Journal:

Article Title: Quantitative Detection of the Free-Living Amoeba Hartmannella vermiformis in Surface Water by Using Real-Time PCR †

doi: 10.1128/AEM.00085-06

Figure Lengend Snippet: Calibration curve for real-time PCR results, using primers Hv1227F and Hv1728R and H. vermiformis ATCC 50237 grown in modified PYNFH medium. The indicated line, derived from 42 real-time PCRs, is defined by an average slope of −3.75 ± 0.18 and an intercept of 28.40 ± 0.95. For each concentration, all obtained data points are given. For log cell number −1.94, only two analyses were conducted.

Article Snippet: Suspensions of H. vermiformis KWR-1, H. vermiformis ATCC 50237, and H. abertawensis and environmental surface water samples were filtered over a 1.2-μm-pore-size RTTP Isopore membrane (Millipore) in a vacuum not exceeding 0.3 × 10 5 Pa. DNA extraction of the filter-retained cells was done using a FastDNA spin kit for soil (BIO 101, Carlsbad, Calif.) following the instructions supplied by the manufacturer.

Techniques: Real-time Polymerase Chain Reaction, Modification, Derivative Assay, Concentration Assay

Journal:

Article Title: Quantitative Detection of the Free-Living Amoeba Hartmannella vermiformis in Surface Water by Using Real-Time PCR †

doi: 10.1128/AEM.00085-06

Figure Lengend Snippet: Recovery of H. vermiformis ATCC 50237 cells spiked into different types of surface water and into PYNFH growth medium. DNA isolations and real-time PCRs were all performed in duplicate. The indicated dilutions are DNA dilutions. Error bars indicate standard deviations.

Article Snippet: Suspensions of H. vermiformis KWR-1, H. vermiformis ATCC 50237, and H. abertawensis and environmental surface water samples were filtered over a 1.2-μm-pore-size RTTP Isopore membrane (Millipore) in a vacuum not exceeding 0.3 × 10 5 Pa. DNA extraction of the filter-retained cells was done using a FastDNA spin kit for soil (BIO 101, Carlsbad, Calif.) following the instructions supplied by the manufacturer.

Techniques:

Journal:

Article Title: Quantitative Detection of the Free-Living Amoeba Hartmannella vermiformis in Surface Water by Using Real-Time PCR †

doi: 10.1128/AEM.00085-06

Figure Lengend Snippet: 18S rRNA gene copy numbers in H. vermiformis ATCC 50237 in relation to maturation state (% cysts). An average DNA extraction efficiency of 62.7% was used in the calculations. The equation of the indicated trend line is y = 0.0026x + 3.0114, and R2 = 0.3314.

Article Snippet: Suspensions of H. vermiformis KWR-1, H. vermiformis ATCC 50237, and H. abertawensis and environmental surface water samples were filtered over a 1.2-μm-pore-size RTTP Isopore membrane (Millipore) in a vacuum not exceeding 0.3 × 10 5 Pa. DNA extraction of the filter-retained cells was done using a FastDNA spin kit for soil (BIO 101, Carlsbad, Calif.) following the instructions supplied by the manufacturer.

Techniques: DNA Extraction

Journal: BMC Cancer

Article Title: A signature of correlated CDC20 and UBCH10 expression indicates poor prognosis in primary head and neck squamous cell carcinoma

doi: 10.1186/s12885-025-14773-x

Figure Lengend Snippet: Correlating CDC20 and UBCH10 expression and its clinical relevance across primary oral malignancies from the Eastern Indian study cohort. A Box-whisker plots of CDC20 and UBCH10 expression between malignant oral tumor ( n = 32) and adjacent normal tissue specimens ( n = 24). Tissue specimens were processed for total RNA extraction and cDNA synthesis, followed by quantitative qRT-PCR using primers specific for CDC20 and UBCH10 and 18 s rRNA as endogenous control. ΔCt values were calculated and represented as dot-plots. The Y axis represents the relative mRNA expression in ΔCt values. In X axis, the red box shows the number of oral tumor samples and the black box plot represents the number of adjacent normal cases. The data were analysed by Mann–Whitney U-Test. * p < 0.05; ns, not significant. B Bar diagram showing the CDC20 and UBCH10 expression in individual oral cancer patients. The Y axis represents relative quantification of values in log scale (Log2 RQ) and X axis shows the corresponding subject identification numbers. The ( *) symbol indicates patients with CDC20-UBCH10 both high expressions. C-D Representative images of immunohistochemical (IHC) analysis of primary oral malignant tissues ( n = 16) and adjacent normal tissues ( n = 16) by using antibodies against Cdc20 and UbcH10. E The representative bar diagrams of correlation by evaluating the staining intensity score of IHC for Cdc20 and UbcH10 in primary oral malignant tissues. The X axis shows the corresponding subject identification numbers. The ( *) symbol indicates patients with CDC20-UBCH10 both high expressions

Article Snippet: For overexpression analysis, cells were transiently transfected with 1 μg of plasmid and harvested after 48 h. Also, human p55 CDC shRNA ( CDC20 ) target specific lentiviral plasmid (Santa Cruz Biotechnology, Inc.) along with packaging and envelope plasmids (psPAX2 and pMD2.G) were transfected into cultured HEK293T cells at 60% confluency.

Techniques: Expressing, Whisker Assay, RNA Extraction, cDNA Synthesis, Quantitative RT-PCR, Control, MANN-WHITNEY, Quantitative Proteomics, Immunohistochemical staining, Staining

Journal: BMC Cancer

Article Title: A signature of correlated CDC20 and UBCH10 expression indicates poor prognosis in primary head and neck squamous cell carcinoma

doi: 10.1186/s12885-025-14773-x

Figure Lengend Snippet: The expression of CDC20 and UBCH10 are correlated in primary head and neck malignancies in global TCGA-HNSC (the cancer genome atlas- head and neck squamous cell carcinoma) cohort. A Box plots, derived from UALCAN database, representing transcript per million (TPM) values of CDC20 across primary head and neck tumor ( n = 520) and adjacent normal tissues ( n = 44), B-H Box plots, depicting TPM values of CDC20 based on ( B ) anatomical subsites (oral cavity and lip, pharynx, and larynx) ( C ) Human papilloma virus (HPV) infection status, D Age status (21–40, 41–60, 61–80, and 81–100 years), E Gender status (male and female), F nodal metastasis status (N0, N1, N2, N3), G tumor grade status (Grade 1, 2, 3, and 4), and ( H ) tumor stage status (I, II, III, and IV). The Y axis represents transcripts per million (TPM) for gene expression. I Box plots, obtained from UALCAN, representing TPM values of UBCH10 across the HNSC primary tumor ( n = 520) and adjacent normal tissues ( n = 44). J-P Box plots, illustrating TPM values of UBCH10 based on the parameters similar to CDC20 . Q-R The representative scatter plot derived from the UCSC Xena and Cancer Cell Line Encyclopedia (CCLE) database, depicts the Pearson’s correlation analysis between the gene expression in log2(TPM + 1) values of CDC20 and UBCH10 in primary HNSC tumor tissues and cell lines respectively. The Pearson correlation coefficient is reported as ‘R’ value. Correlation analysis was performed using R (version 4.4.0). p value was obtained by unpaired student’s t-test. * p < 0.05, ** p < 0.01, *** p < 0.001, **** p < 0.0001, ns; not significant. For all group comparisons, data were represented as mean ± SD

Article Snippet: For overexpression analysis, cells were transiently transfected with 1 μg of plasmid and harvested after 48 h. Also, human p55 CDC shRNA ( CDC20 ) target specific lentiviral plasmid (Santa Cruz Biotechnology, Inc.) along with packaging and envelope plasmids (psPAX2 and pMD2.G) were transfected into cultured HEK293T cells at 60% confluency.

Techniques: Expressing, Derivative Assay, Virus, Infection, Gene Expression

Journal: BMC Cancer

Article Title: A signature of correlated CDC20 and UBCH10 expression indicates poor prognosis in primary head and neck squamous cell carcinoma

doi: 10.1186/s12885-025-14773-x

Figure Lengend Snippet: Correlated overexpression of CDC20 - UBCH10 predicts poor survival in patients with head and neck squamous cell carcinoma (HNSC). A , B Overall survival (OS) probabilities of patients in TCGA-HNSC cohort ( n = 566) from Kaplan Meier plotter dataset with ( A ) CDC20 high and low expression and ( B ) UBCH10 high and low expression group as estimated by Kaplan–Meier analysis. The logrank P value and hazard ratio (HR) for individual analyses are shown. C-E Overall survival (OS), progression-free interval (PFI), and disease-specific survival (DSS) of patients from the TCGA-HNSC cohort with CDC20-UBCH10 both high ( n = 226), CDC20 high- UBCH10 low ( n = 60), and CDC20 low- UBCH10 high expression ( n = 58) group were performed. For statistical analysis log rank P values and hazard ratio (HRs) for individual analyses are shown. * p < 0.05

Article Snippet: For overexpression analysis, cells were transiently transfected with 1 μg of plasmid and harvested after 48 h. Also, human p55 CDC shRNA ( CDC20 ) target specific lentiviral plasmid (Santa Cruz Biotechnology, Inc.) along with packaging and envelope plasmids (psPAX2 and pMD2.G) were transfected into cultured HEK293T cells at 60% confluency.

Techniques: Over Expression, Expressing

Journal: BMC Cancer

Article Title: A signature of correlated CDC20 and UBCH10 expression indicates poor prognosis in primary head and neck squamous cell carcinoma

doi: 10.1186/s12885-025-14773-x

Figure Lengend Snippet: Correlated overexpression of CDC20 - UBCH10 promotes oncogenic properties in HNSC cell line, SCC084. Cells were ectopically transfected with 1000 ng of control or pCDNA5-FLAG-Cdc20 plasmid. Cells was processed for ( A ) Western blot analyses using antibodies against Cdc20, UbcH10 and β-actin (left panel), and their densitometric analyses (right panel); (* p < 0.05, ** p < 0.01, unpaired Student’s t-test), B Clonogenic assay (left panel, representative image & right panel, quantification of colonies); (* p < 0.05, Welch’s t-test), C Wound healing assay (left panel, representative image; top right panel, western blot representative image & bottom right panel, quantification of wound healing) (* p < 0.05, ns; not significant, unpaired student’s t-test), D Matrigel invasion assay (left panel, representative image & right panel, quantification of cell invasion) (* p < 0.05, unpaired student’s t-test), and, E Cell viability (MTT) assay (* p < 0.05, ** p < 0.01, ns; not significant, two way anova, Sidak’s multiple comparison test). F Cells were stably transduced with control or CDC20 -shRNA specific lentiviral vector plasmid. Cells was processed for ( F ) Western blot analyses using antibodies against Cdc20, UbcH10 and β-actin (left panel), and their densitometric analyses (right panel), G Colony formation assay (left panel, representative image & right panel, quantification of colonies), H Matrigel invasion assay (left panel, representative image & right panel, quantification of cell invasion), and, I Cell viability (MTT) assay. For all experiments the statistically analysed data are indicated as mean ± SD of three independent experiments

Article Snippet: For overexpression analysis, cells were transiently transfected with 1 μg of plasmid and harvested after 48 h. Also, human p55 CDC shRNA ( CDC20 ) target specific lentiviral plasmid (Santa Cruz Biotechnology, Inc.) along with packaging and envelope plasmids (psPAX2 and pMD2.G) were transfected into cultured HEK293T cells at 60% confluency.

Techniques: Over Expression, Transfection, Control, Plasmid Preparation, Western Blot, Clonogenic Assay, Wound Healing Assay, Invasion Assay, MTT Assay, Comparison, Stable Transfection, Transduction, shRNA, Colony Assay

Journal: BMC Cancer

Article Title: A signature of correlated CDC20 and UBCH10 expression indicates poor prognosis in primary head and neck squamous cell carcinoma

doi: 10.1186/s12885-025-14773-x

Figure Lengend Snippet: Correlation of CDC20 - UBCH10 expression and its clinical relevance on survival outcome in primary solid tumor malignancies. A-F The representative scatter plots derived from the UCSC Xena database, represent the Pearson’s correlation analysis between the gene expression in log2 (TPM) values of CDC20 and UBCH10 in primary tumor tissues of the representative cancer subtypes (BRCA ( n = 1215), LUAD ( n = 576), LIHC ( n = 421), PRAD ( n = 550), OV ( n = 308), and CESC ( n = 307)). The Pearson correlation coefficient is reported as ‘R’ value. *p < 0.05. G-L Overall survival (OS) data of different primary cancer subtypes across several TCGA cohorts were obtained from the UCSC Xena database. OS probabilities of patients with CDC20-UBCH10 both high, CDC20 high- UBCH10 low, and CDC20 low- UBCH10 high expression group were performed. BRCA, Breast invasive carcinoma; LUAD, Lung adenocarcinoma; LIHC, Liver hepatocellular carcinoma; PRAD, Prostate adenocarcinoma; OV, Ovarian carcinoma; CESC, Cervical squamous cell carcinoma. For statistical analysis p values were obtained by log rank test. Hazard ratio (HRs) for individual analyses are shown. * p < 0.05

Article Snippet: For overexpression analysis, cells were transiently transfected with 1 μg of plasmid and harvested after 48 h. Also, human p55 CDC shRNA ( CDC20 ) target specific lentiviral plasmid (Santa Cruz Biotechnology, Inc.) along with packaging and envelope plasmids (psPAX2 and pMD2.G) were transfected into cultured HEK293T cells at 60% confluency.

Techniques: Expressing, Derivative Assay, Gene Expression

Journal: BMC Cancer

Article Title: A signature of correlated CDC20 and UBCH10 expression indicates poor prognosis in primary head and neck squamous cell carcinoma

doi: 10.1186/s12885-025-14773-x

Figure Lengend Snippet: Correlated overexpression of CDC20 - UBCH10 predicts poor survival in malignancies of several solid organs. A-G Representative progression-free interval (PFI) and disease-specific survival (DSS) data of different primary cancer subtypes across several TCGA cohorts were obtained from the UCSC Xena database. Survival probabilities of patients with CDC20-UBCH10 both high, CDC20 high- UBCH10 low, and CDC20 low- UBCH10 high expression group were performed in ( A ) BRCA, Breast invasive carcinoma; B LUAD, Lung adenocarcinoma; C LIHC, Liver hepatocellular carcinoma; D PRAD, Prostate adenocarcinoma; E OV, Ovarian carcinoma; F CESC, Cervical squamous cell carcinoma, and (G) COAD, Colon adenocarcinoma. For statistical analysis log rank P values and hazard ratio (HRs) for individual analyses are shown. * p < 0.05

Article Snippet: For overexpression analysis, cells were transiently transfected with 1 μg of plasmid and harvested after 48 h. Also, human p55 CDC shRNA ( CDC20 ) target specific lentiviral plasmid (Santa Cruz Biotechnology, Inc.) along with packaging and envelope plasmids (psPAX2 and pMD2.G) were transfected into cultured HEK293T cells at 60% confluency.

Techniques: Over Expression, Expressing