| 1. |
- Beal, Jacob, et al.
(author)
-
Robust estimation of bacterial cell count from optical density
- 2020
-
In: Communications Biology. - : Springer Science and Business Media LLC. - 2399-3642. ; 3:1
-
Journal article (peer-reviewed)abstract
- Optical density (OD) is widely used to estimate the density of cells in liquid culture, but cannot be compared between instruments without a standardized calibration protocol and is challenging to relate to actual cell count. We address this with an interlaboratory study comparing three simple, low-cost, and highly accessible OD calibration protocols across 244 laboratories, applied to eight strains of constitutive GFP-expressing E. coli. Based on our results, we recommend calibrating OD to estimated cell count using serial dilution of silica microspheres, which produces highly precise calibration (95.5% of residuals <1.2-fold), is easily assessed for quality control, also assesses instrument effective linear range, and can be combined with fluorescence calibration to obtain units of Molecules of Equivalent Fluorescein (MEFL) per cell, allowing direct comparison and data fusion with flow cytometry measurements: in our study, fluorescence per cell measurements showed only a 1.07-fold mean difference between plate reader and flow cytometry data.
|
|
| 2. |
- Du, Zi-Ming
(author)
-
Biomarkers in nasopharyngeal carcinoma
- 2012
-
Doctoral thesis (other academic/artistic)abstract
- Nasopharyngeal carcinoma (NPC) is one of the most common malignancies in certain areas of Southern China, Southeastern Asia and Northern Africa. Currently, evaluation of NPC prognosis is mainly based on the tumor-node-metastasis (TNM) staging system. However, NPC patients with the same clinical stage often present different clinical courses, suggesting that the TNM staging is insufficient to predict prognosis of this disease. Therefore, it is important to find molecular biomarkers, which can help clinicians to identify NPC patients with worse prognosis and develop therapeutic interventions in NPC patients. This thesis presents the identification and investigation of mechanism of several novel markers in NPC. In the first paper, Caveolin-1 (Cav-1), a major structural component of caveolae, and CD147 (also known as extracellular matrix metalloproteinase inducer, EMMPRIN), a glycoprotein, were found to be overexpressed in NPC. Both Cav-1 and CD147 expression levels correlated significantly with metastasis and poor prognosis of NPC patients. Further studies revealed that Cav-1 and CD147 enhance NPC cell migration, which is associated with MMP-3 and MMP-11 (active) secretion. The role of microRNA-155 (miR-155) is associated with oncogenesis of several human tumors. In the second paper, miR-155 was found to be upregulated in NPC cell lines and clinical samples. EBV encoded LMP1 and LMP2A could further enhance the expression of miR-155 in NPC CNE1 and TW03 cells. JMJD1A was identified as a direct target of miR-155 in NPC. Downregulation of JMJD1A was significantly correlated with N stage of the TNM classification, a lower five-year survival rate, and a lower five-year disease-free survival rate of NPC patients. Spleen tyrosine kinase (Syk) is a nonreceptor tyrosine kinase and often aberrantly expressed in human cancers. In the third paper, high expression of Syk was detected in 24% of NPC cases. High expression of Syk, resulted partly from LMP2A expression in NPC, is associated with tumor recurrence and poor prognosis of NPC patients. Human chromosome 3 (Chr. 3) contains clusters of tumor suppressor genes (TSGs) involved in many cancer types. In the fourth paper, using Not I Chr. 3 microarray, ten candidate TSGs were found in NPC. Among them, the CpG island in the promoter region of Wingless-type Mouse mammary tumor virus integration site family, member 7A (WNT7a) and the intron 1 region of Integrin α9 (ITGA9) were confirmed to be hypermethylated in NPC by bisulfite sequencing and methylation specific PCR. Demethylating agent 5-aza-2′-deoxycytidine (5-aza-CdR) treatment could restore the expression of WNT7a and ITGA9 in NPC cell lines. Furthermore, WNT7a and ITGA9 were downregulated in NPC clinical samples. As both proteins execute significant functions related to the tumor cell biology, the potential of WNT7a and ITGA9 as diagnosis or therapeutic targets for NPC should be considered.
|
|
| 3. |
- Nawaz, Imran, et al.
(author)
-
Integrin α9 gene promoter is hypermethylated and downregulated in nasopharyngeal carcinoma
- 2015
-
In: Oncotarget. - Albany, NY, United States : Impact Journals LLC. - 1949-2553. ; 6:31, s. 31493-31507
-
Journal article (peer-reviewed)abstract
- Epigenetic silencing of tumor suppressor genes (TSGs) by promoter methylation can be an early event in the multi-step process of carcinogenesis. Human chromosome 3 contains clusters of TSGs involved in many cancer types including nasopharyngeal carcinoma (NPC), the most common cancer in Southern China. Among ten candidate TSGs identified in chromosome 3 using NotI microarray, ITGA9 and WNT7A could be validated. 5-aza-2 deoxycytidine treatment restored the expression of ITGA9 and WNT7A in two NPC cell lines. Immunostaining showed strong expression of these genes in the membrane and cytoplasm of adjacent control nasopharyngeal epithelium cells, while they were weakly expressed in NPC tumor cells. The ITGA9 promoter showed marked differentially methylation between tumor and control tissue, whereas no differentially methylation could be detected for the WNT7A promoter. The expression level of ITGA9 in NPC tumors was downregulated 4.9-fold, compared to the expression in control. ITGA9 methylation was detected by methylation specific PCR (MSP) in 56% of EBV positive NPC-cases with 100% specificity. Taken together, this suggests that ITGA9 might be a TSG in NPC that is involved in tumor cell biology. The possibility of using ITGA9 methylation as a marker for early detection of NPC should further be explored.
|
|
