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Ancestry results for samples from the southeastern portion of the range. Ancestry proportions were determined using Structure with 50,000 and <t>100,000</t> burn‐in and MCMC iterations and the previously determined optimal K ‐value of 2
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Images

1) Product Images from "Population assignment and local adaptation along an isolation‐by‐distance gradient in Pacific cod (Gadus macrocephalus). Population assignment and local adaptation along an isolation‐by‐distance gradient in Pacific cod (Gadus macrocephalus)"

Article Title: Population assignment and local adaptation along an isolation‐by‐distance gradient in Pacific cod (Gadus macrocephalus). Population assignment and local adaptation along an isolation‐by‐distance gradient in Pacific cod (Gadus macrocephalus)

Journal: Evolutionary Applications

doi: 10.1111/eva.12639

Ancestry results for samples from the southeastern portion of the range. Ancestry proportions were determined using Structure with 50,000 and 100,000 burn‐in and MCMC iterations and the previously determined optimal K ‐value of 2
Figure Legend Snippet: Ancestry results for samples from the southeastern portion of the range. Ancestry proportions were determined using Structure with 50,000 and 100,000 burn‐in and MCMC iterations and the previously determined optimal K ‐value of 2

Techniques Used:

2) Product Images from "Employing genome-wide SNP discovery and genotyping strategy to extrapolate the natural allelic diversity and domestication patterns in chickpea"

Article Title: Employing genome-wide SNP discovery and genotyping strategy to extrapolate the natural allelic diversity and domestication patterns in chickpea

Journal: Frontiers in Plant Science

doi: 10.3389/fpls.2015.00162

LD decay (mean r 2 ) estimated in three populations (as defined by population genetic structure) using 3321 desi (A) and 8592 kabuli (B) SNPs, respectively . For LD decay, the r 2 -value of the marker physical distance of 0 kb is considered 1. The plotted curved lines indicate the mean r 2 -values among markers spaced with uniform 100 kb physical intervals from 0 to 1000 kb. The plotted line in uppermost panel I indicate the mean r 2 -values among markers spaced with uniform 10 kb physical intervals from 0 to 100 kb. The marked line in panels I, II indicate the mean r 2 -values among markers spaced with uniform 10 and 20 kb physical intervals from 0 to 100 kb and 0 to 200 kb, respectively. “All” includes the LD decay across entire three populations.
Figure Legend Snippet: LD decay (mean r 2 ) estimated in three populations (as defined by population genetic structure) using 3321 desi (A) and 8592 kabuli (B) SNPs, respectively . For LD decay, the r 2 -value of the marker physical distance of 0 kb is considered 1. The plotted curved lines indicate the mean r 2 -values among markers spaced with uniform 100 kb physical intervals from 0 to 1000 kb. The plotted line in uppermost panel I indicate the mean r 2 -values among markers spaced with uniform 10 kb physical intervals from 0 to 100 kb. The marked line in panels I, II indicate the mean r 2 -values among markers spaced with uniform 10 and 20 kb physical intervals from 0 to 100 kb and 0 to 200 kb, respectively. “All” includes the LD decay across entire three populations.

Techniques Used: Marker

A genome scan plot depicting the density of SNPs physically mapped across eight chromosomes of desi (A) and kabuli (B) genomes at 100-kb sliding window . The SNP density is represented by the number of SNPs mapped within 1-Mb physical intervals across chromosomes.
Figure Legend Snippet: A genome scan plot depicting the density of SNPs physically mapped across eight chromosomes of desi (A) and kabuli (B) genomes at 100-kb sliding window . The SNP density is represented by the number of SNPs mapped within 1-Mb physical intervals across chromosomes.

Techniques Used:

3) Product Images from "Gene Function Prediction Based on Developmental Transcriptomes of the Two Sexes in C. elegans"

Article Title: Gene Function Prediction Based on Developmental Transcriptomes of the Two Sexes in C. elegans

Journal: Cell reports

doi: 10.1016/j.celrep.2016.09.051

Gene Correlation Network Analysis (A) Hierarchical cluster dendrogram groups 21,143 genes into distinct co-expression modules identified using weighted gene correlation network analysis. Six major modules are indicated as colored boxes (Mod1, black; Mod2, salmon; Mod3, brown; Mod4, yellow; Mod5, midnight blue; Mod6, blue). (B) Heatmap showing relative expression of genes in the six major modules across ten samples of two sexes. The color values are the standardized Z scores of gene expression. (C) Percentage of genes that are previously known to be enriched in specific cells or tissues across different modules. Previously known gene lists include for panneural enriched ( Spencer et al., 2011 ), sperm and oocyte enriched ( Reinke et al., 2004 ), and cuticle collagen enriched ( Page and Johnstone, 2007 ). Number of genes was normalized in order to avoid the effect of different module sizes (y axis). (D and E) Tissue-specific expression of reporter transgenes for two C-type lectin domain ( clec ) genes chosen from Mod1 (D) and Mod3 (E) in both sexes. Arrow indicates expression in head neurons in (D) or in vas deferens of male in (E). The magnified view of the arrowed region is shown at the bottom of each image. In all images, anterior is left and posterior is right. The scale bars represent 100 μm.
Figure Legend Snippet: Gene Correlation Network Analysis (A) Hierarchical cluster dendrogram groups 21,143 genes into distinct co-expression modules identified using weighted gene correlation network analysis. Six major modules are indicated as colored boxes (Mod1, black; Mod2, salmon; Mod3, brown; Mod4, yellow; Mod5, midnight blue; Mod6, blue). (B) Heatmap showing relative expression of genes in the six major modules across ten samples of two sexes. The color values are the standardized Z scores of gene expression. (C) Percentage of genes that are previously known to be enriched in specific cells or tissues across different modules. Previously known gene lists include for panneural enriched ( Spencer et al., 2011 ), sperm and oocyte enriched ( Reinke et al., 2004 ), and cuticle collagen enriched ( Page and Johnstone, 2007 ). Number of genes was normalized in order to avoid the effect of different module sizes (y axis). (D and E) Tissue-specific expression of reporter transgenes for two C-type lectin domain ( clec ) genes chosen from Mod1 (D) and Mod3 (E) in both sexes. Arrow indicates expression in head neurons in (D) or in vas deferens of male in (E). The magnified view of the arrowed region is shown at the bottom of each image. In all images, anterior is left and posterior is right. The scale bars represent 100 μm.

Techniques Used: Expressing, Polyacrylamide Gel Electrophoresis

Identification of Semen Protein Genes (A) Schematic of procedure to identify and validate semen protein genes from the RNA-seq data. (B) The anatomical location of seminal vesicle, valve region, and vas deferens in male gonad (gray). (C) Tissue-specific expression of reporter transgenes for three semen candidate genes in male. Arrows indicate expression in seminal vesicle ( ins-31 ), vas deferens ( F59B2.12 ), and the valve region of vas deferens ( B0207.5 ). Arrowhead indicates signal from co-injection marker ttx-3::GFP . In all images, anterior is left and posterior is right. (D) Protein localization identified using translational reporters for ins-31 and F59B2.12 . The Nomarski images show localization within the vesicular structures in the seminal vesicle region for INS-31 and in vas deferens for F59B2.12 protein. (E) Time course images showing transfer of INS-31 from male to hermaphrodite during mating. To facilitate observation of mating behavior, slower-moving unc-119 mutant hermaphrodites were used. INS-31::sfGFP (green) is visible within the seminal vesicle of a male before spicule insertion (a) and moves into the lumen of vas deferens after insertion until ejaculation (b). During ejaculation, INS-31::sfGFP is transferred into the vulva region of the hermaphrodite (c) and remains diffused in the uterus after mating (d). (F) A Venn diagram showing the comparison of semen candidate gene lists obtained from this study, SPELL, and WormNet. The numbers of candidate genes and genes belonging to Mod3 (parentheses) are indicated. The scale bars represent 100 μm in (C) and 20 μm in (D).
Figure Legend Snippet: Identification of Semen Protein Genes (A) Schematic of procedure to identify and validate semen protein genes from the RNA-seq data. (B) The anatomical location of seminal vesicle, valve region, and vas deferens in male gonad (gray). (C) Tissue-specific expression of reporter transgenes for three semen candidate genes in male. Arrows indicate expression in seminal vesicle ( ins-31 ), vas deferens ( F59B2.12 ), and the valve region of vas deferens ( B0207.5 ). Arrowhead indicates signal from co-injection marker ttx-3::GFP . In all images, anterior is left and posterior is right. (D) Protein localization identified using translational reporters for ins-31 and F59B2.12 . The Nomarski images show localization within the vesicular structures in the seminal vesicle region for INS-31 and in vas deferens for F59B2.12 protein. (E) Time course images showing transfer of INS-31 from male to hermaphrodite during mating. To facilitate observation of mating behavior, slower-moving unc-119 mutant hermaphrodites were used. INS-31::sfGFP (green) is visible within the seminal vesicle of a male before spicule insertion (a) and moves into the lumen of vas deferens after insertion until ejaculation (b). During ejaculation, INS-31::sfGFP is transferred into the vulva region of the hermaphrodite (c) and remains diffused in the uterus after mating (d). (F) A Venn diagram showing the comparison of semen candidate gene lists obtained from this study, SPELL, and WormNet. The numbers of candidate genes and genes belonging to Mod3 (parentheses) are indicated. The scale bars represent 100 μm in (C) and 20 μm in (D).

Techniques Used: RNA Sequencing Assay, Expressing, Injection, Marker, Mutagenesis

4) Product Images from "Presphenoidal synchondrosis fusion in DBA/2J mice"

Article Title: Presphenoidal synchondrosis fusion in DBA/2J mice

Journal: Mammalian Genome

doi: 10.1007/s00335-012-9437-8

Histologic analysis of PSS closure in DBA/2J mice. a Photograph of a midline sagittal section through a P1 C57BL/6J mouse cranium; a photomicrograph within the oval contains an enlargement of the area with the PSS superimposed. Photomicrograph on the right is from a C57BL/6J P1 mouse with the PSS in a rostral (R)–caudal (C) orientation. The bilaterally symmetric resting zone (RZ), proliferating zone (PZ), and hypertrophic zone (HZ) chondrocyte-containing regions are indicated. Scale bar 200 μm. b Photomicrographs of midline sagittal sections through the PSS of C57BL/6J (B6) and DBA/2J (D2) mice at 1, 3, 5, and 10 days after birth (P1, P3, P5, P10) stained with hematoxylin and eosin. C57BL/6J and DBA/2J mice have similar looking PSS at P1 and P3, although the rostral–caudal length consistently appears shorter in DBA/2J than in C57BL/6J mice. By P5, the PSS in the DBA/2J mouse has lost rostral–caudal symmetry; instead, the HZ is at the ventral surface ( arrow ) and the RZ bulges from the dorsal surface. At P10, the PSS in the DBA/2J mouse lacks recognizable RZ, PZ, and HZ regions, whereas the RZ region is readily seen in the C57BL/6J PSS. Scale bars 100 μm (Color figure online)
Figure Legend Snippet: Histologic analysis of PSS closure in DBA/2J mice. a Photograph of a midline sagittal section through a P1 C57BL/6J mouse cranium; a photomicrograph within the oval contains an enlargement of the area with the PSS superimposed. Photomicrograph on the right is from a C57BL/6J P1 mouse with the PSS in a rostral (R)–caudal (C) orientation. The bilaterally symmetric resting zone (RZ), proliferating zone (PZ), and hypertrophic zone (HZ) chondrocyte-containing regions are indicated. Scale bar 200 μm. b Photomicrographs of midline sagittal sections through the PSS of C57BL/6J (B6) and DBA/2J (D2) mice at 1, 3, 5, and 10 days after birth (P1, P3, P5, P10) stained with hematoxylin and eosin. C57BL/6J and DBA/2J mice have similar looking PSS at P1 and P3, although the rostral–caudal length consistently appears shorter in DBA/2J than in C57BL/6J mice. By P5, the PSS in the DBA/2J mouse has lost rostral–caudal symmetry; instead, the HZ is at the ventral surface ( arrow ) and the RZ bulges from the dorsal surface. At P10, the PSS in the DBA/2J mouse lacks recognizable RZ, PZ, and HZ regions, whereas the RZ region is readily seen in the C57BL/6J PSS. Scale bars 100 μm (Color figure online)

Techniques Used: Mouse Assay, Staining

5) Product Images from "Brassinosteroids Modulate Meristem Fate and Differentiation of Unique Inflorescence Morphology in Setaria viridis [OPEN]"

Article Title: Brassinosteroids Modulate Meristem Fate and Differentiation of Unique Inflorescence Morphology in Setaria viridis [OPEN]

Journal: The Plant Cell

doi: 10.1105/tpc.17.00816

A Proposed Model for Bsl1 -Dependent BR Control of Spikelet versus Bristle Fate in S. viridis Inflorescence Development. (A) Adjacent sections from an A10.1 wild-type inflorescence primordium at 15 DAS were probed with Bsl1 (left) and SvBd1 (right) and showed adjacent and partially overlapping domains of expression. Bars = 100 μm. (B) One proposed model for bristle versus spikelet differentiation in a wild-type S. viridis inflorescence depends on a diffusible factor that enhances spatiotemporal accumulation of BRs. Paired BMs are indistinguishable during early development; SvKn1 (green circle) is expressed in the meristem tip and Bsl1 (blue semicircle) and SvBd1 (yellow semicircle) in adjacent domains at the sites of lateral organ initiation. BMs are poised to become determinate SMs where opposing levels of SvBd1 expression and BRs maintain the boundary. We propose that the presence of a diffusible factor that promotes BR accumulation over a certain threshold would stimulate rapid cell elongation and cessation of meristem activity, leading to formation of a bristle.
Figure Legend Snippet: A Proposed Model for Bsl1 -Dependent BR Control of Spikelet versus Bristle Fate in S. viridis Inflorescence Development. (A) Adjacent sections from an A10.1 wild-type inflorescence primordium at 15 DAS were probed with Bsl1 (left) and SvBd1 (right) and showed adjacent and partially overlapping domains of expression. Bars = 100 μm. (B) One proposed model for bristle versus spikelet differentiation in a wild-type S. viridis inflorescence depends on a diffusible factor that enhances spatiotemporal accumulation of BRs. Paired BMs are indistinguishable during early development; SvKn1 (green circle) is expressed in the meristem tip and Bsl1 (blue semicircle) and SvBd1 (yellow semicircle) in adjacent domains at the sites of lateral organ initiation. BMs are poised to become determinate SMs where opposing levels of SvBd1 expression and BRs maintain the boundary. We propose that the presence of a diffusible factor that promotes BR accumulation over a certain threshold would stimulate rapid cell elongation and cessation of meristem activity, leading to formation of a bristle.

Techniques Used: Expressing, Activity Assay

Morphological Characterization of Inflorescence Development in the bsl1-1 Mutant by Scanning Electron Microscopy Analysis. (A) and (B) Bristle development was first apparent at 17 DAS in A10.1 wild-type inflorescence primordia (A) and bristle differentiation was obvious by 18 DAS where meristem tips appeared to break off at indentations marked by yellow arrows (B) . Differentiating spikelets are marked by white arrows. Bars = 250 μm. (C) and (D) At 20 DAS, bristles were well developed in the wild-type inflorescences, and within spikelets, an upper floret (white asterisk) developed and a lower floret was visible as a meristematic bulge prior to abortion (red asterisk; [C] ). A mature bristle is marked with a yellow arrow (D) . Bars = 100 μm in (C) and 250 μm in (D) . (E) In the bsl1-1 mutant inflorescence primordium, bristles were not initiated by 18 DAS, but spikelets appeared to develop normally (white arrows). Bar = 250 μm. (F) to (H) At 20 DAS, bristle development was highly reduced in the bsl1-1 mutant and upper (white asterisk) and lower (red asterisk) florets were both developed (G) . Precocious development of numerous rudimentary spikelets (white arrows) was observed at the base of main spikelets (H) . Yellow arrow indicates one of few differentiated bristles formed in the mutant. Bars = 250 μm in (F) and (H) and 100 μm in (G) .
Figure Legend Snippet: Morphological Characterization of Inflorescence Development in the bsl1-1 Mutant by Scanning Electron Microscopy Analysis. (A) and (B) Bristle development was first apparent at 17 DAS in A10.1 wild-type inflorescence primordia (A) and bristle differentiation was obvious by 18 DAS where meristem tips appeared to break off at indentations marked by yellow arrows (B) . Differentiating spikelets are marked by white arrows. Bars = 250 μm. (C) and (D) At 20 DAS, bristles were well developed in the wild-type inflorescences, and within spikelets, an upper floret (white asterisk) developed and a lower floret was visible as a meristematic bulge prior to abortion (red asterisk; [C] ). A mature bristle is marked with a yellow arrow (D) . Bars = 100 μm in (C) and 250 μm in (D) . (E) In the bsl1-1 mutant inflorescence primordium, bristles were not initiated by 18 DAS, but spikelets appeared to develop normally (white arrows). Bar = 250 μm. (F) to (H) At 20 DAS, bristle development was highly reduced in the bsl1-1 mutant and upper (white asterisk) and lower (red asterisk) florets were both developed (G) . Precocious development of numerous rudimentary spikelets (white arrows) was observed at the base of main spikelets (H) . Yellow arrow indicates one of few differentiated bristles formed in the mutant. Bars = 250 μm in (F) and (H) and 100 μm in (G) .

Techniques Used: Mutagenesis, Electron Microscopy

Localization of Bsl1 and SvBd1 mRNAs in A10.1 Wild-Type and bsl1 Mutant Inflorescence Primordia during Development. (A) to (E) An antisense Bsl1 probe was used to examine Bsl1 expression during inflorescence development. (A) and (B) At 14 DAS, Bsl1 mRNAs were localized to the base of primary branches (white arrow; [A] ) and lateral organ boundaries (red arrow) of higher order BMs in A10.1 wild-type inflorescences (B) . (C) and (D) Bsl1 signal (red arrows) marked incipient lateral organs in developing spikelets (C) and floral meristems (D) at 15 and 17 DAS, respectively in wild-type inflorescences. Bsl1 signal was not observed in developing bristles. (E) In bsl1-1 mutants, the Bsl1 signal (red arrow) was expanded and mislocalized to the base of developing spikelet primordia at 16 DAS. (F) A Bsl1 sense probe showed no signal in A10.1 wild-type inflorescence. (G) to (J) An antisense SvBd1 probe was used to examine SvBd1 expression during inflorescence development. (G) At 14 DAS, SvBd1 was expressed in a semicircular domain (yellow arrow) at the base of all AMs prior to spikelet or bristle formation in wild-type inflorescences. (H) and (I) At 15 DAS (H) and 16 DAS (I) , SvBd1 was expressed at the boundaries of incipient lateral organs (yellow arrows) in developing spikelets in A10.1 wild-type inflorescences, but not in bristles. (J) In bsl1-1 mutants, SvBd1 signal was mislocalized to the base of developing spikelets (yellow arrow) at 17 DAS and expression was maintained into later stages of development. (K) A SvBd1 sense probe showed no signal in A10.1 wild-type inflorescence. Bars = 100 μm. BL, bristle; GP, glume primordium; UF, upper floret; LF, lower floret.
Figure Legend Snippet: Localization of Bsl1 and SvBd1 mRNAs in A10.1 Wild-Type and bsl1 Mutant Inflorescence Primordia during Development. (A) to (E) An antisense Bsl1 probe was used to examine Bsl1 expression during inflorescence development. (A) and (B) At 14 DAS, Bsl1 mRNAs were localized to the base of primary branches (white arrow; [A] ) and lateral organ boundaries (red arrow) of higher order BMs in A10.1 wild-type inflorescences (B) . (C) and (D) Bsl1 signal (red arrows) marked incipient lateral organs in developing spikelets (C) and floral meristems (D) at 15 and 17 DAS, respectively in wild-type inflorescences. Bsl1 signal was not observed in developing bristles. (E) In bsl1-1 mutants, the Bsl1 signal (red arrow) was expanded and mislocalized to the base of developing spikelet primordia at 16 DAS. (F) A Bsl1 sense probe showed no signal in A10.1 wild-type inflorescence. (G) to (J) An antisense SvBd1 probe was used to examine SvBd1 expression during inflorescence development. (G) At 14 DAS, SvBd1 was expressed in a semicircular domain (yellow arrow) at the base of all AMs prior to spikelet or bristle formation in wild-type inflorescences. (H) and (I) At 15 DAS (H) and 16 DAS (I) , SvBd1 was expressed at the boundaries of incipient lateral organs (yellow arrows) in developing spikelets in A10.1 wild-type inflorescences, but not in bristles. (J) In bsl1-1 mutants, SvBd1 signal was mislocalized to the base of developing spikelets (yellow arrow) at 17 DAS and expression was maintained into later stages of development. (K) A SvBd1 sense probe showed no signal in A10.1 wild-type inflorescence. Bars = 100 μm. BL, bristle; GP, glume primordium; UF, upper floret; LF, lower floret.

Techniques Used: Mutagenesis, Expressing, Affinity Magnetic Separation

6) Product Images from "Identification of Fitness Determinants during Energy-Limited Growth Arrest in Pseudomonas aeruginosa"

Article Title: Identification of Fitness Determinants during Energy-Limited Growth Arrest in Pseudomonas aeruginosa

Journal: mBio

doi: 10.1128/mBio.01170-17

Validation of fitness determinants identified by Tn-seq. (A) Read counts for insertions across the coxBAC , ackA-pta , and rpoS loci required during carbon limitation, oxygen limitation, or both, respectively. Each locus is divided into 100-bp windows, and the cumulative number of insertions in each window is plotted. (B) Fitness of the corresponding deletion mutants and the complemented strains relative to the WT after 13 days of carbon limitation or 10 days of oxygen limitation. Error bars show the standard deviation of biological replicates ( n = 3). The asterisk indicates a significant fitness defect relative to the WT (paired Student’s t test, P
Figure Legend Snippet: Validation of fitness determinants identified by Tn-seq. (A) Read counts for insertions across the coxBAC , ackA-pta , and rpoS loci required during carbon limitation, oxygen limitation, or both, respectively. Each locus is divided into 100-bp windows, and the cumulative number of insertions in each window is plotted. (B) Fitness of the corresponding deletion mutants and the complemented strains relative to the WT after 13 days of carbon limitation or 10 days of oxygen limitation. Error bars show the standard deviation of biological replicates ( n = 3). The asterisk indicates a significant fitness defect relative to the WT (paired Student’s t test, P

Techniques Used: Standard Deviation

7) Product Images from "Novel insights on colonization routes and evolutionary potential of Colletotrichum kahawae, a severe pathogen of Coffea arabica"

Article Title: Novel insights on colonization routes and evolutionary potential of Colletotrichum kahawae, a severe pathogen of Coffea arabica

Journal: Molecular Plant Pathology

doi: 10.1111/mpp.12726

Boxplots with the r d distribution. Two datasets were used: ck_clone_corrected_dataset and ck_dataset . Each box represents 100 random samples of 50 variants used to calculate an r d distribution and is centred around the mean, with whiskers extending out to 1.5 times the interquartile range. The median is indicated by the centre line. SNP, single nucleotide polymorphism.
Figure Legend Snippet: Boxplots with the r d distribution. Two datasets were used: ck_clone_corrected_dataset and ck_dataset . Each box represents 100 random samples of 50 variants used to calculate an r d distribution and is centred around the mean, with whiskers extending out to 1.5 times the interquartile range. The median is indicated by the centre line. SNP, single nucleotide polymorphism.

Techniques Used:

8) Product Images from "Genome-Wide Analysis of DNA Methylation Dynamics during Early Human Development"

Article Title: Genome-Wide Analysis of DNA Methylation Dynamics during Early Human Development

Journal: PLoS Genetics

doi: 10.1371/journal.pgen.1004868

Unique regulation of tandem repeat-containing regions. A, DNA methylation dynamics of transposable elements. Mean methylation levels of CpGs in various classes of SINEs, LINEs, LTRs and DNA repeats and SVA subfamilies are shown. SVA_A showed an especially high methylation level in blastocysts (59.2%). B, Proportions of repeat copies overlapping > 70% methylated windows in human blastocysts. We analyzed only SINEs, LINEs, LTRs, DNA repeats, SVAs and satellites with > 100 copies in the human genome. The top ten repeat names with the highest proportions are shown. The raw data are shown in S4 Table . C , Relationships between methylation levels and CpG densities. Mean methylation levels of CpGs in SVA_A are plotted against CpG densities. D, MER34C2 copies overlapping > 70% methylated windows in human blastocysts. 39 MER34C2 copies are all tandemly repeated within the PTPRN2 gene locus. E, Proportions of maternal and paternal gDMRs containing VNTRs. Counts of gDMRs with VNTRs and total gDMRs are indicated. F, Proportions of mean methylation levels of CGIs with and without VNTRs in human blastocysts. Only autosomal CGIs hypermethylated in both gametes were analyzed. 118 of 499 CGIs with VNTRs and 31 of 2,222 CGIs without VNTRs showed > 70% methylation ( P = 0, chi-square test). G, Characteristics of VNTRs highly methylated in blastocysts. Using Tandem Repeats Finder [41] , the size of the consensus pattern, the number of tandemly aligned copies and the alignment score were compared between VNTRs of
Figure Legend Snippet: Unique regulation of tandem repeat-containing regions. A, DNA methylation dynamics of transposable elements. Mean methylation levels of CpGs in various classes of SINEs, LINEs, LTRs and DNA repeats and SVA subfamilies are shown. SVA_A showed an especially high methylation level in blastocysts (59.2%). B, Proportions of repeat copies overlapping > 70% methylated windows in human blastocysts. We analyzed only SINEs, LINEs, LTRs, DNA repeats, SVAs and satellites with > 100 copies in the human genome. The top ten repeat names with the highest proportions are shown. The raw data are shown in S4 Table . C , Relationships between methylation levels and CpG densities. Mean methylation levels of CpGs in SVA_A are plotted against CpG densities. D, MER34C2 copies overlapping > 70% methylated windows in human blastocysts. 39 MER34C2 copies are all tandemly repeated within the PTPRN2 gene locus. E, Proportions of maternal and paternal gDMRs containing VNTRs. Counts of gDMRs with VNTRs and total gDMRs are indicated. F, Proportions of mean methylation levels of CGIs with and without VNTRs in human blastocysts. Only autosomal CGIs hypermethylated in both gametes were analyzed. 118 of 499 CGIs with VNTRs and 31 of 2,222 CGIs without VNTRs showed > 70% methylation ( P = 0, chi-square test). G, Characteristics of VNTRs highly methylated in blastocysts. Using Tandem Repeats Finder [41] , the size of the consensus pattern, the number of tandemly aligned copies and the alignment score were compared between VNTRs of

Techniques Used: DNA Methylation Assay, Methylation

9) Product Images from "Evolutionally dynamic L1 regulation in embryonic stem cells"

Article Title: Evolutionally dynamic L1 regulation in embryonic stem cells

Journal: Genes & Development

doi: 10.1101/gad.241661.114

KAP1 coincides with H3K9me3 at the 5′ end of full-length L1 in hES cells. Distribution of ChIP-seq KAP1 peaks relative to the 5′ end of full-length elements ( A ) or the center of truncated L1 elements ( B ) in hES and HEK293 cells. The profiles were normalized to the total number of ChIP-seq peaks for each cell line. ( C ) KAP1 ChIP-seq peak distribution over the first kilobase of L1. The L1 5′ UTR is schematized below , with sense and antisense promoters as red and green boxes, respectively. Sense promoter is diversely depicted as mainly located in the first 100 bp or extending up to 700 bp. ( D ) Overlap of KAP1 and H3K9me3 ChIP-seq tags relative to the 5′ end of full-length L1 elements. ( E ) Relative frequency of KAP1+H3K9me3, KAP1-only, and H3K9me3-only peaks at this location.
Figure Legend Snippet: KAP1 coincides with H3K9me3 at the 5′ end of full-length L1 in hES cells. Distribution of ChIP-seq KAP1 peaks relative to the 5′ end of full-length elements ( A ) or the center of truncated L1 elements ( B ) in hES and HEK293 cells. The profiles were normalized to the total number of ChIP-seq peaks for each cell line. ( C ) KAP1 ChIP-seq peak distribution over the first kilobase of L1. The L1 5′ UTR is schematized below , with sense and antisense promoters as red and green boxes, respectively. Sense promoter is diversely depicted as mainly located in the first 100 bp or extending up to 700 bp. ( D ) Overlap of KAP1 and H3K9me3 ChIP-seq tags relative to the 5′ end of full-length L1 elements. ( E ) Relative frequency of KAP1+H3K9me3, KAP1-only, and H3K9me3-only peaks at this location.

Techniques Used: Chromatin Immunoprecipitation

Evolutionally dynamic and KRAB-ZFP-mediated KAP1–L1 interaction. Percentage of KB full-length (FL) L1 elements per subfamily in hES ( A ) and mES ( B ). (Myr) Million years. ( C ) Screenshot of a representative L1MdF2 element, illustrating RNA-seq coverage plots from control (shEmpty) and Gm6871 knockdown mES cells as well as gm6871 and Kap1 ChIP-seq tracks. ( D ) Putative gm6871 DNA-binding motif identified by computing gm6871 ). ( E ) Relative change in the expression (RPKN [ normalized reads per kilobase]) of murine full-length L1s bound or not bound by KAP1 and/or Gm6871 between Gm6871 knockdown and wild-type mES cells. The raw data were bootstrapped 1000 times with a resampling size of 100 for the plot design. The statistical analyses were calculated on the entire raw data by Wilcoxon nonparametric test. (NS) P > 0.05; (**) P ≤ 0.01.
Figure Legend Snippet: Evolutionally dynamic and KRAB-ZFP-mediated KAP1–L1 interaction. Percentage of KB full-length (FL) L1 elements per subfamily in hES ( A ) and mES ( B ). (Myr) Million years. ( C ) Screenshot of a representative L1MdF2 element, illustrating RNA-seq coverage plots from control (shEmpty) and Gm6871 knockdown mES cells as well as gm6871 and Kap1 ChIP-seq tracks. ( D ) Putative gm6871 DNA-binding motif identified by computing gm6871 ). ( E ) Relative change in the expression (RPKN [ normalized reads per kilobase]) of murine full-length L1s bound or not bound by KAP1 and/or Gm6871 between Gm6871 knockdown and wild-type mES cells. The raw data were bootstrapped 1000 times with a resampling size of 100 for the plot design. The statistical analyses were calculated on the entire raw data by Wilcoxon nonparametric test. (NS) P > 0.05; (**) P ≤ 0.01.

Techniques Used: RNA Sequencing Assay, Chromatin Immunoprecipitation, Binding Assay, Expressing

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Article Snippet: .. Libraries with sample‐specific barcode (eight‐nucleotide) sequences were produced from DNA digested with Pst I. RAD‐seq pools were 100‐bp single‐end sequenced in a lane of an Illumina HiSeq 2000 machine (San Diego, California). .. The sequence data were deposited in the European Nucleotide Archive under submission number PRJEB26929.

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Article Title: Identification of Fitness Determinants during Energy-Limited Growth Arrest in Pseudomonas aeruginosa
Article Snippet: .. The amplified DNA was sequenced using 100-bp single-end reads on the Illumina HiSeq 2500 platform at the Millard and Muriel Jacobs Genetics and Genomics Laboratory at Caltech. .. Sequences were mapped to the UCBPP-PA14 genome sequence using Bowtie ( ) and analyzed using the ARTIST Tn-seq analysis pipeline in MatLab ( ).

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    Illumina Inc 100 bp single end
    Ancestry results for samples from the southeastern portion of the range. Ancestry proportions were determined using Structure with 50,000 and <t>100,000</t> burn‐in and MCMC iterations and the previously determined optimal K ‐value of 2
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    Illumina Inc 100 bp paired single end
    Decreased human endothelial TSP1. (A) Immunofluorescent staining of TSP1 (red) and collagen IV (green) of human CCM and lesion-free brain tissue. Arrowheads, capillary; arrows, venule; asterisks, vascular lumen of CCM lesions. Bar, <t>100</t> µm ( n = 2). (B and C) HUVECs were transduced with shKrit1 or shControl using lentivirus. (B) KRIT1-depleted HUVECs expressed ∼50% as much TSP1 protein as control cells (SEM, n = 3). (C) KRIT1 shRNA 55% decrease in KRIT1 mRNA as determined by RT-qPCR (SEM, n = 4). **, P
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    Image Search Results


    Ancestry results for samples from the southeastern portion of the range. Ancestry proportions were determined using Structure with 50,000 and 100,000 burn‐in and MCMC iterations and the previously determined optimal K ‐value of 2

    Journal: Evolutionary Applications

    Article Title: Population assignment and local adaptation along an isolation‐by‐distance gradient in Pacific cod (Gadus macrocephalus). Population assignment and local adaptation along an isolation‐by‐distance gradient in Pacific cod (Gadus macrocephalus)

    doi: 10.1111/eva.12639

    Figure Lengend Snippet: Ancestry results for samples from the southeastern portion of the range. Ancestry proportions were determined using Structure with 50,000 and 100,000 burn‐in and MCMC iterations and the previously determined optimal K ‐value of 2

    Article Snippet: Libraries were pooled within samples in 10 nM concentrations and sequenced in 100‐bp single‐end reads on a HiSeq2000 (Illumina, Inc., San Diego, CA) at the University of Oregon Genomics and Cell Characterization Core Facility (GC3F, Eugene, Oregon).

    Techniques:

    LD decay (mean r 2 ) estimated in three populations (as defined by population genetic structure) using 3321 desi (A) and 8592 kabuli (B) SNPs, respectively . For LD decay, the r 2 -value of the marker physical distance of 0 kb is considered 1. The plotted curved lines indicate the mean r 2 -values among markers spaced with uniform 100 kb physical intervals from 0 to 1000 kb. The plotted line in uppermost panel I indicate the mean r 2 -values among markers spaced with uniform 10 kb physical intervals from 0 to 100 kb. The marked line in panels I, II indicate the mean r 2 -values among markers spaced with uniform 10 and 20 kb physical intervals from 0 to 100 kb and 0 to 200 kb, respectively. “All” includes the LD decay across entire three populations.

    Journal: Frontiers in Plant Science

    Article Title: Employing genome-wide SNP discovery and genotyping strategy to extrapolate the natural allelic diversity and domestication patterns in chickpea

    doi: 10.3389/fpls.2015.00162

    Figure Lengend Snippet: LD decay (mean r 2 ) estimated in three populations (as defined by population genetic structure) using 3321 desi (A) and 8592 kabuli (B) SNPs, respectively . For LD decay, the r 2 -value of the marker physical distance of 0 kb is considered 1. The plotted curved lines indicate the mean r 2 -values among markers spaced with uniform 100 kb physical intervals from 0 to 1000 kb. The plotted line in uppermost panel I indicate the mean r 2 -values among markers spaced with uniform 10 kb physical intervals from 0 to 100 kb. The marked line in panels I, II indicate the mean r 2 -values among markers spaced with uniform 10 and 20 kb physical intervals from 0 to 100 kb and 0 to 200 kb, respectively. “All” includes the LD decay across entire three populations.

    Article Snippet: These libraries were pooled together (following Elshire et al., ; Spindel et al., ) and sequenced (100-bp single end) using Illumina HiSeq 2000.

    Techniques: Marker

    A genome scan plot depicting the density of SNPs physically mapped across eight chromosomes of desi (A) and kabuli (B) genomes at 100-kb sliding window . The SNP density is represented by the number of SNPs mapped within 1-Mb physical intervals across chromosomes.

    Journal: Frontiers in Plant Science

    Article Title: Employing genome-wide SNP discovery and genotyping strategy to extrapolate the natural allelic diversity and domestication patterns in chickpea

    doi: 10.3389/fpls.2015.00162

    Figure Lengend Snippet: A genome scan plot depicting the density of SNPs physically mapped across eight chromosomes of desi (A) and kabuli (B) genomes at 100-kb sliding window . The SNP density is represented by the number of SNPs mapped within 1-Mb physical intervals across chromosomes.

    Article Snippet: These libraries were pooled together (following Elshire et al., ; Spindel et al., ) and sequenced (100-bp single end) using Illumina HiSeq 2000.

    Techniques:

    Gene Correlation Network Analysis (A) Hierarchical cluster dendrogram groups 21,143 genes into distinct co-expression modules identified using weighted gene correlation network analysis. Six major modules are indicated as colored boxes (Mod1, black; Mod2, salmon; Mod3, brown; Mod4, yellow; Mod5, midnight blue; Mod6, blue). (B) Heatmap showing relative expression of genes in the six major modules across ten samples of two sexes. The color values are the standardized Z scores of gene expression. (C) Percentage of genes that are previously known to be enriched in specific cells or tissues across different modules. Previously known gene lists include for panneural enriched ( Spencer et al., 2011 ), sperm and oocyte enriched ( Reinke et al., 2004 ), and cuticle collagen enriched ( Page and Johnstone, 2007 ). Number of genes was normalized in order to avoid the effect of different module sizes (y axis). (D and E) Tissue-specific expression of reporter transgenes for two C-type lectin domain ( clec ) genes chosen from Mod1 (D) and Mod3 (E) in both sexes. Arrow indicates expression in head neurons in (D) or in vas deferens of male in (E). The magnified view of the arrowed region is shown at the bottom of each image. In all images, anterior is left and posterior is right. The scale bars represent 100 μm.

    Journal: Cell reports

    Article Title: Gene Function Prediction Based on Developmental Transcriptomes of the Two Sexes in C. elegans

    doi: 10.1016/j.celrep.2016.09.051

    Figure Lengend Snippet: Gene Correlation Network Analysis (A) Hierarchical cluster dendrogram groups 21,143 genes into distinct co-expression modules identified using weighted gene correlation network analysis. Six major modules are indicated as colored boxes (Mod1, black; Mod2, salmon; Mod3, brown; Mod4, yellow; Mod5, midnight blue; Mod6, blue). (B) Heatmap showing relative expression of genes in the six major modules across ten samples of two sexes. The color values are the standardized Z scores of gene expression. (C) Percentage of genes that are previously known to be enriched in specific cells or tissues across different modules. Previously known gene lists include for panneural enriched ( Spencer et al., 2011 ), sperm and oocyte enriched ( Reinke et al., 2004 ), and cuticle collagen enriched ( Page and Johnstone, 2007 ). Number of genes was normalized in order to avoid the effect of different module sizes (y axis). (D and E) Tissue-specific expression of reporter transgenes for two C-type lectin domain ( clec ) genes chosen from Mod1 (D) and Mod3 (E) in both sexes. Arrow indicates expression in head neurons in (D) or in vas deferens of male in (E). The magnified view of the arrowed region is shown at the bottom of each image. In all images, anterior is left and posterior is right. The scale bars represent 100 μm.

    Article Snippet: Library preparation followed the protocol described at http://wasp.einstein.yu.edu/index.php/Main_Page , and sequences were determined for 100-bp single-end reads using the Illumina HiSeq2500.

    Techniques: Expressing, Polyacrylamide Gel Electrophoresis

    Identification of Semen Protein Genes (A) Schematic of procedure to identify and validate semen protein genes from the RNA-seq data. (B) The anatomical location of seminal vesicle, valve region, and vas deferens in male gonad (gray). (C) Tissue-specific expression of reporter transgenes for three semen candidate genes in male. Arrows indicate expression in seminal vesicle ( ins-31 ), vas deferens ( F59B2.12 ), and the valve region of vas deferens ( B0207.5 ). Arrowhead indicates signal from co-injection marker ttx-3::GFP . In all images, anterior is left and posterior is right. (D) Protein localization identified using translational reporters for ins-31 and F59B2.12 . The Nomarski images show localization within the vesicular structures in the seminal vesicle region for INS-31 and in vas deferens for F59B2.12 protein. (E) Time course images showing transfer of INS-31 from male to hermaphrodite during mating. To facilitate observation of mating behavior, slower-moving unc-119 mutant hermaphrodites were used. INS-31::sfGFP (green) is visible within the seminal vesicle of a male before spicule insertion (a) and moves into the lumen of vas deferens after insertion until ejaculation (b). During ejaculation, INS-31::sfGFP is transferred into the vulva region of the hermaphrodite (c) and remains diffused in the uterus after mating (d). (F) A Venn diagram showing the comparison of semen candidate gene lists obtained from this study, SPELL, and WormNet. The numbers of candidate genes and genes belonging to Mod3 (parentheses) are indicated. The scale bars represent 100 μm in (C) and 20 μm in (D).

    Journal: Cell reports

    Article Title: Gene Function Prediction Based on Developmental Transcriptomes of the Two Sexes in C. elegans

    doi: 10.1016/j.celrep.2016.09.051

    Figure Lengend Snippet: Identification of Semen Protein Genes (A) Schematic of procedure to identify and validate semen protein genes from the RNA-seq data. (B) The anatomical location of seminal vesicle, valve region, and vas deferens in male gonad (gray). (C) Tissue-specific expression of reporter transgenes for three semen candidate genes in male. Arrows indicate expression in seminal vesicle ( ins-31 ), vas deferens ( F59B2.12 ), and the valve region of vas deferens ( B0207.5 ). Arrowhead indicates signal from co-injection marker ttx-3::GFP . In all images, anterior is left and posterior is right. (D) Protein localization identified using translational reporters for ins-31 and F59B2.12 . The Nomarski images show localization within the vesicular structures in the seminal vesicle region for INS-31 and in vas deferens for F59B2.12 protein. (E) Time course images showing transfer of INS-31 from male to hermaphrodite during mating. To facilitate observation of mating behavior, slower-moving unc-119 mutant hermaphrodites were used. INS-31::sfGFP (green) is visible within the seminal vesicle of a male before spicule insertion (a) and moves into the lumen of vas deferens after insertion until ejaculation (b). During ejaculation, INS-31::sfGFP is transferred into the vulva region of the hermaphrodite (c) and remains diffused in the uterus after mating (d). (F) A Venn diagram showing the comparison of semen candidate gene lists obtained from this study, SPELL, and WormNet. The numbers of candidate genes and genes belonging to Mod3 (parentheses) are indicated. The scale bars represent 100 μm in (C) and 20 μm in (D).

    Article Snippet: Library preparation followed the protocol described at http://wasp.einstein.yu.edu/index.php/Main_Page , and sequences were determined for 100-bp single-end reads using the Illumina HiSeq2500.

    Techniques: RNA Sequencing Assay, Expressing, Injection, Marker, Mutagenesis

    Decreased human endothelial TSP1. (A) Immunofluorescent staining of TSP1 (red) and collagen IV (green) of human CCM and lesion-free brain tissue. Arrowheads, capillary; arrows, venule; asterisks, vascular lumen of CCM lesions. Bar, 100 µm ( n = 2). (B and C) HUVECs were transduced with shKrit1 or shControl using lentivirus. (B) KRIT1-depleted HUVECs expressed ∼50% as much TSP1 protein as control cells (SEM, n = 3). (C) KRIT1 shRNA 55% decrease in KRIT1 mRNA as determined by RT-qPCR (SEM, n = 4). **, P

    Journal: The Journal of Experimental Medicine

    Article Title: Thrombospondin1 (TSP1) replacement prevents cerebral cavernous malformations

    doi: 10.1084/jem.20171178

    Figure Lengend Snippet: Decreased human endothelial TSP1. (A) Immunofluorescent staining of TSP1 (red) and collagen IV (green) of human CCM and lesion-free brain tissue. Arrowheads, capillary; arrows, venule; asterisks, vascular lumen of CCM lesions. Bar, 100 µm ( n = 2). (B and C) HUVECs were transduced with shKrit1 or shControl using lentivirus. (B) KRIT1-depleted HUVECs expressed ∼50% as much TSP1 protein as control cells (SEM, n = 3). (C) KRIT1 shRNA 55% decrease in KRIT1 mRNA as determined by RT-qPCR (SEM, n = 4). **, P

    Article Snippet: RNA libraries were multiplexed and sequenced with 100-bp paired single-end reads (SR100) to a depth of ∼30 million reads per sample on an Illumina HiSeq2500.

    Techniques: Staining, Transduction, shRNA, Quantitative RT-PCR

    TSP1 replacement does not suppress the rise in KLF2 and KLF4 after loss of KRIT1. (A and B) Analysis of TSP1, ZO-1, KLF2, and KLF4 mRNA levels by RT-qPCR in freshly isolated microvasculature from mice at P5 and P7 as indicated. Krit1 fl/fl littermate controls, at each developmental stage, were used to calculate percentage increase or decrease in Krit1 ECKO mice using the following formulas: % increase = 100 × ( X − F )/ F and % decrease = 100 × ABS[( F − X )/ F ], where X and F = mRNA abundance in Krit1 ECKO and Krit1 fl/fl BMECs, respectively (SEM, n = 4 or 6). (C) Representative confocal images of retinal vasculature stained for KLF4 (green), TSP1 (red), or isolectin B4 (turquoise). TSP1 is decreased and KLF4 is increased at areas of condensed vasculature ( n = 5 or 6 mice in each group). Bar, 25 µm. (D and E) Analysis of levels of KLF2 and KLF4 mRNA by RT-qPCR from Krit1 ECKO BMEC (D) or cerebellar tissue from Krit1 ECKO mice (E) treated with 3TSR, TSP1, or vehicle compared with Krit1 fl/fl BMEC or Krit1 fl/fl controls. Data are expressed as percentage increase or decrease in Krit1 ECKO using the same formulas as in A and B (SEM, n = 3 or 4 in each group). (F) HUVECs were transduced with lentivirus encoding shKrit1, KLF2, or KLF4, and the increase in KLF2 or KLF4 mRNA relative to cells transduced with lentivirus encoding GFP was measured by RT-qPCR (SEM, n = 4). (G) HUVECs were transduced with lentivirus encoding ShKrit1, KLF2, or KLF4 as described in F, and the decrease of TSP1 mRNA levels was measured relative to cells transduced with EGFP control lentivirus (SEM, n = 4 or 5). (H) Analysis of TSP1 protein levels in HUVECs transduced with lentivirus encoding KLF2 or KLF4 as assessed by Western blot analysis; lentivirus encoding GFP was used as a control (SEM, n = 4). White lines indicate intervening lanes have been spliced out. (I) Loss of endothelial KRIT1 increases expression of KLF2 and KLF4 transcription factors, contributing to CCM formation by downstream effects including suppressed TSP1 expression. 3TSR (TSP1 derivative) reduces CCM lesion formation by replacing functions of TSP1 such as blocking VEGF signaling. Loss of KRIT1 also leads to ROCK activation in a KLF2-dependent manner, and blocking ROCK can also ameliorate CCMs. Thus, blockade of these and other downstream targets of KLF2 and KLF4 may offer a general strategy to reduce CCM formation in humans. *, P

    Journal: The Journal of Experimental Medicine

    Article Title: Thrombospondin1 (TSP1) replacement prevents cerebral cavernous malformations

    doi: 10.1084/jem.20171178

    Figure Lengend Snippet: TSP1 replacement does not suppress the rise in KLF2 and KLF4 after loss of KRIT1. (A and B) Analysis of TSP1, ZO-1, KLF2, and KLF4 mRNA levels by RT-qPCR in freshly isolated microvasculature from mice at P5 and P7 as indicated. Krit1 fl/fl littermate controls, at each developmental stage, were used to calculate percentage increase or decrease in Krit1 ECKO mice using the following formulas: % increase = 100 × ( X − F )/ F and % decrease = 100 × ABS[( F − X )/ F ], where X and F = mRNA abundance in Krit1 ECKO and Krit1 fl/fl BMECs, respectively (SEM, n = 4 or 6). (C) Representative confocal images of retinal vasculature stained for KLF4 (green), TSP1 (red), or isolectin B4 (turquoise). TSP1 is decreased and KLF4 is increased at areas of condensed vasculature ( n = 5 or 6 mice in each group). Bar, 25 µm. (D and E) Analysis of levels of KLF2 and KLF4 mRNA by RT-qPCR from Krit1 ECKO BMEC (D) or cerebellar tissue from Krit1 ECKO mice (E) treated with 3TSR, TSP1, or vehicle compared with Krit1 fl/fl BMEC or Krit1 fl/fl controls. Data are expressed as percentage increase or decrease in Krit1 ECKO using the same formulas as in A and B (SEM, n = 3 or 4 in each group). (F) HUVECs were transduced with lentivirus encoding shKrit1, KLF2, or KLF4, and the increase in KLF2 or KLF4 mRNA relative to cells transduced with lentivirus encoding GFP was measured by RT-qPCR (SEM, n = 4). (G) HUVECs were transduced with lentivirus encoding ShKrit1, KLF2, or KLF4 as described in F, and the decrease of TSP1 mRNA levels was measured relative to cells transduced with EGFP control lentivirus (SEM, n = 4 or 5). (H) Analysis of TSP1 protein levels in HUVECs transduced with lentivirus encoding KLF2 or KLF4 as assessed by Western blot analysis; lentivirus encoding GFP was used as a control (SEM, n = 4). White lines indicate intervening lanes have been spliced out. (I) Loss of endothelial KRIT1 increases expression of KLF2 and KLF4 transcription factors, contributing to CCM formation by downstream effects including suppressed TSP1 expression. 3TSR (TSP1 derivative) reduces CCM lesion formation by replacing functions of TSP1 such as blocking VEGF signaling. Loss of KRIT1 also leads to ROCK activation in a KLF2-dependent manner, and blocking ROCK can also ameliorate CCMs. Thus, blockade of these and other downstream targets of KLF2 and KLF4 may offer a general strategy to reduce CCM formation in humans. *, P

    Article Snippet: RNA libraries were multiplexed and sequenced with 100-bp paired single-end reads (SR100) to a depth of ∼30 million reads per sample on an Illumina HiSeq2500.

    Techniques: Quantitative RT-PCR, Isolation, Mouse Assay, Staining, Transduction, Western Blot, Expressing, Blocking Assay, Activation Assay

    TSP1 derivative, 3TSR, prevents CCMs and retinal vascular lesions in Krit1 ECKO mice. (A) Experimental protocol: vehicle or 3TSR (1.6 mg/Kg) was administered by retroorbital plexus injection at P5 and P6, and brains and retinas were analyzed at P7. (B) Prominent lesions are present in the cerebellum of Krit1 ECKO mice, whereas administration of 3TSR suppressed lesion formation. (C) Hematoxylin and eosin staining of cerebellar sections from Krit1 ECKO mice after treatment with 3TSR or vehicle ( n = 4 mice in each group). (D) Representative image of whole-mount P7 retinal vasculature at the angiogenic growth front. The marked area in Krit1 ECKO whole-mount retina shows decreased areas of condensed vascular plexus in Krit1 ECKO treated with 3TSR compared with vehicle-treated Krit1 ECKO littermates (SEM, n = 8 mice in each group). (E) Quantification of lesion coverage in Krit1 ECKO mice treated with 3TSR or Vehicle (SEM, n = 8 mice in each group). (F) Administered 3TSR is present in CCM. 3TSR was injected retroorbitally into a Krit1 ECKO ;Thbs1 −/− mouse. After 30 min, the mouse was killed, and its cerebellar cortex was stained for 3TSR (red, using anti-TSP1 antibodies) and endothelial marker PECAM1 (green); DAPI staining (blue) was used to reveal nuclei. 3TSR is observed in CCM. (G) Higher-magnification images of boxed areas in F. (F and G) Asterisks, vascular lumen of CCM. Bars: (B) 1 mm; (C and F) 100 µm; (D) 200 µm; (G) 50 µm. ***, P

    Journal: The Journal of Experimental Medicine

    Article Title: Thrombospondin1 (TSP1) replacement prevents cerebral cavernous malformations

    doi: 10.1084/jem.20171178

    Figure Lengend Snippet: TSP1 derivative, 3TSR, prevents CCMs and retinal vascular lesions in Krit1 ECKO mice. (A) Experimental protocol: vehicle or 3TSR (1.6 mg/Kg) was administered by retroorbital plexus injection at P5 and P6, and brains and retinas were analyzed at P7. (B) Prominent lesions are present in the cerebellum of Krit1 ECKO mice, whereas administration of 3TSR suppressed lesion formation. (C) Hematoxylin and eosin staining of cerebellar sections from Krit1 ECKO mice after treatment with 3TSR or vehicle ( n = 4 mice in each group). (D) Representative image of whole-mount P7 retinal vasculature at the angiogenic growth front. The marked area in Krit1 ECKO whole-mount retina shows decreased areas of condensed vascular plexus in Krit1 ECKO treated with 3TSR compared with vehicle-treated Krit1 ECKO littermates (SEM, n = 8 mice in each group). (E) Quantification of lesion coverage in Krit1 ECKO mice treated with 3TSR or Vehicle (SEM, n = 8 mice in each group). (F) Administered 3TSR is present in CCM. 3TSR was injected retroorbitally into a Krit1 ECKO ;Thbs1 −/− mouse. After 30 min, the mouse was killed, and its cerebellar cortex was stained for 3TSR (red, using anti-TSP1 antibodies) and endothelial marker PECAM1 (green); DAPI staining (blue) was used to reveal nuclei. 3TSR is observed in CCM. (G) Higher-magnification images of boxed areas in F. (F and G) Asterisks, vascular lumen of CCM. Bars: (B) 1 mm; (C and F) 100 µm; (D) 200 µm; (G) 50 µm. ***, P

    Article Snippet: RNA libraries were multiplexed and sequenced with 100-bp paired single-end reads (SR100) to a depth of ∼30 million reads per sample on an Illumina HiSeq2500.

    Techniques: Mouse Assay, Injection, Staining, Marker

    Altered tight junctions are an early phenotypic consequence of Krit1 inactivation. (A) Representative confocal images of ZO-1 (red), claudin5 (CLDN5; turquoise), and VE-cadherin (green) staining in primary BMEC Krit1 ECKO or control Krit1 fl/fl BMECs. Nuclei were counterstained with DAPI (blue; n = 4). Arrows indicate loss of tight junctions but not adherence junctions. (B) Quantification of brain endothelial ZO-1, claudin5, and VE-cadherin protein as assessed by Western blot analysis in Krit1 ECKO compared with Krit1 fl/fl BMEC controls (SEM, n = 3 or 4). (C) Confocal microscopy of cerebellar cortex at P7 stained with anti-PECAM1 (green). (D) Higher-magnification images of boxed areas in C stained for ZO-1 (red), claudin5 (turquoise), and PECAM1 (green). Arrows, staining of tight junction proteins ZO-1 and claudin5; asterisks, vascular lumen of CCM ( n = 3). (E) Quantification of brain endothelial ZO-1, claudin5, and VE-cadherin protein abundance in freshly isolated cerebellar microvasculature in Krit1 ECKO compared with Krit1 fl/fl littermate controls (SEM, n = 3 or 4). (F) Maximum-intensity projection of whole-mount P7 retinal vasculature at the angiogenic growth front stained for ZO-1 (red), claudin5 (turquoise), and an endothelial marker, isolectin B4 (green). (G) Higher-magnification images of boxed areas in F show staining for ZO-1 (red), claudin5 (turquoise), and isolectin B4 (green). (H) Quantification of ZO-1 and claudin5 protein expression in retinal vasculature at the angiogenic front in Krit1 ECKO compared with Krit1 fl/fl littermate controls (SEM, n = 6 mice per group). Bars: (A) 50 µm; (C) 100 µm; (D, F, and G) 25 µm. *, P

    Journal: The Journal of Experimental Medicine

    Article Title: Thrombospondin1 (TSP1) replacement prevents cerebral cavernous malformations

    doi: 10.1084/jem.20171178

    Figure Lengend Snippet: Altered tight junctions are an early phenotypic consequence of Krit1 inactivation. (A) Representative confocal images of ZO-1 (red), claudin5 (CLDN5; turquoise), and VE-cadherin (green) staining in primary BMEC Krit1 ECKO or control Krit1 fl/fl BMECs. Nuclei were counterstained with DAPI (blue; n = 4). Arrows indicate loss of tight junctions but not adherence junctions. (B) Quantification of brain endothelial ZO-1, claudin5, and VE-cadherin protein as assessed by Western blot analysis in Krit1 ECKO compared with Krit1 fl/fl BMEC controls (SEM, n = 3 or 4). (C) Confocal microscopy of cerebellar cortex at P7 stained with anti-PECAM1 (green). (D) Higher-magnification images of boxed areas in C stained for ZO-1 (red), claudin5 (turquoise), and PECAM1 (green). Arrows, staining of tight junction proteins ZO-1 and claudin5; asterisks, vascular lumen of CCM ( n = 3). (E) Quantification of brain endothelial ZO-1, claudin5, and VE-cadherin protein abundance in freshly isolated cerebellar microvasculature in Krit1 ECKO compared with Krit1 fl/fl littermate controls (SEM, n = 3 or 4). (F) Maximum-intensity projection of whole-mount P7 retinal vasculature at the angiogenic growth front stained for ZO-1 (red), claudin5 (turquoise), and an endothelial marker, isolectin B4 (green). (G) Higher-magnification images of boxed areas in F show staining for ZO-1 (red), claudin5 (turquoise), and isolectin B4 (green). (H) Quantification of ZO-1 and claudin5 protein expression in retinal vasculature at the angiogenic front in Krit1 ECKO compared with Krit1 fl/fl littermate controls (SEM, n = 6 mice per group). Bars: (A) 50 µm; (C) 100 µm; (D, F, and G) 25 µm. *, P

    Article Snippet: RNA libraries were multiplexed and sequenced with 100-bp paired single-end reads (SR100) to a depth of ∼30 million reads per sample on an Illumina HiSeq2500.

    Techniques: Staining, Western Blot, Confocal Microscopy, Isolation, Marker, Expressing, Mouse Assay

    Loss of KRIT1 inhibits the expression of TSP1. (A) Genome-wide RNA-seq from three independent biological replicates followed by gene ontology analysis of genes differentially expressed in Krit1 ECKO BMECs compared with Krit1 fl/fl BMECs. Each term listed was the top term in a cluster of related terms, and the corrected p-values were calculated according to Benjamini’s method ( Huang et al., 2009 ). (B) Expression levels of differentially expressed genes represented on a scatter plot; fragments per kilobase of transcript per million mapped reads (FPKM) of individual transcripts are represented on a log2 scale. A few of the most highly suppressed and up-regulated genes are labeled. (C) RT-qPCR confirmation of RNA-seq–identified marked decrease in mRNA of extracellular regulators of angiogenesis in Krit1 ECKO BMECs compared with Krit1 fl/fl BMECs (SEM, n = 3). (D) Quantification of TSP1 protein from three independent biological replicates in Krit1 ECKO (KO) and in Krit1 fl/fl (Flox) BMECs (SEM, n = 3). (E) RT-qPCR analysis of isolated brain microvasculature in Krit1 ECKO compared with Krit1 fl/fl littermate controls (SEM, n = 3). (F) Quantification of TSP1 protein from freshly isolated brain microvasculature in Krit1 ECKO (KO) compared with Krit1 fl/fl (Flox) littermate controls (SEM, n = 3). (G) Confocal microscopy of cerebellar cortex stained for TSP1 (red) and endothelial specific marker PECAM1 (green); DAPI staining (blue) was used to reveal nuclei ( n = 3). (H) Higher-magnification images of boxed areas in G. TSP1 protein expression was decreased in CCM from Krit1 ECKO mice (arrows). Asterisks, vascular lumen of CCM lesions. Bars: (G) 100 µm; (H) 25 µm. *, P

    Journal: The Journal of Experimental Medicine

    Article Title: Thrombospondin1 (TSP1) replacement prevents cerebral cavernous malformations

    doi: 10.1084/jem.20171178

    Figure Lengend Snippet: Loss of KRIT1 inhibits the expression of TSP1. (A) Genome-wide RNA-seq from three independent biological replicates followed by gene ontology analysis of genes differentially expressed in Krit1 ECKO BMECs compared with Krit1 fl/fl BMECs. Each term listed was the top term in a cluster of related terms, and the corrected p-values were calculated according to Benjamini’s method ( Huang et al., 2009 ). (B) Expression levels of differentially expressed genes represented on a scatter plot; fragments per kilobase of transcript per million mapped reads (FPKM) of individual transcripts are represented on a log2 scale. A few of the most highly suppressed and up-regulated genes are labeled. (C) RT-qPCR confirmation of RNA-seq–identified marked decrease in mRNA of extracellular regulators of angiogenesis in Krit1 ECKO BMECs compared with Krit1 fl/fl BMECs (SEM, n = 3). (D) Quantification of TSP1 protein from three independent biological replicates in Krit1 ECKO (KO) and in Krit1 fl/fl (Flox) BMECs (SEM, n = 3). (E) RT-qPCR analysis of isolated brain microvasculature in Krit1 ECKO compared with Krit1 fl/fl littermate controls (SEM, n = 3). (F) Quantification of TSP1 protein from freshly isolated brain microvasculature in Krit1 ECKO (KO) compared with Krit1 fl/fl (Flox) littermate controls (SEM, n = 3). (G) Confocal microscopy of cerebellar cortex stained for TSP1 (red) and endothelial specific marker PECAM1 (green); DAPI staining (blue) was used to reveal nuclei ( n = 3). (H) Higher-magnification images of boxed areas in G. TSP1 protein expression was decreased in CCM from Krit1 ECKO mice (arrows). Asterisks, vascular lumen of CCM lesions. Bars: (G) 100 µm; (H) 25 µm. *, P

    Article Snippet: RNA libraries were multiplexed and sequenced with 100-bp paired single-end reads (SR100) to a depth of ∼30 million reads per sample on an Illumina HiSeq2500.

    Techniques: Expressing, Genome Wide, RNA Sequencing Assay, Labeling, Quantitative RT-PCR, Isolation, Confocal Microscopy, Staining, Marker, Mouse Assay