Journal: Immunity

Article Title: A vaccine-induced public antibody protects against SARS-CoV-2 and emerging variants

doi: 10.1016/j.immuni.2021.08.013

Figure Lengend Snippet:

Article Snippet: NEBNext Immune Sequencing Kit (Human) , New England Biolabs , Cat# E6320.

Techniques: Recombinant, Sequencing, Cell Isolation, Transfection, Infection, Variant Assay, Expressing, Software, Enzyme-linked Immunosorbent Assay

Journal: bioRxiv

Article Title: FFPE DNA shows two major error profiles derived from deamination of cytosine and methylcytosine that can be mitigated using distinct repair strategies

doi: 10.1101/2023.03.02.530819

Figure Lengend Snippet: A . Overall percentage of CG:TA transitions in sequencing reads after library amplification using Q5 (left), Q5U® (center) and Taq DNA polymerase (right), with (DNA repair (orange), UDG (brown)) and without (blue) DNA repair treatment of the lung tumor FFPE sample. Experiments were done in duplicate and error bars are reflecting the variability between replicates. B . Profiles of C to T transitions on read 1 (R1, left) and read 2 (R2, right) as a function of read position (in bp). Libraries were amplified using Q5 (top), Q5U® (middle) and Taq DNA polymerase (bottom). Experiments were done in duplicate. Fraction of C to T is a global count of the of C (on the reference genome) to T (on the mapped reads) normalized to the total number of C to C matches. C . Schema representing the fate of the deaminated strand (gray) and the un-damaged strand (purple) after end repair (red) and amplification with Q5 (left) and Taq or Q5U (right).

Article Snippet: The DNA repair step commonly used in this manuscript corresponds to the NEBNext FFPE DNA Repair v2 Module and contains enzymes and buffers that are optimized to repair FFPE DNA in next generation sequencing workflow including UDG, Endonuclease IV, Fpg, Endonuclease VIII, T4 PDG, Taq DNA ligase and Bst DNA polymerase.

Techniques: Sequencing, Amplification

Journal: bioRxiv

Article Title: FFPE DNA shows two major error profiles derived from deamination of cytosine and methylcytosine that can be mitigated using distinct repair strategies

doi: 10.1101/2023.03.02.530819

Figure Lengend Snippet: A . Overall percentage of CG:TA transitions in sequencing reads for lung (left) and pancreatic (right) tumor FFPE samples. Samples were either left untreated (orange) or treated with DNA repair mix before (red) and after (blue) end repair. B . Breakdown of the fraction of C:T transitions according to Read types, Read 1 (R1, top) and Read 2 (R2, bottom) and position on the read starting from the 5’ end. Two FFPE samples have been used for these experiments : Lung tumor FFPE sample (Blue) and pancreatic tumor FFPE sample (red) treated with DNA repair after end repair (left), before end repair (right) and no treatment (middle). Fraction of C to T is a global count of the of C (on the reference genome) to T (on the mapped reads) normalized to the total number of C to C matches. Red arrows indicate positions of increased C to T transition rate.

Article Snippet: The DNA repair step commonly used in this manuscript corresponds to the NEBNext FFPE DNA Repair v2 Module and contains enzymes and buffers that are optimized to repair FFPE DNA in next generation sequencing workflow including UDG, Endonuclease IV, Fpg, Endonuclease VIII, T4 PDG, Taq DNA ligase and Bst DNA polymerase.

Techniques: Sequencing

Journal: bioRxiv

Article Title: FFPE DNA shows two major error profiles derived from deamination of cytosine and methylcytosine that can be mitigated using distinct repair strategies

doi: 10.1101/2023.03.02.530819

Figure Lengend Snippet: Substitution profiles for low (less than 1% A ) and high (more than 10% B ) allelic frequency substitution. Barplot representing the number of genomic positions per megabases (mb). The barplots are color coded according to the substitution types and organized by contexts (XpA, XpT, XpC and XpG with X= A, C, T or G) and reads (read1, top and read2, bottom). Sequencing depth has been downsample to 300-fold coverage for comparison, thus the variant read number for high (>10%) allelic frequency is above 30 reads supporting the presence of a variant and low (<1%) allelic frequency is below 3 reads supporting the presence of a variant. The equivalent result for medium (1 to 10%) allelic frequency substitution is plotted on and . All reads substitution have a Phred Quality Scores Q>30. CpA context has no high allelic frequency substitution in Read 2 in the DNA repair sample. The excess of G to T can be attributed to oxidative damage.

Article Snippet: The DNA repair step commonly used in this manuscript corresponds to the NEBNext FFPE DNA Repair v2 Module and contains enzymes and buffers that are optimized to repair FFPE DNA in next generation sequencing workflow including UDG, Endonuclease IV, Fpg, Endonuclease VIII, T4 PDG, Taq DNA ligase and Bst DNA polymerase.

Techniques: Sequencing, Variant Assay

Journal: PLoS ONE

Article Title: Evaluation of Providencia rettgeri pathogenicity against laboratory Mediterranean fruit fly strain ( Ceratitis capitata )

doi: 10.1371/journal.pone.0196343

Figure Lengend Snippet: Each bar shows mean ± SE. Different symbols correspond to a significant difference, (*) for the females (F) and (#) for the males (M), (Multivariate analysis, MANOVA).

Article Snippet: Differences between groups were tested using one-way analysis of variance (ANOVA) and a multivariate analysis of variance (MANOVA) (Stat graphics Centurion XVI) using the data that had previously been checked for normality.

Techniques:

Journal: EBioMedicine

Article Title: The displacement of the SARS-CoV-2 variant Delta with Omicron: An investigation of hospital admissions and upper respiratory viral loads

doi: 10.1016/j.ebiom.2022.104008

Figure Lengend Snippet: SARS-CoV-2 positivity, COVID-19 hospitalizations, and variants trends November- December 2021. (a) SARS-CoV-2 daily positivity rates between November and December 2021 for both symptomatic and asymptomatic testing. (b) COVID-19 related admissions between November and December 2021. (c) SARS-CoV-2 variant distribution between November and December 2021 relative to the 7 day rolling average positives from Johns Hopkins system. (d) Percent SARS-CoV-2 variants in November and December 2021.

Article Snippet: Specimen preparation, extractions, and sequencing were performed as described previously., Library preparation for this cohort was performed using the NEBNext® ARTIC SARS-CoV-2 Companion Kit (VarSkip Short SARS-CoV-2 # E7660-L).

Techniques: Variant Assay

Journal: EBioMedicine

Article Title: The displacement of the SARS-CoV-2 variant Delta with Omicron: An investigation of hospital admissions and upper respiratory viral loads

doi: 10.1016/j.ebiom.2022.104008

Figure Lengend Snippet: SARS-CoV-2 IgG levels in upper respiratory samples of infected vaccinated patients. Boost, patients with booster dose; Vax, fully vaccinated patients who didn't receive a booster dose. Dashed lines demarcate the limit of borderline and negative ELISA results as specified per assay's package insert. Statistical analyses, one-way ANOVA. Total numbers per group are shown on top of each scatter.

Article Snippet: Specimen preparation, extractions, and sequencing were performed as described previously., Library preparation for this cohort was performed using the NEBNext® ARTIC SARS-CoV-2 Companion Kit (VarSkip Short SARS-CoV-2 # E7660-L).

Techniques: Infection, Enzyme-linked Immunosorbent Assay

Journal: Microbial Cell Factories

Article Title: Heterologous protein exposure and secretion optimization in Mycoplasma pneumoniae

doi: 10.1186/s12934-024-02574-z

Figure Lengend Snippet: A Structure of the cleavage motif within MPN142(Opt)ss fused to NanoLuc. P3: synthetic promoter P3. B General structure of the vector for the MPN(Opt)ss variants fused to NanoLuc sequence. IR-OR: inverted repeated regions; Tnp: Transposase; CmM438: Cloramphenicol antibiotic resistance. C Scheme of workflow applied for Mpn strains generation included in all the experiments. Vectors were constructed by Gibson assembly reaction, cloned in DH5α E. coli strain for further amplification, and used to transform Mpn 129 strain by electroporation and random transposon insertion. D Luminescence from NanoLuc activity was measured in the culture supernatant of Mpn strains expressing each variant of MPN142(Opt)ss fused to NanoLuc protein. Normalization of each condition was performed by determining total protein concentration by BCA assay. Different amino acid characteristics are represented in greyscale colors. Fold change of NanoLuc activities from different variants with respect to the WT sequence was calculated and T-test was performed from 4 independent experiments. We show the standard deviation of the experiments as error bars and the significance of differences in each variant compared to WT sequences as asterisks ( p value < 0.03 (*), < 0.002 (**), < 0.0002 (***) and < 0.0001 (****)). The scheme was created with BioRender.com

Article Snippet: For cloning purposes, the E. coli NEB 5-alpha High Efficiency strain (New England Biolabs) was grown at 37 °C in LB broth or on LB agar plates supplemented with ampicillin (100 µg mL −1 ).

Techniques: Plasmid Preparation, Sequencing, Construct, Clone Assay, Amplification, Electroporation, Activity Assay, Expressing, Variant Assay, Protein Concentration, BIA-KA, Standard Deviation

Journal: Cell reports

Article Title: Virulence and genomic diversity among clinical isolates of ST1 (BI/NAP1/027) Clostridioides difficile

doi: 10.1016/j.celrep.2023.112861

Figure Lengend Snippet:

Article Snippet: E.coli NEBturbo , NEB , NEB #C2984.

Techniques: Virus, Recombinant, Clone Assay, Purification, SYBR Green Assay, DNA Purification, Ligation, Sequencing, Plasmid Preparation, Software, Variant Assay