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Search Results: 1 - 10 of 81340 matches for " Tze-Tze Liu "
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Complexity of the Mycoplasma fermentans M64 Genome and Metabolic Essentiality and Diversity among Mycoplasmas
Hung-Wei Shu, Tze-Tze Liu, Huang-I Chan, Yen-Ming Liu, Keh-Ming Wu, Hung-Yu Shu, Shih-Feng Tsai, Kwang-Jen Hsiao, Wensi S. Hu, Wailap Victor Ng
PLOS ONE , 2012, DOI: 10.1371/journal.pone.0032940
Abstract: Recently, the genomes of two Mycoplasma fermentans strains, namely M64 and JER, have been completely sequenced. Gross comparison indicated that the genome of M64 is significantly bigger than the other strain and the difference is mainly contributed by the repetitive sequences including seven families of simple and complex transposable elements ranging from 973 to 23,778 bps. Analysis of these repeats resulted in the identification of a new distinct family of Integrative Conjugal Elements of M. fermentans, designated as ICEF-III. Using the concept of “reaction connectivity”, the metabolic capabilities in M. fermentans manifested by the complete and partial connected biomodules were revealed. A comparison of the reported M. pulmonis, M. arthritidis, M. genitalium, B. subtilis, and E. coli essential genes and the genes predicted from the M64 genome indicated that more than 73% of the Mycoplasmas essential genes are preserved in M. fermentans. Further examination of the highly and partly connected reactions by a novel combinatorial phylogenetic tree, metabolic network, and essential gene analysis indicated that some of the pathways (e.g. purine and pyrimidine metabolisms) with partial connected reactions may be important for the conversions of intermediate metabolites. Taken together, in light of systems and network analyses, the diversity among the Mycoplasma species was manifested on the variations of their limited metabolic abilities during evolution.
Sequencing and Comparative Genome Analysis of Two Pathogenic Streptococcus gallolyticus Subspecies: Genome Plasticity, Adaptation and Virulence
I-Hsuan Lin,Tze-Tze Liu,Yu-Ting Teng,Hui-Lun Wu,Yen-Ming Liu,Keh-Ming Wu,Chuan-Hsiung Chang,Ming-Ta Hsu
PLOS ONE , 2012, DOI: 10.1371/journal.pone.0020519
Abstract: Streptococcus gallolyticus infections in humans are often associated with bacteremia, infective endocarditis and colon cancers. The disease manifestations are different depending on the subspecies of S. gallolyticus causing the infection. Here, we present the complete genomes of S. gallolyticus ATCC 43143 (biotype I) and S. pasteurianus ATCC 43144 (biotype II.2). The genomic differences between the two biotypes were characterized with comparative genomic analyses. The chromosome of ATCC 43143 and ATCC 43144 are 2,36 and 2,10 Mb in length and encode 2246 and 1869 CDS respectively. The organization and genomic contents of both genomes were most similar to the recently published S. gallolyticus UCN34, where 2073 (92%) and 1607 (86%) of the ATCC 43143 and ATCC 43144 CDS were conserved in UCN34 respectively. There are around 600 CDS conserved in all Streptococcus genomes, indicating the Streptococcus genus has a small core-genome (constitute around 30% of total CDS) and substantial evolutionary plasticity. We identified eight and five regions of genome plasticity in ATCC 43143 and ATCC 43144 respectively. Within these regions, several proteins were recognized to contribute to the fitness and virulence of each of the two subspecies. We have also predicted putative cell-surface associated proteins that could play a role in adherence to host tissues, leading to persistent infections causing sub-acute and chronic diseases in humans. This study showed evidence that the S. gallolyticus still possesses genes making it suitable in a rumen environment, whereas the ability for S. pasteurianus to live in rumen is reduced. The genome heterogeneity and genetic diversity among the two biotypes, especially membrane and lipoproteins, most likely contribute to the differences in the pathogenesis of the two S. gallolyticus biotypes and the type of disease an infected patient eventually develops.
Common Altered Epigenomic Domains in Cancer Cells: Characterization and Subtle Variations
Yi-Chien Tsai,Chun-Hui Chiao,Ian Yi-Feng Chang,Dow-Tien Chen,Tze-Tze Liu,Kate Hua,Chuan-Hsiung Chang,Ming-Ta Hsu
Cancers , 2011, DOI: 10.3390/cancers3021996
Abstract: We have previously identified large megabase-sized hypomethylated zones in the genome of the breast cancer cell line MCF-7 using the TspRI-ExoIII technique. In this report, we used a more convenient high throughput method for mapping the hypomethylated zones in a number of human tumor genomes simultaneously. The method was validated by the bisulfite sequencing of 39 randomly chosen sites in a demethylated domain and by bisulfite genome-wide sequencing of the MCF-7 genome. This showed that the genomes of the various tumor cell lines, as well as some primary tumors, exhibit common hypomethylated domains. Interestingly, these hypomethylated domains are correlated with low CpG density distribution genome-wide, together with the histone H3K27Me3 landscape. Furthermore, they are inversely correlated with the H3K9Ac landscape and gene expression as measured in MCF-7 cells. Treatment with drugs resulted in en-bloc changes to the methylation domains. A close examination of the methylation domains found differences between non-invasive and invasive tumors with respect to tumorigenesis related genes. Taken together these results suggest that the human genome is organized in epigenomic domains that contain various different types of genes and imply that there are cis- and trans-regulators that control these domain-wide epigenetic changes and hence gene expression in the human genome. The hypomethylated domains are located in gene deserts that contain mainly tissue-specific genes and therefore we hypothesize that tumor cells keep these regions demethylated and silenced in order to save energy and resources and allow higher levels of cell proliferation and better survival (a thrifty tumor genome hypothesis).
Generation and Analysis of the Expressed Sequence Tags from the Mycelium of Ganoderma lucidum
Yen-Hua Huang, Hung-Yi Wu, Keh-Ming Wu, Tze-Tze Liu, Ruey-Fen Liou, Shih-Feng Tsai, Ming-Shi Shiao, Low-Tone Ho, Shean-Shong Tzean, Ueng-Cheng Yang
PLOS ONE , 2013, DOI: 10.1371/journal.pone.0061127
Abstract: Ganoderma lucidum (G. lucidum) is a medicinal mushroom renowned in East Asia for its potential biological effects. To enable a systematic exploration of the genes associated with the various phenotypes of the fungus, the genome consortium of G. lucidum has carried out an expressed sequence tag (EST) sequencing project. Using a Sanger sequencing based approach, 47,285 ESTs were obtained from in vitro cultures of G. lucidum mycelium of various durations. These ESTs were further clustered and merged into 7,774 non-redundant expressed loci. The features of these expressed contigs were explored in terms of over-representation, alternative splicing, and natural antisense transcripts. Our results provide an invaluable information resource for exploring the G. lucidum transcriptome and its regulation. Many cases of the genes over-represented in fast-growing dikaryotic mycelium are closely related to growth, such as cell wall and bioactive compound synthesis. In addition, the EST-genome alignments containing putative cassette exons and retained introns were manually curated and then used to make inferences about the predominating splice-site recognition mechanism of G. lucidum. Moreover, a number of putative antisense transcripts have been pinpointed, from which we noticed that two cases are likely to reveal hitherto undiscovered biological pathways. To allow users to access the data and the initial analysis of the results of this project, a dedicated web site has been created at http://csb2.ym.edu.tw/est/.
Fosmid library end sequencing reveals a rarely known genome structure of marine shrimp Penaeus monodon
Shiao-Wei Huang, You-Yu Lin, En-Min You, Tze-Tze Liu, Hung-Yu Shu, Keh-Ming Wu, Shih-Feng Tsai, Chu-Fang Lo, Guang-Hsiung Kou, Gwo-Chin Ma, Ming Chen, Dongying Wu, Takashi Aoki, Ikuo Hirono, Hon-Tsen Yu
BMC Genomics , 2011, DOI: 10.1186/1471-2164-12-242
Abstract: We found that microsatellite sequences were highly abundant in the P. monodon genome, comprising 8.3% of the total length. The density and the average length of microsatellites were evidently higher in comparison to those of other taxa. AT-rich microsatellite motifs, especially poly (AT) and poly (AAT), were the most abundant. High abundance of microsatellite sequences were also found in the transcribed regions. Furthermore, via self-BlastN analysis we identified 103 novel repetitive element families which were categorized into four groups, i.e., 33 WSSV-like repeats, 14 retrotransposons, 5 gene-like repeats, and 51 unannotated repeats. Overall, various types of repeats comprise 51.18% of the P. monodon genome in length. Approximately 7.4% of the FESs contained protein-coding sequences, and the Inhibitor of Apoptosis Protein (IAP) gene and the Innexin 3 gene homologues appear to be present in high abundance in the P. monodon genome.The redundancy of various repeat types in the P. monodon genome illustrates its highly repetitive nature. In particular, long and dense microsatellite sequences as well as abundant WSSV-like sequences highlight the uniqueness of genome organization of penaeid shrimp from those of other taxa. These results provide substantial improvement to our current knowledge not only for shrimp but also for marine crustaceans of large genome size.Crustaceans (lobster, shrimp, crab, etc.), a remarkable group of organisms filling up all types of habitats in the ocean with a wide array of adaptations, possess the greatest species diversity among marine animals. They are not only abundant in number, but also are among the most commercially exploited food species for human consumption [1]. Given their primarily aquatic habitats, however, they are not as well studied as insects, their terrestrial arthropod relatives.The tiger shrimp (Penaeus monodon) has been one of the most important captured and cultured marine crustaceans in the world, especially in the I
Construction and characterization of an expressed sequenced tag library for the mosquito vector Armigeres subalbatus
George F Mayhew, Lyric C Bartholomay, Hang-Yen Kou, Thomas A Rocheleau, Jeremy F Fuchs, Matthew T Aliota, I-Yu Tsao, Chiung-Yen Huang, Tze-Tze Liu, Kwang-Jen Hsiao, Shih-Feng Tsai, Ueng-Cheng Yang, Nicole T Perna, Wen-Long Cho, Bruce M Christensen, Cheng-Chen Chen
BMC Genomics , 2007, DOI: 10.1186/1471-2164-8-462
Abstract: Six libraries were constructed and used to generate 44,940 expressed sequence tags, of which 38,079 passed quality filters to be included in the annotation project and subsequent analyses. All of these sequences were collapsed into clusters resulting in 8,020 unique sequence clusters or singletons. EST clusters were annotated and curated manually within ASAP (A Systematic Annotation Package for Community Analysis of Genomes) web portal according to BLAST results from comparisons to Genbank, and the Anopheles gambiae and Drosophila melanogaster genome projects.The resulting dataset is the first of its kind for this mosquito vector and provides a basis for future studies of mosquito vectors regarding the cascade of events that occurs in response to infection, and thereby providing insight into vector competence and innate immunity.The perpetuation of mosquito-borne diseases is dependent on the compatibility of the pathogen with its invertebrate and vertebrate hosts, as dictated by each respective genome. The failure of traditional mosquito-borne disease control efforts to reduce the burden of these diseases on public health has created an incentive to develop a more comprehensive understanding of molecular interactions between host and pathogen, in order to develop novel means to control disease transmission. Innate immune responsiveness in the mosquito host is of particular interest in such explorations because extensive research efforts have shown that vector mosquito species produce robust humoral and cellular immune responses against invading pathogens [1-4].A vector species that employs a unique, robust immune response against an invading pathogen is the mosquito, Armigeres subalbatus, a natural vector of the nematode parasites that cause lymphatic filariasis. This debilitating disease affects 120 million people annually, one third of who suffer gross pathology (CDC 2006). Ar. subalbatus is ideally suited for laboratory studies of immune responsiveness because it
Efficient Differentiation of Mouse Embryonic Stem Cells into Insulin-Producing Cells
Szu-Hsiu Liu,Lain-Tze Lee
Experimental Diabetes Research , 2012, DOI: 10.1155/2012/201295
Abstract: Embryonic stem (ES) cells are a potential source of a variety of differentiated cells for cell therapy, drug discovery, and toxicology screening. Here, we present an efficacy strategy for the differentiation of mouse ES cells into insulin-producing cells (IPCs) by a two-step differentiation protocol comprising of (i) the formation of definitive endoderm in monolayer culture by activin A, and (ii) this monolayer endoderm being induced to differentiate into IPCs by nicotinamide, insulin, and laminin. Differentiated cells can be obtained within approximately 7 days. The differentiation IPCs combined application of RT-PCR, ELISA, and immunofluorescence to characterize phenotypic and functional properties. In our study, we demonstrated that IPCs produced pancreatic transcription factors, endocrine progenitor marker, definitive endoderm, pancreatic β-cell markers, and Langerhans α and δ cells. The IPCs released insulin in a manner that was dose dependent upon the amount of glucose added. These techniques may be able to be applied to human ES cells, which would have very important ramifications for treating human disease.
Efficient Differentiation of Mouse Embryonic Stem Cells into Insulin-Producing Cells
Szu-Hsiu Liu,Lain-Tze Lee
Journal of Diabetes Research , 2012, DOI: 10.1155/2012/201295
Abstract: Embryonic stem (ES) cells are a potential source of a variety of differentiated cells for cell therapy, drug discovery, and toxicology screening. Here, we present an efficacy strategy for the differentiation of mouse ES cells into insulin-producing cells (IPCs) by a two-step differentiation protocol comprising of (i) the formation of definitive endoderm in monolayer culture by activin A, and (ii) this monolayer endoderm being induced to differentiate into IPCs by nicotinamide, insulin, and laminin. Differentiated cells can be obtained within approximately 7 days. The differentiation IPCs combined application of RT-PCR, ELISA, and immunofluorescence to characterize phenotypic and functional properties. In our study, we demonstrated that IPCs produced pancreatic transcription factors, endocrine progenitor marker, definitive endoderm, pancreatic β-cell markers, and Langerhans α and δ cells. The IPCs released insulin in a manner that was dose dependent upon the amount of glucose added. These techniques may be able to be applied to human ES cells, which would have very important ramifications for treating human disease. 1. Introduction Human and mouse embryonic stem (ES) cells are capable of spontaneous differentiation into insulin-producing cells, among many other cell types. ES cells can be induced to preferentially differentiate into insulin-producing cells (IPCs) by changing the composition of the culture medium and causing expression of dominant transcription factor genes which are involved in pancreas development [1, 2]. In previous studies, there are two main strategies for the differentiation of ES cells into IPCs: (i) embryoid body formation and (ii) definitive endoderm formation [3–5]. Because after spontaneous differentiation the number of specifically differentiated cell types is relatively low, the application of defined differentiation factors and selection of lineage-specific progenitor cells seems to be necessary for directed differentiation of ES cells into the desired cell types [6, 7]. Differentiated cells can be obtained within approximately 33 days. Until now, there is no report to directly induce definitive endoderm and pancreatic cells in monolayer cells at the same time. Here, we present a strategy for the differentiation of ES cells into IPCs by a two-step differentiation protocol comprising of (i) the formation of definitive endoderm in monolayer culture by activin A, and (ii) this monolayer endoderm being induced to differentiate into IPCs by nicotinamide, insulin, and laminin. The small bioorganic molecules can control cellular
State Price Density Estimation and Nonparametric Pricing of Basket Options  [PDF]
Yuming Kuang, Tze Leung Lai
Journal of Mathematical Finance (JMF) , 2015, DOI: 10.4236/jmf.2015.55038
Abstract:

This paper develops a novel method to price basket options by using an application-driven approach to estimating the state price density of the basket or the joint state price density of the asset prices in the basket. In this connection, we also discuss the difference between the application-driven and the traditional statistical approach to density estimation.

An unusual cause of chyluria after radiofrequency ablation of a renal cell carcinoma: a case report
Tze Wah
Journal of Medical Case Reports , 2011, DOI: 10.1186/1752-1947-5-307
Abstract: During a routine renal examination, an otherwise fit and well 79-year-old Caucasian man was found to have a peripherally situated tumor. He underwent renal radiofrequency ablation as primary treatment. Periodic imaging follow-up over two years showed no evidence of residual or recurrent disease within the zonal ablation. The routine imaging protocol at St James's Hospital included upper abdomen only for kidney assessment; pelvic examination was not included. However, our patient underwent a computed tomography scan of his abdomen and pelvis at the request of his local urologist, around two and a half years after the renal radiofrequency ablation. A fat-fluid level was seen within the urinary bladder, consistent with chyluria. As our patient was asymptomatic, he was treated conservatively.It is important to be aware of chyluria as a possible complication of renal radiofrequency ablation, and to recognize the fat-fluid level sign within the bladder or collecting system on computed tomography scans. As most institutions do not routinely perform computed tomography scans of the pelvis as part of their follow-up protocol after renal radiofrequency ablation, a high index of suspicion is required for diagnosis. Routine urine analysis for fat should be considered, as prompt diagnosis is crucial to guide management for symptomatic patients.Image-guided percutaneous renal radiofrequency ablation (RFA) therapy is now an increasingly popular treatment for small and selected renal cell carcinoma. It has low morbidity, high technical success and good mid-term outcome results [1,2]. After renal RFA, treatment efficacy is usually monitored by periodic cross-sectional imaging, with either computed tomography (CT) or magnetic resonance imaging. Most institutions, especially in Europe, only perform cross-sectional imaging of the kidneys; the pelvis is not routinely imaged as part of the follow-up. I report a case of incidental diagnosis of chyluria on CT in a patient who had undergone
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