1. Biofilms are important characteristics of some bacteria. What are the stages for biofilms formation? Explain the importance of biofilms in the survival of such microorganisms in certain environments.

2. Why are infections caused by eukaryotic parasites harder to treat than those caused by prokaryotes? Explain and give examples. What is the most effective method to treat infections with Cestodes (tape-worms)?  why?

3. If a new bacterial species has been discovered, what are the steps that the researchers would have gone through to confirm its identity?

4. Plasmids are genetic elements found in bacterial cells. What are their main characteristics? Discuss the role of plasmids in bacterial infections and survival.

5. Some bacterial enzymes are essential for virulence. Explain the stages needed to establish microbial infections. Classify bacterial toxins. Provide two examples and describe their mechanism of action on mammalian cells.

1. Can photo system 1 also absorb light and release electrons? How do the electrons be replaced?

2. What happens during non-cyclic electron flow? What product can be generated?

3. Summarize the events of the dark reaction. (All inputs and outputs)

Are most animals vertebrates or invertebrates?

How does bilateral symmetry differ from radial symmetry?

What is cephalization?

1) Discuss biocentrism. Explain its idea. What kinds of observation have led to the

development of this idea? How does this school of thought find support from quantum

physics? What do you think about this ancient idea that has been repackaged as new by

Robert Lanza? A link to an excellent reading about this idea is posted below:

http://discovermagazine.com/2009/may/01-the-biocentric-universe-life-creates-time-space-

cosmos

2) The mechanical philosophy, which arose from the scientific revolution, presents the

universe as a grand machine, one that operates blindly according to invariable laws. From

this mechanical view, the universe is devoid of teleology. As a machine runs according to

its rules, so does the universe. Darwin’s theory in 1859 expanded this non-teleological

conception of the cosmos to the living world. His theory of natural selection presented an

evolutionary process that is random and blind, the result of many accidents, some of

which were beneficial and, therefore, were preserved and have accumulated to drive the

change in form over time. This process gives the impression of an intentional, goal-

oriented process, but as natural selection is random and blind, any appearance of

teleology is an

illusion

. The science of abiogenesis, that studies the natural process

through which life has arisen, has operated since the 1920’s from the assumption that life,

as in its evolution, must also have arisen from a very random and high unlikely accident

of circumstances.

Discuss this non-teleological view of the universe, which has dominated physics and biology

for over 300 years. Do you agree with such a view? Do you see any lines of

evidence/observation that challenges the assumption that the universe operates blindly, that

life has arisen by accident, and that its evolution has come about through a strictly random

process? Regardless if you agree with a non-teleological view of the cosmos or not, support

your views with empirical data and observation.

3) Discuss the difference between technology and science. How are they related to each

other? How do they relate to the ‘Baconian vision’, put forth by Francis Bacon? Would

you say that we have achieved his vision, exactly as he envisioned it? Why or why not?

Finally, explain your position regarding the pros and cons of prioritizing applied research

over basic research. Deal with both sides of the argument. That is, argue why it is best to

prioritize applied over basic research. Then argue from the other side and make a case for

why it is better to prioritize basic research, or at least give equal funding to it. Finally,

explain your own personal position and why you hold it?

4) Discuss what you believe ‘consciousness’ is. Do all living organisms possess it? If not,

which do and which do not? From where do you think it arises? Finally, do you think we

can study understand the phenomenon of consciousness using the tools of reductionism

or do you think an epistemology of holism is needed?

5) In Erwin Schrodinger’s famous little book entitled ‘What is Life”, published in 1944,

Schrodinger looks at the phenomenon of life through the eyes of “a naïve physicist”. He

attempts to address the mystery of living organisms through appeal to physical and

chemical principles. This book has been said to have catalyzed what is now referred to as

the ‘molecular biology revolution’ that gained momentum in the 40’s and currently

dominates the life sciences. While acknowledging decades of productive reductionist

research in the life sciences there are those who argue that a shift to a more organismal

approach is now necessary if we are to truly answer Schrodinger’s question, “what is

life?”. This shift would means considering the organism as a whole without reducing it to

its constituent parts (aka organicism), the opposite of ‘reductionism’. My question to you

is whether you believe that a full explanation of life can be obtained by employing a

purely reductionist methodology? Why or why not?

6) We discussed quite a bit about the evolving role of mathematics in man’s endeavor to

explain the natural world. An eternal question remains: does mathematics exist as an

objectively ‘real’ language/symbolic scheme beyond man’s own mental construct? Or is

the whole of mathematics a contrivance of the human mind that man uses to describe the

universe? How do you personally see this debate? As always, explain your reasoning.

7) The following is a quote from a giant of 20th century biology, Carl Woese:

“Biology today is at a crossroads. The molecular paradigm, which so successfully guided

the discipline throughout most of the 20th century, is no longer a reliable guide. Its vision

of biology now realized,

the molecular paradigm has run its course. Biology,

therefore,

has a choice to make, between the comfortable path of continuing to follow molecular

biology's lead or the more invigorating one of seeking a new and inspiring vision of the

living world, one that addresses the major problems in biology that 20th century biology,

molecular biology, could not handle and, so, avoided. The former course, though highly

productive, is certain to turn biology into an engineering discipline. The latter holds the

promise of making biology an even more fundamental science, one that, along with

physics, probes and defines the nature of reality. This is a choice between a biology that

solely does society's bidding and a biology that is society's teacher.”

Quoted from

A New Biology for a New Century, 2004

Discuss this quote and your thoughts on the matter. Do you agree with Carl Woese? Has

biology become strictly an engineering discipline? If so, is there anything wrong with such

a direction? Do you think biology, as he suggests, has the potential to become a

fundamental science like physics? If so, how? Again, these questions are meant to be

suggestive to get you thinking about this topic. Feel free to discuss in your own way

3. explain the location and role of the endodermis in regulating the movement of substances into and out of the root's vascular cylinder. You musr use, but are not limited to the following: Casparian strip, plasma membrane, endodermis, symplastic, apoplastic.

An alien species was found with the following characteristics Flat feet dominant over round feet A vs a 10 toes dominant to 15 toes B vs b Curved ears dominant to straight ears C vs c A flat footed, curved eared alien with 10 toes was crossed with a round footed, 15 toed, straight eared individual and produced the following offspring

Flat, curved, 10 toes 588

Round, straight, 15 toes 599

Flat, 15 toes, straight 165

Flat 15 toes, curved 159

Round, 10 toes, curved 145

Round, 10 toes, straight 163

Flat, straight, 10 toes 15

Round, curved, 10 toes 23

What gene is in the middle?

How far apart are the genes?

You are interested in mapping the genetic distance between two phage genes. You know from your genetics course that relative gene distance in both bacteria and eukaryotes can be determined by finding the recombination frequency of the two genes.

You infect a bacterial cell with two phages (h+r+ and hr) and you plate the progeny phages onto a bacterial lawn containing both strains of bacteria susceptible to the h mutant phenotype.  

a) Describe all the possible plaque phenotypes you would see and the genotypes associated with each.

b) Which two phenotypes are the most abundant?

c) If the two most abundant plaque phenotypes together total 140 out of 200 plaques, what is the genetic distance between these two genes in map units?

d) What would happen if the double mutant phage (hr) had failed to coinfect the bacterial cell? Would your plate look the same? Why or why not?

What are "cell formation cycles" and why would one want to use them?

Bacterial Endotoxin Limit (EL) is defined as EL=K/m, where K=5 Endotoxin Units (EU) kg of the body weight or 5 EU/kg/hr;m= maximun bolus dose of a product, and the average human body weight is 70kg.The maximun Valid Dilution (MVD) of a product is equal to (EL x Concentration of the product)/sensivity of the lysate

Find the EL for a product whose maximun pediatric dose is 4 mg/ml/kg and concentration is 20mg/ml. Expressthe EL in EU/ml and EU/mg

If the sensivitty of the lysate is EU/ml, the Endotoxin soecification per monograph is EU/mg, the maximun bolus dose is 1ug/kg/min and the concentration is 0.2mg/ml.CAn the monograph specification be used as the Endotoxin limit? Explain

Calculate the MVD based on problem #2

Explain the way of action of antibiotics known as aminoglycosides, tetracyclines and macrolides. Give detailed answer.

Insulin-like growth factor 2 receptor (Igf2r) gene is expressed exclusively from the maternal allele on chromosome 17 due to

A. differential methylation of an Igf2r intron.

B. differential expression of an antisense RNA transcript.

C. transposition of the maternal copy of Igf2r.

D. methylation of an imprinting control region.

1. Define the following terms: allele, incomplete dominance, codominance, pleiotropy, epistasis. What are some examples of each?

18. Entamoeba histolytica is the causative organism in amoebic dysentery. This organism is a(n)
       Protozoan
       Bacterium
       Fungus
       Virus

20. Antibiotic-induced diarrhea is most often caused by an overgrowth of this specific bacterium:
       Clostridium difficile
       Clostridium perfringens
       Candida albicans
       Yersinia pestis

22. Acute glomerulonephritis is a late-developing consequence of which of the following diseases?
       Streptococcal pharyngitis (strep throat)
       Influenza
       Rhinosinusitis
       Pneumonia

31. The opportunistic pathogen often responsible for causing necrotizing fasciitis (also known as the "flesh-eating bacteria") in healthy young adults is called:
       Staphylococcus epidermis
       Streptococcus pyogenes
       Bacillus subtilis
       Streptococcus pneumoniae