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Search Results: 1 - 10 of 342233 matches for " Mei-Yeh J Lu "
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Co-expression of adjacent genes in yeast cannot be simply attributed to shared regulatory system
Huai-Kuang Tsai, Cindy PC Su, Mei-Yeh J Lu, Ching-Hua Shih, Daryi Wang
BMC Genomics , 2007, DOI: 10.1186/1471-2164-8-352
Abstract: Our analyses showed that the proportion of adjacent pairs conserved in five yeast species is relatively low compared to that in the mammalian lineage. The proportion was also low for adjacent gene pairs with shared TFs. Particularly, the statistical analysis suggested that co-expression of adjacent gene pairs was not noticeably associated with the sharing of TFs in these pairs. We further proposed a case of the PAC (polymerase A and C) and RRPE (rRNA processing element) motifs which co-regulate divergent/bidirectional pairs, and found that the shared TFs were not significantly relevant to co-expression of divergent promoters among adjacent genes.Our findings suggested that the commonly shared cis-regulatory system does not solely contribute to the co-expression of adjacent gene pairs in yeast genome. Therefore we believe that during evolution yeasts have developed a sophisticated regulatory system that integrates both TF-based and non-TF based mechanisms(s) for concurrent regulation of neighboring genes in response to various environmental changes.The arrangement and orientation of genes in genomes is often shaped through evolution by mechanisms such as unequal crossing over followed by random genetic drift or natural selection [1,2]. Recent studies indicate that the distribution of genes in genomes does not always happen at random [3-5]. In the human genome, housekeeping genes show a strong tendency to cluster together [6], and genes that participate in the same pathway also tend to lie adjacent to each other in the genome [5,7,8]. Moreover, several studies indicate that adjacent genes in human seem to co-express regardless of their intergenic distance [9-11]. Similar phenomena have been observed in Drosophila, nematode, and yeast [12-16]. Among these observations, the co-expression of adjacent pairs is crucial because changes in such genome organization could alter the co-regulated transcription over the pairs [11,12].How co-expressed genes are regulated is still
A highly efficient β-glucosidase from the buffalo rumen fungus Neocallimastix patriciarum W5
Hsin-Liang Chen, Yo-Chia Chen, Mei-Yeh J Lu, Jui-Jen Chang, Hiaow-Ting C Wang, Tzi-Yuan Wang, Sz-Kai Ruan, Tao-Yuan Wang, Kuo-Yen Hung, Hsing-Yi Cho, Huei-Mien Ke, Wan-Ting Lin, Ming-Che Shih, Wen-Hsiung Li
Biotechnology for Biofuels , 2012, DOI: 10.1186/1754-6834-5-24
Abstract: In this study, a cDNA encoding β-glucosidase was isolated from the buffalo rumen fungus Neocallimastix patriciarum W5 and is named NpaBGS. It has a length of 2,331 bp with an open reading frame coding for a protein of 776 amino acid residues, corresponding to a theoretical molecular mass of 85.1 kDa and isoelectric point of 4.4. Two GH3 catalytic domains were found at the N and C terminals of NpaBGS by sequence analysis. The cDNA was expressed in Pichia pastoris and after protein purification, the enzyme displayed a specific activity of 34.5 U/mg against cellobiose as the substrate. Enzymatic assays showed that NpaBGS was active on short cello-oligosaccharides from various substrates. A weak activity in carboxymethyl cellulose (CMC) digestion indicated that the enzyme might also have the function of an endoglucanase. The optimal activity was detected at 40°C and pH 5?~?6, showing that the enzyme prefers a weak acid condition. Moreover, its activity could be enhanced at 50°C by adding Mg2+ or Mn2+ ions. Interestingly, in simultaneous saccharification and fermentation (SSF) experiments using Saccharomyces cerevisiae BY4741 or Kluyveromyces marxianus KY3 as the fermentation yeast, NpaBGS showed advantages in cell growth, glucose production, and ethanol production over the commercial enzyme Novo 188. Moreover, we showed that the KY3 strain engineered with the NpaNGS gene can utilize 2 % dry napiergrass as the sole carbon source to produce 3.32 mg/ml ethanol when Celluclast 1.5 L was added to the SSF system.Our characterizations of the novel β-glucosidase NpaBGS revealed that it has a preference of weak acidity for optimal yeast fermentation and an optimal temperature of ~40°C. Since NpaBGS performs better than Novo 188 under the living conditions of fermentation yeasts, it has the potential to be a suitable enzyme for SSF.
Functional characterization of cellulases identified from the cow rumen fungus Neocallimastix patriciarum W5 by transcriptomic and secretomic analyses
Tzi-Yuan Wang, Hsin-Liang Chen, Mei-Yeh J Lu, Yo-Chia Chen, Huang-Mo Sung, Chi-Tang Mao, Hsing-Yi Cho, Huei-Mien Ke, Teh-Yang Hwa, Sz-Kai Ruan, Kuo-Yen Hung, Chih-Kuan Chen, Jeng-Yi Li, Yueh-Chin Wu, Yu-Hsiang Chen, Shao-Pei Chou, Ya-Wen Tsai, Te-Chin Chu, Chun-Chieh A Shih, Wen-Hsiung Li, Ming-Che Shih
Biotechnology for Biofuels , 2011, DOI: 10.1186/1754-6834-4-24
Abstract: We have developed an efficient platform that uses a combination of transcriptomic and proteomic approaches to N. patriciarum to accelerate gene identification, enzyme classification and application in rice straw degradation. By conducting complementary studies of transcriptome (Roche 454 GS and Illumina GA IIx) and secretome (ESI-Trap LC-MS/MS), we identified 219 putative GH contigs and classified them into 25 GH families. The secretome analysis identified four major enzymes involved in rice straw degradation: β-glucosidase, endo-1,4-β-xylanase, xylanase B and Cel48A exoglucanase. From the sequences of assembled contigs, we cloned 19 putative cellulase genes, including the GH1, GH3, GH5, GH6, GH9, GH18, GH43 and GH48 gene families, which were highly expressed in N. patriciarum cultures grown on different feedstocks.These GH genes were expressed in Pichia pastoris and/or Saccharomyces cerevisiae for functional characterization. At least five novel cellulases displayed cellulytic activity for glucose production. One β-glucosidase (W5-16143) and one exocellulase (W5-CAT26) showed strong activities and could potentially be developed into commercial enzymes.Cellulosic ethanol produced by microbial fermentation from feedstocks has been proposed to replace fossil fuels in transportation. A key step in cellulosic ethanol production is to break down cellulose into glucose and hemicellulose into xylose, which can subsequently be converted into ethanol by fermentative microbes. Therefore, finding efficient cellulases is important to bioethanol production, as well as for hydrolyzing feedstocks into sugars in general. Neocallimastix species is one of the major anaerobic fungi in the rumen of water buffalo capable of efficiently digesting cellulosic biomass [1-4]. Such anaerobic fungi are potential sources for highly active cellulolytic enzymes that are useful for cellulose hydrolysis [5-7]. Plant cell wall degrading enzymes from rumen fungi such as Neocallimastix patriciarum may
High-Efficiency 6′′ Multicrystalline Black Solar Cells Based on Metal-Nanoparticle-Assisted Chemical Etching
W. Chuck Hsu,Yen-Sheng Lu,Jung-Yi Chyan,J. Andrew Yeh
International Journal of Photoenergy , 2012, DOI: 10.1155/2012/197514
Abstract: Multicrystalline silicon (mc-Si) photovoltaic (PV) solar cells with nanoscale surface texturing by metal-nanoparticle-assisted etching are proposed to achieve high power efficiency. The investigation of average nanorod lengths from 100 nm to 1 μm reveals that the Si wafer decorated with 100 nm thick nanorods has optical reflection of 9.5% inferior than the one with 1 μm thick nanorods (2%). However, the short nanorods improve the doping uniformity and effectively decrease metal contact resistance. After surface passivation using the hydrogenated SiO2/SiNx (5 nm/50 nm) stack, the minority carrier lifetime substantially increases from 1.8 to 7.2 μs for the 100 nm-thick nanorod solar cell to achieve the high power efficiency of 16.38%, compared with 1 μm thick nanorod solar cell with 11.87%.
Calcium Ion Detection Using Miniaturized InN-based Ion Sensitive Field Effect Transistors
Kun-Wei Kao, Yun-Wen Su, Yen-Sheng Lu, Shangjr Gwo, J. Andrew Yeh
International Journal of Automation and Smart Technology , 2012, DOI: 10.5875/ausmt.v2i1.117
Abstract: An Ultrathin (~10 nm) InN ion sensitive field effect transistor (ISFET) with gate regions functionalized with phosphotyrosine (p-Tyr) is proposed to detect calcium ions (Ca2+) in aqueous solution. The ISFET was miniaturized to a chip size of 1.1 mm by 1.5 mm and integrated at the tip of a hypodermic injection needle (18 G) for real-time and continuous monitoring. The sensor shows a current variation ratio of 1.11% with per decade change of Ca2+ and a detection limit of 10-6 M. The response time of 5 sec. reveals its great potential for accomplishing fast detection in chemical and physiological sensing applications. The sensor would be applied in medical diagnosis and used to monitor continuous and real-time variations of Ca2+ levels in human blood in the near future.
Malignant and Nonmalignant Gene Signatures in Squamous Head and Neck Cancer
Maria J. Worsham,Mei Lu,Kang Mei Chen,Josena K. Stephen,Shaleta Havard,Vanessa P. Schweitzer
Journal of Oncology , 2012, DOI: 10.1155/2012/752860
Abstract: Genetic events specific to the pathogenesis of malignancy can offer clues to the tumorigenesis process. The objective of this study was to identify gene alterations that differentiate tumor and nontumor lesions in squamous head and neck cancer (HNSCC). DNA from 220 primary HNSCC with concurrently present tumor and nontumor lesions from the same patient was interrogated for genomic alterations of loss or gain of copy. Conditional logistic regression dealt with tumor and non-tumor records within a patient. Of 113 genes, 53 had univariate effects (<0.01), of which 16 genes remained in the multivariable model with <0.01. The model had a C-index (ROC) of 0.93. Loss of CDKN2B and gain of BCL6, FGF3, and PTP4A3 predicted tumor. Loss of BAK1 and CCND1 and gain of STCH predicted nontumor. This highly powered model assigned alterations in 16 genes specific for malignant versus nonmalignant lesions, supporting their contribution to the pathogenesis of HNSCC as well as their potential utility as relevant targets for further evaluation as markers of early detection and progression.
Environments Aware for Prolonging the Lifetime of Sensor Nodes Deployed in WSNs  [PDF]
Joy Iong-Zong Chen, Lu-Tsou Yeh
Engineering (ENG) , 2012, DOI: 10.4236/eng.2012.42013
Abstract: Providing a pretty adequate environment condition between the transmission and the receiver for a WSN (wireless sensor network), in which deployed sensor nodes and fusion center, is investigated in the paper. Moreover, an algorithm promotes the energy efficient, increases the accuracy of sensing data and prolongs the lifetime of sensor nodes deployed over an WSNs is proposed. On the basis of adopting sensor management, which involves sensor movement sequences, sensor location arrangement, lifetime requirement for sensor nodes deploy surveillance environment, and the data fusion center, are addressed too. Simulation results from the lifetime performance for sensor nodes defeated by parameters about the environment around the WSNs are illustrated. Parameters aforementioned are including sensing distance, path loss factor, number bits of a transmitted packet, and interference suffering from the path of data transmission etc. Furthermore, the algorithm of sensor location arrangement is modified for the purpose of improving the lifetime performance in WSNs environments. In addition, simulation results show that the proposed algorithm in this paper is not only definitely to improve the energy efficient sufficiently, but the sensing accuracy and the lifetime performance of the sensor nodes are also prolonged significantly.
Tract Orientation and Angular Dispersion Deviation Indicator (TOADDI): A framework for single-subject analysis in diffusion tensor imaging
Cheng Guan Koay,Ping-Hong Yeh,John M. Ollinger,M. Okan ?rfano?lu,Carlo Pierpaoli,Peter J. Basser,Terrence R. Oakes,Gerard Riedy
Statistics , 2015, DOI: 10.1016/j.neuroimage.2015.11.046
Abstract: The purpose of this work is to develop a framework for single-subject analysis of diffusion tensor imaging (DTI) data. This framework (termed TOADDI) is capable of testing whether an individual tract as represented by the major eigenvector of the diffusion tensor and its corresponding angular dispersion are significantly different from a group of tracts on a voxel-by-voxel basis. This work develops two complementary statistical tests based on the elliptical cone of uncertainty (COU), which is a model of uncertainty or dispersion of the major eigenvector of the diffusion tensor. The orientation deviation test examines whether the major eigenvector from a single subject is within the average elliptical COU formed by a collection of elliptical COUs. The shape deviation test is based on the two-tailed Wilcoxon-Mann-Whitney two-sample test between the normalized shape measures (area and circumference) of the elliptical cones of uncertainty of the single subject against a group of controls. The False Discovery Rate (FDR) and False Non-discovery Rate (FNR) were incorporated in the orientation deviation test. The shape deviation test uses FDR only. TOADDI was found to be numerically accurate and statistically effective. Clinical data from two Traumatic Brain Injury (TBI) patients and one non-TBI subject were tested against the data obtained from a group of 45 non-TBI controls to illustrate the application of the proposed framework in single-subject analysis. The frontal portion of the superior longitudinal fasciculus seemed to be implicated in both tests as significantly different from that of the control group. The TBI patients and the single non-TBI subject were well separated under the shape deviation test at the chosen FDR level of 0.0005. TOADDI is a simple but novel geometrically based statistical framework for analyzing DTI data.
Adipokine Hormones and Hand Osteoarthritis: Radiographic Severity and Pain
Mei Massengale, Bing Lu, John J. Pan, Jeffrey N. Katz, Daniel H. Solomon
PLOS ONE , 2012, DOI: 10.1371/journal.pone.0047860
Abstract: Introduction Obesity's association with hand osteoarthritis cannot be fully explained by mechanical loading. We examined the relationship between adipokines and radiographic hand osteoarthritis severity and pain. Methods In a pilot study of 44 hand osteoarthritis patients (39 women and 5 men), serum adipokine concentrations and hand x-ray Kallman-scores were analyzed using linear regression models. Secondary analyses examined correlates of hand pain. Results The cohort had a mean age of 63.5 years for women and 72.6 for men; mean (standard deviation) Kallman-scores were 43.3(17.4) for women and 46.2(10.8) for men. Mean body-mass-index was 30 kg/m2 for women and men. Mean leptin concentration was 32.2 ng/ml (women) and 18.5 ng/ml (men); mean adiponectin-total was 7.9 ng/ml (women) and 5.3 ng/ml (men); mean resistin was 7.3 ng/ml (women) and 9.4 ng/ml (men). No association was found between Kallman-scores and adipokine concentrations (R2 = 0.00–0.04 unadjusted analysis, all p-values>0.22). Secondary analyses showed mean visual-analog-scale pain of 4.8(2.4) for women and 6.6(0.9) for men. Leptin, BMI, and history of coronary artery disease were found to be associated with visual-analog-scale scores for chronic hand pain (R2 = 0.36 unadjusted analysis, p-values≤0.04). Conclusion In this pilot study, we found that adipokine serum concentrations were not associated with hand osteoarthritis radiographic severity; the most important correlates of joint damage were age and disease duration. Leptin serum concentration, BMI, and coronary artery disease were associated with the intensity of chronic hand OA pain.
Trends of increase in western medical services in traditional medicine hospitals in china
Jay J Shen, Ying Wang, Fang Lin, Jun Lu, Charles B Moseley, Mei Sun, Mo Hao
BMC Health Services Research , 2011, DOI: 10.1186/1472-6963-11-212
Abstract: 97 TCM hospitals and 103 general hospitals were surveyed in years of 2000 and 2004. Six types of medical service revenue between the two types of hospitals were compared overtime. The national statistics from 1999 to 2008 were also used as complementary evidence.For TCM hospitals, the percentage of service revenue from Western medicine increased from 44.3% to 47.4% while the percentage of service revenue from TCM declined from 26.4% to 18.8% from 1999 to 2004. Percentages of revenue from laboratory tests and surgical procedures for both types of hospitals increased and the discrepancy between the two types of hospitals was narrowed from 1999 to 2004. For TCM hospitals, revenues from laboratory tests increased from 3.64% to 5.06% and revenues from surgical procedures increased from 3.44% to 7.02%. General hospitals' TCM drug revenue in outpatient care declined insignificantly from 5.26% to 3.87%, while the decline for the TCM hospitals was significant from 19.73% to 13.77%. The national statistics from 1999 to 2008 showed similar trends that the percentage of revenue from Western medicine for TCM hospitals increased from 59.6% in 1999 to 62.2% in 2003 and 66.1% in 2008 while the percentage of revenue from TCM for TCM hospitals decreased from 18.0% in 1999, 15.4% in 2003, and 13.7% in 2008.Western medicine has become a vital revenue source for TCM hospitals in the current Chinese health care environment where government subsidies to health care facilities have significantly declined. Policies need to encourage TCM hospitals to identify their own special and effective services, improve public perception, increase demand, strengthen financial sources, and ultimately make contributions to preserving one of the national treasures.As the primary form of healthcare service in many developing countries, complementary and alternative medicine has become more popular in the world including in a number of developed countries in recent years [1]. Given the changes in disease pat
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