Journal: PLoS ONE

Article Title: Correction: Signature Wood Modifications Reveal Decomposer Community History

doi: 10.1371/journal.pone.0126877

Figure Lengend Snippet: Fungal isolates used to assess strength of correlation between wood density loss on birch or pine and two dependent variables, 1) dilute alkali solubility (DAS) and 2) lignin:density loss (L:D).

Article Snippet: Basidio , Polyporales , Resinicium bicolor (Alb. & Schwein.:Fr.) Parmasto , ATCC 44175 , W.

Techniques: Solubility

Journal: Nature Communications

Article Title: Identification of functional non-coding variants associated with orofacial cleft

doi: 10.1038/s41467-025-61734-w

Figure Lengend Snippet: a Schematic of MPRA library construction and execution. BC, barcode. Yellow and red asterisks: non-risk and risk allele, respectively. b Scatter dot plot showing (black dots) 65 SNPs with significant allele-specific effects on reporter activity in the MPRA and (gray dots) 822 SNPs without them. Arrows indicate the functional SNPs identified in this study (two near IRF6 , rs11119348 and rs661849, and one near FOXE1 , rs10984103). Dashed lines indicate the 95th percentile of the reporter activity of scrambled elements; on both axes, zero, i.e., log2(1) represents the reporter activity of the empty vector.

Article Snippet: siRNAs targeting FOXE1 (Santa Cruz, Catalog no. sc-44175) or ETS2 (Santa Cruz, Catalog no. sc-37855) and siRNA controls (Santa Cruz, Catalog no.sc-37007) were transfected into one million HEKn (heterozygous for IRF6 −22 kb SNP) or GMSM-K (homozygous risk for IRF6 -10 kb or −22 kb SNPs).

Techniques: Activity Assay, Functional Assay, Plasmid Preparation

Journal: Nature Communications

Article Title: Identification of functional non-coding variants associated with orofacial cleft

doi: 10.1038/s41467-025-61734-w

Figure Lengend Snippet: a – c UCSC browser views of the human genome, GRCh37/hg19, focused on the OFC-associated SNPs at a , b IRF6 and c FOXE1 . OFC SNPs, SNPs identified by GWAS and evaluated by MPRA at each locus. One SNP at the FOXE1 locus, which was tested in the MPRA but lacked significant effects in it, rs1877431, is outside of the range presented here. MPRA-sig SNPs, SNPs with allele-specific effects in the MPRA. IRF6 enhancers, FOXE1 enhancers, and enhancers for the indicated gene identified using the activity-by-contact (ABC) method and datasets from NHEK (see Methods). Gray arrows, GWAS-meta-analysis P values of the indicated SNPs. Two-sided P values are calculated with an inverse-variance weighted fixed-effects meta-analysis of a transmission disequilibrium test without adjustment for multiple testing and a logistic regression (that had 18 principal components of ancestry as covariates). GM12878 B-cell derived cell line, H1-ESC embryonic stem cells, K562 myelogenous leukemia cell line, HepG2 liver cancer cell line, HUVEC human umbilical vein endothelial cells, HMEC human mammary epithelial cells, HSMM human skeletal muscle myoblasts, NHEK normal human epidermal keratinocytes, NHLF normal human lung fibroblasts. CS 13-20, Carnegie stages for human embryonic face explants . Colored bars, inferred chromatin state from combinatorial analysis of multiple chromatin mark datasets . Orange and yellow, active and weak enhancer element, respectively; bright red, active promoter; light red, weak promoter; purple, inactive/poised promoter; blue, insulator; light green, weakly transcribed; gray, Polycomb repressed; light gray, heterochromatin/repetitive. Additional color bars in the facial explants dataset, green, transcription; green-yellow, transcription weak enhancer; purple, bivalent promoter; light purple, poised promoter.

Article Snippet: siRNAs targeting FOXE1 (Santa Cruz, Catalog no. sc-44175) or ETS2 (Santa Cruz, Catalog no. sc-37855) and siRNA controls (Santa Cruz, Catalog no.sc-37007) were transfected into one million HEKn (heterozygous for IRF6 −22 kb SNP) or GMSM-K (homozygous risk for IRF6 -10 kb or −22 kb SNPs).

Techniques: Activity Assay, Transmission Assay, Derivative Assay

Journal: Nature Communications

Article Title: Identification of functional non-coding variants associated with orofacial cleft

doi: 10.1038/s41467-025-61734-w

Figure Lengend Snippet: a Bar chart of MPRA and luciferase reporter activities for the indicated SNPs at various loci in GMSM-K using elements of the indicated length centered on the SNP. MPRA data are represented as mean ± standard error of the mean (SEM) from the indicated number of replicates. Statistical significance ( P value, two-tailed) of the difference between major and minor allele’s reporter activity is determined by Welch’s t -test, followed by Benjamini–Hochberg false discovery rate correction. P (MPRA) = 0.0452 (rs11110348), 0.0057 (rs661849), 0.9097 (rs642961), 0.6942 (rs4844939), 0.4487 (rs12104876), 0.0238 (rs75436877), 0.7100 (rs79482068), 0.0734 (rs79792381), 0.0125 (rs201265), 0.1206 (rs10124184), 0.0067 (rs10984103), 0.0458 (rs4812449), 0.2945 (rs57369620). For luciferase reporter activities, data are represented as mean ± standard deviation (SD) from four independent experiments. Statistical significance ( P value, two-tailed) is determined by Student’s t -test. P (luciferase) = 0.0006 (rs11110348), <0.0001 (rs661849), 0.3822 (rs642961), <0.0001 (rs4844939), 0.14 (rs12104876), <0.0001 (rs75436877), 0.0693 (rs79482068), 0.5115 (rs79792381), 0.002 (rs201265), <0.0001 (rs10124184), <0.0001 (rs10984103), <0.0001 (rs4812449), 0.1421 (rs57369620). * P < 0.05, ** P < 0.01, *** P < 0.001, **** P < 0.0001, NS non-significant. b – d Scattered dot plots of relative luciferase activity (using the longer elements described in Results) for non-risk and risk alleles of rs11119348, rs661849 and rs10984103 in primary neonatal keratinocytes (HEKn). Value of 1 is that of the empty pGL3 promoter vector. Data are represented as mean ± standard deviation (SD) from four independent experiments. Statistical significance ( P value, two-tailed) is determined by Student’s t -test and P value is indicated on the plot. e – g Scattered dot plot of relative levels of e , f IRF6 or g FOXE1 mRNA in edited induced oral epithelium (iOE) cells homozygous for the non-risk or risk alleles of each SNP, as indicated, assessed by qRT-PCR. Expression levels are normalized against those of ACTB, GAPDH, HPRT1, UBC and CDH1 . Data were represented as mean ± SD from e , f six replicates or g nine replicates of cells harboring each genotype, as indicated in the plot. Each dot represents three technical qPCR replicates. Statistical significance ( P value, two-tailed) is determined by Student’s t -test and P value is indicated on the plot. Source data are provided as a Source Data file.

Article Snippet: siRNAs targeting FOXE1 (Santa Cruz, Catalog no. sc-44175) or ETS2 (Santa Cruz, Catalog no. sc-37855) and siRNA controls (Santa Cruz, Catalog no.sc-37007) were transfected into one million HEKn (heterozygous for IRF6 −22 kb SNP) or GMSM-K (homozygous risk for IRF6 -10 kb or −22 kb SNPs).

Techniques: Luciferase, Two Tailed Test, Activity Assay, Standard Deviation, Plasmid Preparation, Quantitative RT-PCR, Expressing

Journal: Nature Communications

Article Title: Identification of functional non-coding variants associated with orofacial cleft

doi: 10.1038/s41467-025-61734-w

Figure Lengend Snippet: a Consensus FOXE1 binding motif from the JASPAR database of transcription factor DNA-binding preferences (Matrix ID: MA1847.1) and alignment of the variant site in several mammals. The risk allele (A) is the reference allele and has a higher frequency than the non-risk allele (C) in most populations. b , c Percent input identified by ChIP-qPCR for anti-FOXE1 and anti-H3K27Ac, respectively, in iOE cells heterozygous for rs11119348 using primers specific to the IRF6 -10 kb enhancer site or, as a negative control, to a region 103.7 kb upstream of the IRF6 transcription start site that lacked ATAC-Seq and H3K27Ac ChIP-Seq signals in HIOEC or NHEK. Error bars refer to three ChIP replicates and expressed as mean ± SD. Each dot represents three technical qPCR replicates. Statistical significance ( P value, two-tailed) is determined by Student’s t -test and P value is indicated on the plot. NS non-significant. d Sequencing of anti-FOXE1 and anti-H3K27Ac ChIP-PCR products from cells heterozygous for rs11119348 using the indicated antibody. e Scattered dot plot of relative luciferase activity of the IRF6 -10 kb reporter construct (longest version) harboring the risk allele of rs11119348, in wildtype (WT) or a clone of FOXE1 homozygous knockout (KO) GMSM-K cells. Data are represented as mean ± SD from three independent experiments. Statistical significance ( P value, two-tailed) is determined by Student’s t -test and P value is indicated on the plot. f Scattered dot plot of relative levels of IRF6 mRNA in WT and FOXE1 -KO GMSM-K cells assessed by qRT-PCR. Expression levels of IRF6 are normalized against ACTB . Data are represented as mean ± SD from three replicates. Each dot represents three technical qPCR replicates. Statistical significance ( P value, two-tailed) is determined by Student’s t -test and P value is indicated on the plot. g Model showing binding of FOXE1 to the IRF6 -10 kb enhancer, which is favored by the risk allele and which reduces IRF6 expression. Source data are provided as a Source Data file.

Article Snippet: siRNAs targeting FOXE1 (Santa Cruz, Catalog no. sc-44175) or ETS2 (Santa Cruz, Catalog no. sc-37855) and siRNA controls (Santa Cruz, Catalog no.sc-37007) were transfected into one million HEKn (heterozygous for IRF6 −22 kb SNP) or GMSM-K (homozygous risk for IRF6 -10 kb or −22 kb SNPs).

Techniques: Binding Assay, Variant Assay, ChIP-qPCR, Negative Control, ChIP-sequencing, Two Tailed Test, Sequencing, Luciferase, Activity Assay, Construct, Knock-Out, Quantitative RT-PCR, Expressing

Journal: bioRxiv

Article Title: Two non-coding variants associated with isolated orofacial cleft promote binding of transcriptional repressors FOXE1 or ETS2 and reduce expression of IRF6

doi: 10.1101/2024.06.01.596914

Figure Lengend Snippet: FOXE1 KO GMSM-K: Browser view of the human genome, GRCh37/hg19, focused on FOXE1 gene. First track represents a pair of guide RNAs (marked with a block) and primers (marked with arrows) used to generate FOXE1 KO cells. Primer sequences are provided in Table S5. Following color coded bars represent chromatin status revealed by ChIP-Seq to various chromatin marks from the ENCODE Project cell lines and facial explants from human embryos at Carnegie stage (CS) 13-20, encompassing the time when palatal shelves fuse, where yellow bars represent the enhancer element, bright red, active promoter; light red, weak promoter; purple, inactive/poised promoter; grey, Polycomb repressed; dark purple in facial explants dataset, bivalent promoter; GM12878, B-cell derived cell line; ESC, embryonic stem cells; K562, myelogenous leukemia; HepG2, liver cancer; HUVEC, human umbilical vein endothelial cells; HMEC, human mammary epithelial cells; HSMM, human skeletal muscle myoblasts; NHEK, normal human epidermal keratinocytes; NHLF, normal human lung fibroblasts, CS13-CS20 are facial explants from human embryos. The blue region highlights the deleted fragment after CRISPR/Cas9 targeting.

Article Snippet: siRNAs targeting FOXE1 (Santa Cruz Catalog no. sc-44175) or ETS2 (Santa Cruz Catalog no. sc-37855) and siRNA controls (Santa Cruz Catalog no.sc-37007) were transfected into one million HEKn (heterozygous for IRF6 -22 kb SNP) or GMSM-K (homozygous risk for IRF6 -10 kb or -22 kb SNPs).

Techniques: Blocking Assay, ChIP-sequencing, Derivative Assay, CRISPR

Journal: bioRxiv

Article Title: Two non-coding variants associated with isolated orofacial cleft promote binding of transcriptional repressors FOXE1 or ETS2 and reduce expression of IRF6

doi: 10.1101/2024.06.01.596914

Figure Lengend Snippet: A ) Browser view of the human genome, GRCh37/hg19, focused on the GWAS-identified SNPs at FOXE1. First two tracks represent the OFC associated SNPs at FOXE1 and MPRA-identified SNPs at FOXE1 respectively. Next track represents the ABC (Activity by Contact) elements scored using HiC data from NHEK. Next two tracks represent open chromatin peaks detected by ATAC-Seq and H3K27Ac marks in HIOEC respectively. Following color coded bars represent chromatin status revealed by ChIP-Seq to various chromatin marks from the ENCODE Project cell lines and facial explants from human embryos at Carnegie stage (CS) 13-20, encompassing the time when palatal shelves fuse, where orange and yellow bars represent the active and weak enhancer element, respectively; bright red, active promoter; light red, weak promoter; purple, inactive/poised promoter; blue, insulator; light green, weak transcribed; grey, Polycomb repressed; light grey, heterochromatin/repetitive; pale turquoise, light purple and dark purple in facial explants dataset, heterochromatin poised promoter and bivalent promoter respectively; GM12878, B-cell derived cell line; ESC, embryonic stem cells; K562, myelogenous leukemia; HepG2, liver cancer; HUVEC, human umbilical vein endothelial cells; HMEC, human mammary epithelial cells; HSMM, human skeletal muscle myoblasts; NHEK, normal human epidermal keratinocytes; NHLF, normal human lung fibroblasts, CS13-CS20 are facial explants from human embryos. Box in A , a SNP (rs10984103) with significant effect in MPRA lying within an enhancer for FOXE1 in HEKn by the ABC method, and within chromatin marked as an active enhancer in human embryonic faces. B) Browser view of the human genome, GRCh37/hg19, focused on the GWAS-identified SNPs at MAFB associated with orofacial cleft. Tracks and color code are similar as in . Box in B , a SNP (rs4812449) with significant effect in MPRA lying within chromatin marked as an active enhancer in human embryonic faces.

Article Snippet: siRNAs targeting FOXE1 (Santa Cruz Catalog no. sc-44175) or ETS2 (Santa Cruz Catalog no. sc-37855) and siRNA controls (Santa Cruz Catalog no.sc-37007) were transfected into one million HEKn (heterozygous for IRF6 -22 kb SNP) or GMSM-K (homozygous risk for IRF6 -10 kb or -22 kb SNPs).

Techniques: Activity Assay, ChIP-sequencing, Derivative Assay

Journal: bioRxiv

Article Title: Two non-coding variants associated with isolated orofacial cleft promote binding of transcriptional repressors FOXE1 or ETS2 and reduce expression of IRF6

doi: 10.1101/2024.06.01.596914

Figure Lengend Snippet: A) Scattered dot plot of relative levels of IRF6 mRNA in edited iOE cells harboring non-risk (CC) and risk (AA) genotype of rs11119348 assessed by qRT-PCR. Expression levels of IRF6 are normalized against ACTB, GAPDH, HPRT, UBC and CDH1 . Data are represented as mean values +/- s. d. from six replicates of cells harboring each genotype, as indicated in the plot. Statistical significance is determined by Student’s t -test (two-tailed). B) Consensus FOXE1 binding motif from the JASPAR database of transcription factor DNA-binding preferences (Matrix ID: MA1847.1) and alignment of the variant site in different species. At this SNP, the risk allele A has a higher frequency than the non-risk allele, C, in most populations. C and D) Percent input identified by ChIP-qPCR for anti-FOXE1 and anti-H3K27Ac respectively in iOE cells heterozygous for rs11119348 using primers specific to the IRF6 -10 kb enhancer site or, as a negative control, to a region 103.7 kb upstream of the IRF6 transcription start site that did not harbor active elements identified from ATAC-Seq and H3K27Ac ChIP-Seq in HIOEC or NHEK. Error bars refer to three ChIP replicates and expressed as mean values +/- s. d. Statistical significance is determined by Student’s t -test. P value (two-tailed) is indicated on the plot and NS, non-significant. E) Sequencing of anti-FOXE1 and anti-H3K27Ac ChIP-PCR product of cells heterozygous for rs11119348. F) Scattered dot plot of relative luciferase activity using risk allele harboring element in wildtype (WT) and FOXE1 -KO GMSM-K. Data are represented as mean values +/- s. d. from three independent experiments. Statistical significance is determined by Student’s t -test. P value (two-tailed) is indicated on the plot. G) Scattered dot plot of relative levels of IRF6 mRNA in WT and FOXE1 -KO GMSM-K assessed by qRT-PCR. Expression levels of IRF6 are normalized against ACTB . Data are represented as mean values +/- s. d. from three replicates. Statistical significance is determined by Student’s t -test. P value (two-tailed) is indicated on the plot. H) Model for the risk allele of rs11119348 meditated binding of FOXE1 repressor to the IRF6 -10 kb enhancer leading to the reduced IRF6 expression.

Article Snippet: siRNAs targeting FOXE1 (Santa Cruz Catalog no. sc-44175) or ETS2 (Santa Cruz Catalog no. sc-37855) and siRNA controls (Santa Cruz Catalog no.sc-37007) were transfected into one million HEKn (heterozygous for IRF6 -22 kb SNP) or GMSM-K (homozygous risk for IRF6 -10 kb or -22 kb SNPs).

Techniques: Quantitative RT-PCR, Expressing, Two Tailed Test, Binding Assay, Variant Assay, ChIP-qPCR, Negative Control, ChIP-sequencing, Sequencing, Luciferase, Activity Assay

Journal: bioRxiv

Article Title: Two non-coding variants associated with isolated orofacial cleft promote binding of transcriptional repressors FOXE1 or ETS2 and reduce expression of IRF6

doi: 10.1101/2024.06.01.596914

Figure Lengend Snippet: Sequencing of A) anti-FOXE1 and anti-H3K27Ac ChIP-PCR product of cells heterozygous for rs11119348 from two ChIP replicates and B) anti-ETS2 and anti-H3K27Ac ChIP-PCR product of cells heterozygous for rs661849 from two ChIP replicates.

Article Snippet: siRNAs targeting FOXE1 (Santa Cruz Catalog no. sc-44175) or ETS2 (Santa Cruz Catalog no. sc-37855) and siRNA controls (Santa Cruz Catalog no.sc-37007) were transfected into one million HEKn (heterozygous for IRF6 -22 kb SNP) or GMSM-K (homozygous risk for IRF6 -10 kb or -22 kb SNPs).

Techniques: Sequencing

Journal: bioRxiv

Article Title: Two non-coding variants associated with isolated orofacial cleft promote binding of transcriptional repressors FOXE1 or ETS2 and reduce expression of IRF6

doi: 10.1101/2024.06.01.596914

Figure Lengend Snippet: A) Percent input identified by ChIP-qPCR for anti-FOXE1 in GMSM-K harboring non-risk (CC) and risk (AA) genotype of rs11119348 using primers specific to the IRF6 -10 kb enhancer site or, as a negative control, to a region 103.7 kb upstream to the IRF6 transcription start site that did not harbor active elements identified from ATAC-Seq and H3K27Ac ChIP-Seq in HIOEC or NHEK. Error bars refer to 3 ChIP replicates and expressed as mean values +/- s. d. Statistical significance is determined by Student’s t -test. P value (two-tailed) is indicated on the plot. NS, non-significant. B and C) Scattered dot plot of relative levels of FOXE1 mRNA in WT and FOXE1 KO GMSM-K (B) or control siRNA and FOXE1 targeting siRNA transfected GMSM-K (C) assessed by qRT-PCR. Expression levels of FOXE1 are normalized against ACTB. Data are represented as mean values +/- s. d. from three replicates. Statistical significance is determined by Student’s t -test (two-tailed). D) Scattered dot plot of relative luciferase activity for longer construct with risk allele (A) of rs11119348 in GMSM-K transfected with control siRNA or FOXE1 targeting siRNA. Data are represented as mean values +/- s. d. from three independent experiments. Statistical significance is determined by Student’s t -test. P value (two-tailed) is indicated on the plot. E) Scattered dot plot of relative levels of IRF6 mRNA in control siRNA and FOXE1 targeting siRNA transfected GMSM-K assessed by qRT-PCR. Expression levels of IRF6 are normalized against ACTB. Data are represented as mean values +/- s. d. from three replicates. Statistical significance is determined by Student’s t -test (two-tailed). F) Percent input identified by ChIP-qPCR for anti-ETS2 in GMSM-K harboring non-risk (TT) and risk (CC) genotype of rs661849 using primers specific to the IRF6 -22 kb enhancer site or, as a negative control, to a region 103.7 kb upstream IRF6 transcription start site that did not harbor active elements identified from ATAC-Seq and H3K27Ac ChIP-Seq in HIOEC or NHEK. Error bars refer to 3 ChIP replicates and expressed as mean values +/- s. d. Statistical significance is determined by Student’s t -test. P value (two-tailed) is indicated on the plot and NS represents non-significant. G) Scattered dot plot of relative levels of ETS2 mRNA in control siRNA and ETS2 targeting siRNA transfected HEKn assessed by qRT-PCR. Expression levels of ETS2 are normalized against ACTB. Data are represented as mean values +/- s. d. from three replicates. Statistical significance is determined by Student’s t -test (two-tailed). H) Scattered dot plot of relative luciferase activity for longer construct with risk allele (C) of rs661849 in GMSM-K transfected with control siRNA or ETS2 targeting siRNA. Data are represented as mean values +/- s. d. from three independent experiments. Statistical significance is determined by Student’s t -test. P value (two-tailed) is indicated on the plot. I and J) Scattered dot plot of relative levels of IRF6 mRNA (I) or ETS2 mRNA (J) in control siRNA and ETS2 targeting siRNA transfected GMSM-K assessed by qRT-PCR. Expression levels are normalized against ACTB. Data are represented as mean values +/- s. d. from three replicates. Statistical significance is determined by Student’s t -test (two-tailed).

Article Snippet: siRNAs targeting FOXE1 (Santa Cruz Catalog no. sc-44175) or ETS2 (Santa Cruz Catalog no. sc-37855) and siRNA controls (Santa Cruz Catalog no.sc-37007) were transfected into one million HEKn (heterozygous for IRF6 -22 kb SNP) or GMSM-K (homozygous risk for IRF6 -10 kb or -22 kb SNPs).

Techniques: ChIP-qPCR, Negative Control, ChIP-sequencing, Two Tailed Test, Control, Transfection, Quantitative RT-PCR, Expressing, Luciferase, Activity Assay, Construct

Journal: Reports of Biochemistry & Molecular Biology

Article Title: Development of a Cost-Effective Line Probe Assay for Rapid Detection and Differentiation of Mycobacterium Species: A Pilot Study

doi:

Figure Lengend Snippet: Bacteria and reference strains used in this study

Article Snippet: M. avium subsp. silvaticum , DSMZ 44175.

Techniques: Bacteria

Journal: Reports of Biochemistry & Molecular Biology

Article Title: Development of a Cost-Effective Line Probe Assay for Rapid Detection and Differentiation of Mycobacterium Species: A Pilot Study

doi:

Figure Lengend Snippet: GenBank sequence identification numbers (accession number) for Mycobacterium species

Article Snippet: M. avium subsp. silvaticum , DSMZ 44175.

Techniques: Sequencing

Journal: Reports of Biochemistry & Molecular Biology

Article Title: Development of a Cost-Effective Line Probe Assay for Rapid Detection and Differentiation of Mycobacterium Species: A Pilot Study

doi:

Figure Lengend Snippet: Sequences and the parameters of oligonucleotide probes targeting the Mycobacterium ITS. *

Article Snippet: M. avium subsp. silvaticum , DSMZ 44175.

Techniques: Sequencing

Journal: Reports of Biochemistry & Molecular Biology

Article Title: Development of a Cost-Effective Line Probe Assay for Rapid Detection and Differentiation of Mycobacterium Species: A Pilot Study

doi:

Figure Lengend Snippet: Agarose gel electrophoresis of ITS-PCR products for standard Mycobacterium species. Lane 1: M. tuberculosis H37Rv, Lane 2: M. simiae (clinical isolate), Lane 3: M. intracellulare ATCC 13950, Lane 4: M. avium ATCC 25291, Lane 5: M. kansasii TMC 1204, Lane 6: M. chelonae (environmental isolate), Lane 7: M. abscessus DSMZ 44196T, Lane 8: M. fortuitum TMC 1530, Lane 9: M. scrofulaceum ATCC 35785, Lane10: M. ulcerans ATCC 35840, Lane 11: M. marinum (environmental isolate), Lane 12: M. gordonae (clinical isolate). Lane M: 100 bp DNA marker; Lane C-: negative control.

Article Snippet: M. avium subsp. silvaticum , DSMZ 44175.

Techniques: Agarose Gel Electrophoresis, Marker, Negative Control

Journal: Reports of Biochemistry & Molecular Biology

Article Title: Development of a Cost-Effective Line Probe Assay for Rapid Detection and Differentiation of Mycobacterium Species: A Pilot Study

doi:

Figure Lengend Snippet: LPAs for standard Mycobacterium species. Strip 1: M. tuberculosis H37Rv, strip 2: M. simiae (clinical isolate), strip 3: M. intracellulare ATCC 13950, strip 4: M. avium ATCC 25291, strip 5: M. kansasii TMC 1204, strip 6: M. chelonae (environmental isolate), strip 7: M. abscessus DSMZ 44196T, strip 8: M. fortuitum TMC 1530, strip 9: M. scrofulaceum ATCC 35785, strip 10: M. ulcerans ATCC 35840 and M. marinum (environmental isolate), strip 11: M. gordonae (clinical isolate). Briefly, species-specific probes in TE buffer were immobilized onto a nitrocellulose membrane (pore size 0.45 μm; Amersham Pharmacia Biotech) as 16 parallel lines. The membrane was cut into strips and biotinylated PCR products were denatured, added to the membranes, and incubated at 59 ºC for 30 min. The strips were then incubated with a 1:1000-diluted alkaline phosphatase-labeled streptavidin in TBS at pH 8 on a rotating platform at room temperature for 30 min. The strips were washed and BCIP/NBT was added and incubated with shaking at room temperature for 10 min in the dark. The color reactions occurred and the results were visually interpreted with a probe alignment guide, which shows the position of the probes in each line.

Article Snippet: M. avium subsp. silvaticum , DSMZ 44175.

Techniques: Stripping Membranes, Membrane, Pore Size, Incubation, Labeling

Journal: PLoS ONE

Article Title: Correction: Signature Wood Modifications Reveal Decomposer Community History

doi: 10.1371/journal.pone.0126877

Figure Lengend Snippet: Fungal isolates used to assess strength of correlation between wood density loss on birch or pine and two dependent variables, 1) dilute alkali solubility (DAS) and 2) lignin:density loss (L:D).

Article Snippet: Basidio , Russulales , Scytinostroma galactinum (Fr.) Donk , ATCC 44175 , W.

Techniques: Solubility

Journal: PLoS ONE

Article Title: Signature Wood Modifications Reveal Decomposer Community History

doi: 10.1371/journal.pone.0120679

Figure Lengend Snippet: Fungal isolates used to assess strength of correlation between wood density loss on birch or pine and two dependent variables, 1) dilute alkali solubility (DAS) and 2) lignin:density loss (L:D).

Article Snippet: Basidio , Polyporales , Antrodia vaillantii (Alb. & Schwein.:Fr.) Parmasto , ATCC 44175 , W.

Techniques: Solubility