post-script, a GC visual

Taken from: Peters2008. A Combination of cis and trans Control Can Solve the Hotspot Conversion Paradox

This image shows three different gene conversion scenarios in meiosis, where alleles j or i are successfully incorporated into a sister chromatid (1 and 3), or the repair and DSB misses the sequences important for GC and no exchange of alleles takes place (2). 

Research Update

Have been researching Gene Conversion using Ovid, and have so far looked at 7 articles out of 1901 results.

I think I'll need to brush up on many molecular/genetic terms and concepts, including:

• recombination, (in metaphase part of meiosis), crossing-over
• sister chromatids, nonsister chromatids
• homologous sequences, homologous chromosomes
• transcription in general
• histone complexes
• epigenetic modifiers
• acronyms and technical terms such as: NHEJ= non-homologous end-joining, GC= gene conversion, SSA= single-stranded annealing, kb= kilobases, non-reciprocal translocations (GC results in these), inverted dicentric dimers, breakage-fusion bridge cycles (that sounds really visual, though may not be involved in immunology GCs), inverted repeats, gross chormosomal rearrangements, homologous reciprocal recombination, allelic gene conversion, ectopic gene conversion, transposon insertions, 'indels'
• the Rad proteins
• nucleoprotein filaments (this also sounds like it has visual potential)
• Holliday junctions in DNA repair

Some things I've learned about gene conversion:

• it happens in yeast, mice, some plants (arabidopsis and rice), chimpanzees, chickens, and humans (in chromosomes 21 and Y)
• in general, it involves taking sequences from one part of a DNA strand, and incorporating it into another, with the donor DNA remaining unchanged
• it occurs between homologous sequences
• it's one of many repair pathways for double and single-stranded DNA lesions (SSA is another pathway)
• considered 'conservative' because most GC events probably do not produce any changes in recipient DNA
• it can happen with or without crossing-over
• gene conversion can easily be turned off over subsequent generations, 1. if too many point mutations in donor or recipient DNA interfere with their mutual homology, 2. if key sequences that affect gene conversion (i.e. the proteins involved and sequences they bind to, the histones that affect the shape of the DNA and its openness/receptivity to binding) are lost (they may ironically be lost in the gene conversion process)
• this means gene conversion must be beneficial to be maintained, or that a lot of the controlling sequences for GC are located far away from where GC is taking place and changing DNA
• some benefits of GC: 1. it can confer pathogen resistance by introducing variability into a population (or, in the chicken, by helping to create diversity in antigen-binding sites of B-cell antibodies), 2. in some species DSBs that occur with GC trigger formation of 'synaptonemal' complexes (this helps in correct segregation of chromosomes during cell meiosis), 3. GC helps break down linkage disequilibrium (when two genes located close to each other are inherited together more often, instead of being broken apart in recombination): this can prevent deleterious genes from being inherited with beneficial ones
• in yeast, Rad51p is needed to create a nucleoprotein filament which finds and 'invades' homologous sequences in GC
• in yeast, Rad52p is needed for GC (the Rad52p epistasis group includes:  Rad51p, Rad52p, Rad54p, Rad55p, Rad57p, and others)
• gene conversion also occurs in the major histocompatibility complex in chicken T-cells (also antigen-recognizing proteins)
• some say GC homogenizes (by making two homologous genes more similar), others say it introduces variation (i.e. by taking sequences from a pseudogene and inserting them into a functional gene, creating novel sequences, although only a few bases may have been changed)
• Xu 2008: GC in eukaryotes is classified into 2 types: 1. allele conversion (exchange between the same gene on different chromatids; either sister or homologous), 2. repeated genes (i.e. pseudogene example in chicken B-cells; exchange could occur between genes on same chromatid, non-homologous chromatids, homologous chromatids, sister chromatids..)
• gene conversion in rice is more likely between genes on the same chromosome, than pairs on different chromosomes. GC is also more likely when genes are physically closer together on the same chromosome, in yeast, arabidopsis and rice. Upper limit of distance between genes in arabidopsis for successful GC is 40kb.
• some think that human speciation events may have been propelled by GC, between pseudo- and functional genes
• there are gene conversion 'hotspots' in many species, including yeast, mice, humans, some plants, although not fruit flies or c. elegans

I think I'm going to refine my search terms for the remaining articles, possibly focusing on B-cells, and chickens, as I seem to have got a lot of general gene conversion articles that may not relate to GC in the Bursa of Fabricius.

ReCap of First Two MRP Meetings

Master's Research Project

A 3D animation, highlighting Dr. Ratcliffe's research on B  

cell development in the Bursa of Fabricius in the chicken

Committee Members:

Supervisor: Nick Woolridge

Content Supervisor: Dr. Michael J. H. Ratcliffe

Voting Member: Dr. Shelley Wall

Preliminary Goals:

• distill topic of B cell development down to a central focus 
•    a) gene conversion
  
•    b) while still having a strong introduction, and end 
  
•         i) i.e. set the scene by bringing the audience from the macroscopic level of the chick -> bursa -> follicles -> bcells -> cytoplasm -> molecules (DNA strand(s), AID, template repair proteins), and back out again
  
• define target audience, possibly targeting two audiences
•     a) by using two different scripts for the same animation (with vocabulary and concepts geared to undergrads in one, researchers in the second)
  
• have 'scene selection' capabilities in animation
•    a) this will: introduce an element of interactivity
  
•     b) allow a lecturer or presenter to select and replay desired sequences of the animation
  
• possible visual question:
•     a) how to visualize a molecular process, the exact mechanisms of which are still theoretical and not directly observed in nature? (gene conversion)
•         i) three potential mechanisms
  
•        ii) analogs in other species: trypanosome and yeast
  
• interesting visual effects:
•     a) alternating between a static camera view (like a porthole from a submarine, watching a moving landscape outside)
  
•     b) a dynamic camera view observing a static scene (so that the animation appears frozen in time, but the viewer is moving, revolving around, and examining the landscape)
  
•     c) and incorporating 'sliding stills', where a camera moves linearly, or zooms in / out, from a 2D image
•        i) this will provide a visual break or point of contrast interspersed throughout animated scenes
•        ii) will also be an economical (less rendering involved) method of communicating information
•        iii) homework: watch Ken Burns' documentary films, for inspiration
  
•  theme brainstorming:
  
•     a) colour palette?
  
•        i) potentially similar to illustrator / intracellular visualization piece
  
•        ii) golds, purple, an underwater or twilight atmosphere 
•        iii) with illumination radiating from molecules or characters that are the focus of interest
  
•     b) background music?
  
•        i) intro with a fast-paced piano for base and tempo (instead of drums)
  
•        ii) cellos for chorus
  
•        iii) cymbals used for dramatic events (i.e. successful template repair and gene conversion, antigen binding)
  
•        iv) inspiration song: Regina Spektor's 'Us'
  
•        v) may try to recruit friends / colleagues who play cello and piano . . .
  
• timeline and time management:
•     a) make sure not to incorporate too much information
  
•        i) render and design the key elements of the story first
  
•        ii) incorporate extra 'epilogues', intro sequences, and interesting effects (two scripts, scene selection), if there is time
  
• research
•     a) gene conversion
  
•     b) chick anatomy
  
•     c) gene rearrangement
  
•     d) cinematic inspirations