This reading and discussion club is to allow members of cbio to casually work through selected texts and discuss covered topics with each other.

Book: Molecular Biology made simple and fun, 2nd Edition, by David Clark and Lonnie Russell.

This text was chosen to allow those of us with limited biology knowledge to get introduced to the elements of celluar function, genetics, and the current techniques used to study nucleic acids in the laboratory.
 

Next Meeting	Read	Meeting Location
unscheduled	TBD	Our current normal meeting area is the tables outside of the faculty club at Rockefeller Univeristy. If raining or unpleasant, we will meet in the 2nd floor conference room of the Computational Biology Center.

Reading List

chpt	title
2	Bacteria: The Molecular Biologist's Guinea Pigs
3	Basic Genetics
4	Required Reading: The Molecular Basis of Heredity
5	Duplicating the DNA: Replication
6	Getting the Message Out: Transcription of Genes to Produce Messenger RNA
7	Proteins: The Buck Stops Here
8	Sex Among the Low-Lifes and Its Exploitation by Molecular Biologists: Gene Transfer in Bacteria
9	Messing about with DNA
11	Genetic Organization in Higher Organisms
12	Mutations: Things That Go Bump in the Night
13	Inherited Human Disease
14	Cancer and Aging
16	Just Do It! Techniques of Molecular Biology
17	PCR: The Polymerase Chain Reaction and Its Many Uses
19	Gene Creatures, Part I: Viruses, Viroids and Plasmids
20	Gene Creatures, Part II: Jumping Genes and Junk DNA
22	The Molecular Defense Initiative: Your Immune System at Work
23	Sequencing DNA
24	Molecular Evolution: Memories of "The Way We Were" (optional / perhaps not)

Meeting Notes

Sept 21, 2004

Chapter Covered: 24
Present: Lynn, Martine, Robert

• Has original Amino Acid formation of life continued? Is it simply outcompeted by existing organisms?
• Could new life be generated by new Miller experiments? Could we evolve a new system and see it?
• In precambrian there seemed to be more flexibility .. more variety of larger taxonomy groups (phylums..)
• It might be good for us to look at the differences between trait based and molecular sequence based taxonomies
• Retroviral lateral transfer of genes messes up straight percent similarity differences in molecular sequence taxonomies
• How can we explore the lost evolutionary paths? Now we are more regulated / constrained -- especially by DNA repair mechanisms
• How did DNA come in? "Learn to use DNA for genetic storage"??
• How did something come about which could self duplicate?
• Definition of life (consider cell colonies). Definition of death. Is a requirement for "a life" that it naturally die?
• Can DNA be a catalyst like RNA can? Maybe a DNA world..
• Deep sea vents .. sulfer based and heat rather than oxygen
• NASA biology group is asking how we would recognize life if it were different
• Sequencing the ocean (Craig Venter) -- is there enough primordial content to "start again"? Not likely .. there is so much from exchange between bacteria / phages
• Many organisms are present in soil and water which cannot be cultured in lab -- maybe too many dependancies on other present organisms to be isolated
• Can we still get something so different as a new "order" appearing? No reason why things cannot continue to diverge and change
• Speciation not clearly understood. a big change in an individual and you only have 1 who is in the new species .. who will they mate with? How do chromosomes get modified? (subgroups)
• EvoDevo field .. Evolution/Development - genes active in development are more conserved - mutations have much more drammatic effects
• Hard to underline conservation between human and chimp .. so much is conserved .. need to go to more distant species
• Interactions of genes -- harder to study than biochemistry; it makes you make clever tests
• A good book: Coen, "How organisms make themselves"

Sep 2, 2004

Chapter Covered: 23
Present: Lynn, Robert

• Use of dideoxyribose triphosphate mixed with deoxyribose triphosphate to break off replication at various points on a known base.
• Primer walking and m13 ssDNA replication
• Florescent dye primers
• How did the Celera / Human Genome Project compition play out?
  • HGP did not adpot shotgun sequencing - maintained mapping through markers approach
  • Dynamics between Celera, HGSC, TIGR, Smith Kline, Merck
  • Read: 2 papers: nature, science 2/15/2001 on genome sequence
• oligonucleotide array detector
• Followup reading on sequencing: "Genetics" by Hartwell et al.

Aug 2, 2004

Chapter Covered: 22
Present: Martine, Robert

• Two parallel systems:
  1. Main Antibody system - T helper brings antigen to B cell IgM, B cell multiplies and excretes IgG (targeting antibody), and IgE (signals mast cell to make histamine). Antibodies bind to antigens and draw attack by Macrophage, Neutrophil, complement protein complexes.
  2. Free agent system: T killer directly recognizes target cell by presented antigen (on HMC I) and kills it. Does it then present killed cell's antigens to helper T cells?
• Helper cells do not take antigen from infected cells .. only from the other immune system cells, when presented on HMC II. (using CD4 stabilizer)
• Memory cells a very direct explanation of aquired immunity. (this seems simplified)
• What are the mechanisms which constrain the B cell "shuffling" to make valid selections for V, D, J, C regions? (not missing needed ones, not putting too many in?) How is is made random enough to get a good random/regular distribution over the combination space without creating too many illegal combinations?
• Fascinating how Trypanosomes shuffle its surface coat proteins .. using the same system of combinations to defeat the targeted response of the immune system.

July 27, 2004

Chapter Covered: 20
Present: Ethan, Robert

• Transposons -- do they play a role in evolution (similar to crossover?)
• Where did they come from originally? (retrovirus?)
• Why do "hosts" put up with all the overhead (60%, 80%, 40% of genome from retrotransposons?)
• Are transposons necessary for cell to be viable (short term function)? Has experiment been done to remove all transposons from a cell line and see if it is fatal? (to cell, to fly embryo?) What about long term fitness of organism?
• What triggers transposon to replicate/transfer? My guess .. depends on where it is located: when upstream gene is activated, it is activated (to produce transposase,...).
• Wonder why they do not replicate out of control .. First idea is that maybe if they are in a very active site, the amount of transposase is high, forcing them to move to a new (less active) location, where they can remain longer. Second idea is that in individuals where they replicate out of control, it kills the organism before it can reproduce. Are we "saturated" with transposons, in an evolutionary equilibrium?
• RNAi may have evolved to limit retrotransposon proliferation. There must be something keeping it in check
• Idea that large amount of repeat DNA from transposons provides camoflage/decoy from mutation for the "real" genes.
• Why would our immune system develop as a counter to transposons? Can the immune system identify and target them? How? Does our immune system attack cancer cells?

July 12, 2004

Chapter Covered: 19
Present: Ethan, Manda, Martine, Robert

• What is a separate life? How integrated does a genetic sequence have to be before it becomes part of you?
• The question of whether something is working in its own best interest; does it help? The selfish gene
• How do membranes (physically) get wrapped around viral coats? Does the virus facilitate this? How do they get the correct surface proteins? Were these remnants on the old membrane or manufactured by the virus?
• Can T4 / other legged viruses function on an animal cell (no cell wall, cell membrane)?
• Can the immune system act/assist a cell after it has been infected with a virus? (aside from killing the cell)
• Overlapping gene in phiX174 genome -- analogous to computer file compression.
• Stress on issue of "control" over your own replication. Origin of replication. Virus does not have the means of replicating outside of a cell, but it still "controls" its replication. Don't fully understand the authors' message.
• We would like to engage with and apply the material - maybe review upcoming journal club articles and read background material so that we understand the talk better.
• Maybe work in chapters from Molecular Biology text

June 28, 2004

Chapter Covered: Synthetic Life by Gibbs in Scientific American, 2004
Present: Ethan, Manda, Robert

• Philosophical questions more interesting than the techniques.
• Worried about tinkering - something unknown coming about and changing our environment
• Interesting how added funtionality degrades due to mutation - a need to make the added functions mor important to health of he host.
• What's the nature of a "bio brick"? They seem to be on a different level thn "genes" (nature's bio bricks). Too much circuit thinking.
• A goal was to learn about life, but no new insights about life were presented which were found though building stuff.
• Discussion of patenting / intellecutal property issues

June 24, 2004

Chapter Covered: Censors of the Genome by Lau and Bartel in Scientific American, 2003
Present: Ethan, Manda, Martine, Robert

• Is RNAi == siRNA + miRNA?
• Where do siRNA strands come from? mRNA folded over onto itself? How is double stranded made from single stranded RNA? (needed for Dicer, right?)
• Origins from evolutionary perspective .. interesting theory that system was for first for defense, then developed for other purposes later.
• The article gave a good introductory description of the interferon response -- we talked about whether it was a suicide response, a signal to surrounding tissue, whether surrounding cells also are killed by the signal up to a certain distance, etc.. wanted to know more
• Paper describing "high pressure" delivery into mice with hepatitis - did this mean pushing the rna into the liver cells with high pressure, or that the mice were under high pressure atmosphere, or what?
• boinc platform for doing distributed computing .. searching for miRNA sequences.

June 14, 2004

Chapter Covered: 17
Present: Ethan, Manda, Martine, Robert

• Is the primer used in PCR more sticky than the opposite strand somehow? Do strands stay stuck together? No .. the original strands become completely unbound.
• Question/idea about using PCR before running a microarray expression profile. Would this be a good idea? Could it assist in detection, or would we lose calibration?
• Are they really growing gerbils with hippo genes? Why isn't this hitting the news big time?
• Primers do not have to be perfect .. but then can't they hit a bunch of other stuff? We guess yes, but that at a lower rate, and so through exponential growth, these "near hits" would get drowned out by the easier perfect hits
• Does crossover primers have a special "hinge" in the center, or is it just natural that a dna strand could base-pair to two seperate molecules and bring them together?
• Bringing back extinct species - maybe we will have a flip book someday with a dna catalog of animals that kids can make at home (future chemistry set?)
• Lots of talk about education and evolution followed..

June 8, 2004

Chapter Covered: 16
Present: Lynn, Manda, Martine, Robert

• Electrophoresis v. Chromotography -- big things can more faster than small ones in column chromotography - beads have pores and larger molecules will not enter the bead through the pore as often as small molecules.
• Complexity of some of these procedures is surprising (although we realize that things are now much simpler than they used to be). There are many steps
• Filters: If strands are embedded in the filter, isn't it unlikely that stuff will fall exactly in the right place to hybridize? No .. put a *lot* of stuff on the filter, and let the sample "cook" on the filter for a while .. give it time to hybridize .. then pull it through the filter with a vacuum.
• Chromosome walking .. analogy to Leggo blocks
• Subtractive hybridization - seems complicated. Used to isolate DMD gene via mutant with large missing piece (researchers knew that the piece was missing because it could be seen under a microscope .. the missing band pattern.
• Comparitive genomics and "genome on an affy chip" -- not just looking at genes necessarily, can pick evenly spaced landmarks along length of chromosome .. even in IGR. Can have a second level scan with finer resolution (60000 probes)
• Footprint - fragments *all* start from the beginning of the original sequence -- which is why it jumps in observed length over the protein binding region .. there is only one cut per molecule.
• Protein synthesis done in Merrifield lab in Flexnor hall .. Nobel Prise came later after applied to DNA
• Florescence - when you wash away the reporters, they won't be there any more to light up! (duh)
• Melting point: what kind of temperatures are we talking? Depends on salt concentration, length, G-C pairs
• Zoo blotting - is your piece more likely from the coding region? The coding regions are assumed to be more conserved accross species.
• cDNA libraries - look at expression profile of a particular cell -- so if alternative splicing is happening in the cell, it will be represented in the library (introns may be present)
• dose response screening -- handy to use gene fusion to measure changes in expression across dosages (one use)
• X-Ray crystalography - there is a NOVA reference/explanation of the deduction of the helical shape of DNA from using X-Ray C.
• Whose genome was used as "the human genome" -- no particular person (although a name did come up) there were a bunch of donors, and the variations across donors were resoved by some kind of consensus/ majority voting scheme (details unknown). Some bases are marked as "uncertain"

June 1, 2004

Chapter Covered:Efficacy and Safety of a Specific Inhibitor of the bcr-abl Tyrosine Kinase in Chronic Myeloid Leukemia Druker et al. in N Engl J Med 2001
Present: Ethan, Lynn, Manda, Robert, Robyn

• What is myloid? It is a lineage of cells from a stem cell which leads to many white blood cells (phagocyte, lymphocyte, macrophage, granulocyte..)
• Erythrocyte is a red blood cell - they don't have a nucleous! (so some cell differentiation does lead to changes in genetic content)
• B cells are antibody producing cells - they advertise the antibodies they can produce with surface receptors.
• Leukeimia - cells both crowd out other blood cells physically (in the marrow) *and* probably cause "stop" signal reaction to overabundance, which will stop normal cell division.
• What is "clonal expansion" -- all descendants are from a single cell; the disease originates from a single point rather than a wider growth signal.
• Morbidity v. Mortality: in treatments for cancer, more willing to accept morbidity (sickness) due to treatment when only alternative is mortality (death).
• auto/allo/xeno transplants::self/other human/animal
• Do oncologists still totally eliminate bone marrow (with chemo/radiation) and replace it so that patient can recover?
• Alpha-interferon: normally occurs as a cell signal for growth or development - found to be useful for treating CML
• Clinical Trial stages:
  1. dosage testing - often don't see efficacy here because small group and low dose.
  2. dose ranging - bigger group, look for efficacy
  3. efficacy trial - bigger group to prove efficacy
  4. post approval monitoring - maybe done to double check drug which had a fast approval
• This study showed good efficacy in phase 1 and was rationally targeted based on molecular knowledge
• Cancer as a driver of knowledge
• Translocation is a piece of each exchanged (chr9/chr22). Possible agents: transposons, retroviruses
• Original question: is this the cause or a byproduct? It is the cause, because this treatment reversed the disease.
• Is this drug used in other cancers? Yes.
• Issues of making it not interfere with other ATP binding sites - it turned out to be specific enough.
• Some patients develop an immunity to Gleevec - maybe more kinase is made or a change happens which excludes gleevec from blocking
• Would this be an oncogene? Yes (discussion of 1 step to cancer as opposed to 6 steps from last week)
• Might be worth looking into actual reason of death and how this is defined as cancer.
• Pharmakinetics - does it get to the blood and what halflife/concentration curve it follows
• ADMET:
  • Absorbtion
  • Distribution
  • Metabolism
  • Excretion
  • Toxicology

May 25, 2004

Chapter Covered: How Cancer Spreads by Ruoslahti in Scientific American 1996
    A Subway Map of Cancer Pathways Hahn and Weinberg in Nature poster 2002
Present: Ethan, Lynn, Manda, Martine, Robert, Robyn, Ted

• Spread of cancer to downstream organ: do cells die before making a full circuit through the bloodstream?
• We might want to look at breast cancer and kinokines.
• Cancer is heterogenous = generates constant variations in tissues.
• Interested in keeping tumor in the blood stream: it is very very vulnerable there.
• New treatment approaches: antibodies against your own cancer, block angiogenesis, target kinokines to stop sticking
• Ebola: acts similar to cancer ~ disrupts/attacks sticking agents
• Gleevec - story on the abl oncogene | translocation in chromosome turns on kinase; Gleevec blocks it, but some cells evolve other kinases which are not blocked, or amplify production
• Changing pathology: we can do molecular profiling now .. instead of looking at cells with a skilled eye.
• Brain tissue is immune to many cancers -- some species have unusual resistance .. which ones?
• Surgery can sometimes shake cells loose into the blood, perhaps helping in metastesis (kind of scary)
• Usefulness of blood testing - not just for cells, but maybe other blood factors.
• Maybe want to study a treatment: Gleevec or Eressa

May 17, 2004

Chapter Covered: Roots of Cancer by Gibbs in Scientific American, 2003
Present: Ethan, Manda, Martine, Robert, Robyn, Ted

• We appreciated the presentation of multiple (competing) theories - realized that there are several lines of active thought.
• Cancer is population of variety of cells - so it can be resistant to any therapy. Maybe we just don't yet fully understand (our hope)
• What does it mean to "cure" cancer? The potential is always there for reappearance. (me: but isn't the potential always there for everyone? we all have cancer?)
• Idea that a breakthrough for curing cancer might happen in conjunction with developing human immortality.
• Aneuploidy - is there a natural background level for this? No: when it happens we think cells die .. but occasionally one limps along and then it is more likely to become more aneuplodic in descendants.
• Maybe cancer originates from all four of these presented frameworks.
• Idea that in biology the model is not assumed to be truth .. that exceptions are expected.
• Examination of subway map diagram interesting (we will follow up on this next week) - we want to understand these paths better.
• Which comes first: mutations or aneuploidy? This is a key question.
• Want: definition for disease.
• Why does smoking promote cancer? Maybe with damage, normal cells stop dividing but (maybe early) cancer cells proliferate .. because they do not follow the stop signals they have a competitive advantage.
• Manda: "Things that break can break in many different ways"

May 10, 2004

Chapter Covered: 14 (2nd half)
Present: Ethan, Martine, Robert, Robyn

• Cells require signals to keep them alive -- or else they die of "loneliness". "They need constant reassurance"
• Zinc fingers - what are they? guess: a class of proteins recognized by their structure. Is p53 a zinc finger?
• p53 - how do we survive with such a fragile anti-tumor gene?
• What is DCC and "late adenoma"? (definitions)
• Again want definitions: cancer, benign, metastasis .. where is dividing line?
• Lamina is matrix between layers - like basal lamina - compartmentalizes layers of tissues.
• The lymph system and spreading of cancers - is this a completely different system? (different vescles? what's in them?)
• The comment on survivability statistics (that they are inflated due to earlier detection) seems overly harsh - are we *really* making no progress on extending life expectancy?
• 15% of human cancers caused by a virus - hpv, hsv - but is this figure including warts / benign tumors in "cancer" for this statistic?
• Book talks about some advanced therapies - but seems to omit chemotherapy and radiation. What about a comparison?

May 4, 2004

Chapter Covered: Hahn and Weinberg, 2002
Present: Ethan, Manda, Robert, Ted

• Theory of what makes a cancer: 6 steps, and each step gives the cell a new capability. These six steps are seen in *all cancers*.
• Damage to cell and apoptosis - internal and external triggers? Mechanism: lysosome?
• Does the "invasion" capability mean to go somewhere else and grow there? Or go there and transform surrounding tissue? Or transform from a distance? Authors state that the mechanism which allows invasion is not known.
• Interesting: that there might be fast/easy steps (in addition to 6 rate limiting steps) which could be targeted for treatment.
• Words we wanted better definitions for:
  • neoplastic
  • diagnostic
  • prognostic
  • senescence
  • anaplastic
  • epigenetic
  • mitogenic
• Immortal means every cell can continue through infinite replication. Not a time counter - a generation counter.
• What about treatments? Guessing that authors are pointing at steps to target.
• In rats, two steps are enough to get to cancer. Maybe because they don't need to live as long as we do to reproduce?
• Increased genetic instability: due to damaged DNA repair mechanisms

Apr 27, 2004

Chapter Covered: 14 (1st half)
Present: Ethan, Manda, Robert, Robyn

• Clarification of terms: Benign, Metastatic, Malignant
• Is reason why muscle cells don't often procude cancer because they don't divide often enough to progress - or are cells more susceptible to cancer causing mutations during mitosis?
• Smoking's effect of killing cells - does that promote cancer (the killing)
• 5 steps towards cancer .. we want a clear definition of what cancer is. The book seems to indicate that a benign tumor is cancer; we're not sure.
• Viruses as agents to spread oncogenes *within* your body.
• myc figure 14.12 - not sure what this is saying - error in duplication or many copies in genome?
• Signal transcription protein: these are not transcription factors - they may activate transcription factors or form complexes. The transcription factors act in the nucleus, these act in the cytoplasm.
• Is the generation clock mechanism the telomere?
• Importance of the cell cycle - signals which are the gatekeepers of phases.

Apr 19, 2004

Chapter Covered: 13
Present: Ethan, Manda, Robert, Robyn

• Confusion about the need for a deletion mutataion to clone dmd gene: Concluded that researchers did not know the exact composition of the gene, and were using the fragements of mutant chromosome as a filter - soaking up those pieces of the wildtype which were *not* in the gene. The remainder can then be spliced into a plasmid for cloning.
• Why doesn't aerosol gene therapy cure all cases of CF? Guess: some proportion of lung tissue is transformed with new gene, but not all. Partial effects.
• Gene therapy for SCID was exciting. Guess that bone marrow delivery is difficult - done in parts.
• Genetic counciling/engineering for children troubling - idea: you are guided to select the "best" traits for your children. Ethical concerns.
• Observed that retroviruses operate in reverse of the central dogma: RNA makes DNA, which gets inserted into the genome. (information flow is reversed) After insertion, DNA becomes active as a "gene".
• Discussion of history of AIDS, AIDS as a retrovirus.
• Amazed that retrovirus comes packaged with a reverse transcriptase: why not just package the DNA? Guess: with the RNA and reverse transcriptase, the virus can produce more DNA in the host cell than it could have delivered from outside.
• The importance of pathways evident in retrovirus lifecycle diagram.
• p and q arm of chromosome: separated by the centromere.
• Genetic couciling: Fear of regulation of reproduction ("defective" parents).

Apr 13, 2004

Chapter Covered: 12
Present: Ethan, Manda, Robert, Robyn

• Definition seems judgemental: "mistakes" in genetic material. I think of it more as variation then mistake.
• Misense = conservative or radical. Nonsense = new stop codon.
• We thought the term "Nonsense" was confusing. For example, a frame shift mutation leads to "nonsense" but really falls under insertions/deletions.
• Our "mutation tree:"
  Mutation
  • swap (exchange of bases)
  • missense
  • conservative
  • radical
  • nonsense
  • insertion or deletion
  • frame shift
  • non frame shift
• Sensitivity (brittleness) of system in face of mutation and genetic algorithms
• Question: What causes transposons to move? Do they use other machinery?
• Where do transposons come from? What triggers them to move? Are they part of us?
• Why is antibiotic resistance put into gene cassettes? To help you select only the cells that had the gene disrupted
• Hotspots: C->U due to methylated cytosine similar to bromouracil effect.
• Seems like there could be some use we could make of polarity swap reversions (useful mechanism or trigger).
• Maybe cut and patch machinery facilitates movement of transposons.
• Ames hair dye test .. we didn't understand this.

Apr 5, 2004

Chapter Covered: 11
Present: Ethan, Lynn, Manda, Robert

• Do the mitochondria make their own ribosomes? No, but chloroplasts do.
• Are the ribosomes on the ER different than the ribosomes in mitochondria or elsewhere?
• Ribosomes float down to the ER and attach - drawn by signal recognition proteins to the surface.
• DNA is always packaged around histone (even during inerphase)
• There are a variety of histones, some of which are modified through deacetylase methylation as a regulation mechanism.
• Look up term: "Histone Code" in PubMed
• Why is so much "junk DNA" carried forward (e.g. repetitive sequences)
• Idea: make a mouse without "junk" dna. Problem: don't know how to do it (but can't we synthesize entire chromosomes?)
• Analogy to commenting out code - pseudogenes
• Maybe junk kept around to have building blocks for evolution (higher adaptability)
• Highly repetitive areas: jumping genes (ALU). ALU also able to recombine DNA segments by carrying pieces along.
• Why bother having introns? (Seems inefficient) 1) alternative splicing 2) lariats maybe act as a "counter" or signal indicating transcriptional activity.
• Enhancer helps because the looping of DNA helps to hold the whole promoter sequence stuck together -- it stays longer.
• Multiple enhancers or inhibitors can be active (p268 in "Essential Cell Biology")
• Cap and tail are added before splicing.
• Length of tail effects half-life of mRNA in cytoplasm.
• Trypanisomes do trans splicing, but themselves don't have introns. What does this mean? Do they corrupt our mRNA processing? No.. they just cut and splice peices of their own (single exon) trancripts.
• Trans splicing also happens in fruit fly (not mentioned in book)

Mar 30, 2004

Chapter Covered: 9
Present: Lynn, Manda, Robert, Robyn

• How were restriction enzymes identified? (history)
• A prominent maker of restriction enzymes: New England BioLabs
• All restriction enzymes found in nature (not synthesized)
• Aside from ABC techniques for detection: radiation marking
• We stepped through the example on p.105 - making a restriction map. (In order to see how certain orderings had been ruled out)
• Vectors. The need for an origin of replication for the organism which a shuttle vector will travel to.
• Evolving away a cut site (use restriction enzyme at intervals, wait till something survives)
• Discussed a possible field trip to lab or museum so we can run a gel.
• Maybe invite Dr. McCarty from Rockefeller Univeristy for discussion/background.

Mar 22, 2004

Chapter Covered: 8
Present: Manda, Robert, Robyn

• Where did plasmids come from? (Evolutionary origins, how did the first "male" bacteria arise)
• Plasmids which are identical or different enough can coexist, but those which are somewhat similar (same type) cannot. This doesn't make sense. What is the mechanism which allows plasmids to detect "similar" and yet distinguish it from "identical"? What are the limits of "identical"?
• Interested in infection of bacteria (spreading of antibiotic resistance), historical discovery of plasmids
• Discussed our own body's response to viral infection - what is due to virus killing human cells, what is due to immune response?
• What do anti-retroviral drugs do? Do we understand what mechanism HIV uses to progress to AIDS?
• Electroporator - does cell repair this damage to the membrane? How hard is it to recover? (this knocks holes in the membrane yes?)
• Sex Pilus: how is this structure built? How do the genes from the F plasmid allow this to be made? Is the structure like a hair (protein)?
• Discussed the reformation of the plasmid after transduction (semiconservative like DNA replication)
• Origin of transfer ("peelable" point) becomes part of the chromosome after plamid is incorporated into the chromosome.
• Real mystery: during tranformation, how are "the original genes lost"? Why aren't the new genes simply added to the old?

Mar 15, 2004

Chapter Covered: 7
Present: Ethan, Manda, Robert, Robyn

• Why is residue called "residue"?
• Multi-processing makes sense (multiple ribosomes working in parallel - polysome)
• Tail protease understood -- error correction / robust failure response
• Many analogies from computer programming used to help understand concepts
• The need for the chance of errors -- too perfect -- did an error free organism ever survive?
• New models are quickly grasped (perhpas too quickly) through anthropomorphic analogies
• How did this knowledge (from chapter) come about? How was 2 part ribosome figured out?
• Central (1:1) dogma - how much does this hold? Counterexamples?
• What is the difference between a protein and a protein complex/assembly? Maybe any part is a protein if it has some known function in which it acts on the substrate by itself.
• Is the ribosome a protein? no.
• Parallel patterns between transcription and translation:
  • Imperfect binding sites: polymerase enhancer and ribosome binding site.
  • Bootstraps: RNA primers and fMet Amino Acid
  • Batch jobs: Operons and Cistrons
• Reading frames like word alignment in computer data structures/file formats.
• Seems to be lots of new bases:
  • I - Inosine
  • D - Deoxyuracil
  • psi - pseudouracil
• What is variable loop in tRNA and what is it for?
• Idea for future meeting: review summary papers and presentations from researchers (Dr. Nurse?)

Mar 8, 2004

Chapter Covered: 6
Present: Daniel, Ethan, Lynn, Manda, Robert, Robyn

• Discussed basics of transcriptional regulation:

  promoter

  area in upstream region which is recognized by RNA Polymerase

  activator

  protein which binds to upstream region to help RNA Polymerase bind to a (imperfect) promoter

  repressor

  protein which binds to upstream region to block RNA Pol. (Binding site called "operator")

• Stopping transcription with rna hairpin (inverted repeats -> hairpin -> slow down over poly-a tail)
• Question of the start point of the transcribed region .. is 0 the start codon?
• The coding region is the area that codes for amino acids (codons)
• Quorum sensing - intercellular signalling was very interesting
• Perhaps we could expand our representation of cellular pathways to include this kind of group signalling
• Questions of emergent comlexity / emergent intelligence
• Quesions of evolution: how can Quorum sensing evolve? Isn't it useless without the coordination activity of other cells? Question of the evolution of the eye - there still can be a stepwise path
• Global activators and local repressors - the Lac genes
• Cyclic-AMP molecule is like a nucleotide (many signals are)
• Antisense RNA, another mechanism for regulating the use of genes
• Unasked question: when sigma subunit "falls off", how can the RNA Pol. be used again? Does it aquire another?(p.52)
• Unasked question: why are there no operons in eukaryotes? Is this somehow incompatible with the enhanced regulation?

Mar 1, 2004

Chapter Covered: 5
Present: Daniel, Ethan, Manda, Robert

• Okazaki fragments most interesting and confusing concept
• Would like to know length of typical Okazaki fragment, and time scale of segment production compared to action of DNA Helicase
• Who cleans up the RNA primers? POL-III?
• Are there better error correction mechanisms for the lagging end replication? Seems more error prone
• Mismatches in DNA: we think we remember a process of methylation which can introduce mismatches into dna. What happens when a mismatched base pair gets replicated?
• I was confused between reference of chromosome "division" during mitosis versus "duplication" during Synthesis phase
• Nuclear membrane dissolving and reforming -- is the same material reused, or is it remanufactured by the new nuclei?
• Philosophical comment: "every cell of our body knows the answer to these questions" - made me wonder about cellular "knowledge" and "awareness" compared to our own knowledge and awareness, and also compared to the whole "world system"'s knowledge

Feb 26, 2004

Chapter Covered: 4
Present: Ethan, Lynn, Manda, Robert

• Feeling that without hands on experiences, the knowledge doesn't sink in as well (doesn't feel "real")
• Maybe we could take turns "teaching" -- as a way to help us absorb through preparation
• We talked a bit about chemical bonds and chemistry notation. Some confusion about the phosphate/sugar binding site
• 3' and 5' directionality and triphosphate bond during replication (to ensure reliable sequence assembly)
• Felt a desire for a simple course to hit on basic topics for non-bologists (structured teaching)
• Think about prerequisites for each chapter (chemical bonds, e.g.)
• Nucleolus is site for production of ribosomal RNA

Feb 16, 2004

Chapters Covered: 2 and 3
Present: Lynn, Manda, Robert

• Introduced our backgrounds to each other
• The change of understanding: 20 years ago, we didn't know about introns
• Macrophage infection - bacteria can remain alive inside a macrophage - question: how do they harm us then?
• Maybe a good reading club topic for future would be: Statistics for Programmers
• Question of what a gene is .. (unit of genetic inforation?) .. maybe come back to this question after ch7. maybe "single transcriptional event"
• EST = Expressed sequence tag
• cell sex determinants - drosphilla different from human - the role of androgens - c.elegans and cells with different sex in same organism