cells  (New England Biolabs)

Journal: Genome Research

Article Title: Resolving missing human polymorphic inversions and other complex variants from ultralong read data

doi: 10.1101/gr.280867.125

Figure Lengend Snippet: Summary of ONT sequencing experiment results. ( A ) Comparison of the N50 value and the total output of each sequencing run of the four analyzed samples (in different colors). Diverse sequencing protocols using whole-genome sequencing (WGS) or adaptive sampling (AS2/AS3) and DNA isolation methods (Monarch HMW or phenol) are represented by different shapes, whereas empty symbols indicate the use of fresh cells as starting material. ( B ) Enrichment ratio between the read depth inside and outside the targeted regions (depth in/out) of each sample for diverse types of sequencing (black dots), showing a six- to sevenfold average enrichment in AS2 or AS3 compared with WGS (colored bars). ( C ) Average proportion of genotypes obtained for the analyzed inversion regions normalized to the number of AS2 or AS3 targets (percentage, colored bars). Values for each sample (black dots) show considerable variation due mainly to sequencing output differences.

Article Snippet: High-molecular-weight genomic DNA was obtained by two different methods following the protocol specifications: (1) the Monarch HMW DNA extraction kit for cells & blood (New England Biolabs) starting from about 6 million cells and (2) a phenol-based isolation protocol optimized to obtain ultralong reads for ONT sequencing ( ) starting from 20 to 30 million cells.

Techniques: Sequencing, Comparison, Whole-Genome Sequencing, Sampling, DNA Extraction

Journal: JCI Insight

Article Title: Pan-African hybridization of PfSPZ increases antigenic diversity and replicative capacity for malaria vaccine design

doi: 10.1172/jci.insight.207272

Figure Lengend Snippet: ( A ) MAL31 and HL1209 sporozoites exhibit increased liver infectivity compared with NF54. Cryopreserved MAL31 or HL1209 sporozoites were co-inoculated with NF54 mCherry sporozoites, and liver-stage infection was assessed on day 6 by immunofluorescence analysis of at least 100 parasites. Individual FRG NOD huHep mice were injected with 2 × 10 6 cryopreserved NF54 mCherry sporozoites (red) together with 2 × 10 6 MAL31 (purple), HL1209 (gold), or NF54 (gray) sporozoites. Each column represents a single mouse (M1–M3), with colors indicating the proportion of parasites detected across 2 independent liver lobes (± SD). Absolute parasite counts are provided in . ( B ) MAL31, NF54, and NF54 mCherry liver stages show similar sizes, whereas HL1209 liver stages are significantly larger. Each point represents an individual parasite (purple, red, and gray: n = 20; gold: n = 56); gray bars denote median values. Statistical significance was determined by 1-way ANOVA (**** P < 0.0001). ( C ) Liver-stage parasites of MAL31 and HL1209 display nuclear morphology (DAPI, DNA, blue), apicoplast organization (ACP, green), and parasitophorous vacuole membrane expression (EXP1, magenta) comparable to NF54 and NF54 mCherry (mCherry, red). Day 6 liver sections (50 μm) were stained with antibodies against ACP, EXP1, and mCherry. Scale bars: 10 μm.

Article Snippet: Genomic DNA was extracted from large-volume parasite cultures using the Monarch High Molecular Weight DNA Extraction Kit (New England Biolabs).

Techniques: Infection, Immunofluorescence, Analysis, Parasite, Injection, Morphology, Membrane, Expressing, Staining