Journal:

Article Title: Dynamic Partitioning into Lipid Rafts Controls the Endo-Exocytic Cycle of the ?L/? 2 Integrin, LFA-1, during Leukocyte Chemotaxis D⃞

doi: 10.1091/mbc.E05-05-0413

Figure Lengend Snippet: Ratiometric analysis of αL/β 2 enrichment in ruffles

Article Snippet: Cells were then inspected with a laser scanning confocal microscope MRC-1024 (Bio-Rad, Hercules, CA), and the distribution analysis was performed as indicated in legend. table ft1 table-wrap mode="anchored" t5 Table 1. caption a7 αL-GFP/β 2 WGA-TRITC αL-GFP/β 2 + Rab11 wt a 11.7 ± 4.8 b 1.8 ± 0.3 αL-GFP/β 2 + Rab11 S25N 6.4 ± 3.2 1.9 ± 0.7 Open in a separate window a HAfpR-CHO cells were transiently cotransfected with αL-GFP/β 2 and either Rab11 wt or Rab11 S25N constructs.

Techniques:

Journal:

Article Title: Dynamic Partitioning into Lipid Rafts Controls the Endo-Exocytic Cycle of the ?L/? 2 Integrin, LFA-1, during Leukocyte Chemotaxis D⃞

doi: 10.1091/mbc.E05-05-0413

Figure Lengend Snippet: Confocal microscopy analysis of fMLF-induced endosomal localization of αL/β2 in PMN. Primary PMN were labeled at 4°C with a Fab′ fragment of an anti-αL mAb, followed by fMLF stimulation and incubation for the indicated time points. Cells were then fixed, permeabilized, and stained with a Cy3-conjugated goat anti-mouse immunoglobulin antiserum (left). Endogenous Rab11 was detected with an affinity-purified rabbit antiserum followed by an FITC-conjugated goat anti-rabbit antibody (top and middle center panels). Endogenous LAMP-1 was detected with an anti-LAMP-1 mAb (IgG2b) followed by a FITC-conjugated, isotype-specific antiserum (bottom center). Nuclei were detected with Hoechst 33342 (blue fluorescence). Right, merged images.

Article Snippet: Cells were then inspected with a laser scanning confocal microscope MRC-1024 (Bio-Rad, Hercules, CA), and the distribution analysis was performed as indicated in legend. table ft1 table-wrap mode="anchored" t5 Table 1. caption a7 αL-GFP/β 2 WGA-TRITC αL-GFP/β 2 + Rab11 wt a 11.7 ± 4.8 b 1.8 ± 0.3 αL-GFP/β 2 + Rab11 S25N 6.4 ± 3.2 1.9 ± 0.7 Open in a separate window a HAfpR-CHO cells were transiently cotransfected with αL-GFP/β 2 and either Rab11 wt or Rab11 S25N constructs.

Techniques: Confocal Microscopy, Labeling, Incubation, Staining, Affinity Purification, Fluorescence

Journal:

Article Title: Dynamic Partitioning into Lipid Rafts Controls the Endo-Exocytic Cycle of the ?L/? 2 Integrin, LFA-1, during Leukocyte Chemotaxis D⃞

doi: 10.1091/mbc.E05-05-0413

Figure Lengend Snippet: αL/β2 is recycled via a Rab11-positive compartment. CHO cells stably expressing the fMLF receptor were transiently transfected with αL/β2-GFP and either a wt or a Rab11S25N mutant, expressed as monomeric DsRed chimeric constructs. Twenty-four hours posttransfection, cells were fixed and inspected by laser scanning confocal microscopy.

Article Snippet: Cells were then inspected with a laser scanning confocal microscope MRC-1024 (Bio-Rad, Hercules, CA), and the distribution analysis was performed as indicated in legend. table ft1 table-wrap mode="anchored" t5 Table 1. caption a7 αL-GFP/β 2 WGA-TRITC αL-GFP/β 2 + Rab11 wt a 11.7 ± 4.8 b 1.8 ± 0.3 αL-GFP/β 2 + Rab11 S25N 6.4 ± 3.2 1.9 ± 0.7 Open in a separate window a HAfpR-CHO cells were transiently cotransfected with αL-GFP/β 2 and either Rab11 wt or Rab11 S25N constructs.

Techniques: Stable Transfection, Expressing, Transfection, Mutagenesis, Construct, Confocal Microscopy

Journal: Acta Crystallographica. Section F, Structural Biology Communications

Article Title: Full-length nisin immunity protein NisI from Lactococcus lactis in a lipid-free form: crystallization and X-ray analysis

doi: 10.1107/S2053230X17008214

Figure Lengend Snippet: Macromolecule-production information

Article Snippet: To quench the methylation reaction, 1 M Tris–HCl pH 8.0 was added to give a concentration of 100 m M . Finally, the sample was further purified using a Superdex 200 pg 26/600 column (GE Healthcare) equilibrated with 10 m M Tris–HCl pH 8.0, 50 m M NaCl, 2 m M β-mercaptoethanol. table ft1 table-wrap mode="anchored" t5 Table 1 caption a7 Source organism L. lactis subsp. lactis ATCC 11454 DNA source Genomic DNA Forward primer † 5′-CGATAC CATATG CAAACAAGTCATAAAAAGGTGAGG-3′ Reverse primer † 5′-G GAATTC ACTCGAGGTTTCCTACCTTCGTTGCAAGC-3′ Cloning vector pSKB3 (modified pET-28a) Expression vector pSKB3 (modified pET-28a) Expression host E. coli BL21 (DE3) Star Complete amino-acid sequence of the construct produced ‡ MGSSHHHHHHDYDIPTTENLYFQGHM QTSHKKVRFDEGSYTNFIYDNKSYFVTDKEIPQENVNNSKVKFYKLLIVDMKSEKLLSSSNKNSVTLVLNNIYEASDKSLCMGINDRYYKILPESDKGAVKALRLQNFDVTSDISDDNFVIDKNDSRKIDYMGNIYSISDTTVSDEELGEYQDVLAEVRVFDSVSGKSIPRSEWGRIDKDGSNSKQSRTEWDYGEIHSIRGKSLTEAFAVEINDDFKLATKVGN LE Open in a separate window † Restriction sites are underlined.

Techniques: Cloning, Plasmid Preparation, Modification, Expressing, Sequencing, Construct, Produced

Journal: G3: Genes|Genomes|Genetics

Article Title: A long reads-based de-novo assembly of the genome of the Arlee homozygous line reveals chromosomal rearrangements in rainbow trout

doi: 10.1093/g3journal/jkab052

Figure Lengend Snippet: Statistical data summary of the USDA_OmykA_1.1 (Arlee) rainbow trout genome assembly

Article Snippet: The total length of the 710 unplaced scaffolds that are not anchored to a chromosome is ∼108 Mb. table ft1 table-wrap mode="anchored" t5 caption a7 Feature Canu contigs Polished contigs BioNano scaffolds Hi-C scaffolds With linkage information Number of sequences 1,591 1,591 1,044 919 938 Total length 2,340,653,759 2,341,478,269 2,341,947,072 2,342,042,072 2,341,652,372 Maximum length 63,126,076 63,163,333 88,429,459 90,526,592 88,429,459 Minimum length 1,061 1,057 16,956 16,956 16,956 N50 9,835,815 9,837,718 28,011,862 47,542,702 39,165,350 L50 58 58 31 17 22 N90 1,125,404 1,125,715 1,804,217 2,489,804 2,487,114 L90 333 333 170 98 116 BUSCO * C: 95.9% (S: 48.3%; D: 47.6%) C: 96.2% (S: 46.2%; D: 50.0%) NA C: 96.4% (S: 46.7%; D: 49.7%) NA Open in a separate window * Benchmarking Universal Single-Copy Orthologs.

Techniques:

Journal: Human Gene Therapy Methods

Article Title: Adeno-Associated Virus 5 Transduces Adipose-Derived Stem Cells with Greater Efficacy Than Other Adeno-Associated Viral Serotypes

doi: 10.1089/hgtb.2016.123

Figure Lengend Snippet: Lectins used to determine the glycoconjugate profile of adipose-derived stem cells and the corresponding rAAV serotypes that bind to the glycosylation motif

Article Snippet: The cells were mounted with Vectashield mounting medium with DAPI (Vector Laboratories) and images were taken, using a confocal microscope (Olympus FV1000) with a × 60 oil immersion lens. table ft1 table-wrap mode="anchored" t5 Table 1. caption a7 Lectin Ligand motifs AAV binding N -Acetylglucosamine (sialic acid)-binding lectins Maackia amurensis leukoagglutinin (MAL) from Maackia amurensis Neu5Ac/Gcα2,3Galβ1,4Glc(NAc) AAV1, AAV4, AAV5 Wheat germ agglutinin (WGA) from Triticum vulgaris GlcNAcβ1-4GlcNAcβ1-4GlcNAc, Neu5Ac (sialic acid) AAV4, AAV5 N -Acetylgalactosamine (galactose)-binding lectins Peanut agglutinin (PNA) from Arachis hypogaea Galβ1-3GalNAcα1-Ser/Thr AAV9 Ricinus communis agglutinin (RCA) from Ricinus communis Galβ1-4GalNAcβ1-R AAV9 Soybean agglutinin (SBA) from soybean N -Acetylgalactosamine (GalNAc) residues Mannose-binding lectins Concanavalin A (ConA) from Canavalia ensiformis α- d -Mannosyl and α- d -glucosyl residues AAV9 Fucose-binding lectins Ulex europaeus agglutinin (UEA) from Ulex europaeus Fucα1-2Gal-R Open in a separate window rAAV, recombinant adeno-associated virus.

Techniques: Binding Assay

Journal: Nature genetics

Article Title: Minimal phenotyping yields genome-wide association signals of low specificity for major depression

doi: 10.1038/s41588-020-0594-5

Figure Lengend Snippet: a, b, This figure shows the Manhattan plot of neuroticism score (data field 20127, quantitative trait from 0 to 12) in 274,107 individuals and ever smoked status (data field 20160, binary trait of 0 for “No”, and 1 for “Yes”) in 336,066 individuals in UK Biobank using linear regression on all 8,968,716 common SNPs (MAF > 5% in all 337,198 White-British, unrelated samples) for all the above analyses in PLINK (version 1.9)32 with 20 PCs and genotyping array as covariates. We report all associations with P-values smaller than 5×10−8 as genome-wide significant (red). We indicated the SNPs in SVs and the MHC in all Manhattan plots as hollow points instead of solid points due to lack of control for population structure in these regions, and show all top SNPs within peaks (1-Mb regions) in Supplementary Tables 10 and 11.

Article Snippet: This figure shows that at equal sample size and prevalence, GPNoDep (no-MDD Help-seeking phenotype) is the only one showing CNS enrichment, suggesting it may be driving the CNS enrichment signal in GPpsy in . fig ft0 fig @position="anchor" mode=article f4 fig mode="anchored" f5 Extended Data Fig. 5 ∣ fig/graphic|fig/alternatives/graphic mode="anchored" m1 Open in a separate window caption a7 caption a8 GWAS hits from 23andMe are not specific to MDD.

Techniques: Genome Wide, Control

Journal: Nature genetics

Article Title: Minimal phenotyping yields genome-wide association signals of low specificity for major depression

doi: 10.1038/s41588-020-0594-5

Figure Lengend Snippet: ORs are shown for the risk alleles at 27 loci significantly associated with help-seeking definitions of MDD in the UK Biobank (GPpsy and Psypsy), in logistic regression GWAS conducted using MDD definitions based on on CIDI (LifetimeMDD, in purple), help seeking (GPpsy, in red) and no-MDD (GPNoDep, in brown) based definitions of MDD. For comparison, we show the same in conditions other than MDD: neuroticism, smoking and schizophrenia (all in pink). SNPs missing in each panel were not tested in the respective GWAS. For clarity of display, scales on different panels vary to accommodate the different magnitudes of ORs of SNPs in different conditions. ORs at all 27 loci were highly consistent across phenotypes, being completely aligned in direction of effect, regardless of whether it was a definition of MDD or a risk factor or condition other than MDD. All results are shown in Supplementary Table 14. Error bars show the s.e. of the estimates.

Article Snippet: This figure shows that at equal sample size and prevalence, GPNoDep (no-MDD Help-seeking phenotype) is the only one showing CNS enrichment, suggesting it may be driving the CNS enrichment signal in GPpsy in . fig ft0 fig @position="anchor" mode=article f4 fig mode="anchored" f5 Extended Data Fig. 5 ∣ fig/graphic|fig/alternatives/graphic mode="anchored" m1 Open in a separate window caption a7 caption a8 GWAS hits from 23andMe are not specific to MDD.

Techniques: Comparison

Journal: Nature genetics

Article Title: Minimal phenotyping yields genome-wide association signals of low specificity for major depression

doi: 10.1038/s41588-020-0594-5

Figure Lengend Snippet: This figure shows the odds ratios of risk alleles (Risk Allele ORs) at 17 loci significantly associated with help-seeking based definitions of MDD in 23andMe27, in GWAS conducted on CIDI-based (LifetimeMDD, in purple), help-seeking (GPpsy in red) and no-MDD (GPNoDep, in orange) based definitions of MDD, as well as conditions other than MDD: neuroticism, smoking and SCZ (all in brown). SNPs missing in each panel are not tested in the respective GWAS. For clarity of display, scales on different panels vary to accommodate the different magnitudes of ORs of SNPs in different conditions. ORs at all 17 loci are highly consistent across phenotypes, regardless of whether it is a definition or MDD or a risk factor or condition other than MDD. All results are shown in Supplementary Table 20. Error bars show the standard errors of the estimates.

Article Snippet: This figure shows that at equal sample size and prevalence, GPNoDep (no-MDD Help-seeking phenotype) is the only one showing CNS enrichment, suggesting it may be driving the CNS enrichment signal in GPpsy in . fig ft0 fig @position="anchor" mode=article f4 fig mode="anchored" f5 Extended Data Fig. 5 ∣ fig/graphic|fig/alternatives/graphic mode="anchored" m1 Open in a separate window caption a7 caption a8 GWAS hits from 23andMe are not specific to MDD.

Techniques:

Journal: Nature genetics

Article Title: Minimal phenotyping yields genome-wide association signals of low specificity for major depression

doi: 10.1038/s41588-020-0594-5

Figure Lengend Snippet: a, The AUC of PRSs calculated for each definition of depression in the UK Biobank and MDD status indicated in 19 PGC29-MDD cohorts5, while controlling for cohort-specific effects. PRSs were calculated using effect sizes at independent (LD r2 < 0.1) SNPs passing P-value thresholds of 10−4, 0.001, 0.01, 0.05, 0.01, 0.2, 0.5 and 1, in GWAS performed on all definitions of depression in the UK Biobank. b, This figure shows the same analysis performed on downsampled data (7,500 cases and 42,500 controls) for each definition of depression.

Article Snippet: This figure shows that at equal sample size and prevalence, GPNoDep (no-MDD Help-seeking phenotype) is the only one showing CNS enrichment, suggesting it may be driving the CNS enrichment signal in GPpsy in . fig ft0 fig @position="anchor" mode=article f4 fig mode="anchored" f5 Extended Data Fig. 5 ∣ fig/graphic|fig/alternatives/graphic mode="anchored" m1 Open in a separate window caption a7 caption a8 GWAS hits from 23andMe are not specific to MDD.

Techniques:

Journal: Nature genetics

Article Title: Minimal phenotyping yields genome-wide association signals of low specificity for major depression

doi: 10.1038/s41588-020-0594-5

Figure Lengend Snippet: a, This figure shows the Nagelkerke’s r2 of polygenic risk scores (PRS) calculated for each definition of depression in UK Biobank and MDD status indicated in 19 PGC29-MDD cohorts, while controlling for cohort specific effects. PRS were calculated using effect sizes at independent (LD r2 < 0.1) SNPs passing P-value thresholds 10−4, 0.001, 0.01, 0.05, 0.01, 0.2, 0.5 and 1 respectively, in GWAS performed on all definitions of depression in UK Biobank. b, This figure shows the same analysis performed on down-sampled data (7,500 cases, 42,500 controls) for each definition of depression.

Article Snippet: This figure shows that at equal sample size and prevalence, GPNoDep (no-MDD Help-seeking phenotype) is the only one showing CNS enrichment, suggesting it may be driving the CNS enrichment signal in GPpsy in . fig ft0 fig @position="anchor" mode=article f4 fig mode="anchored" f5 Extended Data Fig. 5 ∣ fig/graphic|fig/alternatives/graphic mode="anchored" m1 Open in a separate window caption a7 caption a8 GWAS hits from 23andMe are not specific to MDD.

Techniques:

Journal: Nature genetics

Article Title: Minimal phenotyping yields genome-wide association signals of low specificity for major depression

doi: 10.1038/s41588-020-0594-5

Figure Lengend Snippet: a, This figure shows the relationship between the ratio of effective sample sizes between the full cohort (NFC) and down-sampled (NDS) data for each definition of depression and the ratio of their mean Chi-square (χ2) statistic from GWAS, with black line x = y for reference. Across all definitions of depression, χFC2¯−1χDS2¯−1 is highly correlated with NFCNDS (Pearson r2 = 0.999, P = 5.50×10−7), and NFCNDS has an effect of beta = 1.27 (s.e. = 0.02) on χFC2¯−1χDS2¯−1. b, This figure shows the Nagelkerke’s r2 (Nkr2) for MDD status in PGC29 cohorts predicted for PRS of different definitions of depression at NFC, plotted against their respective empirical Nkr2 at NFC, both at P-value threshold = 1. The Pearson correlation r2 between predicted and actual NKr2 across all definitions were 0.989 (P = 4.46×10−5). c, This figure shows for each definition of depression the effective sample size NX required for each predicted Nkr2 in out-of-sample prediction of MDD status in PGC29 cohorts. While Nx= 274,677 (indicated with orange vertical dotted line) for GPpsy to achieve a Nkr2 of 0.0172 (indicated with orange horizontal dotted line), a smaller Nx= 129,106 (indicated with pink vertical dotted line) is needed to achieve the same Nkr2 for LifetimeMDD.

Article Snippet: This figure shows that at equal sample size and prevalence, GPNoDep (no-MDD Help-seeking phenotype) is the only one showing CNS enrichment, suggesting it may be driving the CNS enrichment signal in GPpsy in . fig ft0 fig @position="anchor" mode=article f4 fig mode="anchored" f5 Extended Data Fig. 5 ∣ fig/graphic|fig/alternatives/graphic mode="anchored" m1 Open in a separate window caption a7 caption a8 GWAS hits from 23andMe are not specific to MDD.

Techniques:

Journal: Pediatric diabetes

Article Title: DNA Methylation and its Role in the Pathogenesis of Diabetes

doi: 10.1111/pedi.12521

Figure Lengend Snippet: Genome Wide DNA Methylation Assays.

Article Snippet: Neither the array based genome wide DNA methylation assays, nor ERRBS adequately profile DNA methylation within the intergenic and enhancer regions of the genome. provides a summary of few genome-wide DNA methylation techniques that are discussed above. table ft1 table-wrap mode="anchored" t5 caption a7 WGBS 450K Infinium Bead Chip Array MethylationEPICInfinium Bead Chip Array ERRBS Regions Sequenced Whole genome including intergenic and enhancer regions Predesigned array based Predesigned array based Determined by Msp1 digestion to enrich for CpG fragments Genome Coverage 15–20 million CpG sites 485,000 methylation sites across the genome 850,000 methylation sites across the genome 3 million CpG sites ~85% of CpG islands, and 60% promoters Assay Details Bisulfite conversion of genomic DNA, followed by next generation sequencing Bisulfite conversion of genomic DNA followed by annealing bead array Bisulfite conversion of the genomic DNA, followed by annealing bead array MspI digestion followed by bisulfite conversion and next generation sequencing Cost per sample $$$ $ $ $$ Input DNA 50–100 ng 500 ng – 1 μg 250 ng 10–300 ng Additional coverage information Comprehensively covers the entire genome including methylated and unmethylated regions.

Techniques: Genome Wide, DNA Methylation Assay, Methylation, Next-Generation Sequencing

Journal: Bone

Article Title: HAJDU CHENEY SYNDROME; REPORT OF A NOVEL NOTCH2 MUTATION AND TREATMENT WITH DENOSUMAB

doi: 10.1016/j.bone.2016.08.025

Figure Lengend Snippet: Genomic DNA from blood samples of the subject with HCS was sequenced by next generation sequencing on Ion Torrent (Thermo Fisher) for the coding sequence of the NOTCH2 gene. The representation of the reads aligned to the reference genome, as provided by the Integrative Genomics Viewer software (IGV v 2.1, Broad Institute), shows a 1:1 signal ratio of C (blue) to T (red) at nucleotide 6667 demonstrating the presence of a heterozygous 6667C>T mutation.

Article Snippet: The 6667C>T mutation in exon 34 of NOTCH2 leads to the creation of a Stop codon and a predicted truncated protein product of 2222 amino acids. fig ft0 fig mode=article f1 fig/graphic|fig/alternatives/graphic mode="anchored" m1 Open in a separate window caption a7 Genomic DNA from blood samples of the subject with HCS was sequenced by next generation sequencing on Ion Torrent (Thermo Fisher) for the coding sequence of the NOTCH2 gene.

Techniques: Next-Generation Sequencing, Sequencing, Software, Mutagenesis