Running_List_of_Goals_Slides_Assignments

Computer lab 14

Computer-lab assignment 14.docx _ as_pdf
Slides on Phamerator.

Goals

Know how to use phamerator
-- select genomes
-- manipulate genome maps
Recognize inteins in phamerator generated genome alignments

Review Session and possibly Lecture 27

Goals

Be ready for the final
Know who Felix d'Hérelle was
Appreciate the images of genome comparisons created in Phamerator.

Assignments

For Friday, recall which intein containing gene you worked on in lab 4
Study for the Final
If you are interested, check out the Wikipedia site on Felix d'Hérelle.

Links

pdf of Exams 5-9 Sorry, not the greatest print-outs.
Training questions with answers
Slides on Felix d'Hérelle and Phamerator.

Lecture 26

Goals

Consider the relationship between genetic drift, population size, and the accumulation of "junk DNA"
Be aware of the discussion of "function" assigned to intergenic DNA by the ENCODE project
Know a few examples for constructive neutral evolution
Know about split inteins and what they are doing

Assignments

Complete Take-Home Exam #9 before Wednesday 11.15am
Have questions ready for review session on Wednesday
Do the SETs, please!
Update your class notebooks. If you do not use the shared One Note book, send it to the instructors on Friday..

Links

Slides on Constructive Neutral evolution, genetic drift and the origins of complexity.

Training Questions to prepare for the final

Other recommended preparation:

read through the list of goals of class 14 - 27. If you think you have not reached a particular goal, look through the slides, and if that does not help, ask a question on the discussion board.
Go through the take home exams.

Computer lab 13

Computer-lab assignment 13.docx _ as_pdf

Goals

Appreciate the power of scripts to run programs repeatedly using different input files
Appreciate the power of scripts to extract information from the verbose output of a program
Know how simple statistics on all protein sequences present in a genome can inform on the physiology and adaptations of an organism
Know that analysis of the genome wide composition of proteins can provide information on optimal growth temperature and adaptation to growth at high salt concentrations.

Assignments for Monday

Read through take home exam #9
refresh your memory on genetic drift and constructive neutral evolution

Lecture 25

Goals

Know about the roles introns play in exon shuffling and in the non-sense mediated mRNA decay pathway
Appreciate the power of scripts to perform repetitive tasks
Appreciate the power of scripts to run programs repeatedly and to extract information from the verbose output of a program
Know how simple statistics on all protein sequences present in a genome can inform on the physiology and adaptations of an organism
Know that analysis of the genome wide composition of proteins can provide information on optimal growth temperature and adaptation to growth at high salt concentrations.

Links

Slides The benefits of spliceosomal introns. The power of simple scripts: genome wide theoretical IEP calculation.

Assignments for Friday

Read through the wikipedia entry on halophiles
Browse through wikipedia entries on
isoelectric points, Zeta potential, and Surface potential

Assignments for Monday

Take home exam #9

Lecture 24

Goals

Appreciate the capabilities of figtree to beautify trees and to create publication ready (nearly) images of phylogenies
Appreciate the pan-genome as a genetic resource for the population (homeoalleles, weakly selected functions, black queen hypothesis)
Know a few examples of new pathways created through gene transfer.
Know the what the terms metagenome, pan-genome and microbiome refer to.
Recall the different types on introns
Be aware that in animals and plants most genes contain more intron than exon sequences
Know about the introns early versus introns debate
Know about the supporting evidence for both sides
Know how Go plots are created, and how they are used to define protein structure building blocks
Know why the finding of the intron in Triose Phosphate Isomerase (TPI) encoding gene from Culex is not an argument for introns early

Links

Slides on Figtree, pan-genome Terminology, Introns, Introns early versus late.

Assignment for Wednesday:

Read Ford Doolittle's article on junk DNA
https://www.pnas.org/doi/10.1073/pnas.1221376110
Read through Michael Lynch's review on genome structure and adaptive evolution
Also available in reading materials.

Assignments for Friday

Read through the wikipedia entry on halophiles
Browse through wikipedia entries on
isoelectric points, Zeta potential, and Surface potential

Computer lab 12

Computer-lab assignment 12.docx _ as_pdf

Goals

Know how to do a PSI Blast search using the web interface
Know that the construction of a PSSM can be done with a different (preferably large and diverse) databank than the final search.
Be able to save a PSSM from a web based or a command line blast search.
Execute PSI-blast searches, and different blast searches using pre-calculated PSSMs
Appreciate the differences between blastp, psibast, and using tblastn with a PSSM
Know that tblastn searches targeting proteins encoded by selfish genetic elements usually give many more results than searches of the annotated proteins.
Appreciate that most eukaryotic genomes are full of remnants of retroviral fragments.

Lecture23

Goals

Know a few examples for the creative power of Gene transfer
Recognize that the pan-genome of a species provides a reservoir of genetic information that goes beyond the genetic content of an individual genome
Know about the relationship between bacteriophages and GTAs
Know that many genes that have not made a functional contribution to the organisms nevertheless show a low level of purifying selection.
Understand how recombination accelerates evolution and prevents the accumulation.
Be aware that rejection of the Null Hypothesis for Neutral evolution (dN/dS<1) does not prove that a gene makes a positive contribution to the fitness of an organisms.
Understand why gene sharing via GTAs is not considered an evolutionary stable strategy

Assignment for Monday 11/27

Read the historical article by Wally Gilbert on "why genes in pieces"
Assignemnts for Friday see below

Lecture 22

Goals

Know that PSIblast lowers the frequency of false negatives as compared to a normal blast search
Know the underlying principle of the iteration in PSI blast
Know what PSI and PSSM stand for
Understand what PSI blast and Hmmer searches might be used for
Be aware that making a PSSM and using it for a search can use different databases.
Appreciate the many contributions horizontal gene transfer makes to the evolution of organisms.
Know a few examples for the creative power of Gene transfer

Assignments for Friday

Read the introduction (section 1) and the caveats (section 4) of the PSI Blast tutorial
For those interested to learn about a popular alternative to PSI Blast:
Read through http://en.wikipedia.org/wiki/HMMER and http://en.wikipedia.org/wiki/Hidden_Markov_model
In case the principle of hidden profiles remains cryptic and for the difference between PSIs and Hmmer, you can try the section in the HMMER manual on "What profile HMMs are" (bottom of page 7 and page 8).

Computer lab 11

Computer-lab assignment 11.docx _ as_pdf

Goals

Understand and be able to apply and evaluate models that test for dN/dS ratios for individual codons.
Be able to use tracer to evaluate estimated parameters and their High Probability Density intervals from MrBayes runs.
Import the sump data (either via tracer, or directly from the sump output) into excel and determine the sites with the highest probability to be under diversifying (positve) selection
Highlight sites that are probably under diversifying selection in protein structures dispayed in chimera.

Lecture 21

Goals

Know that because of the redundancy some mutations do not change the sequence of the encoded protein. These mutations are termed synonymous.
Know that under condition of strict neutral evolution synonymous and non-synonymous substitutions would occur with the same rate.
Know that dN/dS <1 reflects that selection has worked to remove some non-synonymous substitutions.
Know that diversifying selection dN/dS >1 acts on sites in virus genomes that are recognized by the immune system.
Know that the dN/dS>1 approach that can be used to detect positive selection is often difficult to apply in case the alignment is unreliable (which results in overestimating non-synonymous substitutions).
Understand and appreciate Walter Fitch's contribution to identify strains that are likely the parents of next years influenza outbreak
Know that the absence of SNPs in an allele (or surrounding an allele) can be caused by a selective sweep that erases the diversity around the site being selected for.
Be clear about what Bruce Lahn's studies of alleles for brain development genes show and do not show
Think about what this means for science?

Assignments

Read through the excellent articles on Denisovians and on Interbreeding between archaic and modern humans on Wikipedia
Make a contribution on the discussion board regarding the question "Are some scientific facts better left uncovered?" Use the WSF on Bruce Lahn as a starting point (here or in Reading Materials on huskyCT.) This is a difficult topic, be courteous; there may be good arguments on both sides.

Lecture 20

Goals

Know about quartet and bipartition spectra.
Appreciate Neighbor Net as an alternative to trees
Know what the terms positive, negative, and neutral selection mean and the frequent used synonyms for these terms.
Be able to discuss the terms positive and diversifying selection.
Realize the limitations of natural selection with respect to mutations that increase the fitness of an individual.
Know that genes under positive selection are fixed in a population in much shorter time intervals compared to selectively neutral mutations.

Computer lab 10

Computer-lab assignment 10.docx _ as_pdf

Goals

Know about the sump and sumt commands in MrBayes
Understand why the burnin should be excluded from the analysis
Know how to read the bipartition tables and trees created by the sumt command
Know how to evaluate the .p-files with respect to high probability intervals for parameters
Understand why less selection pressure often leads to a higher frequency of A and T in a DNA sequence
Appreciate how total Tree Length and the shape parameter describing Among Site Rate Variation can inform about selection pressures acting on a sequence.

Lecture 19

Goals

Know the different approaches to combine genes into a genome/species tree (super-matrix versus super-tree)
If you concatenate data, make sure that the individual gene phylogenies are compatible with the tree from the concatenated analysis
Worry about what the consensus tree like signal might actually mean
Know the sequencing ebola virus DNA was pivotal in determining the transmission history of the virus
Appreciate that different funeral rites in Congo and West Africa contributed to the severity of the outbreak
Know that the outbreak in West Africa went back to a single transmission from bat to humans

Assignments

Read this article on selective sweeps
Complete the exploration of population genetic simulations at http://www.radford.edu/~rsheehy/Gen_flash/popgen/ (you might need to enable flash in your browser).
- Using the same fitness and frequency for the A1 and A2 allele, explore the impact of population size on drift (w11:1; w12:1, w22=1)? [use a population size of 100, 500 generations, an initial frequency of .5, 5 populations]
- For the same population size (100), explore settings that reflect balancing selection. (w11:.9; w12:1, w22=.9) Compare these results to the above.
- What happens, if you increase or decrease the population size? (Be drastic choose 20 or 1000)
- Using a small initial frequency of allele 1 (freq. of 0.01 in a population of 50, i.e., you have one allele that conveys a 5% fitness advantage) (w11:1; w12:.95, w22=.9). Perform several simulations. (You need to look closely to see that in the majority of the populations the A1 allele, the one that conveys the 5% advantage go extinct quickly). Note that is very different from a population with infinite size.
  - What does this suggest for the effectiveness of natural selection?
- Does natural selection acting on a single advantageous allele work better in a large population? To explore this, increase the population size and lower the frequency, so that you still have one beneficial allele in the population? (e.g., to have one beneficial allele in a population of 500 individuals its freq. is 0.001)**

Lecture 18

Goals

Know the many reasons as to why gene and species trees might differ, and how one can decide if a difference is due to gene transfer or duplication and loss.
Know the similarity and differences between parsimony and maximum likelihood based phylogenetic reconstruction
Understand the differences between Maximum Likelihood Estimation and Bayesian approaches to phylogenetics.
Understand the principle of obtaining posterior probabilities through MCMCMCs

Assignment for Wednesday (11/3)

Play with Paul Lewis's MCRobot. Explore a differing number of heated chains, and different probability landscapes. https://plewis.github.io/applets/mcmc-robot/
Work through Olga's webpage giving an example on Baysian thinging

Computer lab 9

Computer-lab assignment 09

Goals

Know how to do a maximum likelihood ratio test
Know that Maximum Likelihood approaches allow to avoid over parameterization.
Know how different substitution models are defined,
Know how to run iqtree on xanadu (the latest version is invoked with iqtree2, after you loaded the module).
Know what the term Long Branch Attraction Artifact refers to, and that more sophisticated ml-approaches do much better than simple parsimony analysis to avoid LBA (it remains a sad realization that sometimes nature apparently does not follow Okkham's razor).

Assignments for Monday see below.

Lecture 17

Goals

Understand the differences between Parsimony, Maximum Likelihood and Bayesian approaches to phylogenetic reconstruction
Know what non parametric bootstrapping is, and how it can be applied to many different approaches of phylogenetic analysis
Appreciate the huge number of tree topologies for a given number of leaves, and the implications this has for heuristic searches of tree space.
Appreciate the difference between likelihood of a tree or model and the probability of a tree or model

Assignment for Friday

If you have problems wrapping your head around non-parametric bootstrapping, watch this YouTube video (warning some may find the sound track a little strange)

Assignment for Monday (10/30)

Take the quiz from the Tree Thinking Challenge
For additional motivation on the importance of molecular phylogenies meditate about the COVID pandemic. A nice interactive tree is here. There is a play button top left, and you can select different classification schemes and time intervals. I am particularly impressed by the long stem branches that some clades have before they were sampled and diversified (e.g. emerging lineage 22F).

Comments

If you work on a Mac, Java sometimes does not work, also java from ORACLE is only available for free under some conditions. This document on JAVA_and_macOS_X.pdf has instructions on how to install open java version 11.
Updated information on the CURE project / honors conversion project is no the discussion board.

Lecture16

Goals

Know the principle behind parsimony analysis and Occam's razor (or Ockham's razor, aka lex parsimoniae)
Know the similarity and differences between parsimony and maximum likelihood based phylogenetic reconstruction
Understand the differences between Parsimony, and Maximum Likelihood Estimation
Know what non parametric bootstrapping is, and how it can be applied to many different approaches of phylogenetic analysis
Know that swapping branches around a node does not change the meaning of a phylogenetic tree

Assignment for Wednesday (10/27)

Read excerpts of Chapters 5 and 6 from Li's "Molecular Evolution" on HuskyCT
Read through the Wikipedia entry on Occam's razor

Computer lab 8

Computer-lab assignment 08

Goals

be able to use nucmer and dotplot to illustrate the relations between multiple genomes in an all against all comparison.
know how to perform blast searches from the command line.
know how to process the tabular blast output files.

Lecture 15

Goals

Know the different pathways through which gene families can expand in a genome
Know about the fate of duplicated genes
Understand that gene duplication followed by gene loss may be important in erecting post mating hybridization barriers.
Know how gaps, insertions, exons/introns, repeated domains, and regions of low complexity look like in a dotplot analysis.
Appreciate that dotplots (such as Gepard or Mummer) are useful to visualize the comparison between multiple genomes.

Links

slides on gene duplications and dotplots and discussion of lab 6

Assignments

For Friday

Refresh your memory on blast searches and dotplots

For Monday

Contemplate the different ways genes can be duplicated, and how they can persist over long periods of time
Try to understand how pseudogenization can lead to a post mating barrier for diverging populations.

Lecture 14

Goals

Know about some processes in evolution that go beyond natural selection acting on gradual changes
Be aware that many scientific heroes were children of their time
Be aware of the criticisms of the Modern Synthesis

Links

slides on Mutualism and Mutual Aid.

Assignments for Wednesday

Read the brief summary of Jemmy Button at
https://www.darwinproject.ac.uk/orundellico-jemmy-button
Read the article by Lynch and Conery on The Evolutionary Fate and Consequences of Duplicate Genes. The article is available in the Reading Materials on HuskyCT. The abstract is on pubmed.

Computer lab 7

Computer-lab assignment 07

Goals

Know how cumulative strand bias helps to infer genome structure of prokaryotic genomes (Ori, leading/lagging strand, terminus of replication).
Appreciate the power of hashes as on the fly counters and as flexible data structures to associate keys with values.
Appreciate to perform repetitive tasks
Know how to run mummer and create and read mummer plots.

Assignments

See below for suggested readings on cladistics controversies
Take home exam #4 is due on Monday.

Midterm

Lecture 12

Goals

Appreciate that many important characteristics (such as photosynthesis) of living organisms were transferred horizontally
Understand the terminology used in cladistics
Understand the concerns about not considering paraphyletic groups as proper taxonomic units
Know why fish do not exist
Contemplate the utility of a natural taxonomic system in light of endosymbiosis and HGT

Links

Slides on photosynthesis in the ToL and cladistics.

Assignment for Monday (10/16)

Take-home exam #4 is due.
Try to wrap your head around the discussion of shared derived vs shared primitive characters, (see the Wikipedia entry on cladistics -- Ashlock (Ernst Mayr, Lynn Margulis, and others) versus Hennig (Woese, Pace, and others --- for discussion see here, here and here; Jan Sapp's review of the history is here)

The heat of this controversy is reflected in the following excerpt from from Tom Cavalier Smith http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2842702/ :
"Oddly, the school of ‘phylogenetic systematics’ founded by Hennig (1966) grossly downplayed the phylogenetic importance of progressive change compared with splitting, seen by them as so all-important that many Hennigian devotees dogmatically insist that ancestral groups like Bacteria, Protozoa and Reptilia be banned. Hennig called such basal groups with a monophyletic origin ‘paraphyletic’ and redefined monophyly to exclude them and embrace only clades, likewise redefined as including all descendants of their last common ancestor. This redefinition of ‘clade’ is universally accepted, but Hennig's extremely confusing and unwise redefinition of monophyly is not. Though accepted by many, sadly probably the majority (especially the most vociferous and over self-confident, and those fearful of bullying anonymous referees, of whom I have encountered dozens mistakenly insisting without reasoned arguments that paraphyletic taxa are never permissible), it is rightly firmly rejected by evolutionary systematists who consider the classical distinction between polyphyly and paraphyly much more important than distinguishing two forms of monophyly (paraphyly and holophyly, using the precise terminology of Ashlock (1971), where holophyletic equals monophyletic sensu Hennig)."

Computer lab 6

Computer-lab assignment 06

Goals

align sequences in mafft and muscle
be able to define sites in Seaview
safe sections (intein and exteins) from a Multiple Sequence Alignment (MSA) into separate files.
Use chimerax to predict the stucture of putative inteins and theii hostprotein in alphafold
increase your familiarity with FileZilla and the Commnad Line
Assignment for Monday see below.

Lecture 11 (10/6)

Goals

Understand genome structure of prokaryotic genomes (Ori, leading/lagging strand, terminus of replication).
Know two explanations that can explain the preponderance of recombination events between points equidistant to the origin of replication
- (co-occurrence of recombination with replication;
- Architecture Imparting Sequences (AIMS) and strand bias are not disrupted/misplaced (i.e., these are the only recombination events that do not lead to a drop in fitness)
Appreciate the power of hashes as on the fly counters and as flexible data structures to associate keys with values.

Lecture 10, 10/2

Goals

Understand the transitive property of homology and its limitation
Know about the debates concerning the hot origins of life.
Understand the arguments for the domain ancestors being survivors of a catastrophe (impact?) that selected to thermophyly
appreciate that early Earth was a more violent place than today's (no warm little pond, but constant "Tsunamis"
know about the arguments in favor of a vibrant biosphere being present already 3.8 Ga BP
appreciate the difficulties of interpreting ancient microfossils.
know that the temperature under which an organism lives is reflected in sequence composition of proteins and RNAs

Links

Discussion of the transitive property of homology, makeblastdb and blast on the command line, the early evolution of life and impact frustration of an earlier biosphere: Slides

Assignments for Wednesday 10/4

Read through article from Tillier and Collins on Genome rearrangement by replication-directed translocation (also available on HuskyCT). Try to understand Figure 1 and 2. Can you think of alternative explanations?
Make sure that your electronic notebook is in good shape. In particular, you should have reflective statements on every lecture. If you do not use the OneNote class notebook (to which I have access), share the notebook with the instructors via email.
I thought this the notebook sharing was due today, but I was told somewhere it said 10/6. 10/6 before 10am is the final deadline.
Optional, incase you are interested in the early evolution of life, here are a few articles that give more details:

Computer lab 5

Computer-lab assignment 05

Goals

know when an when not the transitive property of homology applies
be able to log into your student account on Xanadu
become familiar with Filezilla and ssh
Be able to align sequences using Mafft or Muscle

Assignment for Monday

read as much of this introduction to the unix shell as you can digest.

Lecture 9 (9/29)

Goals

Know that for pairwise alignments, given a substitution matrix and gap penalties one can find alignments with an optimal alignment score. However, there might be several alignments with the same optimal score.
Have a rough idea of the intricacies of creating multiple sequence alignments
Appreciate the advantages of a command line interface over a Graphics User Interface
Know a few commands from the unix command line (cd ls pwd man cat more)
Know about compute and head-notes on computing clusters

Lecture 8

Know about Margaret Dayhoff's contributions to bioinformatics.
Know the difference between PAM and Blosum matrices.
Know what Dayhoff groups of amino acids are.
How to measure if sequences are significantly similar.
Understand the difference and similarities between P and E values.
Know about "usual" cut-offs for Z-scores, P- and E-values.
Be able to discuss the processes that may lead to the decay of significance
Know what fishing expeditions are about
Know what the Bonferroni correction is, and why it is not popular.
Know what false positives and false negatives are in relation to a databank search
Be able to discuss the processes that may lead to the decay of significance

Computer lab 4

Computer-lab assignment 04:

Goals

Know about bibliography software
Know about the advantage of the databanks accessible through NCBI's Entrez.
Be able to perform literature databank searches at Google scholar, SCOPUS and pubmed
Know how to retrieve full length manuscripts ;-)
Know that the # of publications, # of citations, and the H-index are frequently used to measure productivity and impact of scientists.
Know how to access manuscripts similar to one that you know is relevant to you.
Appreciate that GenBank is highly redundant.
Know that searches at the protein level are more effective than searches at the nucleotide level.

Lecture 7 (9/20)

Goals

Know about Margaret Dayhoff's contributions to bioinformatics.
Know about the Entrez system at the NCBI
Know about the advantages and disadvantages of databanks with or without a gatekeeper.
Know the difference between PAM and Blosum matrices.
Know what Dayhoff groups of amino acids are.
How to measure if sequences are significantly similar.
Understand the difference and similarities between P and E values.
Know about "usual" cut-offs for Z-scores, P- and E-values.
Know about the tree and coral metaphors to depict evolution
Know what false positives and false negatives are in relation to a databank search

Lecture 6 (9/18)

Goals

Understand the relation between substitutions and sequence divergence
Know a few reasons why protein sequences work better to assess similarity than nucleotides
Understand that only slow evolving genes that are under strong selection for function are suitable to trace early events in evolution.
Appreciate Lamarck's contribution to understanding evolution.
Understand the contributions that Woese and Fox made to the classification of life, which molecule they used, and the domains (aka Urkingdoms) they discovered
Understand the power and the limitations of the tree of life image.
Understand the relationship between the 3 domains, and how the tree of life was rooted.
Appreciate that the organismal tree is embedded in the tangled tree or network depicting genome evolution.

Computer lab 3 (9/15)

Computer-lab assignment 03

Inteins: splicing and homing endonuclease domains; proien DNA interactions.

Goals

Know how to identify domains in multi domain proteins in chimera;
create a multiple sequence alignment based on aligned structures in chimera
align structures of very divergent proteins;
inspect protein DNA interactions;
identify the major and minor groove in a DNA molecule;

For the assignments for Monday see class 5 below.

Lecture 5 (9/15)

Goals

Appreciate the problems and limitations faced by attempts to define life
Know who Lynn Margulis was.
Understand the (outline of) Gaia hypothesis, and the problems it faces, and how the ITSNTS approach might overcome these.
Understand the ATP occupancy in the subunits that form the hexamers in the F1 ATPases
Know what inteins are and which enzymatic activities do they have?
Know the scientific definition of symbiosis
Know about the possible symbiotic relationships between organisms, genes, or protein domains?
Know the different phases of the homing cycle.
now that inteins can be associated with a strong selective disadvantage
Know that an environmentally heterogenous environment may allow for the long term persistence of parasites (and thus provide an alternative to the homing cycle).

Links

Assignments

for Monday (9/18)

Draw a sketch for the relation between the number substitutions that occurred in evolution and the percent identity of the two sequences. (I.e. how does the observed similarity change, as more and more substitutions occur?)
What are the endpoints (saturation levels) for 4 letter alphabet and for a 20 letter alphabet assuming a perfect alignment that alignes homologous positions.
How does this relationship change, if some parts of the sequence are so important that the protein becomes non-functional, if a mutation occurs in these positions (i.e., these parts of the sequence are never observed to undergo any change?
If you were to do a realistic calculation and you were to consider a nucleotide sequence, how long would it take to arrive at 20% identity? (tip: how similar are two random sequences that have not been aligned?)
(Note: answering these questions should not require the use of a calculator or a formula, just common sense.)

for Friday (9/15)

go through the slides on inteins,
watch the YouTube presentation.

Lecture 4 (9/13)

Goals

Understand that RNA can be both genetic material and catalyst
Know item that support the RNA world concept, and difficulties faced by the RNA world
Know that ATP binding domains can be of very different types, and what this means for our understanding of homology.
Understand the problems and limitations faced by attempts to define life

Links

Slides on lab#2 ATP binding sites, convergent evolution, the RNA world.
Slides on Life, Natural Selection, and Gaia.pptx

Assignments:

Contemplate the following:

find arguments for an against a virus being considered alive.
if being part of group that can be subject to natural selection is a criterion for being alive, why should this not apply to computer life and computer viruses?
does the stipulation of being a "chemical"-system restrict this to "life as we know it"?
what argues against Traube's cells not being alive?

Read through the slides on Life, Natural Selection and Gaia. You can follow the links, if you are in presentation mode.
Read through take-home exam #1 - Wednesday is the last chance to discuss this in class before the dues date. Remember to work on the exam on your own. THIS IS NOT A TEAM BASED LEARNING EXERCISE!

Computer lab 2 (9/8)

Computer-lab assignment 02:
Aligning divergent sequences and structures in Chimera

Goals:

Have an rough understanding of the content of a protein data bank file
Be able to save individual subunits into distinct pdb files
Align structures of divergent proteins
Use the structure based alignment to align the linear sequences
Align structures of a catalytic subunit during the catalytic cycle
Appreciate that even 80% sequence divergence (or more) can leave the protein structure very, very similar.
Appreciate that for important proteins substitutions occur so rarely that proteins remain recognizable similar in structure AND sequence.

For the assignments for Monday see class 3 below.

Lecture 3 (9/6)

Goals:

The ATPsynthase as rotary motor (Yoshida's experiment, proteolipids)
The role of gene duplication and sequence divergence in the evolution of proteins;
Know about the three domains of life (archaea, bacteria, eukaryotes) and how they are related to one another
Appreciate that molecular evolution can study events that occurred before the last universal common ancestor
Understand the role of ancient gene duplications in rooting the tree of life.

Computer Lab #1 (9/1)

Computer-lab assignment 01:
Intro to Chimera - Binding Pocket Substrate Interactions

Goals:

Be able to launch chimera
Display a 3 D coordinate file from the pdb (1HEW) in chimera
Use different display settings
Display amino acid side chains in the binding pocket of 1HEW and study the interactions between the substrate and the binding pocket.
Calculate a Ramachandran plot, and determine where in this plot alpha helices, beta sheets, and glycine residues fall.
Save your work as image and project.

Assignments for Wednesday (9/8) see below

Lecture 2 (8/30)

Goals:

Understand the concept of homology
Understand that significant similarity between two primary protein sequences (that are - not of low complexity) is a strong indication that the two sequences evolved from the same ancestral sequence.
Know how the field of Bioinformatics is commonly "defined"
Know what terms replication, transcription and translation refer to
Know about primary, secondary and tertiary structure of proteins

Links:

Slides on Homology (we will continue thes on Wednesday 9/8)
Slides on transcription translation protein structure basics
slides selected from Mark Gerstein's Bioinformatics Course.

Assignments for Friday (9/3):

Read through the slides on protein structure
Read through the following entries in Wikipedia:
http://en.wikipedia.org/wiki/Protein_folding
http://en.wikipedia.org/wiki/Ramachandran_plot
Fold an origami crane, write your name on the wings. We will use it as a flag in the class on Friday.
If you want to keep personal copies of the things you do during the computer exercises, bring a laptop and/or memory stick to class on Friday.

Assignments for Wednesday (9/6)

Contemplate the following questions (see the slides on homology for inspiration):

Are most proteins with similar function homologous?
Are all proteins with similar function homologous?
Are most proteins with significant sequence similarity homologous?
Do most homologous proteins have significant sequence similarity?
Do most homologous proteins have similar structure?

Try to answer the following questions:

Would in your opinion maintaining a database on beetles that contains data on where was the beetle collected, its morphology, and where is it stored in the collection fall under bioinformatics?
Would in your opinion determining the 3D structure of a protein using X-ray crystallography fall under bioinformatics?
How many different proteins with length of 100 aa are theoretically possible?
At most how many aa substitutions does one need to turn one of these sequence into an another one?
Formulate a question that you could ask on Wednesday (things you didn't understand, anything you want to hear more details about).
Read through the slides selected from Mark Gerstein's Bioinformatics Course in the Intro slides class 1
Are there any items where you do not agree with Mark Gerstein's delineation?

Read the excerpt from Thomas Mann's book on Dr. Faustus (Dr Faustus) available on HuskyCT. Or at https://www.fadedpage.com/showbook.php?pid=20180329 (go to chapter III). This chapter can provide two insights

Scientific experiments in parlors, salons and living rooms were frequent and common entertainment in the early 1900s.
The distinction between living systems and the mineral world was not established. Apparently life could be easily created from non-living constituents. My favorite example are Traube's cells. In the past I did the experiment in class, but now you have to watch the you tube version instead: How to grow an artificial cell from water and salts ("Traube Cell" experiment).
The membranes that form were the starting point to build the first osmometer and an important step in the development of cell theory. They clearly are not alive, but they grow and do look a lot like red algae.

Ask a question (not limited to Dr. Faustus) on the huskyCT discussion board

Lecture 1 (8/28)

Goals:

Know how to contact the instructor and TA.
Know how your performance will be assessed and graded.
Know that take-home exams and computer lab assignments are an important part of this course, and that they will be graded.
Know that you need to maintain an electronic notebook