Journal: Nature Communications

Article Title: Plasmodium falciparum sexual differentiation in malaria patients is associated with host factors and GDV1-dependent genes

doi: 10.1038/s41467-019-10172-6

Figure Lengend Snippet: GDV1 allele H 217 is over represented in high GCR patient samples. a The frequency of the gdv1 alleles encoding H (black) and P (white) or (B) msp2 FC27 (dark grey) and 3D7 (light grey) family alleles in the high (H) ( n = 20) and low (L) GCR ( n = 19) samples are plotted. Significance was assessed using a Fisher Exact test. b The D4 GCR (%) of each of the samples with gdv1 allele H 217 (H, black dot) or P 217 (P, open circle) or msp2 allele FC27 (dark grey dot) or 3D7 (light grey dot) is plotted with the mean and s.d. indicated. The Kruskal–Wallis test followed a Dunn’s multiple comparison test was used to compare the D4 GCR of the samples with distinct gdv1 or msp2 alleles (Prism GraphPad v7.05). Probability is indicated, p > 0.05 (ns) and p ≤ 0.01(**)

Article Snippet: Fisher’s exact test was used to evaluate the frequency of gdv1 and msp2 alleles in the 2016 and 2017 high and low GCR samples and the Kruskal–Wallis test followed a Dunn’s multiple comparison test was used to compare the GCR of the gdv1 and msp2 alleles (Prism GraphPad v7.05).

Techniques: Comparison

Journal: iScience

Article Title: Methylation of the tyrosine hydroxylase gene is dysregulated by cocaine dependence in the human striatum

doi: 10.1016/j.isci.2021.103169

Figure Lengend Snippet:

Article Snippet: Next, we digested 1ug of gDNA overnight with the MspI restriction enzyme (Cat no. R0106S, New England Biolabs, Ipswich, Massachusetts) and completed RRBS library preparation as follows ( ).

Techniques: Recombinant, High Throughput Screening Assay, Purification, Gel Extraction, Plasmid Preparation, Transfection, Reporter Assay, TaqMan Assay, Sequencing, Methylation, Amplification, Luciferase, Clone Assay, Software

Journal: iScience

Article Title: Trash-to-fuel : Converting municipal waste into transportation fuels by pyrolysis

doi: 10.1016/j.isci.2022.104036

Figure Lengend Snippet:

Article Snippet: MassLib software , MSP Kofel, Zollikofen, Switzerland , https://www.msp.ch/.

Techniques: Recombinant, Software, Mass Spectrometry

Journal: Structure (London, England : 1993)

Article Title: Mechanism of Filamentation-Induced Allosteric Activation of the SgrAI Endonuclease

doi: 10.1016/j.str.2019.08.001

Figure Lengend Snippet: KEY RESOURCES TABLE

Article Snippet: pBAK expressing MspI.M methyltransferase , New England Biolabs, Inc. , N/A.

Techniques: Recombinant, Expressing, Software

Journal: Carcinogenesis

Article Title: Discovery of novel epigenetic markers in non-Hodgkin's lymphoma.

doi: 10.1093/carcin/bgl092

Figure Lengend Snippet: Fig. 1. DNA methylation analysis of six NHL cell lines. (A) Cluster analysis of the methylation microarray data derived from six NHL cell lines using Cluster 3.0 and Treeview software. BCL6 expression was measured by real-time PCR and CD10 expression by flow cytometry as described in Materials and methods. (B and C) Analysis of DNA methylation from 10 pertinent genes in a panel of 6 NHL cell lines. MSP (B) and COBRA (C) were used to determine methylation status of the indicated CpG island loci in cell lines. ‘‘U’’ and ‘‘M’’ indicate either PCR products from unmethylated, and methylated DNA in top two panels (MSP assay), respectively, and BstUI digested fragments resulting from unmethylated and methylated DNA in bottom eight panels (COBRA assay). (D) Bisulfite genomic sequencing of three selected genes in four NHL cell lines. From left to right panels represent CCND1 and CYP27B1 and EFNA5, respectively. Each row represents the sequence of individual clones, closed circles indicate methylated CpG sites, and open circles indicate unmethylated CpG sites. In all the gene-specific analysis described above, normal PBL and in vitro methylated DNA (SssI-treated DNA) serve as negative and positive controls, respectively.

Article Snippet: Membranes were incubated in Tris-buffered saline with 5% non-fat dry milk containing rabbit polyclonal antibodies against DLC-1 (1:200), cyclin D1 (1:200) or GAPDH (1:10000) (Santa Cruz Biotech, Santa Cruz, CA).

Techniques: DNA Methylation Assay, Methylation, Microarray, Derivative Assay, Software, Expressing, Real-time Polymerase Chain Reaction, Cytometry, Combined Bisulfite Restriction Analysis Assay, MSP Assay, Genomic Sequencing, Sequencing, Clone Assay, In Vitro

Journal: Carcinogenesis

Article Title: Discovery of novel epigenetic markers in non-Hodgkin's lymphoma.

doi: 10.1093/carcin/bgl092

Figure Lengend Snippet: Fig. 2. (A) RT–PCR analysis of four selected genes in six NHL cell lines: total RNA (2 mg) isolated from treated (A, DAC; T, TSA; and AT, DAC+TSA) or untreated (C) cells was used to generate cDNA for real-time RT–PCR. cDNA generated from a normal lymph node served as a positive control (set at 100). Expression of GAPDH was used to normalize the gene expression under different conditions. (B) Western blot analysis of the CCND1 and DLC-1 protein expression in lysates (50 mg/lane) of six NHL cell lines and a normal lymph node sample. GAPDH serves as a loading control.

Article Snippet: Membranes were incubated in Tris-buffered saline with 5% non-fat dry milk containing rabbit polyclonal antibodies against DLC-1 (1:200), cyclin D1 (1:200) or GAPDH (1:10000) (Santa Cruz Biotech, Santa Cruz, CA).

Techniques: Reverse Transcription Polymerase Chain Reaction, Isolation, Quantitative RT-PCR, Generated, Positive Control, Expressing, Gene Expression, Western Blot, Control