. Explain the difference Phoresis and Inquilinism?

Phoresis is using the host AS a shelter and inquilinism is going in and taking the home of another species 

What is the significant role of endocytosis?

Nutrient acquisition, antigen presentation, receptor regulation, hypertension, synaptic transmission

what is the role of mitochondria in apoptosis?

mitochondria play an important role in apoptotic signaling pathways. When mitochondria receive the signals of apoptosis, it releases cytochrome c into the cytoplasm. Then, the cytochrome c activates the caspase pathway, apoptosis occurs.

.  How was the evolution of apoptosis helpful for the malarial parasite, Plasmodium?

Apoptosis allowed the parasite to control its replication, which helped keep its host alive long enough so that it can complete its life cycle, and use the resources present for the transmission of malaria.

.  How does biofilm formation portray cooperation in a density-dependent way?

Biofilm formation portrays cooperation because microbes hook onto a surface and onto each other. For this to be accomplished, they must send signals to one another in order to set up a community.  

There are two obligatory symbionts associated with the Mediterranean fruit fly. Who are they, how are they obtained, and what do they do for the fly?

The Mediterranean fruit fly obtains Enterobacter (Panoeoa) agglomerans and Klebsiella pneumoniae through horizontal transmission via bird feces/leaves. First, Enterobacter degrades toxic uric acid into urea. Once converted, Klebsiella can now degrade urea into ammonia for the fly to make proteins.

What are the tradeoffs between nitrogen fixing bacteria and the Rhizobium spp.?

In this symbiotic association, a mutualism occurs when nitrogen fixing bacterium attach to the root surface of a plant. After attachment, the nitrogen fixing bacteria will integrate itself into the plant, forming root nodules. When that occurs, Leghemoglobin from the plant will regulate oxygen levels into an anaerobic environment for the Nitrogen fixing bacteria to thrive. In return, the nitrogen fixing bacteria will offer them precursors for amino acid production by converting N₂ into Ammonia.

What is still unknown or still might need to be figured out about the Rhizopus/Burklholderia relationship? (give one reason that we talked about)

The downside (or cost) to the Burkholderia in the relationship (since producing the toxin is energy expensive secondary metabolic pathway) OR how the fungus is "immune" to the rhizoxin produced by Burkholderia

What are the key differences between Host Sanction Theory and Partner Fidelity Feedback? 

Host Sanction Theory: hosts have evolved to punish cheaters and reward    cooperators, since cheaters are an environmental setback.

Partner Fidelity Theory: symbiotic species have evolved to help hosts (rather than hosts monitoring/punishing their symbionts) because a healthy host feeds back benefits, such as shelter/environment and nutrition, to its symbionts

What does the experiment of infecting mice with P. aeruginosa demonstrate? What were its results and implications?

The results of the experiment showed that a mouse infected only with cooperating bacteria died within a few days, whereas a mouse infected with only cheating bacteria had lower mortality rates. Similarly, mice infected with a mix of both cheaters and cooperators showed the same high survival rates of the only-cheater population. This demonstrates that, though cooperating species are stronger as a society, adding a few cheaters breaks down the success of the population, and could be helpful in decreasing the virulence of some lethal bacterial infections.

. Difference between symbiogenesis and natural selection

In symbiogenesis genomes are acquired while natural selection there is selection thru propagation and elimination of what an organism already has.

How did Thiodendron latens become two microbes Desulfulobacter and Spirochete?

T. lantens is an extreme bacteria thought to be a key microbe who cycled sulfur. When studied in anaerobic vs. aerobic conditions. Bacteria wouldn’t form the same globules. After more study there were actually two microbes working together not one. Living close together that couldn’t be easily differentiated.

What are three mechanism bacteria use to change?

Transformation- bacteria pick up free DNA from a dead bacterium

      Conjugation- A bacterium gets a plasmid transfer from a plasmid donor bacterium

      Transduction- transfer by virus delivery

What are the 3 extracellular factors for Yersinia pestis?

Pesticin 1, coagulase, fibrinolysin

OSCC account for 90% of all oral cancers, why is it ineffective to eliminate or suppress all the microbes in your mouth without discretion? What be one example of targeted microbe elimination?

little is known about the microbiota in the mouth. there are more than 600 bacteria and only half are known. Out of these very few are linked to OSCC. One example would be bacterial phage therapy to target certain bacteria only. 

What is the function of FcR cells?

Bind to antibodies that are attached to pathogens to induce phagocytosis.

Example, FcR allows HIV to piggyback on CMV to be able to attach to pathogens to infect a cell that does not have CD4 receptors.

What happens with HIV and Hepatitis C infect together?

May promote heightened apoptosis of CD4 cells, contributes to the accelerated progression of AIDs, and apoptosis may be a mechanism for increased mortality in HIV/HCV patients. 

How does Yersinia pestis get into your respiratory system?

From lymphatic system:  They will affect the permeability of blood vessels by causing inflammation using cytokines.  This will allow them to be transferred to blood vessels and to the lungs. 

     From respiratory system:  An infected person who has the bacteria already in the lungs will cough up the bacteria which are inhaled by an uninfected person.

What is the possible relationship that has been recently identified in bacteriophage-bacteriophage interactions in a bacterial host?

A bacteriophage can act as a “helper” by aiding other bacteriophage to bind to a bacterium that it normally could not. 

Explain how genetic-based reassortment of influenza strains is used to create vaccines.

. There are two methods that are used to create influenza vaccines.

1.     Traditional egg-based strain assortment where vaccine seed viruses from a vaccine strain and donor strain are co-infected in the egg.  There 256 possible recombinations which are screened for specific surface proteins of interest.

2.     Reverse genetics based virus reassortment where the specific gene segments from vaccine and donor strains are amplified (reverse transcription) and the cDNA of the specific influenza gene segments is cloned into plasmids and grown in cell cultures. Screening is not necessary.

1.     What is the replication cycle of viruses?

A:         1- Adsorption = Attachment to host.

   2- Penetration = Entry to the host cell.

3- Uncoating = release of the nucleic acid + reverse transcription ”RNA viruses”

         4- Biosynthesis = make new viruses parts (i.e nucleic acid and proteins).

         5- Assembly = put parts together (i.e nucleic acid and proteins).

   6- Maturation = inspection, make sure that everything is in order.

         7- Release = leave the cell.

what role does Cytochrome C play when it is leaked form mitochondria?

It starts a series of cascade that leads to apoptosis (programmed cell death

What is Chromalveolate hypothesis?

free-living red algal cell was captured and retained by a nonphotosynthetic heterotrophic protist soon after the evolutionary split of red and green algae, giving rise to the pigmented ancestor of the supergroup "Chromalveolata".

What are two present day amitichondria and what type of cells are they? 

Microsporidia and Giardia. They are anaerobic single celled eukaryotes

What factors are involved in covevolution as evolutionary "arms race”?

a. Adaptations that produce an advantage countered by a neutralizing adaptation.

b. Reciprocal genetic exchange.

c. Traits of one species evolve in response to those traits of other species.

Rhizoxin, a toxin that causes disruption of microtubule formation, produced by Rhizopus microsporus.


False.

Mutualism results from an ancient infection followed by the evolution of a concerted mode of vertical transmission.


True.

Identify 3 of the 6 bacterial species found in high numbers in OSCC patients' saliva.

Prevotella melaninogenica, Capnocytophaga gingivalis, Capnocytophaga ochracea, Eubacterium saburreum, Leptotrichia buccalis, and Streptococcus mitis.

How many different species of bacteria reside within the human mouth?

600 spp.

OSCC accounts for what percent of all oral cancers?    

90%.

What is the function and the consequences of YopJ and YopH proteins of type 3 secretory system in Yersinia Pestis.

YopJ interferes with MAPK pathway, in the infected immune cell, which in turn disrupt the cytokines production. As for YopH, it interferes with the cytoskeleton wedging mechanism to interrupt phagocytosis and allow the bacteria to evade the immune system. 

What are the types of recombination in the viral-viral interaction? 

a. Antigenic drift: minor changes in the nucleic acid of a virus.

 b. Antigenic shift: major changes in the nucleic acid of a virus.

How does Yersinia pestis limit phagocytosis and evade natural immune defenses?

1.     Y. pestis limits phagocytosis by using a Type III secretion system to inject effector proteins into the cytosol of eukaryotic target cells. Yops (Yersinia Outer Proteins) disrupts cytoskeletal element production in so that the cells can no longer make pseudopodia needed for phagocytosis.  (Yops also affect cytokine production.)

What are the six species found at significantly higher levels in the saliva of patients with OSCC than in saliva of oral-free cancer individuals? 

1.     The 6 species are Prevotella melaninogenica, Capnocytophaga gingivalis, Capnocytophaga ochracea, Eubacterium saburreum, Leptotrichia buccalis, and Streptococcus mitis.

What are the 3 microbes that are used as a diagnostic tool to predict 80% of oral cancers?

Caphocytophaga gingivalis, Prevotella Melaninogenica, and Streptococcus Mitis.

1.     What are the three extracellular virulence factors of Yersinia pestis? 

Pesticin I, Coagulase, and Fibrinolysin.

   What are the classifications of a symbiotic relationship? 

Location, persistence, dependence, specificity, and products.

1.     Rhizopus (fungus) harbors Burkholderia (bacteria) for the production of the toxin rhizoxin. How does this toxin benefit the fungus and what happens when Burkholderia is eliminated from the fungus?

Rhizoxin is an efficient chemical agent that helps the fungus defend its habitat against competitors and gaining a supply of nutrient from dead plant matter. When Burkholderia is eliminated from the fungus; the fungus cannot produce spores. 

1.     How do Fc Receptors play a role in CMV and HIV infections? 

FcRs bind to antibodies that are attached to pathogens which in turn induces phagocytosis. HIV then "piggybacks" on CMV and FcRs induced by CMV allow HIV to infect fibroblasts that were not otherwise permissive to HIV infection.

1.     What are the two present-day anaerobic single-celled eukaryotes without mitochondria?

Microsporidia and Giardia. 

How does the leech help in medicinal ways?

With its anti-coagulant the leech draws out new blood from the damaged tissue keeping it fresh to heal or for reattachment of the tissues. They are also used to help reduce swelling.

1.     How can cheaters be used in a positive way?

Virulent bacteria become attenuated in the presence of cheaters.

1.     Why is Komodo dragons bite dangerous? 

Komodo dragons’ saliva contains varieties of multidrug resistant and pathogenic bacteria. 

1.     Why are human bites more serious than dog’s? 

Bacteria living in a dog’s mouth are specific and specifically adapted to living in dogs and not in people. Moreover, dog saliva can kill E. coli and Streptococcus canis. 

1.     How do viral vectors for gene therapy work?

Viral particles encapsulate a modified genome carrying a therapeutic gene cassette in place of the viral genome. 

1.     What are the examples of unicellular organisms and cooperation in a density-dependent way? 

Biofilm formation, siderophore production, quorum sensing, and PCD of malaria pathogens. 

1.     What is CMV?

Cytomegalovirus (CMV) is a member of the herpes virus family. Complete CMV particles contain double-stranded DNA enclosed in an icosahedral capsid and surrounded by an envelope. CMV infects epithelial cells and lymphocytes. It moves into the nucleus where it can produce intranuclear inclusion. 

1.     What does Rhizoxin do? 

Rhizoxin binds beta tubulin in eukaryotic cells disrupting microtubule formation. This, in turn, prevents formation of the mitotic spindle inhibiting cell division. Rhizoxin can also depolymerize assembled microtubules. 

1.     What are the characteristics of mitochondria?

Single strand DNA in a circle bounded by a double membrane, self-replicating by binary fission, genetically identical, semi-autonomous, and the site of ATP production. 

1.     What are the roles of endocytosis?

Nutrient acquisition, antigen presentation, clearance of apoptotic cells, receptor regulation, hypertension, and synaptic transmission.

1.     What are the 4 general subdivisions of symbioses?

Mutualism, commensalism, parasitism, and neutralism.

1.     Define SET.

Serial endosymbiosis theory (SET) proposes that complex living cells arose from evolutionary processes whereby earlier cells merged in a series of combinations and thus formed a larger more complex cell. 

. How do mitochondria divide?

Binary fission

Where did chloroplast originate from

Cyanobacteria

Through which process is genetic material transferred from a bacterium to another by a

virus?

Transduction

Can mitochondria cause disease? 

Name one mitochondria based disease? 

Parkinson, Distonia (dystonia) ,

MERRF(Myoclonic Epilepsy with Ragged Red Fibers), MND (motor neuron diseases),

Corea, Atassia, MELAS (Mitochondrial encephalomyopathy lactic acidosis and stroke-

like episodes)

How does Lynn Margulis theory of endosymbiosis differ from Darwin’s theory of

evolution? 

She believed that symbiosis of species also contributed to evolution.

Evolution is not only based on genetic mutation or survival of the fittest, but also based

on species cooperation.

What does OSCC stand for?Oral Squamous Cell Carcinoma

Oral Squamous Cell Carcinoma

Name one microbe dog saliva can kill?

E.coli or Streptococcus canis

Is it true or false that species relationships are static? 

false

what is eukaryiosis and how is it achieved?

Eukaryosis is when a bacteria transitions into a eukaryote and is achieved by horizontal gene transfer

Which can cause a more serious infection, a dog bite or human bite and why?

    Human bites can cause a more serious infection because dogs have antimicrobial saliva which doesn't cause much harm as much as a human bite can.

When Yersinia pestis is transmitted from person to person, what phase does it go through?

    It is called pneumonic plague when there is a person to person contact

Why do we have to change the influenza vaccine every year?

Because of reassortments that are occurring, which change the virus every year, therefore we have to change the vaccine accordingly. 

What is it called when nutrients are obtained from a dead partner?

Necrotrophic

Please describe a symbiosome and give an example

A Symbiosome is a symbiotic casing that a bacteria is enveloped within a plant cell or structure, and provides the plant with essential nutrients.  An example is Rhizobium spp., which is a Nitrogen-fixing bacteria that lives inside the root nodules in legumes.  

Describe Amitochondrite eukaryotes

Nucleated protists that lack a mitochondria.  There are existing species, such as Giardia intestinalis.  

    Plasmodium spp. to enter the host's (mosquito) _______ to become sexually active and produces many progeny. When activated, it becomes transfered into the RBC where it travels all around the body. This is an example of ___________.

   HIV uses CMV to inhibit Fc receptors in order to penetrate the cell. This is a great example of ....

Explain why caspases have similar homology with  early extracellular proteases. Did a symbiotic relationship develop? If so what kind? Did the type of relationship stay static? If not, what did the relationship transgress to and what was the end result?

Caspases have similar homology with early extracellular proteases due to a microbe entering into another microbe. This initially was a parasitic relationship, in that the foreign microbe would be destroyed by degradative enzymes.  Ultimately this relationship became a mutualistic symbiotic relationship.

There are _______  per mL of saliva.

When a tissue plasminogen activator binds to a plasminogen within the clot, it converts it into ________. 

Plasmin 

False -- it is secondary plastids. 

Give an example of how unicellular organisms cooperate in a density-dependent way. 

Answer: may be Biofilm formation, Quorum-sensing, or Siderophore production. 

Name the 2 different kinds of feedback in a relationship between a host and a symbiont.