DNA Microarray Probe Preparation by Gel Isolation Nested PCR

( Hong Min Wang ),( Wen Li Ma ),( Hai Huang ),( Wei Wei Xiao ),( Yan Wang ),( Wen Ling Zheng ) 생화학분자생물학회 2004 BMB Reports Vol.37 No.3

To develop a simplified method that can rapidly prepare DNA microarray probes in a massive scale, a lambda phage genomic DNA-fragments library was constructed for the microarray-probes collection. Four methods of DNA band recovery from the first PCR products were tested and compared. The DNA microarray probes were collected by a novel method of nested PCR that was mediated by gel isolation of the first PCR products. This method was named GIN-PCR. The probes that were prepared by this GIN-PCR technique were used as subjects to fabricate a DNA microarray. The results showed that a wooden toothpick was superior to the other 3 methods, since this technique can steadily transfer the DNA bands as the template of the second PCR after the first PCR. A group of probes were successfully collected and DNA microarrays were constructed using these probes. Hybridization results demonstrated that this technique of DNA recovery and probe preparation was rapid, efficient, and effective. We developed a cost-effective and less labor-intensive method for DNA microarray probe preparation by nested PCR that is mediated by wooden toothpick transfer of the DNA bands in the gel after electrophoresis.

Characteristics of Mammary Paget's Disease in China: a National-wide Multicenter Retrospective Study During 1999-2008

Zheng, Shan,Song, Qing-Kun,Zhao, Lin,Huang, Rong,Sun, Li,Li, Jing,Fan, Jin-Hu,Zhang, Bao-Ning,Yang, Hong-Jian,Xu, Feng,Zhang, Bin,Qiao, You-Lin Asian Pacific Journal of Cancer Prevention 2012 Asian Pacific journal of cancer prevention Vol.13 No.5

The aim of this study was to detail characteristics of mammary Paget's disease (PD) representing the whole population in China. A total of 4211 female breast cancer inpatients at seven tertiary hospitals from seven representative geographical regions of China were collected randomly during 1999 to 2008. Data for demography, risk factors, diagnostic imaging test, physical examination and pathologic characters were surveyed and biomarker status was tested by immunohistochemistry. The differences of demography and risk factors between PD with breast cancer and other lesions were compared using Chi-square test or t-test, with attention to physical examination and pathological characters. The percentage of PD was 1.6% (68/4211) in all breast cancers. The mean age at diagnosis was 48.1, and 63.2% (43/68) patients were premenopausal. There is no difference in demography and risk factors between PD with breast cancer and other breast cancer (P > 0.05). The main pattern of PD in physical exam and pathologic pattern were patients presenting with a palpable mass in breast (65/68, 95.6%) and PD with underlying invasive cancer (82.4%, 56/68) respectively. The rate of multifocal disease was 7.4% (5/68). PD with invasive breast cancer showed larger tumor size, more multifocal disease, lower ER and PR expression and higher HER2 overexpression than those in other invasive breast cancer (P < 0.05). These results suggested that PD in China is a concomitant disease of breast cancer, and that PD with underlying invasive cancer has more multiple foci and more aggressive behavior compared with other breast invasive cancer. We address the urgent needs for establishing diagnostic and therapeutic guidelines for mammary PD in China.

Endophytic fungi harbored in Panax notoginseng: diversity and potential as biological control agents against host plant pathogens of root-rot disease

Zheng, You-Kun,Miao, Cui-Ping,Chen, Hua-Hong,Huang, Fang-Fang,Xia, Yu-Mei,Chen, You-Wei,Zhao, Li-Xing The Korean Society of Ginseng 2017 Journal of Ginseng Research Vol.41 No.3

Background: Endophytic fungi play an important role in balancing the ecosystem and boosting host growth. In the present study, we investigated the endophytic fungal diversity of healthy Panax notoginseng and evaluated its potential antimicrobial activity against five major phytopathogens causing root-rot of P. notoginseng. Methods: A culture-dependent technique, combining morphological and molecular methods, was used to analyze endophytic fungal diversity. A double-layer agar technique was used to challenge the phytopathogens of P. notoginseng. Results: A total of 89 fungi were obtained from the roots, stems, leaves, and seeds of P. notoginseng, and 41 isolates representing different morphotypes were selected for taxonomic characterization. The fungal isolates belonged to Ascomycota (96.6%) and Zygomycota (3.4%). All isolates were classified to 23 genera and an unknown taxon belonging to Sordariomycetes. The number of isolates obtained from different tissues ranged from 12 to 42 for leaves and roots, respectively. The selected endophytic fungal isolates were challenged by the root-rot pathogens Alternaria panax, Fusarium oxysporum, Fusarium solani, Phoma herbarum, and Mycocentrospora acerina. Twenty-six of the 41 isolates (63.4%) exhibited activity against at least one of the pathogens tested. Conclusion: Our results suggested that P. notoginseng harbors diversified endophytic fungi that would provide a basis for the identification of new bioactive compounds, and for effective biocontrol of notoginseng root rot.

Annexin A2 and CD105 Expression in Pancreatic Ductal Adenocarcinoma is Associated with Tumor Recurrence and Prognosis

Huang, Ya-Kai,Liu, Hong,Wang, Xin-Zheng,Zhu, Shan Asian Pacific Journal of Cancer Prevention 2014 Asian Pacific journal of cancer prevention Vol.15 No.22

To investigate the value of expression of annexin A2, microvessel density (MVD) and CD105 in pancreatic ductal adenocarcinoma (PDAC) tissues and adjacent normal tissues, immunohistochemical staining was used. The positive expression rate of Annexin A2 and the MVD in pancreatic ductal adenocarcinoma tissues was higher than that in in adjacent normal tissues (p<0.005). Expression of Annexin A2 and MVD correlated with histological grade (p<0.05). MVD of cancers in TNM stage IIb was higher than that in TNM stageI~IIa (p<0.026). Cancerous tissues with Annexin A2 staining grade 3+ had lower MVD than the tissues with the other Annexin A2 staining grade (p<0.05). Patients with high MVD had worse prognosis. However, our study did not confirm Annexin A2 was an independent risk factor for patients with PDAC. We confirmed MVD labeled by CD105 was an independent risk factor for patients with PDAC and had moderate predictive value of prognosis.

Prolactin Inhibits BCL6 Expression in Breast Cancer Cells through a MicroRNA-339-5p-Dependent Pathway

Hong Yan,Min Zhao,Shan Huang,Ping Chen,Wen-yong Wu,Jin Huang,Zheng-sheng Wu,Qiang Wu 한국유방암학회 2016 Journal of breast cancer Vol.19 No.1

Purpose: Prolactin (PRL) plays a critical role in breast cancer progression by activating its cognate receptor and promotes the growth and differentiation of breast cancer cells. Studies have shown that B-cell lymphoma 6 (BCL6) is the target gene of microRNA- 339-5p (miR-339-5p) and that BCL6 expression contributes to breast cancer progression. Herein, we identified PRL as a potent suppressor of BCL6 expression in human breast cancer cells. Methods: Western blotting and quantitative reverse transcription-polymerase chain reaction were used to investigate molecular mechanisms underlying miR-339-5p expression and BCL6 manipulation in MCF-7, T47D, and SKBR3 breast cancer cells. Phenotypic changes in these breast cancer cell lines were assessed by performing cell viability (MTT), colony formation, migration, and invasion assays. Results: PRL suppressed BCL6 protein and mRNA expression and upregulated miR-339-5p expression in MCF-7 and T47D breast cancer cells. Selective downregulation of miR-339-5p expression significantly reversed PRL-induced suppression of BCL6 mRNA and protein expression. Exogenous PRL stimulation significantly decreased the proliferation, colony formation, migration, and invasion of breast cancer cells, and suppression of miR-339-5p expression reversed these processes in vitro. Conclusion: These results indicated that PRL inhibited BCL6 expression and regulated breast cancer progression through a miR-339-5p-dependent pathway.

Decreased Expression of LKB1 Correlates with Poor Prognosis in Hepatocellular Carcinoma Patients Undergoing Hepatectomy

Huang, Yue-Han,Chen, Zhen-Kun,Huang, Ka-Te,Li, Peng,He, Bin,Guo, Xu,Zhong, Jun-Qiao,Zhang, Qi-Yu,Shi, Hong-Qi,Song, Qi-Tong,Yu, Zheng-Ping,Shan, Yun-Feng Asian Pacific Journal of Cancer Prevention 2013 Asian Pacific journal of cancer prevention Vol.14 No.3

Aim: To study any correlation of LKB1 expression with prognosis in hepatocellular carcinoma (HCC) cases. Methods: A total of 70 HCC patients and 20 primary intrahepatic stone patients in the first affiliated hospital of Wenzhou Medical College were enrolled in this study. LKB1 expression was detected by immunohistochemistry. Patients were followed-up and prognostic factors were evaluated. Result: LKB1 expression was decreased in the HCC samples. Loss of LKB1 expression in HCC was significantly related to histologic grade (P=0.010), vascular invasion (P=0.025) and TMN stage (P=0.011). Patients showing negative LKB1 expression had a significantly shorter disease-free and overall survival than those with positive expression (P = 0.001, P=0.000, respectively). Multivariate Cox regression analysis indicated that LKB1 expression level was an independent factor of survival (P = 0.033). Conclusion: HCC patients with decreased expression LKB1 have a poor prognosis. The loss of LKB1 expression is correlated with a lower survival rate.

Baicalin Induces Apoptosis in Leukemia HL-60/ADR Cells via Possible Down-regulation of the PI3K/Akt Signaling Pathway

Zheng, Jing,Hu, Jian-Da,Chen, Ying-Yu,Chen, Bu-Yuan,Huang, Yi,Zheng, Zhi Hong,Liu, Ting-Bo Asian Pacific Journal of Cancer Prevention 2012 Asian Pacific journal of cancer prevention Vol.13 No.4

Background: The effect and possible mechanism of traditional Chinese medicine, baicalin, on the PI3K/Akt signaling pathway in drug-resistant human myeloid leukemia HL-60/ADR cells have been investigated in this current study. Methods: HL-60/ADR cells were treated by 20, 40, $80\;{\mu}mol/L$ baicalin followed by cell cycle analysis at 24h. The mRNA expression level of the apoptosis related gene, Bcl-2 and bad, were measured by RT-PCR on cells treated with $80\;{\mu}mol/L$ baicalin at 12, 24 and 48hr. Western blot was performed to detect the changes in the expression of the proteins related to HL-60/ADR cell apoptosis and the signaling pathway before and after baicalin treatment, including Bcl-2, PARP, Bad, Caspase 3, Akt, p-Akt, NF-${\kappa}B$, p-NF-${\kappa}B$, mTOR and p-mTOR. Results: Sub-G1 peak of HL-60/ADR cells appeared 24 h after $20\;{\mu}mol/L$ baicalin treatment, and the ratio increased as baicalin concentration increased. Cell cycle analysis showed 44.9% G0/G1 phase cells 24 h after baicalin treatment compared to 39.6% in the control group. Cells treated with $80\;{\mu}mol/L$ baicalin displayed a trend in decreasing of Bcl-2 mRNA expression over time. Expression level of the Bcl-2 and PARP proteins decreased significantly while that of the PARP, Caspase-3, and Bad proteins gradually increased. No significant difference in Akt expression was observed between treated and the control groups. However, the expression levels of p-Akt, NF-${\kappa}B$, p-NF-${\kappa}B$, mTOR and p-mTOR decreased significantly in a time-dependent manner. Conclusions: We conclude that baicalin may induce HL-60/ADR cell apoptosis through the PI3K/AKT signaling pathway.

Highly Oriented Monolayer Graphene Grown on a Cu/Ni(111) Alloy Foil

Huang, Ming,Biswal, Mandakini,Park, Hyo Ju,Jin, Sunghwan,Qu, Deshun,Hong, Seokmo,Zhu, Zhili,Qiu, Lu,Luo, Da,Liu, Xiaochi,Yang, Zheng,Liu, Zhongliu,Huang, Yuan,Lim, Hyunseob,Yoo, Won Jong,Ding, Feng,Wa American Chemical Society 2018 ACS NANO Vol.12 No.6

<P>Fast-growth of single crystal monolayer graphene by CVD using methane and hydrogen has been achieved on “homemade” single crystal Cu/Ni(111) alloy foils over large area. Full coverage was achieved in 5 min or less for a particular range of composition (1.3 at.% to 8.6 at.% Ni), as compared to 60 min for a pure Cu(111) foil under identical growth conditions. These are the bulk atomic percentages of Ni, as a superstructure at the surface of these foils with stoichiometry Cu<SUB>6</SUB>Ni<SUB>1</SUB> (for 1.3 to 7.8 bulk at.% Ni in the Cu/Ni(111) foil) was discovered by low energy electron diffraction (LEED). Complete large area monolayer graphene films are either single crystal or close to single crystal, and include folded regions that are essentially parallel and that were likely wrinkles that “fell over” to bind to the surface; these folds are separated by large, wrinkle-free regions. The folds occur due to the buildup of interfacial compressive stress (and its release) during cooling of the foils from 1075 °C to room temperature. The fold heights measured by atomic force microscopy (AFM) and scanning tunneling microscopy (STM) prove them to all be 3 layers thick, and scanning electron microscopy (SEM) imaging shows them to be around 10 to 300 nm wide and separated by roughly 20 μm. These folds are always essentially perpendicular to the steps in this Cu/Ni(111) substrate. Joining of well-aligned graphene islands (in growths that were terminated prior to full film coverage) was investigated with high magnification SEM and aberration-corrected high-resolution transmission electron microscopy (TEM) as well as AFM, STM, and optical microscopy. These methods show that many of the “join regions” have folds, and these arise from interfacial adhesion mechanics (they are due to the buildup of compressive stress during cool-down, but these folds are different than for the continuous graphene films-they occur due to “weak links” in terms of the interface mechanics). Such Cu/Ni(111) alloy foils are promising substrates for the large-scale synthesis of single-crystal graphene film.</P> [FIG OMISSION]</BR>

DNA Microarray Probe Preparation by Gel Isolation Nested PCR

Wang, Hong-Min,Ma, Wen-li,Huang, Hai,Xiao, Wei-Wei,Wang, Yan,Zheng, Wen-Ling Korean Society for Biochemistry and Molecular Biol 2004 Journal of biochemistry and molecular biology Vol.37 No.3

To develop a simplified method that can rapidly prepare DNA microarray probes in a massive scale, a lambda phage genomic DNA-fragments library was constructed for the microarray-probes collection. Four methods of DNA band recovery from the first PCR products were tested and compared. The DNA microarray probes were collected by a novel method of nested PCR that was mediated by gel isolation of the first PCR products. This method was named GIN-PCR. The probes that were prepared by this GIN-PCR technique were used as subjects to fabricate a DNA microarray. The results showed that a wooden toothpick was superior to the other 3 methods, since this technique can steadily transfer the DNA bands as the template of the second PCR after the first PCR. A group of probes were successfully collected and DNA microarrays were constructed using these probes. Hybridization results demonstrated that this technique of DNA recovery and probe preparation was rapid, efficient, and effective. We developed a cost-effective and less labor-intensive method for DNA microarray probe preparation by nested PCR that is mediated by wooden toothpick transfer of the DNA bands in the gel after electrophoresis.

Reversible Data Hiding in Block Truncation Coding Compressed Images Using Quantization Level Swapping and Shifting

( Wien Hong ),( Shuozhen Zheng ),( Tung-shou Chen ),( Chien-che Huang ) 한국인터넷정보학회 2016 KSII Transactions on Internet and Information Syst Vol.10 No.6

The existing reversible data hiding methods for block truncation coding (BTC) compressed images often utilize difference expansion or histogram shifting technique for data embedment. Although these methods effectively embed data into the compressed codes, the embedding operations may swap the numerical order of the higher and lower quantization levels. Since the numerical order of these two quantization levels can be exploited to carry additional data without destroying the quality of decoded image, the existing methods cannot take the advantages of this property to embed data more efficiently. In this paper, we embed data by shifting the higher and lower quantization levels in opposite direction. Because the embedment does not change numerical order of quantization levels, we exploit this property to carry additional data without further reducing the image quality. The proposed method performs no-distortion embedding if the payload is small, and performs reversible data embedding for large payload. The experimental results show that the proposed method offers better embedding performance over prior works in terms of payload and image quality.