverted terminal repeats on both ends and the gene itself.
3. The gene is used in order to ensure that transposons can accomplish their job

Transposons are the main player in gene jumping from one chromosome to another.

It looks somewaht similar to an insertion sequence:

1. Entierty of transposon is flanked by _____ ______
2. Also has a core gene, which is made of the gene itself flanked on both ends by _____ _____
3. The core gene is ultimatly used in confering _________ resistance from one bacteria to another

Transposons are the main player in gene jumping from one chromosome to another.

It looks somewaht similar to an insertion sequence:

1. Entierty of transposon is flanked by terminal repeats
2. Also has a core gene, which is made of the gene itself flanked on both ends by insertion sequences
3. The core gene is ultimatly used in confering antibiotic resistance from one bacteria to another

Transposons, if successful, will transplant a gene into an ________ sequence in the target chromosome.

If a transposon inserts a gene into an existing target gene, then that target gene is ____ ____.

Transposons, if successful, will transplant a gene into an intergenic sequence in the target chromosome.

If a transposon inserts a gene into an existing target gene, then that target gene is knocked out.

Transposons can be used to determine what proteins (and by extention, which genes) accomplish a certain task.

In the case of cholora, scientists wanted to determine which surface proteins on cholera were responcible for its suvival in the human gut.

How could they use transposons to determine which surface proteins were responcible for the survival of cholera?

By chosing a gene that will not only transpose into a desired gene to be silence, but one that signals it's presence in the gene and thusly, the silenceing of the gene thought to play a role in survival.

In order to look at which genes allowed cholera to thrive and infect a host, a transposon of the gene ____ was targeted against specific target cholera genes.

This transposon gene was used because it turns X-gal plates ____ when properly recombinated, and it only functions if it is ___ transposed.

In order to look at which genes allowed cholera to thrive and infect a host, a transposon of the gene phoA was targeted against specific target cholera genes.

This transposon gene was used because it turns X-gal plates blue when properly recombinated, and it only functions if it is fully transposed.

Along with phoA, the gene for _______ resistance was transposoned from suicide plasmids into cholera chromosomes.

While phoA was used to ______ for colonies because of the blue color of positive colonies, the resistance gene was used to ______ for colonies with particular characteristics

Along with phoA, the gene for kanamycin resistance was transposoned from suicide plasmids into cholera chromosomes.

While phoA was used to screen for colonies because of the blue color of positive colonies, the resistance gene was used to select for colonies with particular characteristics

After the screening process revealed the positivly selected colonies, those colonies were taken from the kanamycin plate and grown in broths with pHs that resembled _____ conditions and a _____ broth.

The gut pH was set at ___pH, and the control was set around ___pH

After the screening process revealed the positivly selected colonies, those colonies were taken from the kanamycin plate and grown in broths with pHs that resembled gut conditions and a control broth.

The gut pH was set at 6.5pH, and the control was set around 8.0pH

When looking at the broths of phoA/kanamycin resistance in particular broths, the scientists wanted to culture sample that grew well in ____ pH and failed to thrive in ___ pH broths.

Why would this be?

When looking at the broths of phoA/kanamycin resistance in particular broths, the scientists wanted to culture sample that grew well in 6.5 pH and failed to thrive in 8 pH broths.

This is because these were the colines most likely to resemble the originonal gene. Operating well in the control pH would mean that the colony didn't resemble the origional gene very closely

Once the phoA colonies that only grew well in gut pH levels were identified, they were re-inoculated back into mice and the virulence of the cholera strain was observed. 

What did scientists observe, and what could be infered from that?

Scientists found the the virulence of the cholera infected into the mice was severly reduced.

This meant that the gene that was targeted for silencing had a major effect on cholera virulence

DNA Tagged TnphoA Mutagenesis to ID Virulence Genes in S.typhimurium

Give a general overview of why you would just DNA sequence tagging on mutant strains and how that reveals utility and function of certain genes

DNA Tagged TnphoA Mutagenesis to ID Virulence Genes in S.typhimurium

The idea is to infect an animal model with a mutant strain (tagged with specific DNA sequences) so that you can compare the mutant strains that failed to infect or survive in mice and see which genes were silenced in order to determine which strains are needed for infectivity or survival

DNA Tagged TnphoA Mutagenesis to ID Virulence Genes in S.typhimurium

1. Create a DNA sequence tag on a ______ gene for kanamycin resistance
2. Allow the transposon to _______ recombine in the S.typhimurium genome
3. Pool mutants and create a _____ assay out of the individual recombinations by amplifying the probes
4. Infect mice with strains from control pool and collect cells from mouse ______ for comparison
5.  ______ collected probes and compare to the control assay
6. Any probes that fail to light up during observations means that that particular gene was ______ and needed for ______ of the bacteria
7. Determine identify of missing survival genes by _______ corresponding control group

DNA Tagged TnphoA Mutagenesis to ID Virulence Genes in S.typhimurium

1. Create a DNA sequence tag on a transposon gene for kanamycin resistance
2. Allow the transposon to randomly recombine in the S.typhimurium genome
3. Pool mutants and create a control assay out of the individual recombinations by amplifying the probes
4. Infect mice with strains from control pool and collect cells from mouse spleen for conparison
5.  Amplify collected probes and compare to the control assay
6. Any probes that fail to light up during observations means that that particular gene was silenced and needed for survival of the bacteria
7. Determine identify of missing survival genes by cloning corresponding control group

IVET, or ____ _____ _____ ______, can be used to identify virulence genes in bacteria instead of DNA seqence tagging or other methods

IVET, or In Vivo Expression Technology, can be used to identify virulence genes in bacteria instead of DNA seqence tagging or other methods

For IVET techinques to find virulence genes in S.typhirium, the genes ____ and ____ are transformed from a suicide plasmid onto a restion fragmented genome of Salmonella to see what genes in the bacteria have been turned ____. 

For IVET techinques to find virulence genes in S.typhirium, the genes purA and lacz are transformed from a suicide plasmid onto a restion fragmented genome of Salmonella to see what genes in the bacteria have been turned on. 

For the IVET ID of Salmanella genes, the plasmid has the origin ____.

In instances when the origin was not properly used and the purA gene was left out of conjugal transpher onto the bacterial genome, when infected into a mouse the cells will _____.

For the IVET ID of Salmanella genes, the plasmid has the origin R6K.

In instances when the origin was not properly used and the purA gene was left out of conjugal transpher onto the bacterial genome, when infected into a mouse the cells will die.

Both purA and lacZ genes must be downstream of a ______ sequence to be expressed.

After harvesting the bacteria cells from mouse spleens, the cells are plated those that grow either turn blue for ___ lacZ or white for ___ lacZ.

You want ____ colored colonies, because that means the cells survived, but only express lacZ __ ___, not on plates.

Both purA and lacZ genes must be downstream of a promoter sequence to be expressed.

After harvesting the bacteria cells from mouse spleens, the cells are plated those that grow either turn blue for on lacZ or white for off lacZ.

You want white, because that means the cells survived, but only express lacZ in vivo, not on plates.

On X-gal plates, the precence of lactose turs the media _____.

In McConkey plates, the precence of lactose turns the media ____.

On X-gal plates, the precence of lactose turs the media blue.

In McConkey plates, the precence of lactose turns the media red.

Looking back at the IVET expiriment to find virulence factors in Salmanella:

Selection for genes happened in the _____, while screening happened on the ______

Looking back at the IVET expiriment to find virulence factors in Salmanella:

Selection for genes happened in the mice, (surviving bacterial cells muct have purA/lacZ) while screening happened on the plates (White colonies for no lacZ outside mice)

phoA codes for the biosynthysis of ______ ______, which turns surrounding media blue and is useful for screening.

purA is used in _____ biosyntheiss, and is needed for _____ , not virulence.

lacZ is part of a fairly ubiquitus _____ set that helps measure levels of ____ expression and codes for b-glactocydase.

phoA codes for the biosynthysis of alkaline phosphotase, which turns surrounding media blue and is useful for screening.

purA is used in purine biosyntheiss, and is needed for survival, not virulence.

lacZ is part of a fairly ubiquitus operon set that helps measure levels of gene expression and codes for b-glactocydase.

The DFI (____ _____ _____) technique can be used to ID genes expressed by S.typhimurium during the bacteria's intracellular survival in Macrophages.

It basically works by _____, ______, then ______ macrophage products taken from mice spleens after infection

The DFI (Differential Flouroecence Induction) technique can be used to ID genes expressed by S.typhimurium during the bacteria's intracellular survival in Macrophages.

It basically works by tagging, filtering, then screening macrophage products taken from mice spleens after infection

Steps Used in DFI to ID Salmonella Survival Genes:

1. Partially digest Salmonella chromosome and ligate a ____ gene from a plasmid into the peices 
2. Infect macrophages with the tranformed Salmonella and seperate by FACS (____ ____ ___ ______)
3. Take the macrophages with flouroecence and seperate from the rest of the macrophages, then lyse them and grow resulting ______ on media
4. Take the bacteria from the first round of sorting and go through FACS again, creating a group of _______ and ___________ bacteria
5. Take the _______ bacteria and infect into macrophages, and then sort those macrophages in a group with flouroecent bacteria.
6. Analyze the clone sequences in bacteria that glow when grown on _________, but don't glow when grown on ______.

Steps Used in DFI to ID Salmonella Survival Genes:

1. Partially digest Salmonella chromosome and ligate a GFP gene from a plasmid into the peices 
2. Infect macrophages with the tranformed Salmonella and seperate by FACS (Flouroscenet Activated Cell Sorter)
3. Take the macrophages with flouroecence and seperate from the rest of the macrophages, then lyse them and grow resulting bacteria on media
4. Take the bacteria from the first round of sorting and go through FACS again, creating a group of flouroecent and non-flouroecent bacteria
5. Take the NF bacteria and infect into macrophages, and then sort those macrophages in a group with flouroecent bacteria.
6. Analyze the clone sequences in bacteria that glow when grown on macrophages, but don't glow when grown on media

To see what sorts of proteins are expressed on the surface of M.tuberculosis as virulence factors against a host (meaning when the cell is in vivo), scientists can use IVIAT (__ ___ ____ ____ _____) to look at the Ags produced from hosts when infected with TB bacteria

To see what sorts of proteins are expressed on the surface of M.tuberculosis as virulence factors against a host (meaning when the cell is in vivo), scientists can use IVIAT (In Vivo Induced Antigen Technology) to look at the Ags produced from hosts when infected with TB bacteria

______ proteins are usually the virulence factors of bacteria when a host develops symptomes.

Surface proteins are usually the virulence factors of bacteria when a host develops symptomes.

In Vivo Induced Ag technology and TB

1. The immune system makes ____ in responce to Ags. The Ags in this case are the _____ proteins on TB cells that cause virulence.
2. To ID these proteins, first ______the TB genome
3. Digest these fragments and add into a _____ phage library
4. Replicate the library after induction with _____ (to induce lac operon activity)
5. Add to plate with _____ to create plaques
6. Add membrane to plate to capture plaques with TB and transfer to plate with patient _____
7. ______ from patient with previous infection will bind to TB or be free flowing on the plate
8. Remove these Abs and preform an _________ to see which plaques light up (have Ab bound)
9. Isolate and _______ the genetic fragment that was bound to Ab

In Vivo Induced Ag technology and TB

1. The immune system makes Abs in responce to Ags. The Ags in this case are the surface proteins on TB cells that cause virulence.
2. To ID these proteins, first fragment the TB genome
3. Digest these fragments and add into a λgt11 pahge library
4. Replicate the library after induction with IPTG (to induce lac operon activity)
5. Add to plate with E.coli to create plaques
6. Add membrane to plate to capture plaques with TB and transfer to plate with patient serum
7. Abs from patient with previous infection will bind to TB or be free flowing on the plate
8. Remove these Abs and preform an immunoassay to see which plaques light up (have Ab bound)
9. Isolate and sequence the genetic fragment that was bound to Ab

Microarray Scheme Used to Compare In Vivo and In Vitro Examples of Cholera:

1. Isolate the ____ from both samples 
2. Tag the in vitro samples with ___ labled DNA (red)
3. Tag the in vivo smaples with ___ labled DNA (green)
4. Hybridize the two on a microarray and look for ___, _____ , and mixed _____ samples

Microarray Scheme Used to Compare In Vivo and In Vitro Examples of Cholera:

1. Isolate the RNA from both samples 
2. Tag the in vitro samples with Cy5 labled DNA (red)
3. Tag the in vivo smaples with Cy3 labled DNA (green)
4. Hybridize the two on a microarray and look for red, green, and mixed yellow samples

A microarray synthesizes ____ with a sequence of each ____ present in order to get a picture of the entire genome.

Each gene needs a ______ tag, and if you combine two microarrays together, you can see if two different genomes have ________ genes

A microarray synthesizes cDNA with a sequence of each gene present in order to get a picture of the entire genome.

Each gene needs a flouroescent tag, and if you combine two microarrays together, you can see if two different genomes have overlapping genes

Microarrays measure comparitive levels of ______ between different genomes.

It creates a _____ library that requires the use of reverse transcriptase (start with _____, end up with ____)

Microarrays measure comparitive levels of protein between different genomes.

It creates a cDNA library that requires the use of reverse transcriptase (start with RNA, end up with DNA)

 DNA Arrays have advantages and disadvantages.

One big advantage is that expressions from every ____ in a genome can be studied alonside the genes from other _______ too.

However, it is dificult to reproduce the _____ and the preperation of the _____ and _____ design must be precise

 DNA Arrays have advantages and disadvantages.

One big advantage is that expressions from every gene in a genome can be studied alonside the genes from other genomes too.

However, it is dificult to reproduce the results and the preperation of the PCR and RNA design must be precise

The quality of RNA prep may be a limiting factor in DNA arrays, especially when looking at fragile ______ RNA

The quality of RNA prep may be a limiting factor in DNA arrays, especially when looking at fragile bacterial RNA

DNA Arrays Are Usually Made From Either:

1. _____ products amplified from each ____
2. 70 base lone ________ identical to sequences in each ____

DNA Arrays Are Usually Made From Either:

1. PCR products amplified from each ORF
2. 70 base lone oligonucleotides identical to sequences in each ORF

________ is the process of sequencing multiple genomes of organisms in the same enviornment (microbiome)

Metagenomics is the process of sequencing multiple genomes of organisms in the same enviornment (microbiome)

Many metagenomic sequencing techniques will take RNA and use ____ _____ to make a specific DNA product (called ____).

This bypasses the need for _______ of sequencing and allows for massive amounts of _______ sequencing.

Many metagenomic sequencing techniques will take RNA and use Reverse transcriptase to make a specific DNA product (called cDNA).

This bypasses the need for hybridization of sequencing and allows for massive amounts of paralelle sequencing.

cDNA libraries require no ______, only ______ and a way to read the DNA

cDNA libraries require no culturing, only purification and a way to read the DNA

Sequencing of the gut microbiome with metagenomic cDNA libraries revealed that not only was there a ______ amount of bacteria living in the gut, but that certain bacteria were more _______ and that some species were connected with specific ____ _____-like disorders (think IBS and Crohns)

Sequencing of the gut microbiome with metagenomic cDNA libraries revealed that not only was there a massive amount of bacteria living in the gut, but that certain bacteria were more prevelent and that some species were connected with specific immune system-like disorders (think IBS and Crohns)

cDNA metagenomics can be used to determine the entire genetic makeup of a microbiome (like the gut) and can estimate the ______, ______, and _______ potentials of that enviornment

cDNA metagenomics can be used to determine the entire genetic makeup of a microbiome (like the gut) and can estimate the pathogenic, metabolic, and enzymatic potentials of that enviornment

Reverse genetics involves taking existing ______ and looking at the _____ that made it, in order to see the underlying ____ and the ____ they exist in

Reverse genetics involves taking existing proteins and lookign at the RNA that made it, in order to see the underlying DNA and the genes they exist in

Remeber that _____ is an inert molecule that simply codes for something else.

______ are the workhorses of the cell, and in many assay exprirments it is the levels of these molecules that are looked at.

There is little correlation between the amounts of _____ and the amount of coded ______

Remeber that mRNA is an inert molecule that simply codes for something else.

Proteins are the workhorses of the cell, and in many assay exprirments it is the levels of these molecules that are looked at.

There is little coorelation between the amounts of mRNA and the amount of coded proteins

One way to look at the levels of protein in a cell is to look athe the level of ______ occuring in the cell.

One way to look at the levels of protein in a cell is to look athe the level of translation occuring in the cell.

Protein levels can be visualized in a 2D ___-_____ gel.

This gel mainly looks at the ______ point and ____ of fragmented protein segments.

Mass ________ is used on the results of this test to find what _____ acids make up the protein, and thusly, what _____ code for the protein 

Protein levels can be visualized in a 2D SDS-PAGE gel.

This gel mainly looks at the isoelectric point and mass of fragmented protein segments.

Mass spectrometry is used on the results of this test to find what amino acids make up the protein, and thusly, what genes code for the protein 

The isoelectric point of a protein is the ___ at which the protein is a _____ charged molecule.

It is spereated from ____ to ____ , or basic to acidic.

Mass is simply the measurment of the ____ of the protein, and is measured from up to down, _____ fragments to ______ fragments

The isoelectric point of a protein is the pH at which the protein is a neutrally charged molecule.

It is spereated from right to left, or basic to acidic.

Mass is simply the measurment of the size of the protein, and is measured from up to down, lightest fragments to heaviest fragments

Mass spectrometry works by fragmenting proteins wth ______ into ______, then seperating the peptides with HPLC and mass detection into different groups of peptide _____.

These fragments of peptide are then ______ and compared to a database, where their genome and ______ product are identified

Mass spectrometry works by fragmenting proteins wth trypsin into peptides, then seperating the peptides with HPLC and mass detection into different groups of peptide masses.

These fragments of peptide are then sequenced and compared to a database, where their genome and protein product are identified

HPLC stands for ____ _____ ___ ______

HPLC stands for High Preformance Liquid Chromatography

High throughput Mass spec screening starts by taking mixtures of digested proteins and running them through _____ ___ _____ _____ and ____ ____at the same time.

This allows for the identification of an entire spectrum of ______ produced by bacterium in specific ______

High throughput Mass spec screening starts by taking mixtures of digested proteins and running them through HPLC and MS at the same time.

This allows for the identification of an entire spectrum of proteins produced by bacterium in specific conditions

The goal of High throughput Mass Spec screening is to isolate bacteria from an _______ and quickly identify the ______ present.

This gives a spectrum of potential ______ factors

The goal of High throughput Mass Spec screening is to isolate bacteria from an infection and quickly identify the proteins present.

This gives a spectrum of potential virulence factors

Two common ways for antibiotics to kill bacteria is to prevent the synthesis of _____ acid, or to block the polymerization of ________ monomers

Two common ways for antibiotics to kill bacteria is to prevent the synthesis of folic acid, or to block the polymerization of peptidoglycan monomers

_________ are a class of anitbacterials that block the sythesis of folic acid (Vitamin ____)

These sulfa drugs compeate with __-________ acid and create a leathal product instead of folic acid, which kills bacteria

Sulfanilamides are a class of anitbacterials that block the sythesis of folic acid (Vitamin B9)

These sulfa drugs compeate with p-aminobenzoic acid and create a leathal product instead of folic acid, which kills bacteria

How are sulfa drugs dafe to use when they interfere with the production of folic acid, a crucial vitamin?

We cannot produce folic acd in our bodies, so blocking the syntheiss of it only affects the precursors to the product, and not dietaru sources of folic acid

Antibacterials can either halt the growth of a bacteria (________) or outright kill the virus (______)

Antibacterials can either halt the growth of a bacteria (bacteriostatic) or outright kill the virus (bacteriocidal)

Bacteriostatic drugs include ________, which prevents tRNA from binding to mRMA, and bacteriocidal drugs could be _______, which breaks apart or stops the creation of peptidoglycan.

Bacteriostatic drugs include tetracycline, which prevents tRNA from binding to mRMA, and bacteriocidal drugs could be penicillin, which breaks apart or stops the creation of peptidoglycan.

Resistance Mechanisms of Bacteria Against Antibiotics:

1. Synthesis of _______ that break down antibiotics
2. ______ modifications of antbiotics that interuppts activity
3. ______ the intake of antibiotic into cells
4. Increase the ______ rate of drug and lower the _______ in the cell
5. Modify the ______ site of the antibiotic

Resistance Mechanisms of Bacteria Against Antibiotics:

1. Synthesis of enzymes that break down antibiotics
2. Chemical modifications of antbiotics that interuppts activity
3. Inhibit the intake of antibiotic into cells
4. Increase the export rate of drug and lower the concentration in the cell
5. Modify the target site of the antibiotic

One enzyme made by bacteria to combat antibiotics is ________.

It is also called β-________

One enzyme made by bacteria to combat antibiotics is penicillinase.

It is also called β-lactamase

Tetracyclins prevent protein synthesis and are combated by an _____ pump.

Sulfonamides prevent the synthesis of vitamin B9 and are stopped by _____ modification of the enzyme that creates _____

Tetracyclins prevent protein synthesis and are combated by an efflux pump.

Sulfonamides prevent the synthesis of vitamin B9 and are stopped by target modification of the enzyme that creates PBA

Erythromycin antibiotics prevent ______ subunits from binding and are halted by ______ of 23S ribosomal RNA

Quniolones prevent the enzyme DNA _____ from unwinding DNA.

Bacteria like to mutate the genes that code for that enzyme in a form of _______ modification

Erythromycin antibiotics prevent ribosomal subunits from binding and are halted by methylation of 23S ribosomal RNA

Quniolones prevent the enzyme DNA gyrase from unwinding DNA.

Bacteria like to mutate the genes that code of that enzyme in a form of target modification

Vancomycin is another antibacterial that likes to target ________ , and is stoped by both ______ modification and _____

_________ antibiotics are dervived from fungi and are another class of __-______ molecules that target peptidoglycan

Vancomycin is another antibacterial that likes to target peptidoglycan, and is stoped by both target modification and efflux

Cephalosporin antibiotics are dervived from fungi and are another class of β-lactam molecules that target peptidoglycan

The most common way for bacteria to combat antibiotics is by:______

Modification of the target site

The use of antiobiotics creates a _____selective pressure from _______ for bacteria to gain resistance.

The misuse of antibiotics creates a situation in which this genetic pressure creates ______ strains

The use of antiobiotics creates a negative selective pressure from genetics for bacteria to gain resistance.

The misuse of antibiotics creates a situation in which this genetic pressure creates resistant strains

Vancomycin drugs work by interfering with peptioglycan cell wall crossing linking between d-______ and d-_______ terminal chain monomers

D-______ can be linked with d-ala instead for resitance to vancomycin

Vancomycin drugs work by interfering with peptioglycan cell wall crossing linking between d-alamine and d-alamine terminal chain monomers

D-lactate can be linked with d-ala instead for resitance to vancomycin

Outcomes of Multi-Drug Therapy:

1. _______
2. ___________
3. ___________

Outcomes of Multi-Drug Therapy:

1. Synergy
2. Anatagonism
3. Indifference

Antibiotics that are synergistic can be used at the same time and give better results than if used alone.

One such pair is between _______ and ______.

Anitbioticts that are antagonistic tend to weak the effects of one another.

_______ and ______ should not be used together for this reason

Antibiotics that are synergistic can be used at the same time and give better results than if used alone.

One such pair is between Penicillin and gentamycin.

Anitbioticts that are antagonistic tend to weak the effects of one another.

Tetracycline and penicillin should not be used together for this reason

The underlying principle of multi drug therapy is to pair bacteristatic with ___________ , and bacteriocidal with _________.

The underlying principle of multi drug therapy is to pair bacteristatic with bacteriostatic, and bacteriocidal with bacteriocidal.

The _______ and ______ Immune system work together to rid the body of bacterial invaders.

While they both target different characteristics and function in dfferent ways, both systems use _______ and ________ components to carry out the overall function of the immune system

The Innate and Adaptive Immune system work together to rid the body of bacterial invaders.

While they both target different characteristics and function in dfferent ways, both systems use Cellular and Humoral components to carry out the overall function of the immune system

As a general description, cellular components of immunity tend to use different ____ as mediators of immunity.

Humoral components are released _____ and ______ products that may come from the cellular products or from self cells

As a general description, cellular components of immunity tend to use different cells as mediators of immunity.

Humoral components are released protein and peptide products that may come from the cellular products or from self cells

Cellular Components of the Innate Immune System:

1. The first reponder is the ____
2. ______ cells like neutrophils and macrophages
3. ___________ cells 
4. _____ cells for professional killing of bacteria
5. ______ are critical for killing invaders and bridging cellular and humoral immunites

Cellular Components of the Innate Immune System:

1. The first reponder is the skin
2. Phagocytic cells like neutrophils and macrophages
3. Proinflammatory cells 
4. NK cells for professional killing of bacteria
5. APCs are critical for killing invaders and bridging cellular and humoral immunites

Humoral Components of the Innate Immuns System:

1. Antimicrobial _______
2. ______ system of proteins
3. ______ released by cells to trigger signalls
4. _______ released alongside cytokines
5. _______ to degrade and kill microorganims

Humoral Components of the Innate Immuns System:

1. Antimicrobial peptides
2. Compliment system of proteins
3. Cytokines released by cells to trigger signalls
4. Chemokines released alongside cytokines
5. Enzymes to degrade and kill microorganims

Innate Immunity Inducers of Inflammation:

1. Increased ______ supply 
2. Increased _______ permiability 
3. ________ 

Innate Immunity Inducers of Inflammation:

1. Increased blood supply (Erythema)
2. Increased vascular permiability (Edema)
3. Chemotaxis (Induration)

Innate Immunity Inducers of Inflammation:

1. Increased blood supply (________)
2. Increased vascular permiability (_____)
3. Chemotaxis (_______)

Innate Immunity Inducers of Inflammation:

1. Increased blood supply (Erythema)
2. Increased vascular permiability (Edema)
3. Chemotaxis (Induration)

Innate Immunity Inducers of Inflammation:

1. Increased blood supply (Erythema): Brings more ________ cells and proteins to site of infection
2. Increased vascular permiability (Edema): Brings more antimicrobial _____ to site of infection
3. Chemotaxis (Induration): Infiltration of infection site with ________

Innate Immunity Inducers of Inflammation:

1. Increased blood supply (Erythema): Brings more antimicrobial cells and proteins to site of infection
2. Increased vascular permiability (Edema): Brings more antimicrobial proteins to site of infection
3. Chemotaxis (Induration): Infiltration of infection site with Erythrocytes

Skin has a multitude of components that allows it to be the first line of innate immunity.

Firstly, the _______ epithelium layer of the skin gives physical protection against invaders. The frequent shedding of skin cells, caused by ______ of straified epithlium, is another method of removing invaders. The _____ junctions that join the skin epithlial cells prevent microorganisms from colonizing on the skin.

Skin has a multitude of components that allows it to be the first line of innate immunity.

Firstly, the keratinized epithelium layer of the skin gives physical protection against invaders. The frequent shedding of skin cells, caused by desquamation of straified epithlium, is another method of removing invaders. The tight junctions that join the skin epithlial cells prevent microorganisms from colonizing on the skin.

Aside from the physical components of skin, there are chemical defenses that the skin uses to stop microbial invasions.

Chemicals called ______ found on the skin kill bacretia and fungi alongside _______ that target bacterial RNA. Sweat glands release ______ as another bacteriociadal chemical. ___ ____ from sebaceous glands inhibit bacterial growth.

Enzymes like ______ from tears and ______from skin hydrolyse bacterial peptidoglycan.

Aside from the physical components of skin, there are chemical defenses that the skin uses to stop microbial invasions.

Chemicals called defensins found on the skin kill bacretia and fungi alongside ribonuceases that target bacterial RNA. Sweat glands release dermcidin as another bacteriociadal chemical. Fatty acids from sebaceous glands inhibit bacterial growth.

Enzymes like lysozyme from tears and amidase from skin hydrolyse bacterial peptidoglycan.

Mucus membranes are another important part of the innate immune system that works closely with the skin to prevent infection.

Mucus coated hairs in the ____ , _____ epithelium in the throat and lungs, and coughing and sneezing all remove microorgamisms from the body. Chemicals like ______ kill bacteria while _________ in intestinal ______ cells destroy surface components of bacteria not killed by the ___ of the gut.

Mucus membranes are another important part of the innate immune system that works closely with the skin to prevent infection.

Mucus coated hairs in the nose, cilliar epithelium in the throat and lungs, and coughing and sneezing all remove microorgamisms from the body. Chemicals like defensins kill bacteria while phospholipidases in intestinal Paneth cells destroy destroy surface components of bacteria not killed by the pH of the gut.

One very important component of the innate immune system for killing bacteria is the normal _____ flora of the body.

This flora competes with forign microbes for _____ and releases _____ ment to kill other populations of bacteria

One very important component of the innate immune system for killing bacteria is the normal bacterial flora of the body.

This flora competes with forign microbes for nutrients and releases peptides ment to kill other populations of bacteria

Innate Immue System Anti-Microbial Peptides

Phospholipidases are found in ______ cells of the intestine and Neutrophil _______. They are active against Gram _______ and Gram ______ bacteria.

BPI, or _____/____ _____ protein, comes from the granules of ______ and works with phospholipidases to target Gram-______ bacteria

Innate Immue System Anti-Microbial Peptides

Phospholipidases are found in Paneth cells of the intestine and Neutrophil granules. They are active against Gram positive and Gram negative bacteria.

BPI, or Bacteriocidal/Permiability Increasing protein, comes from the granules of Neutrophils and works with phospholipidases to target Gram-negative bacteria

Innate Immue System Anti-Microbial Peptides

Innate Immue System Anti-Microbial Peptides

Innate Immue System Anti-Microbial Peptides

Innate Immue System Anti-Microbial Peptides

The main recogntion strategy of the innate immune systems is using _____ to look at bacterial _____.

PAMPs come in many forms, the most common being ____, ________, and ____

The main recogntion strategy of the innate immune systems is using PRRs to look at bacterial PAMPs.

PAMPs come in many forms, the most common being LPS, peptidoglycan, and TLRs

Important Cell Membrane Innate Immunity Recptors:

TLR___, TLR__, and TLR__ are all cell membrane TLRs that reocgnize very popular bacterial and fungal elements. CD___, ______, and ______ sugar receptors are also membrane receptors that help recognize bacterial elements.

Important Cell Membrane Innate Immunity Recptors:

TLR2, TLR4, and TLR5 are all cell membrane TLRs that reocgnize very popular bacterial and fungal elements. CD14, Scavenger, and Mannose sugar receptors are also membrane receptors that help recognize bacterial elements.

Endosomal Innate Immunity Receptors:

TLR__,TLR__, TLR__, and TLR__ are all Toll-Like Receptors on the inside of host cells that recognize some form of bacterial or viral genome.

Endosomal Innate Immunity Receptors:

TLR3, TLR7, TLR8, and TLR9 are all Toll-Like Receptors on the inside of host cells that recognize some form of bacterial or viral genome.

Cytoplasmic Innate Immunty Receptors:

NOD__ and NOD__ bind to peptidoglycan on Gran-positive bacteria and induce inflammatory responces.                                                    

Cytoplasmic Innate Immunty Receptors:

NOD1 and NOD2 bind to peptidoglycan on Gran-positive bacteria and induce inflammatory responces.                                                    

Cell Membrane Innate Immune Receptors:

1. TLR2: Recognzes bacterial lipo______, lipo______ acids, and _________
2. TLR4: Recognizes bacterial ____ when co-recpeting with MD-2
3. TLR5: Recognized bacterial cilliar ______
4. Scavenger Receptors: _______ charged polymers
5. Mannose Receptor: Recognizes ______ sugars on bacteria

Cell Membrane Innate Immune Receptors:

1. TLR2: Recognzes bacterial lipoproteins, lipotechoic acids, and peptidoglycan
2. TLR4: Recognizes bacterial LPS when co-recpeting with MD-2
3. TLR5: Recognized bacterial cilliar flagella
4. Scavenger Receptors: Negativly charged polymers
5. Mannose Receptor: Recognizes mannose sugars on bacteria

Endosomal Innate Immune Receptors:

1. TLR3: _____ stranded ___ from viruses
2. TLR7 and TLR8: _____ Stranded ____
3. TLR9: ____

Endosomal Innate Immune Receptors:

1. TLR3: Double stranded RNA from viruses
2. TLR7 and TLR8: Single Stranded RNA
3. TLR9: DNA

Cytoplasmic Innate Immune Receptors:

1. NOD1 and NOD2: ________

Cytoplasmic Innate Immune Receptors:

1. NOD1 and NOD2: Peptidoglycan 

Some Innate Immune receptirs can be ______ and travel through the blood stream binding to particular PAMPs.

Soluble CD___ and Mannose-binding ____ are two examples

Some Innate Immune receptirs can be secreated and travel through the blood stream binding to particular PAMPs.

Soluble CD14 and Mannose binding lectin are two examples

When PRRs bind to PAMPs, the resulting pairing causes the follows two steps, regardless of the secific PRR or PAMP:

1. The activation of _____ and ______ cells 
2. Resulting _______ from those activated cells
3. The release of pro-_________ mediators
4. Preping for the activation of the _____ immune system

When PRRs bind to PAMPs, the resulting pairing causes the follows two steps, regardless of the secific PRR or PAMP:

1. The activation of macrophages and dendritic cells 
2. Resulting Phagocytosis from those activated cells
3. The release of pro-inflammatory mediators
4. Preping for the activation of the adaptive immune system

Bacterial syrface proteins like LPS can make it hard for phagocytes and host immune cells to bind to the bacteria.

To overcome this, the body has developed a ______ System of proteins that cover and allow for the lysing of bacteria

Bacterial syrface proteins like LPS can make it hard for phagocytes and host immune cells to bind to the bacteria.

To overcome this, the body has developed a Compliment System of proteins that cover and allow for the lysing of bacteria

The Compliment System is made of 3 Pathways:

1. ______ Pathway
2. ______ Pathway
3. ______ Pathway

All 3 pathways lead to the creation of the MAC (____ ____ _____)

The Compliment System is made of 3 Pathways:

1. Classical Pathway
2. Alternate Pathway
3. Lectin Pathway

All 3 pathways lead to the creation of the MAC (Membrane Attack Complex)

The Classical Compliment Pathway:

1. Compliment proteins C1__ binds to the ___ portion of Abs and activates C1__
2. Activated C1__ is cleaved and generates a protein that cleaves C1__
3. Cleaved C1__ produces a protein that cleaves C2 and C4 into C__ and C__
4. C2a and C4b bind on the membrane of bacteria and form the __/__ convertase pump 

The Classical Compliment Pathway:

1. Compliment proteins C1q binds to the Fc portion of Abs and activates C1r
2. Activated C1r is cleaved and generates a protein that cleaves C1s
3. Cleaved C1s produces a protein that cleaves C2 and C4 into C2a and C4b
4. C2a and C4b bind on the membrane of bacteria and form the C3/C5 convertase pump 

The Alternate Compliment Pathway:

1. Factor B holds the same function as C__ in the classical pathway and is activated when cleaved by Factor __
2. Factor Bb binds to C___ to form the C3/C5 convertase pump and Factor __ stabilizes the pair

The Alternate Compliment Pathway:

1. Factor B holds the same function as C2 in the classical pathway and is activated when cleaved by Factor D
2. Factor Bb binds to C3b to form the C3/C5 convertase pump and Factor P stabilizes the pair

The Lectin Compliment Pathway:

1. _____ on microbial surfaces is bound to by mannose binding _____
2. MASP 1 and 2 (__-____ _____ 1 and 2) bind with MBL and cleave C2 and C4 into C2__ and C4__
3. C2a and C4b form the same __/__ convertase pump as in the classical pathway

The Lectin Compliment Pathway:

1. Mannose on microbial surfaces is bound to by mannose binding lectin 
2. MASP 1 and 2 (MBL-Associated Proteases 1 and 2) bind with MBL and cleave C2 and C4 into C2a and C4b
3. C2a and C4b form the same C3/C5 convertase pump as in the classical pathway

In all 3 Compliment pathways, the goal is to make a __/___ convertase pump, either out of ___/___ or __/___.

This pump ultimatly makes up an important part of the _____

In all 3 Compliment pathways, the goal is to make a C3/C5 convertase pump, either out of C2a/C4b or Bb/C3b.

This pump ultimatly makes up an important part of the MAC

Once C2a/C4b (or Bb/C3b) bind on microbial surfaces, C3 is cleaved into C3b and C3a.

C3__remains and binds to the C2a/C4b (Bb/C3b) complex and cleaves C5 into C5b and C5a.

C5__ joins compliment proteins C__, C__, C__, and C__ into making the fully functional Membrane Attack Complex.

Once C2a/C4b (or Bb/C3b) bind on microbial surfaces, C3 is cleaved into C3b and C3a.

C3b remains and binds to the C2a/C4b (Bb/C3b) complex and cleaves C5 into C5b and C5a.

C5b joins compliment proteins C6, C7, C8, and C9 into making the fully functional Membrane Attack Complex.

The formation of the MAC depends on a process called Diapedesis, which is the migration of ______ out of the ______ tissues of blood vessels towards high gradients of C5__

This is a ______ action of cellular movement

The formation of the MAC depends on a process called Diapedesis, which is the migration of Phagocytes out of the endothelial tissues of blood vessels towards high gradients of C5a

This is a chemotactic action of cellular movement

As the MAC is being formed, the bacterial cells (now covered in Ab-C3b) are ______ into phagocytes.

This opsonization happens as phagocytes bind to the C3__/___ pairing and engulf the cell in a zipper formation.

Once fully engulfed, the bacteria is contained on a vesicle, called the ______, and PMNs bind to the infected cell and release granulocytes in to the vesicle, forming the _____.

As the MAC is being formed, the bacterial cells (now covered in Ab-C3b) are opsonized into phagocytes.

This opsonization happens as phagocytes bind to the C3b/Ab pairing and engulf the cell in a zipper formation.

Once fully engulfed, the bacteria is contained on a vesicle, called the phagosome, and PMNs bind to the infected cell and release granulocytes in to the vesicle, forming the phagolysosome 

The MAC causes holes in the membranes of targeted bacteria, which allows for the followng to occur:

1. The holes allow the ________ of PMNs to attack the inside of the cell
2. The holes cause changes in _______ and lead to a lack of an _________ gradient due to the loss of cellular protons

The MAC causes holes in the membranes of targeted bacteria, which allows for the followng to occur:

1. The holes allow the granulocytes of PMNs to attack the inside of the cell
2. The holes cause changes in osmolarity and lead to a lack of an electrochemical gradient due to the loss of cellular protons

Gram negative cells are more suseptable to MACs because they have an outer _______ , which Gram positive cells do not (although G+ is still targeted by MAC)

Gram negative cells are more suseptable to MACs because they have an outer membrane, which Gram positive cells do not (although G+ is still targeted by MAC)

Phagocytes are the go-to killing components of the immune system, doing more work than the compliment system.

They are a major components of the _____ immune system, although they help modulate _____ immune responces 

Phagocytes are the go-to killing components of the immune system, doing more work than the compliment system.

They are a major components of the innate immune system, although they help modulate adaptive immune responces 

Stem cells differentiate into ____ cells and ________ cells.

Progenitor cells include _____ and ______ progenitors

Myeloid cells become _____, Basophil, Neutrophil, and ______ cells

Lymphoid progenitors become ___ and ___ cells

Monocytes further differentiate into _________ 

Stem cells differentiate into NK cells and Progenitor cells.

Progenitor cells include Myeloid and Lymphoid progenitors

Myeloid cells become Mast, Basophil, Neutrophil, and Monocyte cells

Lymphoid progenitors become B and T cells

Monocytes further differentiate into Macrophages 

______ are the precursors to Macrophages.

They circulate continuously in the bloodstream and can be stimulated to quickly _____ in batches

Neutrophils have a ______ life span, but are highly ______ and will swarm infection sites

Monocytes are the precursors to Macrophages.

They circulate continuously in the bloodstream and can be stimulated to quickly mature in batches

Neutrophils have a shorter life span, but are highly bacteriocidal and will swarm infection sites

Dendritic cells mainly work as _____ and ______.

They are called Langerhans cells when in the ___ and Kuppfer cells in the ____

Dendritic cells mainly work as APCs and Phagocytes.

They are called Langerhans cells when in the skin and Kuppfer cells in the liver

Neutrophils are part of a family of cells including Eosinophils and Basophils called ____________ Leukocytes (PMNs)

They function mainly in ______  of target cells and in _______, and are a big part of _________ towards C5a gradients

Neutrophils are part of a family of cells including Eosinophils and Basophils called Polymorphonuclear Leukocytes (PMNs)

They function mainly in degranulation of target cells and in phagocytosis, and are a big part of diapedesis towards C5a gradients

Eosinophils and Basophils aren't as large of players in immunity as Neutrophils are, but they do serve specfic functions

Eosinophils act against ________, espcially ______, while Basophils release ____________  molecules

Eosinophils and Basophils aren't as large of players in immunity as Neutrophils are, but they do serve specfic functions

Eosinophils act against parasites, espcially helminths, while Basophils release proinflammatory molecules

Aside from maturing into macrophages, Monocytes also act as _______ and secreate cytokinese that promote _____ and ______.

Aside from maturing into macrophages, Monocytes also act as phagocytes and secreate cytokinese that promote adherence and diapedesis.

Macrophages do a ton of shit

They are primarily ________, but they also sectreat a large array of _______, which may be chemokines or cytokines. They produce many lyseing ______.

In the adaptive immune system, they function in Antigen ______ and ______ and help produce ____ molecules for self cell recognition

Macrophages do a ton of shit

They are primarily phagocytes, but they also sectreat a large array of Interluekins, which may be chemokines or cytokines. They produce many lyseing enzymes.

In the adaptive immune system, they function in Antigen processing and recognition and help produce MHC molecules for self cell recognition

T cells can either be ______ cells, _______ cells, or _____ cells that all modulate the adaptive immune responce.

B cells work as _____ and can differentiate into _____ B cells and serum _____ cells

T cells can either be Helper cells, Cytotoxic cells, or Effector cells that all modulate the adaptive immune responce.

B cells work as APCs and can differentiate into memory B cells and serum plasma cells

Neutrophils release two different types of granules, _____ and ______ (also called primary and secondary)

Neutrophils release two different types of granules, azurophils and specific (also called primary and secondary)

Both types of granulocytes release by neutrophils have ______ dependent and independent mechanisms for degrading bacteria

Both types of granulocytes release by neutrophils have oxygen dependent and independent mechanisms for degrading bacteria

Azurophil (Primary Granule) Antimicrobials:

1. α-______, _____, and _____ (oxygen independent)
2. ________ (oxygen-dependent)

Azurophil (Primary Granule) Antimicrobials:

1. α-Defensins, BPI, and Lysozomes (oxygen independent)
2. Myeloperoxidase (oxygen-dependent)

Specific (Secondary Granule) Antimicrobials:

1. ______ and ______ (oxygen independent)
2. ______ oxidase cofactors (oxygen-dependent)
3. Bacterial _______ receptors
4. C___ Receptors

Specific (Secondary Granule) Antimicrobials:

1. Lactoferrin and Lysozomes (oxygen independent)
2. NADPH oxidase cofactors (oxygen-dependent)
3. Bacterial chemotaxin receptors
4. C5a Receptors

Mediators of Inflammation:

1. C3__ and C5__
2. ______
3. ___________
4. _____-α
5. IL-__ and ___
6. ____ and ___ chemokine receptors

Mediators of Inflammation:

1. C3a and C5a
2. Histamine
3. Prostidoglandins
4. TNF-α
5. IL-1 and 6
6. CXC and CC chemokine receptors

Mediators of Inflammation:

1. C3a and C5a: Induce the release of _______ from mast cells
2. Histamine: Increased vaso_______and vaso______
3. Prostidoglandins: Vaso_______ and vaso______as well as ______
4. CXC and CC chemokine receptors: Chemokine attraction of _____ and ___ cells (respectivly)

Mediators of Inflammation:

1. C3a and C5a: Induce the release of Histamine from mast cells
2. Histamine: Increased vasopermiability and vasodialation
3. Prostidoglandins: Vasodialation and vasocontriction as well as edema
4. CXC and CC chemokine receptors: Chemokine attraction of PMNs and T cells (respectivly)

TNF-α is responsible for _______ and is the main  actovator of _____.

It also causes the activation of ______ and PMN cells, and the ________ of fat and protein.

IL-1 fulfills similar roles and is activated by _______ cells 

IL-6 is special in that it causes ___ cell differentiation

TNF-α is responsible for inflammation and is the main  actovator of fever.

It also causes the activation of endothilial and PMN cells, and the catabolization of fat and protein.

IL-1 fulfills similar roles and is activated by endothelial cells 

IL-6 is special in that it causes B cell differentiation

NK cells will not kill self cells if those cells present _____ molecules that can bind to the NK cells inhibitory receptor (_____)

NK cells will not kill self cells if those cells present MHC molecules that can bind to the NK cells inhibitory receptor (KIR)

Another name for compliment fragments like C3a, C4a, and C5a is __________.

Another name for compliment fragments like C3a, C4a, and C5a is Anaphylatoxin.

Steps to Initiate the Adaptive Immune System from the Innate immune System:

1. Microbial ____ enter the body
2. ______ cells regocnize PAMPs on bacteria
3. Dendritic cells take bacteria to lymph nodes and acts as ____
4. Dentritic cells present ___ cell stimulating cell surface molecules
5. Processing of Ag and binding to self MHC Class ___ molecules
6. Presentation of __-___ to T cells
7. Secreation of T cell activating _______
8. _____, _______, and ________ of Ag-specific T cells
9. Generation of Ag specific _______ Cells
10. _______ of Ag 

Steps to Initiate the Adaptive Immune System from the Innate immune System:

1. Microbial Ags enter the body
2. Dendritic cells regocnize PAMPs on bacteria
3. Dendritic cells take bacteria to lymph nodes and acts as APCs
4. Dentritic cells present T cell stimulating cell surface molecules
5. Processing of Ag and binding to self MHC Class II molecules
6. Presentation of Ag-MHC to T cells
7. Secreation of T cell activating cytokines
8. Activation, proliferation, and differentiation of Ag-specific T cells
9. Generation of Ag specific Effector Cells
10. Elimination of Ag 

Differences between Innate and Adaptive Immunity:

1. Innate Receptors are _______ encoded, while Apative immune receptors are all _____ _______
2. Innate Immune receptors are expressed by ______ cell types, while Adaptive immune receptors are _______ expressed on lymphocytes
3. Innate Immune receptors have a ______ repertoire, while adaptive immune receptors can recognize _____ different types of Ags
4. Innate immune receptors have no ______, while adaptive immune receptors are strengthened by previous _______ to Ag

Differences between Innate and Adaptive Immunity:

1. Innate Receptors are germline encoded, while Apative immune receptors are all somatically recombined
2. Innate Immune receptors are expressed by many cell types, while Adaptive immune receptors are clonally expressed on lymphocytes
3. Innate Immune receptors have a small repertoire, while adaptive immune receptors can recognize many different types of Ags
4. Innate immune receptors have no memory, while adaptive immune receptors are strengthened by previous exposure to Ag

Portions of an Immunoglobulin (Antibody):

1. _____ and _____ Chains
2. ________ and _______Regions
3. _____ and ____ Portions

Portions of an Immunoglobulin (Antibody):

1. Heavy and Light Chains
2. Variable and Constant Regions
3. Fab and Fc Portions

Abs have a Y shape with a movable ______ region in the middle that allows for flexability

The _____ portion is the arms of the Y, and the ___ portion is the stem of the Y.

The Ab can be digested into the seperate arms and stem by _____ cleavage, or have the stem digestested and the arms intact with ______ cleavage

Abs have a Y shape with a movable hinge region in the middle that allows for flexability

The Fab portion is the arms of the Y, and the Fc portion is the stem of the Y.

The Ab can be digested into the seperate arms and stem by papain cleavage, or have the stem digestested and the arms intact with pepsin cleavage

Immunoglobulin Types:

1. IgG: _____ Ab that fights most of infections
2. IgA: _______ into intestinal lumen
3. IgD: Can activate ___ cells
4. IgM: __mer or ___mer shape, used as initial indicator of ______, gangs up on bacteria to help phagocytes
5. IgE: _______ release from Mast cells

Immunoglobulin Types:

1. IgG: Soluble Ab that fights most of infections
2. IgA: Secreatable into intestinal lumen
3. IgD: Can activate B cells
4. IgM: Dimer or pentamer shape, used as initial indicator of infection, gangs up on bacteria to help phagocytes
5. IgE: Histamine release from Mast cells

Valence refers to the amount of ____ binding sites on an ____.

Each Y shaped Immunoglobulin monomer has a valence of ____

Valence refers to the amount of Ag binding sites on an Ab.

Each Y shaped Immunoglobulin monomer has a valence of two