Energy spread of ultracold electron bunches extracted from a laser cooled gas

Ultrashort and ultracold electron bunches created by near-threshold femtosecond photoionization of a laser-cooled gas hold great promise for single-shot ultrafast diffraction experiments. In previous publications the transverse beam quality and the bunch length have been determined. Here the longitudinal energy spread of the generated bunches is measured for the first time, using a specially developed Wien filter. The Wien filter has been calibrated by determining the average deflection of the electron bunch as a function of magnetic field. The measured relative energy spread $\frac{\sigma_{U}}{U} = 0.64 \pm 0.09\%$ agrees well with the theoretical model which states that it is governed by the width of the ionization laser and the acceleration length

Additional file 2: of The genomic and transcriptomic landscape of anaplastic thyroid cancer: implications for therapy

Supplementary file outlining the detailed sequencing methodology and additional figures. (DOCX 434 kb

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

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

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

Y-box binding protein 1 (YB-1) binds to specific sites within the epidermal growth factor receptor (EGFR) promoter

<p><b>Copyright information:</b></p><p>Taken from "Epidermal growth factor receptor (EGFR) is transcriptionally induced by the Y-box binding protein-1 (YB-1) and can be inhibited with Iressa in basal-like breast cancer, providing a potential target for therapy"</p><p>http://breast-cancer-research.com/content/9/5/R61</p><p>Breast cancer research : BCR 2007;9(5):R61-R61.</p><p>Published online 17 Sep 2007</p><p>PMCID:PMC2242657.</p><p></p> (a) Sequence of the EGFR2a oligonucleotide used in the gel shift assays (-979 to -934). Highlighted sequences are the potential YB-1 binding sites. The substitutions made in the two mutants are given under the wild-type sequence. (b) Direct evidence for YB-1 binding to the EGFR promoter using gel shift assays. Nuclear extract from SUM149, MDA-MB-468 or HCC1937 cells were incubated in the presence of the EGFR oligonucleotide spanning -979 to -934. There was no binding in the absence of protein (lanes 1, 5 and 10), whereas the addition of the nuclear extract (lanes 2, 6 and 11) resulted in strong binding that could be inhibited with the unlabelled oligonucleotide (lanes 3, 7 and 12). The addition of a YB-1 antibody caused a supershift (lane 4, 8 and 13) that did not occur when the non-related CREB antibody was used (lanes 9 and 14). (c) Nuclear extracts from 6 primary BLBC samples were pooled and used in a gel shift assay for the EGFR 2a site. Lane 1 contains EGFR2a biotin-labelled oligo only. Binding to the probe is evident in lane 2, which was competed off in lane 3 and supershifted with a YB-1 antibody in lane 4. A CREB antibody was used to demonstrate specificity of the supershift (lane 5). (d) Validation of putative YB-1-responsive elements on the EGFR promoter. SUM149 nuclear extracts were incubated with either wild-type (lane 1) or mutant biotin oligo nucleotides (lanes 3, 4, and 5). A competition reaction was carried out against the wild-type (lane 2). nuclear extract bound to the wild-type sequence (lane 1), but was unable to bind the mutants (lanes 3, 4 and 5)

Y-box binding protein 1 (YB-1) binds to the epidermal growth factor receptor (EGFR) promoter

<p><b>Copyright information:</b></p><p>Taken from "Epidermal growth factor receptor (EGFR) is transcriptionally induced by the Y-box binding protein-1 (YB-1) and can be inhibited with Iressa in basal-like breast cancer, providing a potential target for therapy"</p><p>http://breast-cancer-research.com/content/9/5/R61</p><p>Breast cancer research : BCR 2007;9(5):R61-R61.</p><p>Published online 17 Sep 2007</p><p>PMCID:PMC2242657.</p><p></p> (a) Chromatin immunoprecipitation was performed on SUM149 cells. YB-1 binds to the EGFR promoter in the basal-like cells where the 2a loci is the preferred binding site (lane 2). Weak binding was also detected with the 1b primers (lane 1). No binding was observed in the 2b or 3 sites (lanes 3 to 4), nor was there any non-specific binding detected in the IgY negative controls (lanes 5 to 8). Input DNA was diluted fourfold and amplified to demonstrate that the primer produced an expected product (lanes 9 to 12). The no input controls (lanes 13 to 16) are presented to show a lack of non-specific amplifications. (b) Serial ChIP was performed by sequentially pulling down YB-1 and then immunoprecipitating with a phospho-serine antibody. This demonstrated that at least some of the YB-1 is serine phosphorylated when bound to the EGFR 2a site. YB-1 binds to the 2a site (lane 1) as expected. Similarly, the phospho-serine antibody pulls down a complex that can be amplified with the 2a primers (lane 2). Re-ChIP with the YB-1 antibody and subsequently with the phospho-serine antibody also bound to EGFR at the 2a site (lane 3). A phospho-serine YB-1 complex bound to the 2a site on EGFR (lane 3). Species-matched IgG and IgY controls were included to show that the binding was specific (lane 4). The input DNA and no DNA controls were also included (lanes 5 and 6). (c) ChIP was carried out using a phospho-YB-1 antibody (S102), and binding was detected for the EGFR 2a region (lane 4). There was no binding observed when immunoprecipitation was performed using IgG as a control (lane 3). Input DNA was diluted fourfold and amplified to demonstrate that the primer produced an expected product (lanes 5 and 6). Lane 1 is the DNA ladder

Additional file 1: of Comprehensive whole genome sequence analyses yields novel genetic and structural insights for Intellectual Disability

Supplementary Methods - Additional details on methods presented succinctly in main text. (DOCX 53 kb

Additional file 5: Supplementary Figures. of Comprehensive whole genome sequence analyses yields novel genetic and structural insights for Intellectual Disability

Figure S1. IGV image and Sanger verification trace files for indel in ARID1B and missense variation in UPF1. Figure S2. UK10K mutation load – counts as per variant annotation type on one patient. Figure S3. Histogram of mutation burden per patient in the UK10K cohort. Figure S4. Pathway interactions showing convergence onto UPP pathway. Figure S5. Plots for CNV distribution for two chromosomes as called by CNAseq. (DOCX 1972 kb

Inhibiting epidermal growth factor receptor (EGFR) suppresses the growth of basal-like breast cancer cells

<p><b>Copyright information:</b></p><p>Taken from "Epidermal growth factor receptor (EGFR) is transcriptionally induced by the Y-box binding protein-1 (YB-1) and can be inhibited with Iressa in basal-like breast cancer, providing a potential target for therapy"</p><p>http://breast-cancer-research.com/content/9/5/R61</p><p>Breast cancer research : BCR 2007;9(5):R61-R61.</p><p>Published online 17 Sep 2007</p><p>PMCID:PMC2242657.</p><p></p> (a) Inhibition of EGFR with Iressa (0.25, 0.5, 1 and 2 μM) blocks the growth of basal-like breast cancer cells by up to 40% when the cells were treated for 72 h (0.5 μM = 0.02, 1 μM = 0.02, 2 μM = 0.07). Each experiment was performed in replicates of six on two separate occasions. (b) Anchorage-independent growth was measured by counting colonies formed after 4 weeks exposure to Iressa or vehicle control. Representative images of colonies following each treatment are shown, with average colony number/well shown underneath. The ability to form colonies was completely lost in the presence of concentrations of Iressa as low as 0.25 μM in SUM149 cells. (c) The ability of HCC1937 cells to form colonies was not effected by Iressa alone; however, knockdown of YB-1 significantly reduced the number of colonies (< 0.001). The addition of Iressa further reduced the number of colonies. This was highly significant at all concentrations (< 0.001). Statistical analysis carried out using students -test; *< 0.05, **< 0.01