bj fibroblast cells  (ATCC)

Journal: Carbohydrate polymers

Article Title: Nitric oxide-releasing dextran surface with enhanced albumin affinity mitigates infection and foreign body reaction

doi: 10.1016/j.carbpol.2025.124855

Figure Lengend Snippet: Biocompatibility evaluation of surfaces. (A) Surface adsorbed bovine serum albumin after 90 mins incubation at physiology conditions ( N > 4). (B) Indirect contact cytotoxicity screening of sample groups against BJ human fibroblast cells (24h) showed the viability of cells across all sample groups tested ( N > 5). (C) Percent hemolysis of the film samples (N > 4). 2–5 % hemolytic activity is considered slightly hemolytic, and > 5 % activity is considered hemolytic according to ASTM F756. Error bars represent standard deviation. **** represents statistical significance ( p < 0.0001).

Article Snippet: BJ fibroblast cells (BJ CRL-2522) were derived from stocks previously acquired from the American Type Culture Collection.

Techniques: Incubation, Activity Assay, Standard Deviation

Journal: Nucleic Acids Research

Article Title: High-throughput mapping of spontaneous mitotic crossover and genome instability events with sci-L3-Strand-seq

doi: 10.1093/nar/gkag119

Figure Lengend Snippet: sci-L3-Strand-seq enables the detection of all seven mitotic CO outcomes. ( A–G ) Schematics of the seven types of mitotic CO outcomes with example sci-L3-Strand-seq data. Homologs with SNVs are shown in black and blue (green and purple for translocation), each containing two identical sister chromatids. Oval indicates centromere. Read counts in the example data show Watson (W) reads colored dark yellow and Crick ( C ) reads colored dark green. This color code for strand directionality is used throughout this paper unless noted otherwise. Overlapping reads in the example data show the locations of overlaps, with nearby locations offset on the y-axis. Each location belongs to one of three categories based on the type of overlap: dark green represents overlapping C strand reads, dark yellow represents overlapping W strand reads, and gray represents overlapping reads of opposite strands. Each point for the haplotype1 (hap1) fraction is the phased allelic fraction of ∼50 binned SNVs for Patski and 15 for BJ-5ta. LOH calls are shaded in pink. ( A ) SCE. Both the chromosome heterozygosity and copy number remain unchanged after SCE. Only a strand-switch on the replication template strand (solid arrows) can be detected by Strand-seq. Without an SCE, the template strands map continuously to either Watson or Crick (black homolog). With an SCE, the template strands are exchanged. In the example, SCEs are marked by a black triangle in the “Call” track. ( B ) cnLOH. Inter-homolog (IH) CO leads to reciprocal cnLOH (shaded in pink) in the daughter cells. Note that with reciprocal events, if both daughter cells are sequenced together with bulk WGS, every position will appear heterozygous given the 1:1 ratio of the two alleles. ( C ) CNV. Insertion or deletions between intra-chromatid sequences with high similarity as an example, resulting from NAHR. ( D ) Inversions. Intra-chromatid reversal of sequences end-to-end, for example between repeats at the two vertical bar, results in no change in chromosome heterozygosity or copy number. Just like with SCE, a double strand-switch on the replication template strand (two inward facing blue triangles) can be detected by Strand-seq. However, confident identification of inversions requires the detection of a shared strand state across multiple cells that negatively correlate with the stand state of the adjoining regions. ( E ) Translocations. Exchange of sequence between nonhomologous chromosomes. Translocations can be unbalanced, where recombined chromatids segregate apart and result in the loss or gain of chromosomal segments in the daughter cells (not shown); or balanced, where the co-segregation of recombined chromatids results in an equal exchange of chromosomal segments with no change in copy number of heterozygosity. Similar to inversions, the identification of balanced translocations requires the detection of a shared strand state across multiple cells that positively correlates (as opposed to negatively correlating in inversions) between the translocated chromosomes. In black and blue, green and purple are the homologs of two different chromosomes. ( F ) Aneuploidy. Aberrant COs can cause nondisjunction, resulting in monosomy and trisomy in the reciprocal daughter cells. Example data (trisomy) is shown for only one of the daughter cells. ( G ) UPD. Reciprocal UPD is shown with example data for only one of the daughter cells. Other routes leading to UPD include the duplication of a monosomy or the loss of the nonallelic chromosome from a trisomy. ( H ) sci-L3-Strand-seq workflow overview. IVT: in-vitro transcription; RT: reverse transcription. See .

Article Snippet: BJ-5ta (CRL-4001, ATCC) and Patski (gift from Disteche lab) cells were cultured in DMEM medium supplemented with 10% FBS and 1× Pen–Strep.

Techniques: Translocation Assay, Sequencing, In Vitro, Reverse Transcription

Journal: Nucleic Acids Research

Article Title: High-throughput mapping of spontaneous mitotic crossover and genome instability events with sci-L3-Strand-seq

doi: 10.1093/nar/gkag119

Figure Lengend Snippet: SCE rate and genomic hotspots. ( A ) sci-L3-Strand-seq example data. Top panel shows a haploid human cell (HAP1; median reads per Mb: 97, about 2.1% coverage), while the bottom panel shows a diploid human (BJ-5ta; median reads per Mb: 99) cell. Reads were counted across 200 Kb bins. ( B ) Number of SCE per haploid genome for each cell line. Significant difference level (*** < 0.001, ** <0.01, * <0.05) calculated using Mann–Whitney U, HAP1 versus HAP1lig4− (BH adjusted P -value: 0.00038; MAD for HAP1 1.48, HAP1lig4− 1.48) and BJ-5ta versus Patski (BH adjusted P -value: 0.003; MAD for BJ-5ta 0.74, Patski 1.48). Cells with a high number of loss or gain annotations were excluded. ( C ) Genome-wide distribution of scaled features and SCE correlation domainograms. Domainograms show Spearman correlation between increasing number of 1 Mb bins at windows of 10, 25, 50, 75, 100, 125 Mb. BJ-5ta cell feature tracks are plotted at 1 Mb resolution, while Patski are plotted at 3 Mb.

Article Snippet: BJ-5ta (CRL-4001, ATCC) and Patski (gift from Disteche lab) cells were cultured in DMEM medium supplemented with 10% FBS and 1× Pen–Strep.

Techniques: MANN-WHITNEY, Genome Wide

Journal: Nucleic Acids Research

Article Title: High-throughput mapping of spontaneous mitotic crossover and genome instability events with sci-L3-Strand-seq

doi: 10.1093/nar/gkag119

Figure Lengend Snippet: Phasing of SNVs and digital information for calling LOH and CNV. ( A ) Phasing accuracy of Patski cells across the mm10 genome. The phasing accuracy was plotted at a 1 Mb bin resolution. In general only WC read (around half) will be informative for phasing. The SNV coverage from reads in the WC regions is shown in the top two panels, with the mean chromosome coverage shown under each chromosome label. Phasing by sci-L3-Strand-seq was compared to the existing references to evaluate accuracy. Raw phasing accuracies are slightly different between the two haplotypes (third and fourth panel). Bottom panel shows the final phasing accuracy after inference of the opposite haplotype, conflict removal, phasing with chr4 LOH, and inversion correction ( and and ). Sharp decreases in accuracy can be explained by inversion . ( B ) LOH calls and rescues. LOH calls (pink) on chr4 in two BJ-5ta cells are shown (left panels) with strand switch-based segmentation (two black triangles within call track). Three additional BJ-5ta cells (right panels) are shown without breakpoint calls for which the LOH calls were rescued (blue) and segmentation based on shared LOH with other cells. Read counts and overlapping reads are plotted as in Fig. . Red vertical lines within the call track represent centromere bounds. Breakdown of LOH calling and rescue is provided in and . ( C ) Diagram of digital information within overlapping reads used for chromosome copy number counts. Random genome fragmentation, barcode insertion and T7 promoter ligation (red arrows) is mediated by the Tn5 transposase dimer. IVT amplicon structure is depicted post ligation. The insertion leaves behind a 9 nt single-stranded overhang that is shared between adjacent fragments and ligated to the end of the Tn5 mosaic end duplex sequence (highlighted in red). Due to this shared 9nt sequence, to identify overlapping reads, an overlap is required to be >12 bp (9 nt gap + 3 bp offset for deduplication). With IVT, each unique genomic fragment is linearly amplified that creates blocks of IVT duplicates (gray horizontal dashed lines with inward arrows). A disomic region (top left panel) will contain at most one overlap of two unique insertion patterns (ignoring IVT duplicates), each of which must originate from one of the parental homologs if heterozygous. In the event of a CNV gain, an overlap with three unique insertion patterns will be observed (top right panel). With a CNV loss, there will be no overlapping insertion patterns observed and only homozygous SNVs will be present (bottom left panel). The presence of overlapping insertion patterns and homozygous SNVs distinguishes cnLOH from CNV loss (bottom right panel).

Article Snippet: BJ-5ta (CRL-4001, ATCC) and Patski (gift from Disteche lab) cells were cultured in DMEM medium supplemented with 10% FBS and 1× Pen–Strep.

Techniques: Ligation, Amplification, Sequencing

Journal: Nucleic Acids Research

Article Title: High-throughput mapping of spontaneous mitotic crossover and genome instability events with sci-L3-Strand-seq

doi: 10.1093/nar/gkag119

Figure Lengend Snippet: Annotation and quantification of mutational mitotic CO outcomes. ( A ) Heatmap of Patski SV annotation. The heatmap shows only cells with annotated events. Cumulative percentages of cells with an annotation are shown in the top panel. Each row represents a single cell. Cells were ordered and grouped using hierarchical clustering. The chosen 29 clusters (not plotted with the 177 optimal number of clusters here) are shown on the right. Only cell counts (n) of clusters with >20 cells are shown. Clusters containing a single annotated event representing founder populations are indicated with a gray bar on the left. The cluster with multiple trisomies is highlighted in dark red. Heatmaps of mutational SVs in BJ-5ta, HAP1 and HAP1 lig4− cells are shown in . ( B ) Diffusion maps of mutational SVs in Patski cells. Diffusion components 1 (DC1) and 2 (DC2) are shown in the top panel colored by segmental loss on chr2 (separated out by DC1, x-axis) and monosomy on chromosome 12 (separated out by DC2, y-axis). The bottom panel shows DC2 and DC4 colored by different combinations of trisomy. DC3 separated out two specific clusters, examined in . Each point represents a unique set of annotated SVs, while the size of each point represents the number of cells that share the same set of annotated outcomes. High gain and high loss cells were excluded. Multiple trisomy represents cells with trisomy on chromosome 1, 3, 5, 6, 10, 15, 17, and/or 19 (dark red highlight in A). ( C ) SCE rates within subsets of Patski SV outcomes. In the right panel, cells were divided into groups based on the presence of chr4 monosomy or chr4 UPD or the absence of both (other category), while the left panel was divided based on the presence or absence of monosomy on chr12. The fold change of the median SCE counts per cell are shown for pairs of annotated events above the relevant plots. Significant differences for the left and right panels were calculated with the Mann–Whitney U test, comparing chr4 Monosomy versus chr4 UPD ( P -value: 1.54 × 10 −11 ); chr4 Monosomy versus Other ( P -value: 2 × 10 −03 ); chr4 UPD versus Other ( P -value: 4.6 × 10 −02 ); chr12 Monosomy versus Other ( P -value: 1.94 × 10 −13 ). Significant differences with additional summary statistics such as median, MAD, and fold change are provided in . ( D, E ) Pre-existing events (see ) and chromosomes without any event annotation are not plotted. Plotted events were counted per chromosome and normalized by the total number of cells and the ploidy of respective cell line. Sex chromosomes were excluded from BJ-5ta cells. Error bars show the 95% confidence interval. ( D ) Normalized counts of mutational SVs. Significant differences were calculated with chi-squared for HAP1 lig4− versus HAP1 with segmental DTZ ( P -value 5.18 × 10 −04 ; 1.7×), whole chromosome gain ( P -value: 5.32 × 10 −12 ; 2.5×). Contingency tables of additional event combinations with normalized counts, fold change and chi-squared P -values are provided in . Color code for the types of annotation is the same as in panel (A) and same for panel ( E ) sci-L3. ( E ) Comparison of Patski SV annotations from three methods for a subset of 40 cells. Each row represents a single cell, with columns showing chromosomes genome-wide (labels for 11, 13, 15, 17, 19 not shown). Each method produced the following number of contiguous SV segments: SVM – 175; aneufinder – 3517; scTRiP lenient filter – 4859. For scTRiP, 2 out of the 40 cells did not pass the initial QC filter and thus have no annotations . Note that the population of chr4 UPD is not annotated by both previous tools.

Article Snippet: BJ-5ta (CRL-4001, ATCC) and Patski (gift from Disteche lab) cells were cultured in DMEM medium supplemented with 10% FBS and 1× Pen–Strep.

Techniques: Single Cell, Diffusion-based Assay, MANN-WHITNEY, Comparison, Genome Wide, Produced

Journal: Nucleic Acids Research

Article Title: High-throughput mapping of spontaneous mitotic crossover and genome instability events with sci-L3-Strand-seq

doi: 10.1093/nar/gkag119

Figure Lengend Snippet: Detecting inversions with sci-L3-Strand-seq. ( A ) A universal inversion on chr8 in BJ-5ta. The left panel shows chr8 heatmaps from a subset of 449 single cells with both chromosomes in the C strand orientation. Each row represents a single cell plotted at an approximate resolution of 200 Kb. W reads are plotted in red (representing background reads except for the inversion), and C reads are in blue. Masked regions are in gray. The same bin size and color code are used for heatmaps in Figs – unless noted otherwise. Arrows highlight an inversion at the start of chr8. The right panel shows the pileup tracks of the heatmaps zoomed-in on the inversion, showing the median value for each bin across all plotted cells. The pileup for the W read heatmap of CC chromosomes is shown on the top track, and the C read heatmap of CC chromosomes is shown on the middle track. The bottom track shows our inversion call. ( B ) Genome-wide locations of inversion calls. Inversions identified across the three human cell lines are shown in the top panel. Patski inversions are shown on the bottom panel. The size of inversions have been scaled to a minimum of 1Mb to allow visualization. Inversions found in at least two cell lines were classed as global. There are no inversions private to HAP1 cells (all shared with HAP1 lig4− ). Even chromosomes are shaded gray for visual clarity. Calls overlapping with previously published inversions are highlighted with an asterisk [ , ]. ( C ) Inversion detected from double strand switch hotspots in HAP1 lig4− cells. The sub-clonal inversion measuring 27.98–33.8Mb was observed as a hotspot (red) of coincident strand switches shown in the top left bar plot. Matching whole chromosome heatmaps are shown underneath, where each row represents a single cell with at least two strand switches on chr3. The heatmaps show the inversion as a block of strand state change in a subpopulation of cells. Each roughly 200 kb bin shows the subtraction of W from C read counts. A zoom-in on the breakpoints within the hotspots is shown in the right panel, revealing 9 cells that contain paired strand switches in this region. The list of subclonal inversions with exact coordinates is provided in . ( D ) Inversion detected from double strand switch hotspots in Patski cells. The subclonal inversion measuring 4.9–14.5Mb was observed as a hotspot (red) of coincident breakpoints shown in the top left bar plot. Whole chromosome heatmaps are shown underneath, same as in panel (C). The zoom-in on breakpoints within the hotspots is shown in the right panel, revealing 55 cells that contain paired strand switches in this region .

Article Snippet: BJ-5ta (CRL-4001, ATCC) and Patski (gift from Disteche lab) cells were cultured in DMEM medium supplemented with 10% FBS and 1× Pen–Strep.

Techniques: Single Cell, Genome Wide, Blocking Assay

Journal: Bioresources and Bioprocessing

Article Title: Box-Behnken optimized copper oxide nanoparticles from Thymus vulgaris potentiate efficacy against multidrug-resistant bacterial pathogens and exhibit anticancer activity

doi: 10.1186/s40643-026-01008-5

Figure Lengend Snippet: Comprehensive Evaluation of TE-CuONPs Anticancer Activity and Apoptotic Mechanism in MCF-7 Breast Cancer Cells. Concentration-dependent cytotoxicity and mechanistic analysis. a , b MTT dose–response curves against MCF-7 breast cancer cells and normal human skin fibroblasts (HSF). c , d Representative phase-contrast micrographs (200 × magnification) of MCF-7 cells after 24 h treatment at respective IC₅₀ concentrations, showing c minimal morphological changes with TE treatment versus d characteristic apoptotic features with TE-CuONPs treatment, including cell shrinkage (red arrows), membrane blebbing (yellow arrows), chromatin condensation, and cellular detachment. e Flow cytometric scatter plots (FSC-H vs. SSC-H) demonstrating consistent cell populations across treatments (10,000 events gated per sample). ( f ) Schematic proposal for anticancer mechanisms. g Annexin V-FITC/propidium iodide (PI) dual-staining flow cytometric analysis

Article Snippet: MCF-7 breast adenocarcinoma cells (ATCC HTB-22) and normal human skin fibroblasts (HSF, CRL-2522) were obtained from Nawah Scientific (Cairo, Egypt) and cultured in RPMI-1640 medium (Gibco, USA) supplemented with 10% FBS, 100 U/mL penicillin, and 100 μg/mL streptomycin at 37 °C in 5% CO2.

Techniques: Activity Assay, Concentration Assay, Membrane, Staining