Thu Ho - Academia.edu (original) (raw)

Papers by Thu Ho

Copyright information:Taken from "Headloop suppression PCR and its applic... more Copyright information:Taken from "Headloop suppression PCR and its application to selective amplification of methylated DNA sequences"Nucleic Acids Research 2005;33(14):e127-e127.Published online 9 Aug 2005PMCID:PMC1184225.© The Author 2005. Published by Oxford University Press. All rights reserved Headloop PCR with mixtures of bacterial DNAs as shown were performed using the control primer NR-Fli and primers EHL2a or EHL48 to suppress rDNA amplification (), with primer SAHL to suppress rDNA amplification ( and ). Melting profiles of PCR products were determined to distinguish amplicons from different species. The left peak (86–88°C) corresponds to the amplicon and the right peak (91–93°C) to the amplicons from the thermophilic bacteria and

Copyright information:Taken from "Headloop suppression PCR and its applic... more Copyright information:Taken from "Headloop suppression PCR and its application to selective amplification of methylated DNA sequences"Nucleic Acids Research 2005;33(14):e127-e127.Published online 9 Aug 2005PMCID:PMC1184225.© The Author 2005. Published by Oxford University Press. All rights reserved Sequences from the and 16S rRNA genes are shown below that from the gene. Dashes indicate identity to the sequence and 'Δ' deletions. The position of the forward base primer NR-Fli is shown as are the head sequences EHL2a and EHL48 targeted to suppress rDNA amplification, and SAHL targeted to suppress amplification of rDNA. Mismatches to non-target sequences are shown in boldface.

I would like to thank Vietnam Education Foundation (VEF), who sponsored my graduate study at UT A... more I would like to thank Vietnam Education Foundation (VEF), who sponsored my graduate study at UT Austin in the international education exchange program to improve Vietnamese Science and Technology capacities. I wish to express my gratitude to my advisor, Dr. Michael D. Engelhardt. His support, guidance, patience and profound knowledge have motivated me a lot from the beginning of my master's program and through the study in this thesis. Without him, this thesis could not be completed. Finally, I would like to thank my parents, Ho Thu Quang and Nguyen Thi Hue, whose unconditional love and encouragement always enlighten the road that I go and provide me the strength to overcome many difficulties in the life.

Release of hypermethylated DNA from tumour cells affords the opportunity to develop an early diag... more Release of hypermethylated DNA from tumour cells affords the opportunity to develop an early diagnostic for cancer by DNA isolated from blood or other bodily fluids. However, using standard methylation-specific PCR, DNA frist needs to be treated with bisulfite and sensitivity can be limited due to mispriming. Once formed, unwanted products amplify efficiently and can prevent detection of the target. To overcome this we have developed a system which does not require bisulfite treatment of DNA and in which selectivity is maintained throughout the amplification.

Cold Spring Harbor Monograph Archive, 1996

In the early genetic studies of mammalian cells in culture there was ongoing controversy about th... more In the early genetic studies of mammalian cells in culture there was ongoing controversy about the sources of heritable variability (for review, see Holliday 1991). On the one hand, it was believed that mammalian cells could be handled essentially in the same way as microorganisms; that is, by the isolation and study of gene mutations. On the other hand, it was maintained that these cells were derived from tissues containing specialized genes, most of which were not transcribed, as well as standard housekeeping genes. Changes in the activity of specialized genes in cells in culture would be expected to have an epigenetic basis. This controversy was apparently ended by two definitive reviews (De Mars 1974; Siminovitch 1976), which established beyond doubt that classic mutations could be induced in cultured mammalian cells and that these had the inherited stability expected of such mutations. There was still a problem, because established cell lines had at least a diploid number of ch...

Copyright information: Taken from "Headloop suppression PCR and its application to selective... more Copyright information: Taken from "Headloop suppression PCR and its application to selective amplification of methylated DNA sequences"Nucleic Acids Research 2005;33(14):e127-e127.Published online 9 Aug 2005PMCID:PMC1184225.© The Author 2005. Published by Oxford University Press. All rights reserved Sequences are shown for the promoter region of the gene () and the intragenic region, top strand () or bottom strand (). For each the unmodified sequence is shown (W) and below it the expected sequences after bisulphite treatment if the DNA were methylated (M) or unmethylated (U). Numbering of CpG sites relative to the transcription start site is shown above the sequences. Primer regions are boxed and shaded yellow. Head regions are boxed and shaded blue. T residues resulting from conversion of a C are shown as lower case (t); I = inosine. Cs or Ts at the position of CpG sites and the discriminatory A bases in the head sequence are highlighted in red.

Bioorganic & Medicinal Chemistry Letters, 2020

High-throughput screening methods have been used to identify two novel series of inhibitors that ... more High-throughput screening methods have been used to identify two novel series of inhibitors that disrupt progranulin binding to sortilin. Exploration of structure-activity relationships (SAR) resulted in compounds with sufficient potency and physicochemical properties to enable co-crystallization with sortilin. These co-crystal structures supported observed SAR trends and provided guidance for additional avenues for designing compounds with additional interactions within the binding site.

Energies, 2020

This study conducted a questionnaire-led survey to explore the financial feasibility and socio-en... more This study conducted a questionnaire-led survey to explore the financial feasibility and socio-environmental impacts of stand-alone solar home systems (SHS) through stratified random sampling. Based on the above consideration, fifteen cases of studies of various watt peak (Wp) capacities have been investigated to evaluate the economic viability of solar home systems. The results revealed that most of the cases have positive net present value (NPV) and low payback periods, with an internal rate of return (IRR) value ranging from 16% to 131%, which signifies a high rate of investment exchange. Solar home systems are economically profitable for micro-enterprises and households with low-income generation activities as opposed to the households using it only for lighting. The study found that solar home systems with a capacity above 30 Wp are the most economically viable option, which can also avoid 6.15 to 7.34 tonnes of CO2 emissions during the 20 years of life-cycle, while providing d...

Methods in molecular biology (Clifton, N.J.), 2018

Over the last few years a number of restriction enzymes that cut DNA only if cytosines within the... more Over the last few years a number of restriction enzymes that cut DNA only if cytosines within their recognition sequences are methylated have been characterized and become commercially available. Cleavage with these enzymes to release DNA fragments in a methylation-dependent manner can be combined with a novel method of amplification, Helper Dependent Chain Reaction (HDCR), to selectively amplify these fragments. HDCR uses "Helper" oligonucleotides as templates for extension of the free 3' end of target fragments to incorporate tag sequences at the ends of fragments. These tag sequences are then used for priming of amplification of target fragments. Modifications to the amplification primers (Drivers) and the Helpers ensure that there is selection for the sequences within target fragments with each cycle of amplification. The combination of methylation-dependent enzymes and HDCR allows the sensitive and selective amplification of methylated DNA sequences without the ne...

Analytical chemistry, Jan 20, 2016

The local electrochemical behavior of a solid-liquid interface can be studied by electrochemical ... more The local electrochemical behavior of a solid-liquid interface can be studied by electrochemical impedance spectroscopy (EIS). The investigated surface area can be delimited by adding a drop of solution, which forms an interface between the liquid drop and the working electrode, and performing the measurements inside. The size of the drop must be sufficiently small for a simultaneous wettability characterization (from the contact angle measurement) and appropriately large so that wettability is not influenced by the presence of the working and the counter electrode inserted in the droplet. In this work, we showed that EIS measurements can be performed in a solution droplet of 2 to 4 μL, although the electrochemical cell lacks the usual geometry. For our measurements, we studied a model system consisting of a KCl aqueous solution of [Fe(CN)6](3-/4-) redox couple at a Pt electrode. All the results were compared with those obtained for a bulk configuration. The sessile drop configurati...

Genes, Jan 15, 2016

Solid tumors shed DNA into circulation, and there is growing evidence that the detection of circu... more Solid tumors shed DNA into circulation, and there is growing evidence that the detection of circulating tumor DNA (ctDNA) has broad clinical utility, including monitoring of disease, prognosis, response to chemotherapy and tracking tumor heterogeneity. The appearance of ctDNA in the circulating cell-free DNA (ccfDNA) isolated from plasma or serum is commonly detected by identifying tumor-specific features such as insertions, deletions, mutations and/or aberrant methylation. Methylation is a normal cell regulatory event, and since the majority of ccfDNA is derived from white blood cells (WBC), it is important that tumour-specific DNA methylation markers show rare to no methylation events in WBC DNA. We have used a novel approach for assessment of low levels of DNA methylation in WBC DNA. DNA methylation in 29 previously identified regions (residing in 17 genes) was analyzed in WBC DNA and eight differentially-methylated regions (DMRs) were taken through to testing in clinical samples...

Http Www Theses Fr, 2012

Ce travail a été réalisé au laboratoire interfaces et systèmes électrochimiques. Je tiens tout d'... more Ce travail a été réalisé au laboratoire interfaces et systèmes électrochimiques. Je tiens tout d'abord à remercier Dr. François HUET, Professeur à l'UPMC, de m'avoir accueillie dans son laboratoire. J'adresse également mes profondes gratitudes et sincère reconnaissance à Dr. Hubert PERROT, Directeur de recherches, qui m'a ouvert les portes de son équipe. Grâce à eux, j'ai pu passer mes trois années de thèse dans les meilleures conditions de travail et dans une ambiance si humaine ! Je voudrais présenter toute ma sincère reconnaissance et mes profondes gratitudes à Dr. Mireille TURMINE, Maître de conférences à l'UPMC, qui a dirigé cette thèse et sans qui tout ce travail n'aurait pas pu être mené. Ses remarques avisées, sa rigueur et ses compétences scientifiques m'ont permis d'acquérir des connaissances dans plusieurs domaines. Merci pour le soutien, la gentillesse, le suivi de ce travail quotidiennement tout en me laissant une grande liberté ainsi les petites pensées qu'elle m'a apportées lors qu'elle est en voyage !!! Pour moi, elle n'est pas une simple directrice de thèse et je n'oublirai jamais mon

International Journal of Pest Management, 1993

A trial was conducted to evaluate people's perception and measurement of the swath width... more A trial was conducted to evaluate people's perception and measurement of the swath widths produced by a spray nozzle held at three different heights above the ground whilst spraying. Nineteen individuals, having no previous experience of pesticide application, consistently underestimated the swath width compared with measurements made by three experienced spray operators. Half of another 22 participants failed to calculate correctly the amount of pesticide required to spray a 1 ha field, but all but one individual successfully made up a 20% solution of a hypothetical pesticide mixture. The results suggest that more detail on the measurement of swath widths is required in instruction manuals, and that training courses need to take particular account of the inability of many operators to perform simple calculations.

Genes & cancer, 2011

An uncharacterized gene locus (Chr16:hCG_1815491), now named colorectal neoplasia differentially ... more An uncharacterized gene locus (Chr16:hCG_1815491), now named colorectal neoplasia differentially expressed (gene symbol CRNDE), is activated early in colorectal neoplasia. The locus is unrelated to any known protein-coding gene. Microarray analysis of 454 tissue specimens (discovery) and 68 previously untested specimens (validation) showed elevated expression of CRNDE in >90% of colorectal adenomas and adenocarcinomas. These findings were confirmed and extended by exon microarray studies and RT-PCR assays. CRNDE transcription start sites were identified in CaCo2 and HCT116 cells by 5'-RACE. The major transcript isoforms in colorectal cancer (CRC) cell lines and colorectal tissue are CRNDE-a, -b, -d, -e, -f, -h, and -j. Except for CRNDE-d, the known CRNDE splice variants are upregulated in neoplastic colorectal tissue; expression levels for CRNDE-h alone demonstrate a sensitivity of 95% and specificity of 96% for adenoma versus normal tissue. A quantitative RT-PCR assay measur...

Epigenetics : official journal of the DNA Methylation Society, 2014

The CAHM gene (Colorectal Adenocarcinoma HyperMethylated), previously LOC100526820, is located on... more The CAHM gene (Colorectal Adenocarcinoma HyperMethylated), previously LOC100526820, is located on chromosome 6, hg19 chr6:163 834 097-163 834 982. It lacks introns, encodes a long non-coding RNA (lncRNA) and is located adjacent to the gene QKI, which encodes an RNA binding protein. Deep bisulphite sequencing of ten colorectal cancer (CRC) and matched normal tissues demonstrated frequent hypermethylation within the CAHM gene in cancer. A quantitative methylation-specific PCR (qMSP) was used to characterize additional tissue samples. With a threshold of 5% methylation, the CAHM assay was positive in 2/26 normal colorectal tissues (8%), 17/21 adenomas (81%), and 56/79 CRC samples (71%). A reverse transcriptase-qPCR assay showed that CAHM RNA levels correlated negatively with CAHM % methylation, and therefore CAHM gene expression is typically decreased in CRC. The CAHM qMSP assay was applied to DNA isolated from plasma specimens from 220 colonoscopy-examined patients. Using a threshold ...

Somatic Cell and Molecular Genetics, 1995

NHuman diploid fibroblasts, strain MRC-5, were perrneabilized by electroporation and treated with... more NHuman diploid fibroblasts, strain MRC-5, were perrneabilized by electroporation and treated with 5-methyl deoxycytidine triphosphate (5-methyl dCTP) in the S phase of the cell cycle. The frequency of TG n HPRT cells was increased up to 20-fold in comparison to control untreated cultures. Representative TG R clones were unable to grow in HA T, and these were treated with 5-azacytidine (5-aza-CR). In many cases subsequent growth in HA T medium was observed, but in others it is likely that the cells had run out of growth potential. The results provide the first evidence of the silencing and reactivation of a gene in normal diploid mammalian cells.

Copyright information:Taken from "Headloop suppression PCR and its applic... more Copyright information:Taken from "Headloop suppression PCR and its application to selective amplification of methylated DNA sequences"Nucleic Acids Research 2005;33(14):e127-e127.Published online 9 Aug 2005PMCID:PMC1184225.© The Author 2005. Published by Oxford University Press. All rights reserved Sequences from the and 16S rRNA genes are shown below that from the gene. Dashes indicate identity to the sequence and 'Δ' deletions. The position of the forward base primer NR-Fli is shown as are the head sequences EHL2a and EHL48 targeted to suppress rDNA amplification, and SAHL targeted to suppress amplification of rDNA. Mismatches to non-target sequences are shown in boldface.