Genetic interactions between and known or potential regulators of cell death in the eye

<p><b>Copyright information:</b></p><p>Taken from ", required for interommatidial cell sorting and cell death in the pupal retina, encodes a protein with homology to ubiquitin-specific proteases"</p><p>http://www.biomedcentral.com/1471-213X/7/82</p><p>BMC Developmental Biology 2007;7():82-82.</p><p>Published online 5 Jul 2007</p><p>PMCID:PMC1950886.</p><p></p> To the right is a schematic depicting known or suggested interactions between death regulators in the fly. The question mark separating Debcl/Buffy from Ark indicates the uncertainy as to the roles these proteins play in regulating Ark activation or activity. GMR-driven transgenes of the indicated genotype were introduced into the background, or into a wildtype background in the presence of GMR-ec-SF1. For each death regulator tested, similar phenotypes were observed in the presence of GMR-ec-SF2 (data not shown)

Flies with mutations in CG2904 have rough eyes, defects in IOC sorting, an increase in IOC number (A-F) SEM views of adult fly eyes of various genotypes

<p><b>Copyright information:</b></p><p>Taken from ", required for interommatidial cell sorting and cell death in the pupal retina, encodes a protein with homology to ubiquitin-specific proteases"</p><p>http://www.biomedcentral.com/1471-213X/7/82</p><p>BMC Developmental Biology 2007;7():82-82.</p><p>Published online 5 Jul 2007</p><p>PMCID:PMC1950886.</p><p></p> (G-O) Pupal retinas of various genotypes stained with anti-Dlg. (A, G) Wildtype flies have regularly spaced ommatidia and an invariant number of IOCs. Cell types indicated are bristle (B), 2°, 3°, and asterisk represent extra IOCs. (B,H) flies obtained from the Bloomington Stock center have rough eyes and a modest number of extra 2° and 3° pigment cells. (C,I) GMR-driven RNAi of CG2904 results in flies with rough eyes and a large increase in IOCs, with many stacked side-by-side in parallel rows. (D,J) Flies homozygous for a deletion in CG2904, , have rough eyes, a large increase in IOCs, with many cells stacked side-by-side in parallel rows. (E,K) GMR-dependent expression of ec-SF1 has no effect on the adult eye and does not cause any excess death of IOCs. (F,L) Expression of GMR-ec-SF1 restores normal levels of IOC death to flies. (M,N) Pupal eyes from two independent stocks of outcrossed for 5 generations. There are increased numbers of IOCs as compared with the original stock, and many extra cells are aligned side-by-side in parallel rows. (O) Pupal eyes from flies have a modest increase in IOC number and few defects in cell sorting

Echinus does not require deubiquitinating activity to promote normal IOC death

<p><b>Copyright information:</b></p><p>Taken from ", required for interommatidial cell sorting and cell death in the pupal retina, encodes a protein with homology to ubiquitin-specific proteases"</p><p>http://www.biomedcentral.com/1471-213X/7/82</p><p>BMC Developmental Biology 2007;7():82-82.</p><p>Published online 5 Jul 2007</p><p>PMCID:PMC1950886.</p><p></p> (A-D) SEMs of adult eyes of various genotypes. (E-H) Pupal retinas of various genotypes stained with anti-Dlg. (A,E) GMR-driven expression of a microRNA targeting ec-SF1 results in an echinus phenotype. (B,F) eyes. (C,G) Eyes of genotype ; GMR-ec-SF2/+. (D,H) Eyes of genotype ; GMR-ec-SF3/+. Expression of versions of Echinus that lack essential USP catalytic residues rescues the phenotype

Specificity of individual restriction fragments and patterns based on exact and experimental sizing tolerance

<p><b>Copyright information:</b></p><p>Taken from "A BAC clone fingerprinting approach to the detection of human genome rearrangements"</p><p>http://genomebiology.com/2007/8/10/R224</p><p>Genome Biology 2007;8(10):R224-R224.</p><p>Published online 22 Oct 2007</p><p>PMCID:PMC2246298.</p><p></p> dIII restriction fragment specificity for the human genome for fragments within the experimental size range of 500 bp to 30 kb. For a given fragment size, the vertical scale represents the fraction of fragments in the genome that are indistinguishable by size in the case of either exact sizing (fragments in common between two fingerprints must be of identical size) or within experimental tolerance (fragments in common between two fingerprints must be within experimental sizing error; Figure 3) on a fingerprinting gel. When sizing is exact, fragment specificity follows approximately the exponential distribution of fragment sizes and spans a range of 3.5 orders of magnitude. When experimental tolerance is included, the number of distinguishable fragment size bins is reduced and the range of fragment specificity drops to two orders of magnitude. The specificity of a fingerprint pattern of a given size in the human genome. Fingerprint pattern size is measured in terms of number of fragments. Regions with identical patterns are those in which there is a 1:1 mapping within tolerance between all sizeable fragments. The specificity of experimental fingerprint patterns is cumulatively affected by specificity of individual fragments. The specificity of fragments is sufficiently low (that is, due to high experimental precision) so that 96.5% of the genome is uniquely represented by fragment patterns of 8 fragments or more

Detailed reconciliation of sequence and fingerprint alignments for clone 3F05, which contains at least four internal breakpoints

<p><b>Copyright information:</b></p><p>Taken from "A BAC clone fingerprinting approach to the detection of human genome rearrangements"</p><p>http://genomebiology.com/2007/8/10/R224</p><p>Genome Biology 2007;8(10):R224-R224.</p><p>Published online 22 Oct 2007</p><p>PMCID:PMC2246298.</p><p></p> FPP is capable of dissecting complex rearrangements in a clone, as illustrated in this figure showing the internal structure of M0003F05. This BAC was sequenced [26] and found to be composed of content from at least five distinct regions (A-E). FPP detected 4/5 of these regions. BLAT (grey rectangles with alignment orientation arrows) and FPP (thin black lines) alignments of M0003F05 are shown; values underneath coordinate pairs are differences in edge positions between BLAT and FPP alignments

Simulation results of sensitivity and spatial error of rearrangement detection by FPP using experimental sizing tolerance

<p><b>Copyright information:</b></p><p>Taken from "A BAC clone fingerprinting approach to the detection of human genome rearrangements"</p><p>http://genomebiology.com/2007/8/10/R224</p><p>Genome Biology 2007;8(10):R224-R224.</p><p>Published online 22 Oct 2007</p><p>PMCID:PMC2246298.</p><p></p> Sensitivity is measured as the fraction of clone regions of a given size with successful FPP alignments and is plotted for five digests (labeled 1-5). Spatial error is measured by the median distance between FPP and theoretical alignment positions. The largest improvement in both sensitivity and spatial error is realized by migrating FPP from one digest to two. With two fingerprint patterns used to align the clone, 50% of >25 kb clone regions are aligned (90% of >45 kb regions) with a spatial error of 1.7 kb