Journal: Viruses

Article Title: Cinnamaldehyde Inhibits the Replication of Porcine Reproductive and Respiratory Syndrome Virus Type 2 In Vitro

doi: 10.3390/v17040506

Figure Lengend Snippet: Cinnamaldehyde suppresses PRRSV infection in Marc-145 cells. ( A , B ) The effect of different concentrations (40, 80, 160 μM) of CA on PRRSV (MOI = 1) replication in Marc-145 cells was investigated by RT-qPCR ( A ) and a viral titer assay ( B ). ( C – F ) Western blotting ( C ) and an immunofluorescence assay ( E ) were used to detect the expression of PRRSV N protein at 24 hpi in the presence of CA (40, 80, 160 μM). Statistical analysis of Western blotting ( D ) and the IFA ( F ). Bar = 100 µm. The data are the results of three independent experiments (means ± SD). Significant differences are denoted by * p < 0.05 and ** p < 0.01.

Article Snippet: Subsequently, reverse transcription was conducted with the HiScript ® ⅢRT SuperMix for qPCR (+gDNA wiper) Vazyme Code: R323-01 100 rxns (Vazyme, China), based on the manufacturer’s instructions.

Techniques: Infection, Quantitative RT-PCR, Titer Assay, Western Blot, Immunofluorescence, Expressing

Journal: Viruses

Article Title: Cinnamaldehyde Inhibits the Replication of Porcine Reproductive and Respiratory Syndrome Virus Type 2 In Vitro

doi: 10.3390/v17040506

Figure Lengend Snippet: Cinnamaldehyde suppresses PRRSV infection in PAM cells. ( A ) The cytotoxicity of CA on PAM cells was evaluated using the CCK-8 assay. The non-toxic concentration of CA was determined to be 80 μM. ( B , C ) The effect of different concentrations (40, 80 μM) of CA on PRRSV (MOI = 1) replication in PAM cells was investigated by RT-qPCR ( B ) and a viral titer assay ( C ). ( D , E ) An immunofluorescence assay ( D ) was used to detect the expression of PRRSV N protein at 24 hpi in the presence of CA (40, 80 μM). Statistical analysis of the IFA ( E ). Bar = 100 µm. The data are the results of three independent experiments (means ± SD). Significant differences are denoted by * p < 0.05 and ** p < 0.01.

Article Snippet: Subsequently, reverse transcription was conducted with the HiScript ® ⅢRT SuperMix for qPCR (+gDNA wiper) Vazyme Code: R323-01 100 rxns (Vazyme, China), based on the manufacturer’s instructions.

Techniques: Infection, CCK-8 Assay, Concentration Assay, Quantitative RT-PCR, Titer Assay, Immunofluorescence, Expressing

Journal: Viruses

Article Title: Cinnamaldehyde Inhibits the Replication of Porcine Reproductive and Respiratory Syndrome Virus Type 2 In Vitro

doi: 10.3390/v17040506

Figure Lengend Snippet: Cinnamaldehyde exerts anti-PRRSV ability in different treatment modes. ( A ) The diagram shows three different administration treatment modes. Pre-treatment: Marc-145 cells were pre-treated with CA at 160 μM at different times (2, 4, 6, 8 h) and then infected with PRRSV for another 2 h. Co-treatment: Marc-145 cells were infected with PRRSV and incubated with CA (160 μM) for 2 h. Post-treatment: Marc-145 cells were infected with PRRSV for 2 h, then treated with CA at 160 μM at different times (2, 4, 6, 8 h). Samples were harvested at 24 hpi. ( B ) RT-qPCR was used to determine viral ORF7 expression. ( C ) The expression of PRRSV N protein was detected by an IFA. ( D ) Statistical analysis of the IFA. ( E ) Cell supernatants were collected for the TCID 50 assay. Bar = 100 µm. The data are the results of three independent experiments (means ± SD). Significant differences are denoted by * p < 0.05 and ** p < 0.01.

Article Snippet: Subsequently, reverse transcription was conducted with the HiScript ® ⅢRT SuperMix for qPCR (+gDNA wiper) Vazyme Code: R323-01 100 rxns (Vazyme, China), based on the manufacturer’s instructions.

Techniques: Infection, Incubation, Quantitative RT-PCR, Expressing

Journal: Viruses

Article Title: Cinnamaldehyde Inhibits the Replication of Porcine Reproductive and Respiratory Syndrome Virus Type 2 In Vitro

doi: 10.3390/v17040506

Figure Lengend Snippet: Cinnamaldehyde blocks the binding, entry, replication, and release of PRRSV. ( A ) A schematic diagram of PRRSV binding, entry, replication, and release. ( B ) A viral binding assay was performed. PRRSV was inoculated in the presence or absence of CA at 4 °C for 2 h. RT-qPCR was used to detect viral ORF7 expression. ( C ) A viral entry assay was performed. After virus binding, cells were transferred to 37 °C for another 2 h. RT-qPCR was used to analyze viral ORF7 expression. ( D ) Viral replication assays were performed. Cells were infected with PRRSV for 4 h (including binding and entry) and then treated with CA for another 6, 12, and 24 h. Cells were collected for RT-qPCR analysis. ( E ) A viral release assay was performed. Marc-145 cells were infected with PRRSV for 24 h. Then, cells were treated with CA for another 8 h. Cell supernatants were collected for the TCID 50 assay. The data are the results of three independent experiments (means ± SD). Significant differences are denoted by * p < 0.05 and ** p < 0.01.

Article Snippet: Subsequently, reverse transcription was conducted with the HiScript ® ⅢRT SuperMix for qPCR (+gDNA wiper) Vazyme Code: R323-01 100 rxns (Vazyme, China), based on the manufacturer’s instructions.

Techniques: Binding Assay, Quantitative RT-PCR, Expressing, Virus, Infection, Release Assay

Journal: Journal of the American Heart Association

Article Title: Stroke Causes DNA Methylation at Ncx1 Heart Promoter in the Brain Via DNMT1/MeCP2/REST Epigenetic Complex

doi: 10.1161/jaha.123.030460

Figure Lengend Snippet: Figure 1. The epigenetic factors DNMT1 and MeCP2 and the transcriptional factor REST are involved in the negative modulation of Ncx1 mRNA and protein expression. A and B, qRT-PCR for DNMT1 and MECP2 transcripts in SH-SY5Y cells transfected for 48 hours with siDNMT1 or siMeCP2 at a final concentration of 50 nM. An siCTL was used as scrambled. *P≤0.05 vs siCTL by Student’s t test (n=3). C, Ncx1 mRNA and protein expression in SH-SY5Y cells transfected for 48 hours with siCTL, siDNMT1, siMeCP2, and siREST. *P≤0.05 vs siCTL by 1-way ANOVA analysis followed by Tukey’s post hoc test (n=3/4). D and E, qRT-PCR for DNMT1 and MECP2 transcripts in SH-SY5Y transfected for 48 hours with vector overexpressing DNMT1 or MeCP2. pcDNA3.1 vector was used as EV. *P≤0.05 vs EV by Student’s t test (n=3). F, Ncx1 mRNA and protein expression in SH-SY5Y cells transfected for 48 hour with EV, DNMT1, MeCP2, or REST plasmids. *P≤0.05 vs EV by 1-way ANOVA analysis followed by Tukey’s post hoc test (n=3/4). CTL indicates control; DNMT1, DNA-methyltransferase-1; EV, empty vector; MeCP2, methyl-CpG binding protein 2; NCX1, sodium/calcium exchanger 1; qRT-PCR, quantitative real time polymerase chain reaction; REST, repressor element 1-silencing transcription factor; si, small interfering; and siCTL, control siRNA.

Article Snippet: Chromatin lysates were incubated overnight with 3 μg of antibody for DNMT1 (Mouse mAb, cod: sc- 271 729 Santa Cruz Biotechnology, dilution 1:500), MeCP2 (Rabbit mAb, cod: 3456 Cell Signaling, dilution 1:1000), REST, HDAC1, and HDAC2.3 Normal rabbit IgG was used as negative control.

Techniques: Expressing, Quantitative RT-PCR, Transfection, Concentration Assay, Plasmid Preparation, Control, Binding Assay, Real-time Polymerase Chain Reaction

Journal: Journal of the American Heart Association

Article Title: Stroke Causes DNA Methylation at Ncx1 Heart Promoter in the Brain Via DNMT1/MeCP2/REST Epigenetic Complex

doi: 10.1161/jaha.123.030460

Figure Lengend Snippet: Figure 4. DNMT1 and MeCP2 bind Ht, but not Br promoter sequence, in the temporoparietal cortex 24 hours after tMCAO. Chromatin immunoprecipitation with anti-DNMT1 (A), anti-MeCP2 (B) anti-REST (C), anti-HDAC1 (D), anti-HDAC2 (E), antibodies followed by qPCR of Ncx1 brain promoter (Br) (white columns) and Ncx1 heart promoter (Ht) (gray columns) in peri-ischemic cortex of mice euthanized 12 or 24 hours after tMCAO. IgG was used as negative control. *P≤0.05 vs Sham immunopreciptated with IgG antibody by 1-way ANOVA analysis followed by Tukey’s post hoc test (n=3). DNMT1 indicates DNA-methyltransferase-1; HDAC, histone deacetylase; IP, immunoprecipitation; MeCP2, methyl-CpG binding protein 2; NCX1, sodium/calcium exchanger 1; qRT-PCR, quantitative real time polymerase chain reaction; REST, repressor element 1-silencing transcription factor; and tMCAO, transient middle cerebral artery occlusion.

Article Snippet: Chromatin lysates were incubated overnight with 3 μg of antibody for DNMT1 (Mouse mAb, cod: sc- 271 729 Santa Cruz Biotechnology, dilution 1:500), MeCP2 (Rabbit mAb, cod: 3456 Cell Signaling, dilution 1:1000), REST, HDAC1, and HDAC2.3 Normal rabbit IgG was used as negative control.

Techniques: Sequencing, Chromatin Immunoprecipitation, Negative Control, Histone Deacetylase Assay, Immunoprecipitation, Binding Assay, Quantitative RT-PCR, Real-time Polymerase Chain Reaction

Journal: Oncotarget

Article Title: CIP2A is an Oct4 target gene involved in head and neck squamous cell cancer oncogenicity and radioresistance

doi:

Figure Lengend Snippet: (A) Immunohistochemical staining of CIP2A in the adult mouse testis show highest CIP2A-positivity in spermatogonial cells locating most basally in seminiferous tubules (arrows). The bar represents 25 μm. (B) Representative CT scan image from mouse and tissue specific X-irradiation scattering. Radiation distribution in a mouse can be seen in colours and in axial and AP directions. Testes are contoured with red lines, where radiation dose is 4 Gy. (C) Expression of spermatogonial cell-associated markers in adult mouse testis 0–144 hours after X-irradiation. Steady state levels of CD9 and Plzf mRNA were elevated by the treatment, whereas c-Kit and Stra8 levels were reduced. CIP2A and Oct4 levels were relatively stable and closely mimicked each other's pattern of expression. GOI, gene of interest; n = 3–7, SEM; a, p < 0.001; b, p < 0.05 when compared to 0 h (= control) value; c, p < 0.05 when compared to 6 hours after X-irradiation. Statistical significancies were tested using one-way ANOVA and Dunnett post hoc tests. Letters a, b and c next to the error bars are in different colors based on the color of the line marking the gene.

Article Snippet: After blocking with 3% BSA PBS for 10 min the slides were rinsed in Tris-HCl (pH 7.4), and incubated overnight with primary antibodies against CIP2A (1:10000 rabbit polyclonal anti-CIP2A [ ], Oct4 (1:200 mouse monoclonal, sc-5279 Santa Cruz), ki-67 (1:5000 mouse monoclonal anti-ki67 (M7240, Dako)), or c-Myc (1:200 mouse monoclonal 9E10 (Nordic Biosite).

Techniques: Immunohistochemical staining, Staining, Computed Tomography, Irradiation, Expressing, Control

Journal: Oncotarget

Article Title: CIP2A is an Oct4 target gene involved in head and neck squamous cell cancer oncogenicity and radioresistance

doi:

Figure Lengend Snippet: (A) Western blot analysis of CIP2A, Oct4 and Nanog expression levels from two different testicular cancer cell lines (Tcam2 and Tera 1) 72 hr after transfection with normal medium (negative control), scrambled siRNA (Scr) and CIP2A siRNA (siCIP2A). Actin was used as a loading control. (B) Western blot analyses of CIP2A expression after transfection with scrambled siRNA (Scr), CIP2A siRNA (siCIP2A) and two different Oct4 siRNAs (siOct4-1, siOct4-2) from Tcam2. (C) Quantitation of CIP2A protein levels from three independent siCIP2A and siOct4 experiments identical to shown in B. Shown is mean +SD of three experiments. *** p < 0.001. (D) Time course analysis of CIP2A expression in Oct4 siRNA transfected cells. (E) Oct4 and CIP2A qRT-PCR analyze in Tcam2 cell line after 5 days treatment with Oct4 or CIP2A siRNA. (F) Regulation of CIP2A promoter activity by Oct4. Tcam2 cells transiently transfected with CIP2A promoter/luciferase constructs were transfected with Oct4 siRNA and the relative promoter activity was analysed after 72 hours. Shown is mean +SD of 3 experiments. *** p < 0.001. (G) Schematic figure of CIP2A promoter constructs and putative Oct4 binding region. Red box indicates Oct4 binding region in CIP2A promoter, which is absent from both -865CIP2Aluc and -1802ΔCIP2Aluc constructs. (H) -865CIP2Aluc fragment significantly decreased promoter activity in Tcam2 cells. Shown is mean ± SEM of 3 experiments. * p < 0.05. (I) Deletion of putative Oct4 binding region decreased promoter activity of -1802CIP2Aluc significantly in Tcam2 cells, but the inhibition did not fully reach the level of inhibition observed by Oct4 RNAi (red line). Shown is mean ± SEM of 3 experiments. * p < 0.05. (J) Western blot analyses of CIP2A and Oct4 expression in mESC model where Oct4 downregulation and ES cell differentiation is achieved after doxycycline addition (Zhbtc4f). (K) Protein expression of CIP2A, Oct4 and p-S62MYC from Tcam2 cells 72 hr after transfection with scrambled or two different Oct4 siRNA.

Article Snippet: After blocking with 3% BSA PBS for 10 min the slides were rinsed in Tris-HCl (pH 7.4), and incubated overnight with primary antibodies against CIP2A (1:10000 rabbit polyclonal anti-CIP2A [ ], Oct4 (1:200 mouse monoclonal, sc-5279 Santa Cruz), ki-67 (1:5000 mouse monoclonal anti-ki67 (M7240, Dako)), or c-Myc (1:200 mouse monoclonal 9E10 (Nordic Biosite).

Techniques: Western Blot, Expressing, Transfection, Negative Control, Control, Quantitation Assay, Quantitative RT-PCR, Activity Assay, Luciferase, Construct, Binding Assay, Inhibition, Cell Differentiation

Journal: Oncotarget

Article Title: CIP2A is an Oct4 target gene involved in head and neck squamous cell cancer oncogenicity and radioresistance

doi:

Figure Lengend Snippet: Representative images after CIP2A, MYC, ki67 and Oct4 immunohistochemical staining in two different human testicular cancer samples, seminoma and embryonal carcinoma. Black bar represents 100 μm.

Article Snippet: After blocking with 3% BSA PBS for 10 min the slides were rinsed in Tris-HCl (pH 7.4), and incubated overnight with primary antibodies against CIP2A (1:10000 rabbit polyclonal anti-CIP2A [ ], Oct4 (1:200 mouse monoclonal, sc-5279 Santa Cruz), ki-67 (1:5000 mouse monoclonal anti-ki67 (M7240, Dako)), or c-Myc (1:200 mouse monoclonal 9E10 (Nordic Biosite).

Techniques: Immunohistochemical staining, Staining

Journal: Oncotarget

Article Title: CIP2A is an Oct4 target gene involved in head and neck squamous cell cancer oncogenicity and radioresistance

doi:

Figure Lengend Snippet: Immunopositivity of CIP2A, MYC, ki67 and Oct4 expression among testicular cancer patient samples

Article Snippet: After blocking with 3% BSA PBS for 10 min the slides were rinsed in Tris-HCl (pH 7.4), and incubated overnight with primary antibodies against CIP2A (1:10000 rabbit polyclonal anti-CIP2A [ ], Oct4 (1:200 mouse monoclonal, sc-5279 Santa Cruz), ki-67 (1:5000 mouse monoclonal anti-ki67 (M7240, Dako)), or c-Myc (1:200 mouse monoclonal 9E10 (Nordic Biosite).

Techniques: Expressing

Journal: Oncotarget

Article Title: CIP2A is an Oct4 target gene involved in head and neck squamous cell cancer oncogenicity and radioresistance

doi:

Figure Lengend Snippet: (A) Western blot analyses of CIP2A and Oct4 expression in testicular cancer (Tera1, Tcam2) and four different HNSCC cell lines (UT-SCC). (B-C) Relative mRNA expression levels of CIP2A, Oct4 and Nanog were studied with quantitative PCR (qPCR) from 15 different HNSCC cells lines (UT-SCC). RPL19 (ribosomal protein L19) was used as an endogenous control gene to normalize expression levels of CIP2A, Oct4 and Nanog before linear regression analysis. (D-F) Representative dot plot figures from UT-SCC2, -7 and -9 cell line cell sorting. Percentages for CD44+ and CD44+/CD24+ side populations are means of three independent experiments per cell line. (G-I) Representative figures of western blot analysis of CIP2A and Oct4 expression levels in sorted CD44+ and CD44+/CD24+ UT-SCC2, -7 and -9 cell populations. GAPDH was used as a loading control.

Article Snippet: After blocking with 3% BSA PBS for 10 min the slides were rinsed in Tris-HCl (pH 7.4), and incubated overnight with primary antibodies against CIP2A (1:10000 rabbit polyclonal anti-CIP2A [ ], Oct4 (1:200 mouse monoclonal, sc-5279 Santa Cruz), ki-67 (1:5000 mouse monoclonal anti-ki67 (M7240, Dako)), or c-Myc (1:200 mouse monoclonal 9E10 (Nordic Biosite).

Techniques: Western Blot, Expressing, Real-time Polymerase Chain Reaction, Control, FACS

Journal: Oncotarget

Article Title: CIP2A is an Oct4 target gene involved in head and neck squamous cell cancer oncogenicity and radioresistance

doi:

Figure Lengend Snippet: (A) Representative figures of negative and high CIP2A or Oct4 expression in HNSCC. White bar represents 100 μm. (B) The Kaplan–Meier 5 year overall survival curve from the HNSCC material ( n = 52). The higher (blue) curve (1) represents the patients with a negative CIP2A expressing tumor, red curve (2) represents low CIP2A positivity and the lowest (green) curve (3) represents HNSCC patients having strong CIP2A expression. (C) The distribution as a percentage of poorly and well-differentiated tumours in Oct4/CIP2A double positive HNSCCs. (D) The Kaplan–Meier 5 year overall survival curve from the HNSCC patients treated with radiotherapy ( n = 29). The higher (blue) curve represents the patients with Oct4 negative tumor and the lower (red) curve represents patients with double Oct4 and CIP2A positivity. (E) Relative Oct4/CIP2A mRNA expression values of six different HNSCC cell lines with highest and lowest double Oct4/CIP2A expression index were compared to radioresistancy expressed in area under the survival curve (AUC) values.

Article Snippet: After blocking with 3% BSA PBS for 10 min the slides were rinsed in Tris-HCl (pH 7.4), and incubated overnight with primary antibodies against CIP2A (1:10000 rabbit polyclonal anti-CIP2A [ ], Oct4 (1:200 mouse monoclonal, sc-5279 Santa Cruz), ki-67 (1:5000 mouse monoclonal anti-ki67 (M7240, Dako)), or c-Myc (1:200 mouse monoclonal 9E10 (Nordic Biosite).

Techniques: Expressing

Journal: Oncotarget

Article Title: CIP2A is an Oct4 target gene involved in head and neck squamous cell cancer oncogenicity and radioresistance

doi:

Figure Lengend Snippet: Immunopositivity of CIP2A and Oct4 expression in head and neck squamous cell carcinoma (HNSCC) patient samples

Article Snippet: After blocking with 3% BSA PBS for 10 min the slides were rinsed in Tris-HCl (pH 7.4), and incubated overnight with primary antibodies against CIP2A (1:10000 rabbit polyclonal anti-CIP2A [ ], Oct4 (1:200 mouse monoclonal, sc-5279 Santa Cruz), ki-67 (1:5000 mouse monoclonal anti-ki67 (M7240, Dako)), or c-Myc (1:200 mouse monoclonal 9E10 (Nordic Biosite).

Techniques: Expressing

Journal: Oncotarget

Article Title: CIP2A is an Oct4 target gene involved in head and neck squamous cell cancer oncogenicity and radioresistance

doi:

Figure Lengend Snippet: (A-B) Relative mRNA expression levels of CIP2A and Oct4 in six different HNSCC cell lines (UT-SCC) were studied with qPCR. Xenograft capacity demonstrates how easily HNSCC cell line is capable to grow in nude mice. ND = not determined. (C) Xenoraft experiment where HNSCC cell lines containing low (UT-SCC-50) and high (UT-SCC-14) Oct4/CIP2A mRNA expression levels were injected into nude mouse subcutaneous and followed for five weeks. (D) CIP2A expression is important for HNSCC tumorigenicity and radioresistancy. In the context of Oct4 positive cells with increased stemness, Oct4-driven CIP2A expression contributes to clinical radioresistance and tumorigenesis by affecting oncogenic pathways involved in proliferation and apoptosis resistance.

Article Snippet: After blocking with 3% BSA PBS for 10 min the slides were rinsed in Tris-HCl (pH 7.4), and incubated overnight with primary antibodies against CIP2A (1:10000 rabbit polyclonal anti-CIP2A [ ], Oct4 (1:200 mouse monoclonal, sc-5279 Santa Cruz), ki-67 (1:5000 mouse monoclonal anti-ki67 (M7240, Dako)), or c-Myc (1:200 mouse monoclonal 9E10 (Nordic Biosite).

Techniques: Expressing, Injection

Journal: Oncotarget

Article Title: CIP2A is an Oct4 target gene involved in head and neck squamous cell cancer oncogenicity and radioresistance

doi:

Figure Lengend Snippet: Relative CIP2A and Oct4 mRNA expression and logarithmic AUC radiosensitivity values of HNSCC cell lines

Article Snippet: After blocking with 3% BSA PBS for 10 min the slides were rinsed in Tris-HCl (pH 7.4), and incubated overnight with primary antibodies against CIP2A (1:10000 rabbit polyclonal anti-CIP2A [ ], Oct4 (1:200 mouse monoclonal, sc-5279 Santa Cruz), ki-67 (1:5000 mouse monoclonal anti-ki67 (M7240, Dako)), or c-Myc (1:200 mouse monoclonal 9E10 (Nordic Biosite).

Techniques: Expressing

Journal: bioRxiv

Article Title: Genomic and microscopic evidence of stable high density and maternally inherited Wolbachia infections in Anopheles mosquitoes

doi: 10.1101/2020.10.29.357400

Figure Lengend Snippet: a , Wolbachia prevalence rates in wild adult female mosquitoes for the w AnM strain in An. demeilloni and w AnM strain in An. moucheti are denoted in blue and green respectively. b, Mosquito COII phylogenetic tree with the highest log likelihood (−4605.97). The analysis involved 130 nucleotide sequences with a total of 735 positions in the final dataset. Filled circles = Wolbachia -infected individuals, open squares = uninfected individuals. c, Mosquito ITS2 phylogenetic tree with the highest log likelihood (−11797.51). The analysis involved 71 nucleotide sequences. Codon positions included were 1st+2nd+3rd+Noncoding. There was a total of 1368 positions in the final dataset. Filled circles = Wolbachia -infected individuals, open squares = uninfected individuals. b,c Reference numbers of additional sequences obtained from GenBank (accession numbers) are shown unless subtree is compressed. The trees are drawn to scale, with branch lengths measured in the number of substitutions per site.

Article Snippet: Normalised qPCR Wolbachia 16S rRNA gene copies per μL were compared using unpaired t-tests in GraphPad Prism 7.

Techniques: Infection

Journal: bioRxiv

Article Title: Genomic and microscopic evidence of stable high density and maternally inherited Wolbachia infections in Anopheles mosquitoes

doi: 10.1101/2020.10.29.357400

Figure Lengend Snippet: a , Wild caught mosquitoes were offered a blood meal to support egg development and offered an oviposition site. Eggs were hatched and the prevalence of vertically transmitted Wolbachia was determined in the F1 larvae, pupae or adults using qPCR. b, Wolbachia was primarily located to the ovarian follicles (A-H). Coloured boxes indicate area of magnification for subsequent images. Within the same ovary, some ovarian follicles are sparsely infected with Wolbachia (E and magnification in G) while others have a heavy infection (C, D and H; E and F). Asterisks indicate infection in the secondary follicles. Wolbachia was imaged with an Alexa 590 labelled probe targeting the Wolbachia 16S rRNA gene (red) and DNA was stained with DAPI (blue). No probe control images (I – L) show no fluorescent signal (I & J and K & L are two separate individuals). FISH analysis found nine out of 16 individuals positive for infection.

Article Snippet: Normalised qPCR Wolbachia 16S rRNA gene copies per μL were compared using unpaired t-tests in GraphPad Prism 7.

Techniques: Infection, Staining, Control

Journal: bioRxiv

Article Title: Genomic and microscopic evidence of stable high density and maternally inherited Wolbachia infections in Anopheles mosquitoes

doi: 10.1101/2020.10.29.357400

Figure Lengend Snippet: a, normalised Wolbachia strain densities measured using qPCR of the conserved Wolbachia 16S rRNA gene. A synthetic oligonucleotide standard was used to calculate Wolbachia 16S rDNA gene copies per ng total DNA using a ten-fold serial dilution standard curve. b, Relative Wolbachia abundance in the mosquito microbiome. Average relative taxonomic abundance of bacterial ASVs within the 16S rDNA microbiomes of An. demeilloni and An. moucheti using QIIME2 . Wolbachia is represented in black, all other bacteria are represented in grey (more information available in Extended data Fig. 5). Wolbachia % abundance of total 16S rDNA bacterial load is seen through box-and-whisker plots.

Article Snippet: Normalised qPCR Wolbachia 16S rRNA gene copies per μL were compared using unpaired t-tests in GraphPad Prism 7.

Techniques: Serial Dilution, Bacteria, Whisker Assay

Journal: bioRxiv

Article Title: Genomic and microscopic evidence of stable high density and maternally inherited Wolbachia infections in Anopheles mosquitoes

doi: 10.1101/2020.10.29.357400

Figure Lengend Snippet: Insect hosts without a known Wolbachia strain are highlighted in grey, whilst those with a known Wolbachia infection are highlighted in green. Analysis includes An. gambiae from previously published studies (●), Burkina Faso - Baldini et al. 2014 (○) and newly sequenced An. gambiae from the DRC (◊) and An. coluzzii from Ghana samples sequenced during our study. a, Heatmap of coverage from published genome sequencing datasets after first mapping to the associated host genome and subsequently to a selection of Wolbachia genomes. Shades of blue represent low values in either depth or breadth of coverage and shades of red represent high values. Samples from arthropods not known to contain Wolbachia have comparatively low depth and breadth of coverage for against Wolbachia genomes. A complete results table is available in Supplementary table 4. b, Average mapping coverage of Wolbachia and host mosquito genomes. The average minimum and maximum coverage are shown comparing Anopheles species and arthropods that have a known or unknown Wolbachia strain.

Article Snippet: Normalised qPCR Wolbachia 16S rRNA gene copies per μL were compared using unpaired t-tests in GraphPad Prism 7.

Techniques: Infection, Sequencing, Selection

Journal: bioRxiv

Article Title: Genomic and microscopic evidence of stable high density and maternally inherited Wolbachia infections in Anopheles mosquitoes

doi: 10.1101/2020.10.29.357400

Figure Lengend Snippet: a , Heatmap showing the results of FastANI, comparing a total of 48 Wolbachia genomes against each other for similarity. High values represent close genetic similarity and a smaller phylogenetic distance, vice versa with low values, as shown by the colour key to the top left. The colour bar to the left of the heatmap indicates previously known clade organisation of the analysed Wolbachia species. b, Clustering analysis of the same Wolbachia genomes, with colour scheme preserved from the colour bar in panel a . The complete results matrix is available in supplementary table 8 . c, Representation of the cif genes within the assembled Wolbachia genomes, with predicted protein domains overlaid. Each gene pair is drawn in relation to the contig they have been annotated on (x-axis, nucleotides). Domains were detected using the HHPred webserver

Article Snippet: Normalised qPCR Wolbachia 16S rRNA gene copies per μL were compared using unpaired t-tests in GraphPad Prism 7.

Techniques:

Journal: ACS Infectious Diseases

Article Title: Two Years into the COVID-19 Pandemic: Lessons Learned

doi: 10.1021/acsinfecdis.2c00204

Figure Lengend Snippet: Origins of different coronaviruses. In the 21st century, three highly pathogenic betacoronaviruses have emerged from bats to cause respiratory disease in humans. In 2002, a betacoronavirus called severe acute respiratory syndrome coronavirus (SARS-CoV) emerged in Guangdong Province, China, and caused respiratory disease in humans. One decade later, another betacoronavirus called Middle East respiratory syndrome coronavirus (MERS-CoV) was reported in Saudi Arabia. Both SARS-CoV and MERS-CoV emerged from bats and were transmitted to humans via civets and dromedary camels, respectively. Later, in December 2019, a novel betacoronavirus called severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) emerged from bats and caused a pandemic disease called coronavirus disease 2019 (COVID-19). It was likely transmitted to humans by pangolins, although its origin is still being investigated. In summary, coronaviruses represent an example of emerging zoonotic viruses that have crossed the species barrier to cause disease in the human population. The possibility of a new, highly pathogenic coronavirus emerging from wild animals in the next few years cannot be ruled out. This figure was created with Biorender.com .

Article Snippet: Preclinical tests confirmed the anti-SARS-CoV-2 activity of remdesivir in mice and non-human primate models., Since the first in vitro / in vivo evidence, remdesivir has been clinically tested in patients with COVID-19.

Techniques:

Journal: ACS Infectious Diseases

Article Title: Two Years into the COVID-19 Pandemic: Lessons Learned

doi: 10.1021/acsinfecdis.2c00204

Figure Lengend Snippet: Schematic of the SARS-CoV-2 virus particle and genome architecture. The top panel illustrates the general structure of the SARS-CoV-2 viral particle, indicating its structural proteins and genome. The bottom panel illustrates the genome organization of SARS-CoV-2, including the 5′ cap, the region that encodes the nonstructural proteins required for viral replication (nsp1–nsp16), the region that encodes accessory and structural proteins (spike [S] protein, membrane [M] protein, envelope [E] protein, and nucleocapsid [N] proteins), and the poly-A tail. This figure was created with Biorender.com .

Article Snippet: Preclinical tests confirmed the anti-SARS-CoV-2 activity of remdesivir in mice and non-human primate models., Since the first in vitro / in vivo evidence, remdesivir has been clinically tested in patients with COVID-19.

Techniques:

Journal: ACS Infectious Diseases

Article Title: Two Years into the COVID-19 Pandemic: Lessons Learned

doi: 10.1021/acsinfecdis.2c00204

Figure Lengend Snippet: The SARS-CoV-2 replication cycle. SARS-CoV-2 enters the host cell via an endosomal pathway or through fusion of the viral envelope with the host cell membrane. Briefly, viral entry is initiated by binding of the RBD of the spike (S) protein to the human host cell receptor (ACE2). After the RBD–receptor interaction, the S protein undergoes proteolytic cleavage, which can be catalyzed by several host proteases, such as TMPRSS2, furin, and cathepsin B/L. Following viral entry, SARS-CoV-2 releases its genomic RNA into the cytoplasm and utilizes both the host’s and its own enzymatic machinery to replicate its genetic material and assemble new viral particles. The viral RNA genome is first translated into viral replicase polyproteins (pp1a and pp1ab), which are then cleaved into 16 nsps. In the process of genome replication and transcription mediated by the replication–transcription complex (RTC), the negative-sense (− sense) genomic RNA is synthesized and used as a template to generate a positive-sense (+ sense) genomic RNA and subgenomic RNAs. Viral assembly is aided by the interaction between viral genomic RNA and structural proteins located in the endoplasmic reticulum (ER) and ER–Golgi intermediate compartment (ERGIC). Finally, these virions are released to the plasma membrane via deacidified lysosomes and secreted from the infected cell via exocytosis. This figure was created with Biorender.com .

Article Snippet: Preclinical tests confirmed the anti-SARS-CoV-2 activity of remdesivir in mice and non-human primate models., Since the first in vitro / in vivo evidence, remdesivir has been clinically tested in patients with COVID-19.

Techniques: Binding Assay, Synthesized, Infection

Journal: ACS Infectious Diseases

Article Title: Two Years into the COVID-19 Pandemic: Lessons Learned

doi: 10.1021/acsinfecdis.2c00204

Figure Lengend Snippet: Major modes of SARS-CoV-2 human-to-human transmission. Transmission can be through direct contact of airborne infectious particles deposited in respiratory droplets and aerosols. Indirect contact by infectious particles deposited on fomites represents another potential route for viral transmission. This figure was created with Biorender.com .

Article Snippet: Preclinical tests confirmed the anti-SARS-CoV-2 activity of remdesivir in mice and non-human primate models., Since the first in vitro / in vivo evidence, remdesivir has been clinically tested in patients with COVID-19.

Techniques: Transmission Assay

Journal: ACS Infectious Diseases

Article Title: Two Years into the COVID-19 Pandemic: Lessons Learned

doi: 10.1021/acsinfecdis.2c00204

Figure Lengend Snippet: Clinical manifestations of COVID-19. Patients infected with SARS-CoV-2 can be asymptomatic, develop mild disease with diverse symptoms, or progress to severe illness. COVID-19 cases with severe complications are more frequently presented by patients from the high-risk group. This figure was created with Biorender.com .

Article Snippet: Preclinical tests confirmed the anti-SARS-CoV-2 activity of remdesivir in mice and non-human primate models., Since the first in vitro / in vivo evidence, remdesivir has been clinically tested in patients with COVID-19.

Techniques: Infection

Journal: ACS Infectious Diseases

Article Title: Two Years into the COVID-19 Pandemic: Lessons Learned

doi: 10.1021/acsinfecdis.2c00204

Figure Lengend Snippet: Overview of different methods for COVID-19 diagnosis. SARS-CoV-2 can be directly detected in humans using molecular approaches, such as RT-qPCR, DNA sequencing, RT-LAMP, CRISPR/Cas systems, and sensors. Imaging tests, including chest computed tomography (CT), have been widely used as a complementary approach to diagnose COVID-19 patients. Additionally, human antibodies produced against SARS-CoV-2 antigens can be detected in blood samples via serological methods, including enzyme-linked immunosorbent assay (ELISA), chemiluminescence immunoassay (CLIA), immunofluorescence assay (IFA), and lateral flow assay (LFA). This figure was created with Biorender.com .

Article Snippet: Preclinical tests confirmed the anti-SARS-CoV-2 activity of remdesivir in mice and non-human primate models., Since the first in vitro / in vivo evidence, remdesivir has been clinically tested in patients with COVID-19.

Techniques: Quantitative RT-PCR, DNA Sequencing, CRISPR, Imaging, Computed Tomography, Produced, Enzyme-linked Immunosorbent Assay, Chemiluminescence Immunoassay, Immunofluorescence, Lateral Flow Assay

Journal: ACS Infectious Diseases

Article Title: Two Years into the COVID-19 Pandemic: Lessons Learned

doi: 10.1021/acsinfecdis.2c00204

Figure Lengend Snippet: Kinetics of viral load and immune response during SARS-CoV-2 infection. During the first week after SARS-CoV-2 exposure, a period when patients are typically presymptomatic, the viral load increases and reaches its peak during the initial days after symptom onset. Seroconversion in infected patients begins in the second week after symptom onset. Three to four weeks after symptom onset, the IgM and IgG levels both reach their peaks and then begin to drop—more rapidly for IgM than for IgG. To avoid false-negative results when COVID-19 diagnostic tests are performed, the kinetics of viral load and immune response should be taken into consideration. The figure was adapted from the template in Biorender.com .

Article Snippet: Preclinical tests confirmed the anti-SARS-CoV-2 activity of remdesivir in mice and non-human primate models., Since the first in vitro / in vivo evidence, remdesivir has been clinically tested in patients with COVID-19.

Techniques: Infection, Diagnostic Assay

Journal: ACS Infectious Diseases

Article Title: Two Years into the COVID-19 Pandemic: Lessons Learned

doi: 10.1021/acsinfecdis.2c00204

Figure Lengend Snippet: Vaccine platforms currently being developed against SARS-CoV-2 infection. Since the emergence of SARS-CoV-2, great efforts have been made by research groups and companies around the world toward the development of effective vaccines. Briefly, the graph in (A) shows current vaccine candidates in the clinical phase. Vaccine platforms currently being developed against SARS-CoV-2 infection include those based on (B) RNA, (C) DNA, (D) replicating viral vectors, (E) inactivated viruses, (F) attenuated viruses, (G) viruslike particles (VLPs), (H) nonreplicating viral vectors, (I) protein subunits, and (J) modified antigen-presenting cells (APCs). Abbreviations: S, spike protein; LNP, lipid nanoparticle; LV, lentiviral vector; DC, dendritric cell. This figure was created with Biorender.com .

Article Snippet: Preclinical tests confirmed the anti-SARS-CoV-2 activity of remdesivir in mice and non-human primate models., Since the first in vitro / in vivo evidence, remdesivir has been clinically tested in patients with COVID-19.

Techniques: Infection, Modification, Plasmid Preparation

Journal: ACS Infectious Diseases

Article Title: Two Years into the COVID-19 Pandemic: Lessons Learned

doi: 10.1021/acsinfecdis.2c00204

Figure Lengend Snippet: SARS-CoV-2 variants of concern (VOCs). (A) Schematic of the SARS-CoV-2 genome architecture. (B) Definition of nonsynonymous mutations and deletions of each VOC. Nucleotide alterations without predicted or confirmed impact on protein structure and/or function are shown in black. Nucleotide alterations with predicted or confirmed impact on protein structure and/or function are shown in red. (C) Phenotypic characteristics of VOCs. Global distributions are according to the PANGO lineages website ( https://cov-lineages.org/index.html ). This figure was created with Biorender.com .

Article Snippet: Preclinical tests confirmed the anti-SARS-CoV-2 activity of remdesivir in mice and non-human primate models., Since the first in vitro / in vivo evidence, remdesivir has been clinically tested in patients with COVID-19.

Techniques:

Journal: JAMA Ophthalmology

Article Title: Biomarker Detection and Validation for Corneal Involvement in Patients With Acute Infectious Conjunctivitis

doi: 10.1001/jamaophthalmol.2024.2891

Figure Lengend Snippet: A, Each data point represents the mean area under the receiver operating characteristic curve (AUROC) of logistic regression models that left out the respective gene over 1000 randomized training and validation splits. The red dotted line represents the mean AUROC for all splits of the full model of all 13 genes. The blue dotted lines represent the 95% CIs of the full model. Error bars represent 95% CIs for the individual models. B, Validation of APOE in conjunctival samples of 48 patients with presumed acute infectious conjunctivitis using quantitative reverse transcription polymerase chain reaction (RT-qPCR) analysis. APOE expression was normalized to glyceraldehyde 3-phosphate dehydrogenase and expressed as Δ threshold cycle (Δ CT). P value was calculated using the Mann-Whitney U test.

Article Snippet: The Fisher exact test was used to determine the discriminability of APOE RT-qPCR with clinical findings of corneal involvement (GraphPad version 10).

Techniques: Reverse Transcription, Polymerase Chain Reaction, Quantitative RT-PCR, Expressing, MANN-WHITNEY