Journal: Cells

Article Title: ‘Shared-Hook’ and ‘Changed-Hook’ Binding Activities of Herpesviral Core Nuclear Egress Complexes Identified by Random Mutagenesis

doi: 10.3390/cells11244030

Figure Lengend Snippet: Qualitative and quantitative analyses of HCMV AD169-GFP ΔUL53 virus reconstitution on the different recombinant HFF cell populations. HFFs that express pUL53, pUL53-Flag or pUL53::sHook1-Flag were transfected with the infectious bacterial artificial chromosome of HCMV ΔUL53. ( A ) Images of the GFP signals and the respective brightfield illuminations were taken at indicated time points; scale bar in panel A, picture 1 marks 500 μm. ( B ) Quantitative analysis of fluorescence-positive cells was achieved with automated counting by the CellReporterXpress ® software (Molecular Devices LLC, San Jose, CA, USA). Counting parameters for positive nuclei were set to an intensity of at least 100, a minimal width of 7 and a maximal width of 30. Measurements were performed in biological sextuplicates per cell population of 5.05% area of the well and mean values ± SD are given. ( C ) qPCR-based assay for the determination of viral genome equivalents referring to the respective recombinant HFF populations. Viral supernatants were harvested at day 24 p.t. and subjected to IE1-specific qPCR. Calculations were performed in biological sextuplicates per cell population; mean values ± SD are shown. ( B , C ) Statistical analysis was performed using an ordinary two-way ANOVA and post-hoc Tukey correction; ****, p < 0.0001; **, p < 0.01; *, p < 0.1; ns, not significant; no significant differences were noted for values between 1–20 d p.t. ( B ). ( D ) Wb-based expression analysis of the conditionally expressing HFF populations. Recombinant protein expression in the three HFF populations of HFF-UL53, HFF-UL53-Flag and HFF-UL53::sHook1-Flag cells was either uninduced (-) or induced (500 ng/mL Dox). Cells were either infected with HCMV ΔUL53 or remained mock-infected. At 24 h p.t., cells were harvested and lysed. Total lysate samples were subjected to standard Wb analysis using tag-specific or protein-specific monoclonal antibodies as indicated.

Article Snippet: For measurement of HCMV AD169-GFP ΔUL53-positive cells, signals were counted with the ImageXpress ® Pico device (Molecular Devices LLC, San Jose, CA, USA) using CellReporterXpress ® software (version 2.9.3.1183, Molecular Devices LLC) by the system-integrated cell count assay.

Techniques: Virus, Recombinant, Transfection, Fluorescence, Software, Expressing, Infection, Bioprocessing

Journal: Cells

Article Title: ‘Shared-Hook’ and ‘Changed-Hook’ Binding Activities of Herpesviral Core Nuclear Egress Complexes Identified by Random Mutagenesis

doi: 10.3390/cells11244030

Figure Lengend Snippet: Viral replication kinetics of HCMV ΔUL53 and its revertant (HCMV Rev) determined by quantitation of GFP-positive cells and HCMV-specific qPCR on the different recombinant HFF populations. 80,000 inducibly expressing HFFs in 24-well plates were infected with HCMV ΔUL53 or HCMV Rev at a viral dose of 5 × 10 6 genome copies. pUL53, pUL53-Flag or pUL53::sHook1-Flag protein expression was either Dox-induced (+Dox) or remained non-induced (−Dox). ( A ) The number of HCMV-infected cells was measured by detection of GFP signal-positive cells at indicated time points with the CellReporterXpress ® software using the ImageXpress ® Pico device. Values represent 25.04 % of the area of a well and are given as a mean value ± SD of two independently infected wells. ( B ) Viral supernatants were harvested at indicated time points and viral genome equivalents were determined by qPCR. Each value represents the mean ± SD of two independent biological replicates, each measured twice. ( A , B ) Statistical analysis was performed using an ordinary two-way ANOVA and post-hoc Sidak correction; ****, p < 0.0001; ***, p < 0.001; *, p < 0.1; ns, not significant; no significant differences were noted for values between 1–13 d p.i. ( A ) or 1–11 d p.i. ( B ), respectively.

Article Snippet: For measurement of HCMV AD169-GFP ΔUL53-positive cells, signals were counted with the ImageXpress ® Pico device (Molecular Devices LLC, San Jose, CA, USA) using CellReporterXpress ® software (version 2.9.3.1183, Molecular Devices LLC) by the system-integrated cell count assay.

Techniques: Quantitation Assay, Recombinant, Expressing, Infection, Software

Journal: PLoS ONE

Article Title: Neuroinflammation, body temperature and behavioural changes in CD1 male mice undergoing acute restraint stress: An exploratory study

doi: 10.1371/journal.pone.0259938

Figure Lengend Snippet: The results of automated behaviour analysis (with HCS) showing behaviour from before and after exposure to restraint stress in mice undergoing each method of handling (NAH-T, TH or NAH-M). P-values refer to comparison between pre-post R&L stress on all animals. Walking and Rearing frequencies significantly declined following stress, although the Total Distance mice moved (metres) tended to decline, not significantly. The average duration of bouts (in seconds) of Grooming increased. Handling method had no significant effects.

Article Snippet: Automated behaviour analysis software ( www.cleversysinc.com ) was used to record the spontaneous unconstrained behaviour of the mice.

Techniques: Comparison

Journal: Clinical Epigenetics

Article Title: Identification of influential probe types in epigenetic predictions of human traits: implications for microarray design

doi: 10.1186/s13148-022-01320-9

Figure Lengend Snippet: Distinction between two primary analysis methods in the present study. We employed both variance components and penalised regression models in order to examine the amount of phenotypic variance captured by each respective probe set (n = 18 in total, see Methods). Variance component estimates were obtained using the restricted maximum likelihood method in OSCA. Here, we were able to estimate the amount of phenotypic variance captured by all probes in a given probe set in the training sample (n ≤ 4450). We also employed penalised regression to build linear DNAm-based predictors of traits using probes in a given probe set in the training sample. We then applied the predictors to the test sample (n ≤ 2578) in order to estimate how much variance in a given trait the predictor could explain over basic covariates (such as age and sex). This coefficient reflected the incremental R 2 estimate and pertained to an out-of-sample setting as the predictor was applied to a sample outside of that in which it was derived. LASSO, least absolute shrinkage and selection operator; OSCA, OmicS data-based complex trait analysis. Image created using Biorender.com

Article Snippet: For this, we used OmicS-data-based complex trait analysis (OSCA) software in which the correlation structure among all input probes is used to create an omic-data-based relationship matrix (ORM).

Techniques: Derivative Assay, Selection

Journal: Clinical Epigenetics

Article Title: Identification of influential probe types in epigenetic predictions of human traits: implications for microarray design

doi: 10.1186/s13148-022-01320-9

Figure Lengend Snippet: Variance captured in complex traits by all available probes and four subsets of decreasing size. Restricted maximum likelihood was used to estimate variance components in the training sample (n ≤ 4450, OSCA software). The four traits (out of seventeen biochemical and complex traits) with the highest proportion of variance captured by DNAm are shown. Five different sets of probes were compared. ‘All available probes’ denotes probes that were common to the Illumina EPIC and 450K arrays and passed quality control procedures in the training sample within Generation Scotland (n = 393,654 probes). The ‘variable non-mQTL probes’ set consisted of probes without reported non-genetic influences and mean Beta-values between 10 and 90%. The remaining three probe subsets contained the 50,000, 20,000 and 10,000 most variable non-mQTL probes (ranked by their standard deviations). The five sets of probes therefore had decreasing numbers of probes but increasing mean variabilities. Vertical bars show 95% confidence intervals. DNAm, DNA methylation; mQTL, methylation quantitative trait locus; OSCA, OmicS data-based complex trait analysis

Article Snippet: For this, we used OmicS-data-based complex trait analysis (OSCA) software in which the correlation structure among all input probes is used to create an omic-data-based relationship matrix (ORM).

Techniques: Software, Control, DNA Methylation Assay, Methylation

Journal: Frontiers in Neurology

Article Title: Angiogenin in the Neurogenic Subventricular Zone After Stroke

doi: 10.3389/fneur.2021.662235

Figure Lengend Snippet: SH-SY5Y neurite differentiation: (A) timeline of the experimental procedure. (B) Box plots and representative images showing axonal/neurite outgrowth in the presence of Retinoic Acid (RA) as expected, but not with angiogenin stimulation; n = 5–6. The insert in RA shows a micrograph representative of the WimNeuron analysis. Box plots represent median (IQR) of the percentage vs. control values of each independent experiment, *** p < 0.001 vs. control.

Article Snippet: Finally, WimNeuron automated analysis software (Wimasis Image Analysis®) was used for quantification by measuring the circuitry length and the total thin neurite length.

Techniques: Control