2012 29 August

===JMB's summary of class progress===
#Progress in wiki development: participation patterns
#Web site organization
#Communication among editors and between editors and instructor
#Class notes?
===Matters Arising===
#Student issues and questions (based on class work, textbook, or anything else)
#Student reaction to editing process and communication from instructor
#Use of Email and Twitter
#Class notes-- collective or assigned?
#Reactions to EverNote?
===Better editing practice===
#Page linking
#Citations
#Sources for graphics (demonstrate Google image search)
#Use of Edit summary space
#Categories
#Tracking your contributions
===Review of new pages and major edits===
*Allele
*Biochemistry
*Biodiversity
*Bioinformatics
*Gene
*Genetic information
*Genetic map
*Genetics
*Genome
*Genomics
*Genotype
*Metagenome
*Phenotype
*Selection
===Genetics, Biochemistry, Genomics, Metagenomics, Proteomics, Otheromics, and Systems Biology===
#Forward genetics and genetic maps
#Reverse genetics
#What can we learn from genetics?
#What does biochemical analysis tell us?
#Combining genetics and biochemistry
#Genomics
#Metagenomics
#Proteomics, otheromics, and systems biology
===Assignments===
#Please send JMB an email that links your wikia name to your real name.
#Continue to add content in 'Concepts and Jargon'. Remember that you are free to add any new topics that you think will be useful.
#Chapter 1 Exercises
#Chapter 1 Problems
#Chapter 1 Weblems
#Write new problems (and proposed solutions) based on textbook and class work to date.
===Class notes:===
Better editing practice:
*page linking: link terms that are already on our pages together. Also, include a link to a wikipedia article or any internet source which information is directly derived from.
*add references: provide references when the information is taken from another page, the same should be done also with images
*image tracking on Google images: it is possible to find a picture original site by simply dragging the image file from the PC into the image search bar
*wikimedia commons: freely usable images, freely modifiable
​
*Genetics x Biochemistry x Genomics: Genetics and biochemistry are very complementary to each other and are used in conjunction when studying disease, whereas genomics integrates all the information and provides a broad overview.
*Biochemistry: Dissassembles and identifies various components of an organism. These components are broken apart to understand their physical interaction and structures. It is focused on the structure of molecules and their effect on chemical processes. Biochemistry = Structure.
*Genetics: Identifies particular genes that have mutated or can be induced to mutate. Genes can be modified and phenotypes observed to gather information about their function. Genetics = Function.
*Genomics: Techniques that allows us to collect extensive genome-wide data in organisms. When seen at a metagenomics level, it is possible to gather vast genetic information from different allelic expression among and within populations. It adds globalism to the biochem-genetics analysis.
*Genetically tractable systems = model organisms (ex. mice & E.Coli). With model organisms it is possible to work with lethal mutations to discover the purpose of most important components in living organisms.
*Humans are not model organisms due to ethical limitations and are targeted for research when they already exchibit a particular disease. This becomes an obstacle when researching rare genetic diseases and lethal mutation.
*Lethal Mutations: lethal mutations are easy to study in model organisms, but not humans. Such mutations do occur but can not be researched because many of them result in embyonic death and termination of the pregnancy via miscarrage.
*Conditional Mutation: Mutation-induced organism that will express a particular phenotype, tested under restrictive condition. E.g. Temperature-sensitive mutations.
*Omics (i.e. genomics, proteomics, transcriptomics, metabolomics, ionomics), have to be analyzed with bioinformatics tools that can allow the user to better visualize and clean the data.
*Mendelian genetics is a simplification of genetics, where a single gene is linked to a single trait, which is diallelic. (Mendelian Genetics: "1 gene/1 trait /2 alleles"). Mendel explained genetics using a selective-breeding model in a subset of a population. John Burke- "The problem with it is that it is a lie. It oversimplifies biological reality".
*Newer genetics study the interaction of several genes (and the environment) with more than two alleles. Mendelian genetics does not take into account that a majority of phenotpes are contributed to by more than one gene, and that each gene often times has more than two alleles.Allele is a version of a gene that can lead to an observable difference. Any sequence variation in a gene may be an allele.No gene comes in only two different phenotypes. For example, skin color is the result of >25 genes.
Category:Class notes