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Lamb HJ, Nguyen LT, Copley JP, Engle BN, Hayes BJ, Ross EM. Imputation strategies for genomic prediction using nanopore sequencing. BMC Biol 2023; 21:286. [PMID: 38066581 PMCID: PMC10709982 DOI: 10.1186/s12915-023-01782-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2023] [Accepted: 11/27/2023] [Indexed: 12/18/2023] Open
Abstract
BACKGROUND Genomic prediction describes the use of SNP genotypes to predict complex traits and has been widely applied in humans and agricultural species. Genotyping-by-sequencing, a method which uses low-coverage sequence data paired with genotype imputation, is becoming an increasingly popular SNP genotyping method for genomic prediction. The development of Oxford Nanopore Technologies' (ONT) MinION sequencer has now made genotyping-by-sequencing portable and rapid. Here we evaluate the speed and accuracy of genomic predictions using low-coverage ONT sequence data in a population of cattle using four imputation approaches. We also investigate the effect of SNP reference panel size on imputation performance. RESULTS SNP array genotypes and ONT sequence data for 62 beef heifers were used to calculate genomic estimated breeding values (GEBVs) from 641 k SNP for four traits. GEBV accuracy was much higher when genome-wide flanking SNP from sequence data were used to help impute the 641 k panel used for genomic predictions. Using the imputation package QUILT, correlations between ONT and low-density SNP array genomic breeding values were greater than 0.91 and up to 0.97 for sequencing coverages as low as 0.1 × using a reference panel of 48 million SNP. Imputation time was significantly reduced by decreasing the number of flanking sequence SNP used in imputation for all methods. When compared to high-density SNP arrays, genotyping accuracy and genomic breeding value correlations at 0.5 × coverage were also found to be higher than those imputed from low-density arrays. CONCLUSIONS Here we demonstrated accurate genomic prediction is possible with ONT sequence data from sequencing coverages as low as 0.1 × , and imputation time can be as short as 10 min per sample. We also demonstrate that in this population, genotyping-by-sequencing at 0.1 × coverage can be more accurate than imputation from low-density SNP arrays.
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Affiliation(s)
- H J Lamb
- Centre for Animal Science, Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St. Lucia, QLD, 4067, Australia.
| | - L T Nguyen
- Centre for Animal Science, Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St. Lucia, QLD, 4067, Australia
| | - J P Copley
- Centre for Animal Science, Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St. Lucia, QLD, 4067, Australia
| | - B N Engle
- USDA, ARS, U.S. Meat Animal Research Centre, Clay Centre, NE, 68933, USA
| | - B J Hayes
- Centre for Animal Science, Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St. Lucia, QLD, 4067, Australia
| | - E M Ross
- Centre for Animal Science, Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St. Lucia, QLD, 4067, Australia
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Idzuchi H, Pientka F, Huang KF, Harada K, Gül Ö, Shin YJ, Nguyen LT, Jo NH, Shindo D, Cava RJ, Canfield PC, Kim P. Unconventional supercurrent phase in Ising superconductor Josephson junction with atomically thin magnetic insulator. Nat Commun 2021; 12:5332. [PMID: 34504077 PMCID: PMC8429564 DOI: 10.1038/s41467-021-25608-1] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2021] [Accepted: 08/22/2021] [Indexed: 11/23/2022] Open
Abstract
In two-dimensional (2D) NbSe2 crystal, which lacks inversion symmetry, strong spin-orbit coupling aligns the spins of Cooper pairs to the orbital valleys, forming Ising Cooper pairs (ICPs). The unusual spin texture of ICPs can be further modulated by introducing magnetic exchange. Here, we report unconventional supercurrent phase in van der Waals heterostructure Josephson junctions (JJs) that couples NbSe2 ICPs across an atomically thin magnetic insulator (MI) Cr2Ge2Te6. By constructing a superconducting quantum interference device (SQUID), we measure the phase of the transferred Cooper pairs in the MI JJ. We demonstrate a doubly degenerate nontrivial JJ phase (ϕ), formed by momentum-conserving tunneling of ICPs across magnetic domains in the barrier. The doubly degenerate ground states in MI JJs provide a two-level quantum system that can be utilized as a new dissipationless component for superconducting quantum devices. Our work boosts the study of various superconducting states with spin-orbit coupling, opening up an avenue to designing new superconducting phase-controlled quantum electronic devices. Van der Waals structures provide a new platform to explore novel physics of superconductor/ferromagnet interfaces. Here, NbSe2 Josephson junction with Cr2Ge2Te6 enables non-trivial Josephson phase by spin-dependent interaction, boosting the study of superconducting states with spin-orbit coupling and phase-controlled quantum electronic device.
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Affiliation(s)
- H Idzuchi
- Department of Physics, Harvard University, Cambridge, MA, USA.,WPI Advanced Institute for Materials Research and Center for Science and Innovation in Spintronics, Tohoku University, Sendai, Japan
| | - F Pientka
- Department of Physics, Harvard University, Cambridge, MA, USA.,Institut für Theoretische Physik, Goethe-Universität, Frankfurt am Main, Germany
| | - K-F Huang
- Department of Physics, Harvard University, Cambridge, MA, USA
| | - K Harada
- Center for Emergent Matter Science (CEMS), RIKEN, Hatoyama, Saitama, Japan
| | - Ö Gül
- Department of Physics, Harvard University, Cambridge, MA, USA
| | - Y J Shin
- Department of Physics, Harvard University, Cambridge, MA, USA.,Center for Functional Nanomaterials, Brookhaven National Laboratory, Upton, NY, USA
| | - L T Nguyen
- Department of Chemistry, Princeton University, Princeton, NJ, USA
| | - N H Jo
- Department of Physics and Astronomy, Iowa State University, Ames, IA, USA.,Ames Laboratory, Iowa State University, Ames, IA, USA
| | - D Shindo
- Center for Emergent Matter Science (CEMS), RIKEN, Hatoyama, Saitama, Japan
| | - R J Cava
- Department of Chemistry, Princeton University, Princeton, NJ, USA
| | - P C Canfield
- Department of Physics and Astronomy, Iowa State University, Ames, IA, USA.,Ames Laboratory, Iowa State University, Ames, IA, USA
| | - P Kim
- Department of Physics, Harvard University, Cambridge, MA, USA.
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McBride B, O'Neil JD, Hue TT, Eni R, Nguyen CV, Nguyen LT. Improving health equity for ethnic minority women in Thai Nguyen, Vietnam: qualitative results from an mHealth intervention targeting maternal and infant health service access. J Public Health (Oxf) 2019; 40:ii32-ii41. [PMID: 30252117 PMCID: PMC6294030 DOI: 10.1093/pubmed/fdy165] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2018] [Accepted: 08/29/2018] [Indexed: 11/12/2022] Open
Abstract
Background Ethnic minority women (EMW) in Vietnam experience disproportionately high infant and maternal mortality rates due to low social status, poverty and remoteness from health centres. This project piloted and evaluated a low-cost mobile health (mHealth) intervention called mMom utilizing behaviour change communication (BCC) to improve access to maternal, newborn and child health (MNCH) services and health equity among EMW living in remote areas. Methods The mMom intervention built an integrated mHealth platform which sent timely MNCH information and BCC text messages to participants, and engaged health workers towards increasing their interaction and building demand for quality natal care. Mid-term and final qualitative evaluations were conducted to assess the intervention's acceptability and impact. Results In evaluations, all participants expressed satisfaction with the quality, timeliness and convenience of the messages, and health workers reported increased efficiency and quality of care. The use of BCC increased care-seeking from EMW and strengthened relationships with health providers. Conclusion The mMom project demonstrated the acceptability of mHealth in a remote Vietnamese region with a high proportion of disadvantaged EMW. The messages promoted increased contact between participants and health providers, which holds potential to address the marginalization of EMW from the health system. Keywords behaviour change communication, eHealth, ethnic minorities, health equity, mHealth, MNCH, mobile health, Vietnam.
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Affiliation(s)
- B McBride
- School of Population and Public Health, University of British Columbia, Canada
| | - J D O'Neil
- Faculty of Health Sciences, Simon Fraser University, Burnaby, Canada
| | - Trinh T Hue
- Institute of Population, Health and Development, Hanoi, Vietnam
| | - R Eni
- School of Population and Public Health, University of British Columbia, Canada
| | - C Vu Nguyen
- Institute of Population, Health and Development, Hanoi, Vietnam
| | - L T Nguyen
- Institute of Population, Health and Development, Hanoi, Vietnam.,Nossal Institute for Global Health, University of Melbourne, Australia
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4
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Nguyen LT, Nguyen UDT, Nguyen TDT, Ho-Pham LT, Nguyen TV. Contribution of bone turnover markers to the variation in bone mineral density: a study in Vietnamese men and women. Osteoporos Int 2018; 29:2739-2744. [PMID: 30196375 DOI: 10.1007/s00198-018-4700-9] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/09/2018] [Accepted: 09/04/2018] [Indexed: 11/28/2022]
Abstract
UNLABELLED The present cross-sectional study constructed reference ranges for bone resorption marker beta isomerized form of C-terminal crosslinking telopeptides of type I collagen (beta-CTX) and bone formation marker procollagen type 1 N-terminal propeptide (PINP) for the Vietnamese population. We have further shown that for a given age and weight, higher levels of beta-CTX were significantly associated with bone mineral density in men and women. INTRODUCTION Normal bone is constantly renewed by two opposing processes of resorption and formation which can be reflected by bone turnover markers (BTMs). This study sought to define the contribution of BTMs to the variation in bone mineral density (BMD) in normal individuals. METHODS The study involved 205 men and 432 women aged between 18 and 87, who were randomly selected from various districts within Ho Chi Minh City, Vietnam. Fasting serum levels of PINP and beta-CTX were determined by electrochemiluminescence (Roche, ECLIA). BMD at the lumbar spine (LS) and femoral neck (FN) was measured by dual-energy x-ray absorptiometry (Hologic, Waltham, MA, USA). RESULTS Among those aged < 50 years, women had lower PINP and beta-CTX levels than men, but among those aged > 50 years, women had higher PINP and beta-CTX levels than men. In the multiple linear regression analysis, beta-CTX-but not PINP-was significantly associated with both femoral neck (P = 0.008) and lumbar spine BMD (P = 0.008) and the association was independent of gender, age, and body weight. The proportion of variance in BMD attributable to beta-CTX was 1% for femoral neck BMD and 2% for lumbar spine BMD. CONCLUSION The elevation in bone formation marker PINP and bone resorption marker beta-CTX in postmenopausal women was greater than in elderly men. However, only beta-CTX was modestly but significantly associated with BMD.
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Affiliation(s)
- L T Nguyen
- Bone and Muscle Research Group, Ton Duc Thang University, 19 Nguyen Huu Tho, Tan Phong, District 7, Ho Chi Minh, 700000, Vietnam
- Faculty of Applied Sciences, Ton Duc Thang University, Ho Chi Minh, Vietnam
| | - U D T Nguyen
- Bone and Muscle Research Group, Ton Duc Thang University, 19 Nguyen Huu Tho, Tan Phong, District 7, Ho Chi Minh, 700000, Vietnam
- Department of Internal Medicine, Pham Ngoc Thach University of Medicine, Ho Chi Minh, Vietnam
| | - T D T Nguyen
- Bone and Muscle Research Group, Ton Duc Thang University, 19 Nguyen Huu Tho, Tan Phong, District 7, Ho Chi Minh, 700000, Vietnam
| | - L T Ho-Pham
- Bone and Muscle Research Group, Ton Duc Thang University, 19 Nguyen Huu Tho, Tan Phong, District 7, Ho Chi Minh, 700000, Vietnam.
- Department of Internal Medicine, Pham Ngoc Thach University of Medicine, Ho Chi Minh, Vietnam.
| | - T V Nguyen
- Bone and Muscle Research Group, Ton Duc Thang University, 19 Nguyen Huu Tho, Tan Phong, District 7, Ho Chi Minh, 700000, Vietnam
- School of Biomedical Engineering, University of Technology Sydney, Ultimo, Australia
- Bone Biology Division, Garvan Institute of Medical Research, Sydney, Australia
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Nguyen LT, Zacchi LF, Schulz BL, Moore SS, Fortes MRS. Adipose tissue proteomic analyses to study puberty in Brahman heifers. J Anim Sci 2018; 96:2392-2398. [PMID: 29788311 DOI: 10.1093/jas/sky128] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2018] [Accepted: 05/17/2018] [Indexed: 12/31/2022] Open
Abstract
The adipose tissue has been recognized as an active endocrine organ which can modulate numerous physiological processes such as metabolism, appetite, immunity, and reproduction. The aim of this study was to look for differentially abundant proteins and their biological functions in the abdominal adipose tissue between pre- and postpubertal Brahman heifers. Twelve Brahman heifers were divided into 2 groups and paired on slaughter day. Prepubertal heifers had never ovulated and postpubertal heifers were slaughtered on the luteal phase of their second estrous cycle. After ensuring the occurrence of puberty in postpubertal heifers, abdominal adipose tissue samples were collected. Mass spectrometry proteomic analysis identified 646 proteins and revealed that 171 proteins showed differential abundance in adipose tissue between the pre- and postpuberty groups (adjusted P-value < 0.05). Data are available via ProteomeXchange with identifier PXD009452. Using a list of 51 highly differentially abundant proteins as the target (adjusted P-value < 10-5), we found 14 enriched pathways. The results indicated that gluconeogenesis was enhanced when puberty approached. The metabolism of glucose, lipids, and AA in the adipose tissue mainly participated in oxidation and energy supply for heifers when puberty occurred. Our study also revealed the differentially abundant proteins were enriched for estrogen signaling and PI3K-Akt signaling pathways, which are known integrators of metabolism and reproduction. These results suggest new candidate proteins that may contribute to a better understanding of the signaling mechanisms that relate adipose tissue function to puberty. Protein-protein interaction network analysis identified 4 hub proteins that had the highest degrees of connection: PGK1, ALDH5A1, EEF2, and LDHB. Highly connected proteins are likely to influence the functions of all differentially abundant proteins identified, directly or indirectly.
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Affiliation(s)
- L T Nguyen
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Australia.,Faculty of Biotechnology, Vietnam National University of Agriculture, Hanoi, Vietnam
| | - L F Zacchi
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Australia.,Australian Research Council Training Centre for Biopharmaceutical Innovation, Australian Institute of Bioengineering and Nanotechnology, The University of Queensland, Brisbane, Australia
| | - B L Schulz
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Australia.,Australian Research Council Training Centre for Biopharmaceutical Innovation, Australian Institute of Bioengineering and Nanotechnology, The University of Queensland, Brisbane, Australia
| | - S S Moore
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Brisbane, Australia
| | - M R S Fortes
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Australia
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6
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Fortes MRS, Zacchi LF, Nguyen LT, Raidan F, Weller MMDCA, Choo JJY, Reverter A, Rego JPA, Boe-Hansen GB, Porto-Neto LR, Lehnert SA, Cánovas A, Schulz BL, Islas-Trejo A, Medrano JF, Thomas MG, Moore SS. Pre- and post-puberty expression of genes and proteins in the uterus of Bos indicus heifers: the luteal phase effect post-puberty. Anim Genet 2018; 49:539-549. [PMID: 30192028 DOI: 10.1111/age.12721] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/26/2018] [Indexed: 12/17/2022]
Abstract
Progesterone signaling and uterine function are crucial in terms of pregnancy establishment. To investigate how the uterine tissue and its secretion changes in relation to puberty, we sampled tissue and uterine fluid from six pre- and six post-pubertal Brahman heifers. Post-pubertal heifers were sampled in the luteal phase. Gene expression of the uterine tissue was investigated with RNA-sequencing, whereas the uterine fluid was used for protein profiling with mass spectrometry. A total of 4034 genes were differentially expressed (DE) at a nominal P-value of 0.05, and 26 genes were significantly DE after Bonferroni correction (P < 3.1 × 10-6 ). We also identified 79 proteins (out of 230 proteins) that were DE (P < 1 × 10-5 ) in the uterine fluid. When we compared proteomics and transcriptome results, four DE proteins were identified as being encoded by DE genes: OVGP1, GRP, CAP1 and HBA. Except for CAP1, the other three had lower expression post-puberty. The function of these four genes hypothetically related to preparation of the uterus for a potential pregnancy is discussed in the context of puberty. All DE genes and proteins were also used in pathway and ontology enrichment analyses to investigate overall function. The DE genes were enriched for terms related to ribosomal activity. Transcription factors that were deemed key regulators of DE genes are also reported. Transcription factors ZNF567, ZNF775, RELA, PIAS2, LHX4, SOX2, MEF2C, ZNF354C, HMG20A, TCF7L2, ZNF420, HIC1, GTF3A and two novel genes had the highest regulatory impact factor scores. These data can help to understand how puberty influences uterine function.
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Affiliation(s)
- M R S Fortes
- School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, QLD 4072, Australia
| | - L F Zacchi
- School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, QLD 4072, Australia
| | - L T Nguyen
- School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, QLD 4072, Australia.,Faculty of Biotechnology, Vietnam National University of Agriculture, Gialam, Hanoi, Vietnam
| | - F Raidan
- Animal Science Department, Universidade Federal de Viçosa, Vicosa, Minas Gerais, 36570-900, Brazil
| | - M M D C A Weller
- CSIRO Agriculture and Food, Queensland Bioscience Precinct, Brisbane, QLD 4072, Australia
| | - J J Y Choo
- School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, QLD 4072, Australia
| | - A Reverter
- Animal Science Department, Universidade Federal de Viçosa, Vicosa, Minas Gerais, 36570-900, Brazil
| | - J P A Rego
- Instituto Federal de Educação, Ciência e Tecnologia do Ceara, Fortaleza, Ceará, 62930-000, Brazil
| | - G B Boe-Hansen
- School of Veterinary Sciences, The University of Queensland, Gatton, QLD 4343, Australia
| | - L R Porto-Neto
- Animal Science Department, Universidade Federal de Viçosa, Vicosa, Minas Gerais, 36570-900, Brazil
| | - S A Lehnert
- Animal Science Department, Universidade Federal de Viçosa, Vicosa, Minas Gerais, 36570-900, Brazil
| | - A Cánovas
- Department of Animal Biosciences, Centre of Genetic Improvement for Livestock, University of Guelph, Guelph, ON, N1G 2W1, Canada
| | - B L Schulz
- School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, QLD 4072, Australia
| | - A Islas-Trejo
- Department of Animal Science, University of California Davis, Davis, CA, 95616, USA
| | - J F Medrano
- Department of Animal Science, University of California Davis, Davis, CA, 95616, USA
| | - M G Thomas
- Department of Animal Science, Colorado State University, Fort Collins, CO, 80523, USA
| | - S S Moore
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Brisbane, QLD 4072, Australia
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Bui KC, Nguyen TML, Riebold M, Xing J, Bhuria V, Nguyen LT, Le HS, Velavan TP, Wilkens L, Malek NP, Bozko P, Plentz RR. Role of adiponectin signaling in cholangiocarcinoma. Z Gastroenterol 2018. [DOI: 10.1055/s-0038-1668968] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Affiliation(s)
- KC Bui
- Medical University Hospital, Department of Internal Medicine I, Tübingen, Deutschland
- Vietnam Military Medical University, Department of Pathophysiology, Hanoi, Vietnam
- Medical University Hospital, Institute of Tropical Medicine, Tübingen, Deutschland
| | - TML Nguyen
- Medical University Hospital, Department of Internal Medicine I, Tübingen, Deutschland
- Vietnam Military Medical University, Department of Biochemistry, Hanoi, Vietnam
- Vietnamese-German Center of Excellence in Medical Research, Hanoi, Vietnam
| | - M Riebold
- Medical University Hospital, Department of Internal Medicine I, Tübingen, Deutschland
| | - J Xing
- Medical University Hospital, Department of Internal Medicine I, Tübingen, Deutschland
| | - V Bhuria
- Medical University Hospital, Department of Internal Medicine I, Tübingen, Deutschland
| | - LT Nguyen
- Vietnam Military Medical University, Department of Pathophysiology, Hanoi, Vietnam
| | - HS Le
- Vietnamese-German Center of Excellence in Medical Research, Hanoi, Vietnam
- 108 Military Central Hospital, Hanoi, Vietnam
| | - TP Velavan
- Medical University Hospital, Institute of Tropical Medicine, Tübingen, Deutschland
- Vietnamese-German Center of Excellence in Medical Research, Hanoi, Vietnam
| | - L Wilkens
- Hannover Regional Hospital, Institute of Pathology, Hannover, Deutschland
| | - NP Malek
- Medical University Hospital, Department of Internal Medicine I, Tübingen, Deutschland
| | - P Bozko
- Medical University Hospital, Department of Internal Medicine I, Tübingen, Deutschland
| | - RR Plentz
- Medical University Hospital, Department of Internal Medicine I, Tübingen, Deutschland
- Bremen-Nord Hospital, Department of Internal Medicine II, Bremen, Deutschland
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Fonseca PADS, Id-Lahoucine S, Casellas J, Miglior F, Reverter A, Fortes MR, Nguyen LT, Porto-Neto LR, Sargolzaei M, Brito LF, Miller SP, Schenkel FS, Lohuis M, Medrano JF, Canovas A. 25 Functional Characterization of Genes Mapped in Transmission Ratio Distortion Regions of the Bovine Genome Affecting Reproduction. J Anim Sci 2018. [DOI: 10.1093/jas/sky073.023] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Affiliation(s)
| | - S Id-Lahoucine
- Centre for Genetic Improvement of Livestock, Department of Animal Biosciences, University of Guelph, Guelph, ON, Canada
| | - J Casellas
- Universitat Autònoma de Barcelona, Bellaterra, Spain
| | - F Miglior
- Canadian Dairy Network, Guelph, ON, Canada
| | | | - M R Fortes
- The University of Queensland, Queensland Alliance for Agriculture and Food Innovation, St Lucia, Australia
| | - L T Nguyen
- The University of Queensland, School of Chemistry and Molecular Biosciences, St Lucia, Australia
| | | | - M Sargolzaei
- Centre for Genetic Improvement of Livestock, Department of Animal Biosciences, University of Guelph, Guelph, ON, Canada
| | - L F Brito
- Centre for Genetic Improvement of Livestock, University of Guelph, Guelph, ON, Canada
| | | | - F S Schenkel
- Centre for Genetic Improvement of Livestock, Department of Animal Biosciences, University of Guelph, Guelph, ON, Canada
| | | | - J F Medrano
- Department of Animal Science, University of California, Davis, CA
| | - A Canovas
- University of Guelph, Guelph, ON, Canada
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9
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Nguyen LT, Reverter A, Cánovas A, Venus B, Islas-Trejo A, Porto-Neto LR, Lehnert SA, Medrano JF, Moore SS, Fortes MRS. Global differential gene expression in the pituitary gland and the ovaries of pre- and postpubertal Brahman heifers. J Anim Sci 2017; 95:599-615. [PMID: 28380590 DOI: 10.2527/jas.2016.0921] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
To understand genes, pathways, and networks related to puberty, we characterized the transcriptome of two tissues: the pituitary gland and ovaries. Samples were harvested from pre- and postpubertal Brahman heifers (same age group). Brahman heifers () are older at puberty compared with , a productivity issue. With RNA sequencing, we identified differentially expressed (DEx) genes and important transcription factors (TF) and predicted coexpression networks. The number of DEx genes detected in the pituitary gland was 284 ( < 0.05), and was the most DEx gene (fold change = 4.12, = 0.01). The gene promotes bone mineralization through transforming growth factor-β (TGFβ) signaling. Further studies of the link between bone mineralization and puberty could target . In ovaries, 3,871 genes were DEx ( < 0.05). Four highly DEx genes were noteworthy for their function: (a γ-aminobutyric acid [GABA] transporter), (), and () and its receptor . These genes had higher ovarian expression in postpubertal heifers. The GABA and its receptors and transporters were expressed in the ovaries of many mammals, suggesting a role for this pathway beyond the brain. The pathway has been known to influence the timing of puberty in rats, via modulation of GnRH. The effects of at the hypothalamus, pituitary gland, and ovaries have been documented. and its receptors are known factors in the release of GnRH, similar to and GABA, although their roles in ovarian tissue are less clear. Pathways previously related to puberty such as TGFβ signaling ( = 6.71 × 10), Wnt signaling ( = 4.1 × 10), and peroxisome proliferator-activated receptor (PPAR) signaling ( = 4.84 × 10) were enriched in our data set. Seven genes were identified as key TF in both tissues: , , , , , , and a novel gene. An ovarian subnetwork created with TF and significant ovarian DEx genes revealed five zinc fingers as regulators: , , , , and . Recent work of hypothalamic gene expression also pointed to zinc fingers as TF for bovine puberty. Although some zinc fingers may be ubiquitously expressed, the identification of DEx genes in common across tissues points to key regulators of puberty. The hypothalamus and pituitary gland had eight DEx genes in common. The hypothalamus and ovaries had 89 DEx genes in common. The pituitary gland and ovaries had 48 DEx genes in common. Our study confirmed the complexity of puberty and suggested further investigation on genes that code zinc fingers.
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Fortes MRS, Nguyen LT, Weller MMDCA, Cánovas A, Islas-Trejo A, Porto-Neto LR, Reverter A, Lehnert SA, Boe-Hansen GB, Thomas MG, Medrano JF, Moore SS. Transcriptome analyses identify five transcription factors differentially expressed in the hypothalamus of post- versus prepubertal Brahman heifers. J Anim Sci 2017; 94:3693-3702. [PMID: 27898892 DOI: 10.2527/jas.2016-0471] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Puberty onset is a developmental process influenced by genetic determinants, environment, and nutrition. Mutations and regulatory gene networks constitute the molecular basis for the genetic determinants of puberty onset. The emerging knowledge of these genetic determinants presents opportunities for innovation in the breeding of early pubertal cattle. This paper presents new data on hypothalamic gene expression related to puberty in (Brahman) in age- and weight-matched heifers. Six postpubertal heifers were compared with 6 prepubertal heifers using whole-genome RNA sequencing methodology for quantification of global gene expression in the hypothalamus. Five transcription factors (TF) with potential regulatory roles in the hypothalamus were identified in this experiment: , , , , and . These TF genes were significantly differentially expressed in the hypothalamus of postpubertal versus prepubertal heifers and were also identified as significant according to the applied regulatory impact factor metric ( < 0.05). Two of these 5 TF, and , were zinc fingers, belonging to a gene family previously reported to have a central regulatory role in mammalian puberty. The gene belongs to the family of homologues of Drosophila sine oculis () genes implicated in transcriptional regulation of gonadotrope gene expression. Tumor-related genes such as and are known to affect basic cellular processes that are relevant in both cancer and developmental processes. Mutations in were associated with puberty in humans. Mutations in these TF, together with other genetic determinants previously discovered, could be used in genomic selection to predict the genetic merit of cattle (i.e., the likelihood of the offspring presenting earlier than average puberty for Brahman). Knowledge of key mutations involved in genetic traits is an advantage for genomic prediction because it can increase its accuracy.
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Dias MM, Cánovas A, Mantilla-Rojas C, Riley DG, Luna-Nevarez P, Coleman SJ, Speidel SE, Enns RM, Islas-Trejo A, Medrano JF, Moore SS, Fortes MRS, Nguyen LT, Venus B, Diaz ISDP, Souza FRP, Fonseca LFS, Baldi F, Albuquerque LG, Thomas MG, Oliveira HN. SNP detection using RNA-sequences of candidate genes associated with puberty in cattle. Genet Mol Res 2017; 16:gmr-16-01-gmr.16019522. [PMID: 28340271 DOI: 10.4238/gmr16019522] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
Fertility traits, such as heifer pregnancy, are economically important in cattle production systems, and are therefore, used in genetic selection programs. The aim of this study was to identify single nucleotide polymorphisms (SNPs) using RNA-sequencing (RNA-Seq) data from ovary, uterus, endometrium, pituitary gland, hypothalamus, liver, longissimus dorsi muscle, and adipose tissue in 62 candidate genes associated with heifer puberty in cattle. RNA-Seq reads were assembled to the bovine reference genome (UMD 3.1.1) and analyzed in five cattle breeds; Brangus, Brahman, Nellore, Angus, and Holstein. Two approaches used the Brangus data for SNP discovery 1) pooling all samples, and 2) within each individual sample. These approaches revealed 1157 SNPs. These were compared with those identified in the pooled samples of the other breeds. Overall, 172 SNPs within 13 genes (CPNE5, FAM19A4, FOXN4, KLF1, LOC777593, MGC157266, NEBL, NRXN3, PEPT-1, PPP3CA, SCG5, TSG101, and TSHR) were concordant in the five breeds. Using Ensembl's Variant Effector Predictor, we determined that 12% of SNPs were in exons (71% synonymous, 29% nonsynonymous), 1% were in untranslated regions (UTRs), 86% were in introns, and 1% were in intergenic regions. Since these SNPs were discovered in RNA, the variants were predicted to be within exons or UTRs. Overall, 160 novel transcripts in 42 candidate genes and five novel genes overlapping five candidate genes were observed. In conclusion, 1157 SNPs were identified in 62 candidate genes associated with puberty in Brangus cattle, of which, 172 were concordant in the five cattle breeds. Novel transcripts and genes were also identified.
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Affiliation(s)
- M M Dias
- Departamento de Zootecnia, Faculdade de Ciências Agrárias e Veterinárias, Universidade Estadual Paulista, Jaboticabal, SP, Brasil
| | - A Cánovas
- Centre for Genetic Improvement of Livestock, Department of Animal Bioscience, University of Guelph, Guelph, ON, Canada
| | - C Mantilla-Rojas
- Department of Animal Science, Texas A&M University, College Station, TX, USA
| | - D G Riley
- Department of Animal Science, Texas A&M University, College Station, TX, USA
| | - P Luna-Nevarez
- Departamento de Ciencias Agronómicas y Veterinarias, Instituto Tecnológico de Sonora, Ciudad Obregón, SON, México
| | - S J Coleman
- Department of Animal Sciences, Colorado State University, Fort Collins, CO, USA
| | - S E Speidel
- Department of Animal Sciences, Colorado State University, Fort Collins, CO, USA
| | - R M Enns
- Department of Animal Sciences, Colorado State University, Fort Collins, CO, USA
| | - A Islas-Trejo
- Department of Animal Science, University of California, Davis, CA, USA
| | - J F Medrano
- Department of Animal Science, University of California, Davis, CA, USA
| | - S S Moore
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Brisbane, Australia
| | - M R S Fortes
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, St Lucia, Australia
| | - L T Nguyen
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, St Lucia, Australia.,Faculty of Biotechnology, Vietnam National University of Agriculture, Vietnam
| | - B Venus
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Brisbane, Australia
| | - I S D P Diaz
- Departamento de Zootecnia, Faculdade de Ciências Agrárias e Veterinárias, Universidade Estadual Paulista, Jaboticabal, SP, Brasil
| | - F R P Souza
- Departamento de Ecologia, Zoologia e Genética, Universidade Federal de Pelotas, Pelotas, RS, Brasil
| | - L F S Fonseca
- Departamento de Zootecnia, Faculdade de Ciências Agrárias e Veterinárias, Universidade Estadual Paulista, Jaboticabal, SP, Brasil
| | - F Baldi
- Departamento de Zootecnia, Faculdade de Ciências Agrárias e Veterinárias, Universidade Estadual Paulista, Jaboticabal, SP, Brasil
| | - L G Albuquerque
- Departamento de Zootecnia, Faculdade de Ciências Agrárias e Veterinárias, Universidade Estadual Paulista, Jaboticabal, SP, Brasil
| | - M G Thomas
- Department of Animal Sciences, Colorado State University, Fort Collins, CO, USA
| | - H N Oliveira
- Departamento de Zootecnia, Faculdade de Ciências Agrárias e Veterinárias, Universidade Estadual Paulista, Jaboticabal, SP, Brasil
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12
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Nguyen LA, Do DH, Nguyen LT, Do NT, Nguyen HH, Nguyen VT, Vu DQ, Nguyen HT, Kato M, Jordan MR, Bui DD. A13 HIV drug resistance over a decade of antiretroviral therapy scale-up for HIV/AIDS patients in Vietnam. Virus Evol 2017; 3:vew036.012. [PMID: 28845273 PMCID: PMC5565985 DOI: 10.1093/ve/vew036.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Affiliation(s)
- L A Nguyen
- National Institute of Hygiene and Epidemiology, Vietnam
| | - D H Do
- National Institute of Hygiene and Epidemiology, Vietnam
| | - L T Nguyen
- National Institute of Hygiene and Epidemiology, Vietnam
| | - N T Do
- Vietnam Authority for HIV AIDS Control
| | | | | | - D Q Vu
- Hanoi Medical University, Vietnam
| | - H T Nguyen
- National Institute of Hygiene and Epidemiology, Vietnam
| | - M Kato
- World Health Organization, Vietnam
| | - M R Jordan
- Tuffs University School of Medicine, Massachusetts, USA
| | - D D Bui
- Vietnam Authority for HIV AIDS Control
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13
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Chu DH, Stevenson MA, Nguyen LV, Isoda N, Firestone SM, Nguyen TN, Nguyen LT, Matsuno K, Okamatsu M, Kida H, Sakoda Y. A cross-sectional study to quantify the prevalence of avian influenza viruses in poultry at intervention and non-intervention live bird markets in central Vietnam, 2014. Transbound Emerg Dis 2017; 64:1991-1999. [PMID: 28120423 DOI: 10.1111/tbed.12605] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2016] [Indexed: 11/26/2022]
Abstract
In Vietnam, live bird markets are found in most populated centres, providing the means by which fresh poultry can be purchased by consumers for immediate consumption. Live bird markets are aggregation points for large numbers of poultry, and therefore, it is common for a range of avian influenza viruses to be mixed within live bird markets as a result of different poultry types and species being brought together from different geographical locations. We conducted a cross-sectional study in seven live bird markets in four districts of Thua Thien Hue Province in August and December, 2014. The aims of this study were to (i) document the prevalence of avian influenza in live bird markets (as measured by virus isolation); and (ii) quantify individual bird-, seller- and market-level characteristics that rendered poultry more likely to be positive for avian influenza virus at the time of sale. A questionnaire soliciting details of knowledge, attitude and avian influenza practices was administered to poultry sellers in study markets. At the same time, swabs and faecal samples were collected from individual poultry and submitted for isolation of avian influenza virus. The final data set comprised samples from 1,629 birds from 83 sellers in the seven live bird markets. A total of 113 birds were positive for virus isolation; a prevalence of 6.9 (95% CI 5.8-8.3) avian influenza virus-positive birds per 100 birds submitted for sale. After adjusting for clustering at the market and individual seller levels, none of the explanatory variables solicited in the questionnaire were significantly associated with avian influenza virus isolation positivity. The proportions of variance at the individual market, seller and individual bird levels were 6%, 48% and 46%, respectively. We conclude that the emphasis of avian influenza control efforts in Vietnam should be at the individual seller level as opposed to the market level.
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Affiliation(s)
- D-H Chu
- Laboratory of Microbiology, Department of Disease Control, Graduate School of Veterinary Medicine, Hokkaido University, Sapporo, Hokkaido, Japan.,Department of Animal Health, Ministry of Agriculture and Rural Development, Hanoi, Vietnam
| | - M A Stevenson
- Asia-Pacific Centre for Animal Health, Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, Vic., Australia
| | - L V Nguyen
- Department of Animal Health, Ministry of Agriculture and Rural Development, Hanoi, Vietnam
| | - N Isoda
- Unit of Risk Analysis and Management, Research Center for Zoonosis Control, Hokkaido University, Sapporo, Hokkaido, Japan.,Global Station for Zoonosis Control, Global Institution for Collaborative Research and Education (GI-CoRE), Hokkaido University, Sapporo, Hokkaido, Japan
| | - S M Firestone
- Asia-Pacific Centre for Animal Health, Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, Vic., Australia
| | - T N Nguyen
- Department of Animal Health, Ministry of Agriculture and Rural Development, Hanoi, Vietnam
| | - L T Nguyen
- Laboratory of Microbiology, Department of Disease Control, Graduate School of Veterinary Medicine, Hokkaido University, Sapporo, Hokkaido, Japan
| | - K Matsuno
- Laboratory of Microbiology, Department of Disease Control, Graduate School of Veterinary Medicine, Hokkaido University, Sapporo, Hokkaido, Japan.,Global Station for Zoonosis Control, Global Institution for Collaborative Research and Education (GI-CoRE), Hokkaido University, Sapporo, Hokkaido, Japan
| | - M Okamatsu
- Laboratory of Microbiology, Department of Disease Control, Graduate School of Veterinary Medicine, Hokkaido University, Sapporo, Hokkaido, Japan
| | - H Kida
- Global Station for Zoonosis Control, Global Institution for Collaborative Research and Education (GI-CoRE), Hokkaido University, Sapporo, Hokkaido, Japan.,World Organization for Animal Health Reference Laboratory for Highly Pathogenic Avian Influenza and Low Pathogenic Avian Influenza, Sapporo, Hokkaido, Japan
| | - Y Sakoda
- Laboratory of Microbiology, Department of Disease Control, Graduate School of Veterinary Medicine, Hokkaido University, Sapporo, Hokkaido, Japan.,Global Station for Zoonosis Control, Global Institution for Collaborative Research and Education (GI-CoRE), Hokkaido University, Sapporo, Hokkaido, Japan.,World Organization for Animal Health Reference Laboratory for Highly Pathogenic Avian Influenza and Low Pathogenic Avian Influenza, Sapporo, Hokkaido, Japan
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14
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Nguyen LT, Reverter A, Cánovas A, Venus B, Islas-Trejo A, Porto-Neto LR, Lehnert SA, Medrano JF, Moore SS, Fortes MRS. Global differential gene expression in the pituitary gland and the ovaries of pre- and postpubertal Brahman heifers. J Anim Sci 2017. [DOI: 10.2527/jas2016.0921] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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15
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Masoud ST, Vecchio LM, Bergeron Y, Hossain MM, Nguyen LT, Bermejo MK, Kile B, Sotnikova TD, Siesser WB, Gainetdinov RR, Wightman RM, Caron MG, Richardson JR, Miller GW, Ramsey AJ, Cyr M, Salahpour A. Increased expression of the dopamine transporter leads to loss of dopamine neurons, oxidative stress and l-DOPA reversible motor deficits. Neurobiol Dis 2014; 74:66-75. [PMID: 25447236 DOI: 10.1016/j.nbd.2014.10.016] [Citation(s) in RCA: 103] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2014] [Revised: 10/07/2014] [Accepted: 10/22/2014] [Indexed: 01/17/2023] Open
Abstract
The dopamine transporter is a key protein responsible for regulating dopamine homeostasis. Its function is to transport dopamine from the extracellular space into the presynaptic neuron. Studies have suggested that accumulation of dopamine in the cytosol can trigger oxidative stress and neurotoxicity. Previously, ectopic expression of the dopamine transporter was shown to cause damage in non-dopaminergic neurons due to their inability to handle cytosolic dopamine. However, it is unknown whether increasing dopamine transporter activity will be detrimental to dopamine neurons that are inherently capable of storing and degrading dopamine. To address this issue, we characterized transgenic mice that over-express the dopamine transporter selectively in dopamine neurons. We report that dopamine transporter over-expressing (DAT-tg) mice display spontaneous loss of midbrain dopamine neurons that is accompanied by increases in oxidative stress markers, 5-S-cysteinyl-dopamine and 5-S-cysteinyl-DOPAC. In addition, metabolite-to-dopamine ratios are increased and VMAT2 protein expression is decreased in the striatum of these animals. Furthermore, DAT-tg mice also show fine motor deficits on challenging beam traversal that are reversed with l-DOPA treatment. Collectively, our findings demonstrate that even in neurons that routinely handle dopamine, increased uptake of this neurotransmitter through the dopamine transporter results in oxidative damage, neuronal loss and l-DOPA reversible motor deficits. In addition, DAT over-expressing animals are highly sensitive to MPTP-induced neurotoxicity. The effects of increased dopamine uptake in these transgenic mice could shed light on the unique vulnerability of dopamine neurons in Parkinson's disease.
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Affiliation(s)
- S T Masoud
- Department of Pharmacology and Toxicology, University of Toronto, 1 King's College Circle - Rm 4302, Toronto, ON M5S 1A8, Canada.
| | - L M Vecchio
- Department of Pharmacology and Toxicology, University of Toronto, 1 King's College Circle - Rm 4302, Toronto, ON M5S 1A8, Canada.
| | - Y Bergeron
- Department of Medical Biology, Université du Québec à Trois-Rivières, QC G9A 5H7 Canada.
| | - M M Hossain
- Environmental and Occupational Health Sciences Institute, Rutgers, 170 Frelinghuysen Road, EOHSI 340, Piscataway, NJ 08854, USA.
| | - L T Nguyen
- Department of Pharmacology and Toxicology, University of Toronto, 1 King's College Circle - Rm 4302, Toronto, ON M5S 1A8, Canada.
| | - M K Bermejo
- Department of Pharmacology and Toxicology, University of Toronto, 1 King's College Circle - Rm 4302, Toronto, ON M5S 1A8, Canada.
| | - B Kile
- Department of Chemistry, University of North Carolina at Chapel Hill, NC 27599, USA.
| | - T D Sotnikova
- Neuroscience and Brain Technologies, Italian Institute of Technology, Via Morego 30, Genova 16163, Italy; Faculty of Biology and Soil Science, St. Petersburg State University, St. Petersburg 199034, Russia.
| | - W B Siesser
- Department of Cell Biology, Duke University Medical Center, Durham, NC 27710, USA.
| | - R R Gainetdinov
- Neuroscience and Brain Technologies, Italian Institute of Technology, Via Morego 30, Genova 16163, Italy; Faculty of Biology and Soil Science, St. Petersburg State University, St. Petersburg 199034, Russia; Skolkovo Institute of Science and Technology, Skolkovo, 143025 Moscow Region, Russia.
| | - R M Wightman
- Department of Chemistry, University of North Carolina at Chapel Hill, NC 27599, USA.
| | - M G Caron
- Department of Cell Biology, Duke University Medical Center, Durham, NC 27710, USA.
| | - J R Richardson
- Environmental and Occupational Health Sciences Institute, Rutgers, 170 Frelinghuysen Road, EOHSI 340, Piscataway, NJ 08854, USA.
| | - G W Miller
- Department of Environmental Health, Emory University, Atlanta, GA 30322, USA; Department of Pharmacology, Emory University, Atlanta, GA 30322, USA; Department of Neurology, Emory University, Atlanta, GA 30322, USA.
| | - A J Ramsey
- Department of Pharmacology and Toxicology, University of Toronto, 1 King's College Circle - Rm 4302, Toronto, ON M5S 1A8, Canada.
| | - M Cyr
- Department of Medical Biology, Université du Québec à Trois-Rivières, QC G9A 5H7 Canada.
| | - A Salahpour
- Department of Pharmacology and Toxicology, University of Toronto, 1 King's College Circle - Rm 4302, Toronto, ON M5S 1A8, Canada.
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16
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Nguyen NT, Tran HV, Tran THT, Stephen MJ, Nguyen LT, Nguyen MTT, Pham MD. OR13-1 * FACTORS ASSOCIATED WITH RETENTION IN VIETNAM'S METHADONE MAINTENANCE PROGRAM (MMT): A 24-MONTH-COHORT STUDY IN HAI PHONG AND HO CHI MINH CITY. Alcohol Alcohol 2014. [DOI: 10.1093/alcalc/agu053.60] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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17
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Nguyen LT, Nguyen MV, Trinh HTX. P2.025 Etiology of Respiratory Tract Infection in HIV/AIDS Patients at the National Hospital of Tropical Diseases (NHTD) Hanoi, Vietnam. Br J Vener Dis 2013. [DOI: 10.1136/sextrans-2013-051184.0290] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
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18
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Nguyen LT, Hamilton CD, Xia Q, Stout JE. Mortality before or during treatment among tuberculosis patients in North Carolina, 1993-2003. Int J Tuberc Lung Dis 2011; 15:257-i. [PMID: 21219691 PMCID: PMC3805270] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/30/2023] Open
Abstract
SETTING North Carolina, United States. OBJECTIVE To investigate the demographic and behavioral risk factors associated with death among tuberculosis (TB) patients in North Carolina. DESIGN Retrospective cohort of all TB patients reported in North Carolina, 1993-2003 (inclusive). A surveillance dataset based upon Report of Verified Case of Tuberculosis (RVCT) records was cross-linked with the National Death Index (NDI) to confirm date of death and capture additional deaths. RESULTS Among 5311 TB patients, 181 died before initiation of TB treatment, and 540 died before completion of TB treatment. Increasing age, miliary/meningeal disease, and human immunodeficiency virus (HIV) infection were associated with increased risk of death before treatment, during early treatment (initial 8 weeks) and later in TB treatment. In addition to these factors, excess alcohol use (HR 1.62, 95%CI 1.13-2.32) and residence in a nursing home (HR 1.65, 95%CI 1.20-2.29) were associated with a significantly increased risk of death during the first 8 weeks of treatment. CONCLUSION Many of the deaths in TB patients occurred in the most vulnerable populations, such as the elderly or those with HIV infection, and may be attributable to delayed diagnosis and poor functional status.
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Affiliation(s)
- L. T. Nguyen
- Department of Medicine, Duke University Medical Center, Durham, North Carolina
| | - C. D. Hamilton
- Department of Medicine, Duke University Medical Center, Durham, North Carolina
| | - Q. Xia
- Research Triangle Institute International, Research Triangle Park, North Carolina, USA
| | - J. E. Stout
- Correspondence to: Jason Stout, Box 102359, Duke University Medical Center, Durham, NC 27710, USA. Tel: (+1) 919 668 0826. Fax: (+1) 919 681 7494.
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Weingarten TN, Flores AS, McKenzie JA, Nguyen LT, Robinson WB, Kinney TM, Siems BT, Wenzel PJ, Sarr MG, Marienau MS, Schroeder DR, Olson EJ, Morgenthaler TI, Warner DO, Sprung J. Obstructive sleep apnoea and perioperative complications in bariatric patients. Br J Anaesth 2010; 106:131-9. [PMID: 20959329 DOI: 10.1093/bja/aeq290] [Citation(s) in RCA: 90] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
BACKGROUND The objective of this study was to determine the relationship between perioperative complications and the severity of obstructive sleep apnoea (OSA) in patients undergoing bariatric surgery who had undergone preoperative polysomnography (PSG). METHODS The records of 797 patients, age >18 yr, who underwent bariatric operations (442 open and 355 laparoscopic procedures) at Mayo Clinic and were assessed before operation by PSG, were reviewed retrospectively. OSA was quantified using the apnoea-hypopnoea index (AHI) as none (≤ 4), mild (5-15), moderate (16-30), and severe (≥ 31). Pulmonary, surgical, and 'other' complications within the first 30 postoperative days were analysed according to OSA severity. Logistic regression was used to assess the multivariable association of OSA, age, sex, BMI, and surgical approach with postoperative complications. RESULTS Most patients with OSA (93%) received perioperative positive airway pressure therapy, and all patients were closely monitored after operation with pulse oximetry on either regular nursing floors or in intensive or intermediate care units. At least one postoperative complication occurred in 259 patients (33%). In a multivariable model, the overall complication rate was increased with open procedures compared with laparoscopic. In addition, increased BMI and age were associated with increased likelihood of pulmonary and other complications. Complication rates were not associated with OSA severity. CONCLUSIONS In obese patients evaluated before operation by PSG before bariatric surgery and managed accordingly, the severity of OSA, as assessed by the AHI, was not associated with the rate of perioperative complications. These results cannot determine whether unrecognized and untreated OSA increases risk.
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Affiliation(s)
- T N Weingarten
- Department of Anaesthesiology, College of Medicine, Mayo Clinic, Rochester, MN, USA
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Nguyen LT, Muhlhausler BS, Botting KJ, Morrison JL. Maternal undernutrition alters fat cell size distribution, but not lipogenic gene expression, in the visceral fat of the late gestation guinea pig fetus. Placenta 2010; 31:902-9. [PMID: 20728936 DOI: 10.1016/j.placenta.2010.07.014] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/03/2010] [Revised: 07/24/2010] [Accepted: 07/27/2010] [Indexed: 12/19/2022]
Abstract
This study investigated the development of adipose tissue in the guinea pig and the impact of maternal undernutrition on the structural and functional characteristics of perirenal adipose tissue in the dam and fetus. Date-mated guinea pigs were provided with either ad libitum feed (Control, C) or 85% of food intake per body weight of the Controls (Undernutrition, UN). Maternal (C, n = 6; UN, n = 7) perirenal adipose tissue (PAT) was collected at 60 d gestation and fetal PAT was collected at 50 d (C, n = 4) and 60 d (C, n = 8 and UN, n = 7) gestation (term, 69 d). The expression of stearoyl-CoA desaturase (SCD-1), fatty acid synthase (FAS), lipoprotein lipase (LPL), leptin and glycerol 3 phosphate dehydrogenase (G3PDH) mRNA and glucose transporters 1 and 4 (GLUT1 and GLUT4) was determined by Real Time PCR. There was no effect of maternal UN on total or relative PAT mass in the pregnant dam. There was an increase in G3PDH, but not LPL, leptin, FAS or GLUT4 mRNA expression, in UN dams compared to Controls (P < 0.05). In the fetal guinea pig there was no effect of maternal UN on total or relative PAT mass, however, the UN fetuses had a higher percentage of larger lipid locules in their PAT compared to Controls (P < 0.05). The expression of FAS, LPL, SCD-1, leptin, G3PDH and GLUT4 mRNA in PAT was not different between the Control and UN fetuses. These results support previous studies which have demonstrated that maternal undernutrition is associated with an increased accumulation of visceral adipose tissue in utero, and extend them by showing that maternal undernutrition results in early changes in the size distribution of lipid locules in visceral fat depots that precede changes in lipogenic gene expression.
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Affiliation(s)
- L T Nguyen
- Early Origins of Adult Health Research Group, Sansom Institute for Health Research, School of Pharmacy and Medical Sciences, University of South Australia, Adelaide, SA 5001, Australia
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Nghiemphu PL, Omuro AM, Cloughesy T, Mellinghoff IK, Norden AD, Nguyen LT, Rajangam K, Wen PY. A phase I safety and pharmacokinetic study of XL765 (SAR245409), a novel PI3K/TORC1/TORC2 inhibitor, in combination with temozolomide (TMZ) in patients (pts) with newly diagnosed malignant glioma. J Clin Oncol 2010. [DOI: 10.1200/jco.2010.28.15_suppl.3085] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
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22
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Edelman G, Bedell C, Shapiro G, Pandya SS, Kwak EL, Scheffold C, Nguyen LT, Laird A, Baselga J, Rodon J. A phase I dose-escalation study of XL147 (SAR245408), a PI3K inhibitor administered orally to patients (pts) with advanced malignancies. J Clin Oncol 2010. [DOI: 10.1200/jco.2010.28.15_suppl.3004] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
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23
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Moldovan C, Soria J, LoRusso P, Guthrie T, Song C, Nguyen LT, Martini J, Infante JR, Burris HA. A phase I safety and pharmacokinetic (PK) study of the PI3K inhibitor XL147 (SAR245408) in combination with erlotinib in patients (pts) with advanced solid tumors. J Clin Oncol 2010. [DOI: 10.1200/jco.2010.28.15_suppl.3070] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
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Nguyen LT, Uchida T, Tsukamoto Y, Kuroda A, Okimoto T, Kodama M, Murakami K, Fujioka T, Moriyama M. Helicobacter pylori dupA gene is not associated with clinical outcomes in the Japanese population. Clin Microbiol Infect 2009; 16:1264-9. [PMID: 19832706 DOI: 10.1111/j.1469-0691.2009.03081.x] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
The dupA gene of Helicobacter pylori was suggested to be a risk factor for duodenal ulcer but protective against gastric cancer. The present study aimed to re-examine the role of dupA in H. pylori-infected Japanese patients. We found that dupA status was not associated with any gastroduodenal disease, histological score of chronic gastritis or with the extent of interleukin-8 production from gastric cell lines. These results indicate that dupA is unlikely to be a virulence factor of H. pylori in the Japanese population.
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Affiliation(s)
- L T Nguyen
- Department of Molecular Pathology, Faculty of Medicine, Oita University, Yufu City, Oita, Japan
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Nguyen LT, Uchida T, Tsukamoto Y, Kuroda A, Okimoto T, Kodama M, Murakami K, Fujioka T, Moriyama M. Helicobacter pylori dupA gene is not associated with clinical outcomes in the Japanese population. Clin Microbiol Infect 2009. [PMID: 19832706 DOI: 10.1111/j.1469-0691.2009.03081] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
The dupA gene of Helicobacter pylori was suggested to be a risk factor for duodenal ulcer but protective against gastric cancer. The present study aimed to re-examine the role of dupA in H. pylori-infected Japanese patients. We found that dupA status was not associated with any gastroduodenal disease, histological score of chronic gastritis or with the extent of interleukin-8 production from gastric cell lines. These results indicate that dupA is unlikely to be a virulence factor of H. pylori in the Japanese population.
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Affiliation(s)
- L T Nguyen
- Department of Molecular Pathology, Faculty of Medicine, Oita University, Yufu City, Oita, Japan
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Smith DC, Britten C, Clary DO, Nguyen LT, Woodard P, Hurwitz HI. A phase I study of XL228, a potent IGF1R/AURORA/SRC inhibitor, in patients with solid tumors or hematologic malignancies. J Clin Oncol 2009. [DOI: 10.1200/jco.2009.27.15_suppl.3512] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
3512 Background: XL228 is a protein kinase inhibitor targeting IGF1R, the AURORA kinases, FGFR1–3, ABL and SRC family kinases. It is being evaluated in a phase 1 trial in patients (pts) with advanced malignancies. Methods: XL228 is administered as weekly 1-hour IV infusions. Cohorts of pts with refractory solid tumors or lymphoma are evaluated for determination of the maximum tolerated dose, pharmacokinetics, and pharmacodynamic effects using FDG-PET, signal pathway analysis in tumor and normal tissue biopsies, and plasma marker analysis. MTD expansion cohorts will include pts with multiple myeloma and colorectal cancer. Results: Thirty-six pts have been treated at doses ranging from 0.45 to 8.0mg/kg. The maximum administered dose was defined as 8.0mg/kg as a result of the dose limiting toxicities of Grade (Gr) 4 neutropenia, and Gr 3 neutropenia requiring dose skipping. XL228 is generally well tolerated; one serious adverse event of drug-related Gr 3 vomiting has been observed. Common drug-related adverse events include Gr 1 nausea, fatigue, decreased appetite, and flushing, and Grade 1–2 hyperglycemia (fasting) lasting up to 4 hours post- infusion. XL228 exposure was approximately dose-proportional; the mean terminal half-life (t1/2, z) ranged from 27 to 54 hours. Low accumulation was observed after weekly administration. Protein phosphorylation measurements in skin, hair, and blood samples demonstrate inhibition of IGF1R, SRC and FGFR1 signaling by XL228, including reductions in hair follicle phospho-IGF1R and phospho-FAK1 of 39% and 42%, respectively, in a pt dosed at 5.4mg/kg. Evidence of clinical activity includes one non-small cell lung cancer pt with an unconfirmed partial response (confirmation pending) and 9 additional pts (of 30 evaluable) with stable disease (SD) lasting >3 months, including a small cell lung cancer pt on study for 13.3+ months after failing carboplatin/etoposide. For pts with SD, the median time on study is currently 5.9 months (range 3.3+ to 13.3+). Conclusions: XL228 is generally well tolerated and has shown encouraging preliminary clinical and pharmacodynamic activity. [Table: see text]
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Affiliation(s)
- D. C. Smith
- University of Michigan, Ann Arbor, MI; University of California, Los Angeles, Los Angeles, CA; Exelixis, Inc., South San Francisco, CA; Duke University, Durham, NC
| | - C. Britten
- University of Michigan, Ann Arbor, MI; University of California, Los Angeles, Los Angeles, CA; Exelixis, Inc., South San Francisco, CA; Duke University, Durham, NC
| | - D. O. Clary
- University of Michigan, Ann Arbor, MI; University of California, Los Angeles, Los Angeles, CA; Exelixis, Inc., South San Francisco, CA; Duke University, Durham, NC
| | - L. T. Nguyen
- University of Michigan, Ann Arbor, MI; University of California, Los Angeles, Los Angeles, CA; Exelixis, Inc., South San Francisco, CA; Duke University, Durham, NC
| | - P. Woodard
- University of Michigan, Ann Arbor, MI; University of California, Los Angeles, Los Angeles, CA; Exelixis, Inc., South San Francisco, CA; Duke University, Durham, NC
| | - H. I. Hurwitz
- University of Michigan, Ann Arbor, MI; University of California, Los Angeles, Los Angeles, CA; Exelixis, Inc., South San Francisco, CA; Duke University, Durham, NC
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Tsukamoto Y, Uchida T, Karnan S, Noguchi T, Nguyen LT, Tanigawa M, Takeuchi I, Matsuura K, Hijiya N, Nakada C, Kishida T, Kawahara K, Ito H, Murakami K, Fujioka T, Seto M, Moriyama M. Genome-wide analysis of DNA copy number alterations and gene expression in gastric cancer. J Pathol 2008; 216:471-82. [PMID: 18798223 DOI: 10.1002/path.2424] [Citation(s) in RCA: 98] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Genomic copy number aberrations (CNAs) are believed to play a major role in the development and progression of human cancers. Although many CNAs have been reported in gastric cancer, their genome-wide transcriptional consequences are poorly understood. In this study, to reveal the impact of CNAs on genome-wide expression in gastric cancer, we analysed 30 cases of gastric cancers for their CNAs by array comparative genomic hybridization (array CGH) and 24 of these 30 cases for their expression profiles by oligonucleotide-expression microarray. We found that with the application of laser microdissection, most CNAs were detected at higher frequency than in previous studies. Notably, gain at 20q13 was detected in almost all cases (97%), suggesting that this may play an important role in the pathogenesis of gastric cancer. By comparing the array CGH data with expression profiles of the same samples, we showed that both genomic amplification and deletion strongly influence the expression of genes in altered genomic regions. Furthermore, we identified 125 candidate genes, consisting of 114 up-regulated genes located in recurrent regions (>10%) of amplification and 11 down-regulated genes located in recurrent regions of deletion. Up-regulation of several candidate genes, such as CDC6, SEC61G, ANP32E, BYSL and FDFT1, was confirmed by immunohistochemistry. Interestingly, some candidate genes were localized at genomic loci adjacent to well-known genes such as EGFR, ERBB2 and SMAD4, and concordantly deregulated by genomic alterations. Based on these results, we propose that our list of candidate genes may contain novel genes involved in the pathogenesis of advanced gastric cancer.
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Affiliation(s)
- Y Tsukamoto
- Department of Molecular Pathology, Faculty of Medicine, Oita University, Oita, Japan
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Nakada C, Matsuura K, Tsukamoto Y, Tanigawa M, Yoshimoto T, Narimatsu T, Nguyen LT, Hijiya N, Uchida T, Sato F, Mimata H, Seto M, Moriyama M. Genome-wide microRNA expression profiling in renal cell carcinoma: significant down-regulation of miR-141 and miR-200c. J Pathol 2008; 216:418-27. [PMID: 18925646 DOI: 10.1002/path.2437] [Citation(s) in RCA: 228] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
We investigated expression profiles of microRNA (miRNA) in renal cell carcinoma [clear cell carcinomas (CCC) and chromophobe renal cell carcinomas (ChCC)] and in normal kidneys by using a miRNA microarray platform which covers a total of 470 human miRNAs (Sanger miRBase release 9.1). Unsupervised hierarchical cluster analysis revealed that CCC and ChCC were separable and that no subgroups were identified in CCCs. We found that 43 miRNAs were differentially expressed between CCC and normal kidney, of which 37 were significantly down-regulated in CCC and the other 6 were up-regulated. We also found that 57 miRNAs were differentially expressed between ChCC and normal kidney, of which 51 were significantly down-regulated in ChCC and the other 6 were up-regulated. Together, these observations indicate that expression of miRNAs tends to be down-regulated in both CCC and ChCC compared with normal kidney. We observed that miR-141 and miR-200c were the most significantly down-regulated miRNAs in CCCs. Indeed, in all cases of CCC analysed, both miR-141 and miR-200c were down-regulated in comparison with normal kidney. Microarray data and quantitative RT-PCR showed that these two miRNAs were expressed concordantly. TargetScan algorithm revealed that ZFHX1B mRNA is a hypothetical target of both miR-141 and -200c. We established by quantitative RT-PCR that, in CCCs in which miR-141 and miR-200c were down-regulated, ZFHX1B, a transcriptional repressor for CDH1/E-cadherin, tended to be up-regulated. Furthermore, we found that overexpression of miR-141 and miR-200c caused down-regulation of ZFHX1B and up-regulation of E-cadherin in two renal carcinoma cell lines, ACHN and 786-O. On the basis of these findings, we suggest that down-regulation of miR-141 and miR-200c in CCCs might be involved in suppression of CDH1/E-cadherin transcription via up-regulation of ZFHX1B.
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Affiliation(s)
- C Nakada
- Department of Molecular Pathology, Faculty of Medicine, Oita University, Japan
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29
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Dorn SD, Kaptchuk TJ, Park JB, Nguyen LT, Canenguez K, Nam BH, Woods KB, Conboy LA, Stason WB, Lembo AJ. A meta-analysis of the placebo response in complementary and alternative medicine trials of irritable bowel syndrome. Neurogastroenterol Motil 2007. [PMID: 17640177 DOI: 10.1111/j.1365-2982.2007.00937] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 03/13/2023]
Abstract
Among patients with irritable bowel syndrome (IBS) enrolled in clinical trials of conventional medical therapy, the placebo response rate is high. IBS patients also frequently use complementary and alternative medicine (CAM), which may act through an 'enhanced placebo effect'. The purpose of this study was to estimate the magnitude of the placebo response rate in CAM trials for IBS and to identify factors that influence this response. We performed a systematic review and meta-analysis of randomized, placebo-controlled clinical trials of CAM therapies for IBS identified from MEDLINE/EMBASE/PsychLIT databases from 1970 to 2006. Placebo and active treatment response rates for global symptom improvement were assessed. Nineteen studies met the inclusion criteria. The pooled estimate of the placebo response rate was 42.6% (95% confidence interval, 38.0-46.5%). Significant heterogeneity existed across trials (range 15.0-72.2%, P < 0.00001). Higher placebo response rates correlated with a longer duration of treatment (r = 0.455, P = 0.05) and a greater number of office visits (r = 0.633, P = 0.03). Among IBS patients in CAM trials, the placebo response rate is high. That this rate is similar in magnitude to that seen in conventional medicine trials suggests that the placebo response is independent of the type of therapy used and that it is not particularly 'enhanced' in CAM trials.
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Affiliation(s)
- S D Dorn
- Brigham and Women's Hospital, Boston, MA, USA
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30
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Dorn SD, Kaptchuk TJ, Park JB, Nguyen LT, Canenguez K, Nam BH, Woods KB, Conboy LA, Stason WB, Lembo AJ. A meta-analysis of the placebo response in complementary and alternative medicine trials of irritable bowel syndrome. Neurogastroenterol Motil 2007; 19:630-7. [PMID: 17640177 DOI: 10.1111/j.1365-2982.2007.00937.x] [Citation(s) in RCA: 77] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Among patients with irritable bowel syndrome (IBS) enrolled in clinical trials of conventional medical therapy, the placebo response rate is high. IBS patients also frequently use complementary and alternative medicine (CAM), which may act through an 'enhanced placebo effect'. The purpose of this study was to estimate the magnitude of the placebo response rate in CAM trials for IBS and to identify factors that influence this response. We performed a systematic review and meta-analysis of randomized, placebo-controlled clinical trials of CAM therapies for IBS identified from MEDLINE/EMBASE/PsychLIT databases from 1970 to 2006. Placebo and active treatment response rates for global symptom improvement were assessed. Nineteen studies met the inclusion criteria. The pooled estimate of the placebo response rate was 42.6% (95% confidence interval, 38.0-46.5%). Significant heterogeneity existed across trials (range 15.0-72.2%, P < 0.00001). Higher placebo response rates correlated with a longer duration of treatment (r = 0.455, P = 0.05) and a greater number of office visits (r = 0.633, P = 0.03). Among IBS patients in CAM trials, the placebo response rate is high. That this rate is similar in magnitude to that seen in conventional medicine trials suggests that the placebo response is independent of the type of therapy used and that it is not particularly 'enhanced' in CAM trials.
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Affiliation(s)
- S D Dorn
- Brigham and Women's Hospital, Boston, MA, USA
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Lema C, Fuessel-Haws AL, Lewis LR, Rady PL, Lee P, Turbat-Herrera EA, He Q, Nguyen LT, Tyring SK, Dao DD. Association between HLA-DQB1 and cervical dysplasia in Vietnamese women. Int J Gynecol Cancer 2006; 16:1269-77. [PMID: 16803516 DOI: 10.1111/j.1525-1438.2006.00459.x] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
Host genetic background seems to play a key role in cervical carcinogenesis as only a small subset of women infected with high-risk human papillomaviruses (HPVs) develop cervical cancer. The rate of cervical cancer in Vietnamese women is notably high. To explore the association of human leukocyte antigen (HLA)-DQB1 alleles, HPV infection, and cervical dysplasia in this population, cervical smears were obtained from 101 women attending the obstetrics and gynecology clinic of Da Nang General Hospital in Vietnam. Besides the Papanicolaou test, HPV and HLA-DQB1 genotyping were performed using cervical smear DNA. Additionally, a subset of 30 blood samples was used as the gold standard for HLA genotyping. HLA-DQB1 alleles showed no association with HPV infection status. However, a positive association with cervical dysplasia was found for HLA-DQB1*0302 (P= 0.0229, relative risk (RR) = 4.737) and HLA-DQB1*0601 (P= 0.0370, RR = 4.038), whereas HLA-DQB1*0301 (P= 0.0152, RR = 0.221) was found negatively associated. The low diversity of HLA-DQB1 alleles, wide spectrum of HPV genotypes, and high prevalence of HPV 16 and HPV 18 observed in the study population suggest a permissive/susceptible genetic background that deserves further research. Total concordance of HLA-DQB1 genotyping results between blood and cervical cells confirms the potential value of cervical smears as an effective tool for the development of cervical cancer biomarkers.
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Affiliation(s)
- C Lema
- Life Sciences & Health Group, Houston Advanced Research Center, 4800 Research Forest Drive, The Woodlands, TX 77381, USA
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Abstract
BACKGROUND Bronchiectasis is a suppurative airway disease characterised by persistent cough and sputum production associated with bronchial dilatation. A study was undertaken to determine whether cough sensitivity is increased in bronchiectatic patients. METHODS Twenty two patients with bronchiectasis and 20 healthy non-smoking controls matched for age and sex were recruited into the study. Quality of life (Leicester Cough Questionnaire score), total cough symptom score, and extent of bronchiectasis on HRCT scans were recorded. Cough sensitivity was assessed using incremental inhalation of capsaicin concentrations; the concentration at which 5 or more coughs occurred (C5) was recorded. RESULTS Patients with bronchiectasis had increased sensitivity to capsaicin compared with controls (mean (SE) log10 C5 1.22 (0.20) v 1.89 (0.21); p<0.03). Capsaicin sensitivity correlated positively with the Leicester Cough Questionnaire score (r = 0.64; p = 0.005) and inversely with the total cough symptom score (r = -0.58; p = 0.004), but not with the extent of the disease. It also correlated with forced expiratory volume in 1 second (FEV1) in litres (r = 0.58; p = 0.005) but not with FEV1 % predicted. Capsaicin sensitivity was not related to the presence of infected sputum or to corticosteroid or bronchodilator use. CONCLUSIONS : Patients with bronchiectasis have a sensitive cough reflex which reflects the severity of cough symptoms. A measure of cough severity could be part of health assessment for patients with bronchiectasis.
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Affiliation(s)
- A Torrego
- National Heart and Lung Institute, Imperial College, Dovehouse Street, London SW3 6LY, UK
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33
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Lema C, Fuessel-Haws AL, Lewis LR, Rady PL, Lee P, Turbat-Herrera EA, He Q, Nguyen LT, Tyring SK, Dao DD. Association between HLA-DQB1 and cervical dysplasia in Vietnamese women. Int J Gynecol Cancer 2006. [DOI: 10.1136/ijgc-00009577-200605000-00048] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022] Open
Abstract
Host genetic background seems to play a key role in cervical carcinogenesis as only a small subset of women infected with high-risk human papillomaviruses (HPVs) develop cervical cancer. The rate of cervical cancer in Vietnamese women is notably high. To explore the association of human leukocyte antigen (HLA)-DQB1 alleles, HPV infection, and cervical dysplasia in this population, cervical smears were obtained from 101 women attending the obstetrics and gynecology clinic of Da Nang General Hospital in Vietnam. Besides the Papanicolaou test, HPV and HLA-DQB1 genotyping were performed using cervical smear DNA. Additionally, a subset of 30 blood samples was used as the gold standard for HLA genotyping. HLA-DQB1 alleles showed no association with HPV infection status. However, a positive association with cervical dysplasia was found for HLA-DQB1*0302 (P = 0.0229, relative risk (RR) = 4.737) and HLA-DQB1*0601 (P = 0.0370, RR = 4.038), whereas HLA-DQB1*0301 (P = 0.0152, RR = 0.221) was found negatively associated. The low diversity of HLA-DQB1 alleles, wide spectrum of HPV genotypes, and high prevalence of HPV 16 and HPV 18 observed in the study population suggest a permissive/susceptible genetic background that deserves further research. Total concordance of HLA-DQB1 genotyping results between blood and cervical cells confirms the potential value of cervical smears as an effective tool for the development of cervical cancer biomarkers.
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Nguyen LT, Bui KM. 17 COMPARISON OF FARMING AND NON-FARMING MOTHERS IN THAI NGUYEN, VIETNAM. J Investig Med 2006. [DOI: 10.2310/6650.2005.x0004.16] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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Srinivasan V, Nam HM, Nguyen LT, Tamilselvam B, Murinda SE, Oliver SP. Prevalence of Antimicrobial Resistance Genes inListeria monocytogenesIsolated from Dairy Farms. Foodborne Pathog Dis 2005; 2:201-11. [PMID: 16156701 DOI: 10.1089/fpd.2005.2.201] [Citation(s) in RCA: 105] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Antimicrobial resistance of Listeria monocytogenes (n = 38) isolated from the four dairy farms to 15 antimicrobial agents was evaluated. All 38 L. monocytogenes isolates from the four farms evaluated were resistant to more than one antimicrobial in different combinations. All L. monocytogenes isolates evaluated were resistant to cephalosporin C (minimum inhibitory concentration [MIC] > or = 512 microg/mL), streptomycin (MIC > or = 32) and trimethoprim (MIC > or = 512). Most L. monocytogenes isolates were resistant to ampicillin (92%, MIC > or = 2), rifampicin (84%, MIC > or = 4), rifamycin (84%, MIC > or = 4), and florfenicol (66%, MIC > or = 32) and some were resistant to tetracycline (45%, MIC > or = 16), penicillin G (40%, MIC > or = 2) and chloramphenicol (32%, MIC > or = 32). All L. monocytogenes isolates were susceptible to amoxicillin, erythromycin, gentamicin, kanamycin and vancomycin. Susceptibility of L. monocytogenes to the antimicrobials evaluated was quite consistent among the dairy farms evaluated. However, some variability in antimicrobial susceptibility among dairy farms was noted. Nineteen of 38 L. monocytogenes isolates contained more than one antimicrobial resistance gene sequence. A high frequency of floR (66%) was found in L. monocytogenes followed by penA (37%), strA (34%), tetA (32%), and sulI (16%). Other tetracycline resistance genes (tetB, tetC, tetD, tetE, and tetG) and other antimicrobial resistance genes (cmlA, strB, aadA, sulI, vanA, vanB, ampC, ermB, ereA, and ereB) were not found in any of the L. monocytogenes isolates from the four dairy farms. Results of the present study demonstrated that L. monocytogenes isolated from the dairy farm environment were resistant to many antimicrobials and contained one or more antimicrobial resistance genes.
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Affiliation(s)
- V Srinivasan
- Food Safety Center of Excellence, University of Tennessee, 59 McCord Hall, Knoxville, TN 37996, USA
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Nguyen LT, Gillespie BE, Nam HM, Murinda SE, Oliver SP. Detection ofEscherichia coliO157:H7 andListeria monocytogenesin Beef Products by Real-Time Polymerase Chain Reaction. Foodborne Pathog Dis 2004; 1:231-40. [PMID: 15992285 DOI: 10.1089/fpd.2004.1.231] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Rapid methods for the detection of Escherichia coli O157:H7 and Listeria monocytogenes in food products are important to the food industry and for public health. Conventional microbiological methods and newly developed molecular-based techniques such as polymerase chain reaction (PCR)-based methods are time consuming. In this study, a faster method based on utilization of a hybridization probe with real-time PCR, was developed and applied for detection of E. coli O157:H7 and L. monocytogenes from artificially contaminated raw ground beef and fully cooked beef hotdogs. Target genes for E. coli O157:H7 and L. monocytogenes were rfbE and hylA, respectively. An analysis of 169 bacterial strains showed that the chosen primers and probes were specific for detection of E. coli O157:H7 and L. monocytogenes by real-time PCR. The assay was positive for nine of 10. E. coli O157:H7 strains, and all L. monocytogenes (7/7) strains evaluated. Bacterial strains lacking these genes were not detected by these assays. Detection limits of real-time PCR assays ranged from 10(3) to 10(8) colony forming units (CFU)/ml for E. coli O157:H7 in modified tryptic soy broth and 10(4) to 10(8) CFU/mL for L. monocytogenes in Fraser Broth. Detection sensitivity ranged from 10(3) to 10(4) CFU/g of raw ground beef or hotdog without enrichment for E. coli and L. monocytogenes. Approximately 1.4-2.2 CFU/g of E. coli O157:H7 in raw ground beef were detected following an enrichment step of 4 h. Approximately 1.2-6.0 CFU/g of L. monocytogenes in beef hotdogs were detected following an enrichment step of 30 h. The real-time PCR assays for detection of E. coli O157:H7 and L. monocytogenes in raw ground beef and beef hotdogs were specific, sensitive and rapid.
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Affiliation(s)
- L T Nguyen
- The University of Tennessee Food Safety Center of Excellence, Knoxville, Tennessee 37996, USA.
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Abstract
BACKGROUND Increased hydrogen and reduced chloride ionic environments of the airways are conducive to the stimulation of cough. However, the constituents of the local milieu of the airways of patients with chronic cough are unknown. METHODS The pH and chloride levels in exhaled breath condensate and capsaicin cough threshold (C5) were measured in 50 patients with chronic cough and in 16 healthy controls. pH and chloride measurements were repeated after capsaicin challenge in those with cough. The cause of cough was asthma (n = 13), postnasal drip/rhinitis (n = 7), gastro-oesophageal reflux (n = 5), bronchiectasis (n = 5), but remained unidentified in 20. RESULTS Compared with controls, patients with chronic cough had lower pH (mean 7.9 v 8.3, 95% CI of difference -0.5 to -0.2, p<0.0001), chloride levels (median 4 v 6 mmol/l, 95% CI -3.1 to -0.2, p = 0.007), and C5 (median 3.9 v 125 micro M, 95% CI -270.0 to -17.6, p = 0.002). The pH levels were different in the six subgroups including controls, and were reduced in all diagnostic subgroups of patients with cough compared with controls but did not differ between them. Chloride levels were significantly different in the six subgroups but were lower than controls in only the gastro-oesophageal reflux subgroup. There was a weak but significant correlation between chloride levels and C5 when all participants were analysed together, but not between pH and C5 or chloride levels. pH and chloride levels did not change after capsaicin challenge. CONCLUSIONS The epithelial lining fluid of patients with chronic cough has a reduced pH and reduced chloride levels which could contribute to the enhanced cough reflex.
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Affiliation(s)
- A Niimi
- Department of Thoracic Medicine, National Heart and Lung Institute, Imperial College and Royal Brompton Hospital, Dovehouse Street, London SW3 6LY, UK
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Nakamura M, Tohya Y, Miyazawa T, Mochizuki M, Phung HTT, Nguyen NH, Huynh LMT, Nguyen LT, Nguyen PN, Nguyen PV, Nguyen NPT, Akashi H. A novel antigenic variant of Canine parvovirus from a Vietnamese dog. Arch Virol 2004; 149:2261-9. [PMID: 15503211 DOI: 10.1007/s00705-004-0367-y] [Citation(s) in RCA: 129] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2004] [Accepted: 04/29/2004] [Indexed: 10/26/2022]
Abstract
Nine isolates of Canine parvovirus (CPV) were obtained from Vietnamese dogs and cats. One canine isolate showed a unique antigenic property which indicates a novel antigenic variant of CPV-2b when examined with hemagglutination inhibition tests using our monoclonal antibodies, 21C3 and 19D7, which were recently developed. This isolate had an amino acid substitution of residue 426, Asp to Glu, and the same substitution has recently been found in CPV from Italian dogs. This study first showed that such substitution caused an antigenic difference demonstrable by monoclonal antibodies and that a similar evolution may have occurred in CPV in Vietnam.
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Affiliation(s)
- M Nakamura
- Department of Veterinary Microbiology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan
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Murinda SE, Nguyen LT, Nam HM, Almeida RA, Headrick SJ, Oliver SP. Detection of Sorbitol-Negative and Sorbitol-Positive Shiga Toxin-ProducingEscherichia coli,Listeria monocytogenes,Campylobacter jejuni, andSalmonellaspp. in Dairy Farm Environmental Samples. Foodborne Pathog Dis 2004; 1:97-104. [PMID: 15992268 DOI: 10.1089/153531404323143611] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Six visits were conducted to four dairy farms to collect swab, liquid, and solid dairy farm environmental samples (165 to 180/farm; 15 sample types). The objective of the study was to determine on-farm sources of Campylobacter jejuni, Salmonella spp., Listeria monocytogenes, and Shiga toxin-producing Escherichia coli (STEC), which might serve as reservoirs for transmission of pathogens. Samples were analyzed using mostly U.S. Food and Drug Administration's Bacteriological Analytical Manual protocols; however, Salmonella spp., L. monocytogenes and STEC were co-enriched in universal pre-enrichment broth. Campylobacter jejuni were enriched in Bolton broth containing Bolton broth supplement. Pathogens were isolated on agar media, typed biochemically, and confirmed using multiplex polymerase chain reaction protocols. Campylobacter jejuni, Salmonella spp., L. monocytogenes, Sorbitol-negative (SN)-STEC O157:H7, and sorbitol-positive (SP)-STEC, respectively, were isolated from 5.06%, 3.76%, 6.51%, 0.72%, and 17.3% of samples evaluated. Whereas other pathogens were isolated from all four farms, SN-STEC O157:H7 were isolated from only two farms. Diverse serotypes of SP-STEC including O157:H7, O26:H11, O111, and O103 were isolated. None of the five pathogen groups studied were isolated from bulk tank milk (BTM). Most pathogens (44.2%) were isolated directly from fecal samples. Bovine fecal samples, lagoon water, bedding, bird droppings, and rat intestinal contents constituted areas of major concern on dairy farms. Although in-line milk filters from two farms tested positive for Salmonella or L. monocytogenes, none of the pathogens were detected in the corresponding BTM samples. Good manure management practices, including control of feral animals, are critical in assuring dairy farm hygiene. Identification of on-farm pathogen reservoirs could aid with implementation of farm-specific pathogen reduction programs.
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Affiliation(s)
- S E Murinda
- Food Safety Center of Excellence, The University of Tennessee, Knoxville, Tennessee 37996, USA
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Nam HM, Murinda SE, Nguyen LT, Oliver SP. Evaluation of Universal Pre-Enrichment Broth for Isolation ofSalmonellaspp.,Escherichia coliO157:H7, andListeria monocytogenesfrom Dairy Farm Environmental Samples. Foodborne Pathog Dis 2004; 1:37-44. [PMID: 15992260 DOI: 10.1089/153531404772914446] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Use of universal pre-enrichment broth (UPB) as a primary enrichment medium for detection of Salmonella spp., Escherichia coli O157:H7, and Listeria monocytogenes from dairy farm environmental samples was evaluated. There were no differences in bacterial growth between UPB and selective primary enrichment broths for each pathogen inoculated individually or in combination at 10(1) and 10(2) colony forming units/mL. In addition, no differences were observed when UPB and selective primary enrichment broths were compared for detection efficiency of pathogens in artificially contaminated raw milk and fecal samples. Listeria enrichment broth (LEB) was compared with UPB to support growth of L. monocytogenes from naturally contaminated environmental samples. Listeria monocytogenes was isolated from seven of 30 samples enriched in UPB and six of 30 samples enriched in LEB. Dairy farm environmental samples were examined for recovery of the three pathogens using UPB. Subsequent isolation was achieved using selective secondary enrichment of each pathogen. Listeria monocytogenes, Salmonella spp., and E. coli O157:H7 were isolated in 13.4% (30 of 224), 8.9% (20 of 224), and 2.2% (five of 224) of samples, respectively. Isolation rates of the three pathogens were somewhat higher than in previous reports. Overall, UPB supported growth of test pathogens to detectable levels within 24 h. Our results demonstrate that UPB has potential for routine use in isolation of foodborne pathogens from diverse environmental samples.
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Affiliation(s)
- H M Nam
- University of Tennessee Food Safety Center of Excellence, Knoxville 37996, USA
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Jouaville LF, Annesi-Maesano I, Nguyen LT, Bocage AS, Bedu M, Caillaud D. Interrelationships among asthma, atopy, rhinitis and exhaled nitric oxide in a population-based sample of children. Clin Exp Allergy 2004; 33:1506-11. [PMID: 14616861 DOI: 10.1046/j.1365-2222.2003.01800.x] [Citation(s) in RCA: 92] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
BACKGROUND Exhaled nitric oxide (eNO) has attracted increasing interest as a non-invasive marker of airway inflammation in asthma. However, little evidence exists on the influences exerted on eNO by the interrelations among atopic status, asthma and rhinitis. METHODS Among the 1156 children who participated in a large-scale epidemiological survey on asthma and allergies (ISAAC II: International Study of Asthma and Allergies in Childhood Phase II) in the city of Clermont-Ferrand, 53 asthmatics without corticosteroid treatment and 96 non-asthmatics were invited to perform eNO and skin prick tests (SPTs) to 12 common allergens. RESULTS Atopic asthmatic children had higher eNO than non-atopic asthmatic children (28.9+/-9.1 vs. 17.1+/-13.1 p.p.b.; P=0.0004) with a significant increase when one SPT or more are positive (26.5+/-7.8 vs. 17.1+/-13.1 p.p.b.; P=0.03). Similarly, non-asthmatic, atopic subjects had higher eNO than non-atopic subjects with a significant increase when two SPTs or more are positive (19.4+/-9.8 vs. 11.7 +/-6.7 p.p.b.; P=0.003). In the case of equal levels of positive SPTs (0, 1, >/=2), asthmatic children always had higher eNO than non-asthmatic ones. Furthermore, among non-asthmatic children, the eNO level increased only in atopics who had rhinitis (20.7+/-13 vs. 12.5+/-6.4 p.p.b. in atopic controls (subjects without rhinitis and asthma) and 12.3+/-6.6 p.p.b. in non-atopic controls; P=0.001), whereas among asthmatic children, eNO level increased in atopics independently of rhinitis (28.2+/-9.5 p.p.b. in those with rhinitis and 30.9+/-8.1 p.p.b. in those without) as well as in non-atopics with rhinitis (22.5+/-17.2 p.p.b.). CONCLUSIONS Our data suggest that besides atopy and asthma, allergic rhinitis should also be taken into account in the assessment of eNO.
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Affiliation(s)
- L F Jouaville
- Physiology and Pulmonary Department, Clermont-Ferrand, France
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Gerhard DS, Nguyen LT, Zhang ZY, Borecki IB, Coleman BI, Rader JS. A relationship between methylenetetrahydrofolate reductase variants and the development of invasive cervical cancer. Gynecol Oncol 2003; 90:560-5. [PMID: 13678724 DOI: 10.1016/s0090-8258(03)00368-8] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
OBJECTIVE Low red blood cell folate levels have been associated with hypomethylation of DNA in dysplastic tissue and an increased risk for cervical intraepithelial neoplasia in human papillomavirus (HPV)-infected women. Methylenetetrahydrofolate reductase (MTHFR) is a critical enzyme regulating the metabolism of folate and methionine, the important components of DNA synthesis and methylation. Two common genetic polymorphisms, causing reduced MTHFR activity, have been identified. Therefore, the goal of this study was to evaluate these MTHFR variations as risk factors for invasive cervical cancer. METHODS To overcome the failure to properly match cases and controls that can cause false-positive inferences due to population stratification and unrecognized variables in a traditional case-control study, a family-based transmission/disequilibrium test (TDT) was used. We obtained samples from nuclear families of 102 women with invasive cervical cancer (ICC). One polymorphism was typed by a PCR-RFLP method, while a template-directed dye-terminator assay was developed for the other. RESULTS AND CONCLUSIONS We were unable to confirm a strong association of MTHFR polymorphisms and ICC using family-based controls and a transmission/disequilibrium test. The overall results of the TDT showed chi(2) (1 df) of 0.28 (P = 0.60) for exon 4, chi(2) (1 df) of 0.81(P = 0.37) for exon 7, and chi(2) (3 df) of 2.56 (P = 0.46) for the haplotype, meaning that there was no transmission of those alleles significantly in excess of Mendelian expectations to affected women. In addition, there was no effect of these variants with increased parity or infection with high-risk-type human papillomavirus.
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Affiliation(s)
- D S Gerhard
- Department of Genetics, Washington University School of Medicine, St. Louis, MO 63110, USA.
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Abstract
BACKGROUND/PURPOSE The aim of this study was to review the presentations of gastrointestinal duplication (GID) and to assess the influence of prenatal diagnosis on treatment. METHODS Retrospective review of all GID at 2 pediatric hospitals from 1980-2002 was conducted. RESULTS Seventy-three patients (M43:F30) were identified: 21 neonates, 28 infants (1 to 24 months), 15 children (1 to 10 years), 9 adolescents (>/=11 years). GID location by frequency was ileum (31.5%), ileocaecal valve (30.2%), duodenum (9.6%), stomach (8.2%), jejunum (8.2%), colon (6.8%), and rectum (5.5%). In neonates and infants, vomiting and distension were the most common presentations. Volvulus, caused by a duplication, occurred in 23.8% of neonates and caused the death of one neonate. Intussusception was identified in 10.9% of patients. In older children and adolescents, pain and vomiting were the most common associations. Six of these patients were being treated for Crohn's disease, with the diagnosis of duplication made at laparotomy. Eighteen patients had a prenatal diagnosis by ultrasound scan, with 77.2% of these asymptomatic after birth. Most prenatal diagnoses occurred after 1991 (77.8%). When comparing an earlier period (1980 to 1991; 29 patients) with the current (1992 to 2002; 44 patients), a greater proportion of the latter patients were asymptomatic (36.4 v 13.8%) and had a lower incidence of complications (volvulus/intussusception). CONCLUSIONS GID can lead to life-threatening complications. Prenatal diagnosis should lead to expeditious postnatal investigation and treatment before the onset of symptoms or complications. GID in older children can mimic Crohn's disease. Laparoscopy/laparotomy should be considered in patients with atypical Crohn's disease or when the diagnosis of an intraabdominal mass is unclear.
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Affiliation(s)
- P S Puligandla
- Divisions of Division of Pediatric Surgery and Pathology, The Montreal Children's Hospital, Montreal, Quebec, Canada
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Nguyen LT, Bachmann MF, Ohashi PS. Contribution of LCMV transgenic models to understanding T lymphocyte development, activation, tolerance, and autoimmunity. Curr Top Microbiol Immunol 2002; 263:119-43. [PMID: 11987812 DOI: 10.1007/978-3-642-56055-2_7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Affiliation(s)
- L T Nguyen
- Department of Immunology, Ontario Cancer Institute, 610 University Avenue, Toronto, Ontario, Canada, M5G 2M9
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Murinda SE, Nguyen LT, Ivey SJ, Gillespie BE, Almeida RA, Draughon FA, Oliver SP. Molecular characterization of Salmonella spp. isolated from bulk tank milk and cull dairy cow fecal samples. J Food Prot 2002; 65:1100-5. [PMID: 12117241 DOI: 10.4315/0362-028x-65.7.1100] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
The consumption of meat from cull dairy cows and of raw milk has been associated with foodborne salmonellosis. This survey was conducted to establish the prevalence of Salmonella in cull dairy cow fecal samples and bulk tank milk and to determine the proportion of Salmonella-positive dairy farms (n = 30) in east Tennessee. Food and Drug Administration bacteriological analytical protocols were generally used for Salmonella isolation. Primary enrichment was performed with lactose broth, and secondary enrichment was conducted with tetrathionate broth. Eosin methylene blue, hektoen enteric, xylose lysine desoxycholate, bismuth sulfite, and brilliant green (BG) were used as isolation agars. BG agars supplemented with individual antibiotics and/or sulfur compounds were also evaluated. Six of 268 (2.24%) bulk tank milk samples and 9 of 415 (2.17%) fecal samples from 7 of 30 (25.3%) dairy farms were Salmonella-positive. Most isolates (11 of 15) were obtained between September and December. Salmonella isolates were further characterized using polyvalent somatic O Salmonella antiserum, o-nitrophenyl-beta-D-galactopyranoside (ONPG), and Analytical Profile Index (API) 20E strips for Enterobacteriaceae. Serological evaluation of presumptive positive Salmonella isolates resulted in substantial numbers of false positives (41.2%). ONPG and API 20E tests enabled further biochemical distinction of the majority of Salmonella spp. from Salmonella Arizonae and closely related members of Enterobacteriaceae like Citrobacter youngae. Pulsed-field gel electrophoresis of SpeI-digested Salmonella DNA was used to subtype isolates. The isolates grouped into four clusters. The baseline information generated in this survey is being used to develop preharvest pathogen reduction programs on selected farms.
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Affiliation(s)
- S E Murinda
- University of Tennessee Food Safety Center of Excellence, Knoxville 37996, USA
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Murinda SE, Nguyen LT, Ivey SJ, Gillespie BE, Almeida RA, Draughon FA, Oliver SP. Prevalence and molecular characterization of Escherichia coli O157:H7 in bulk tank milk and fecal samples from cull cows: a 12-month survey of dairy farms in east Tennessee. J Food Prot 2002; 65:752-9. [PMID: 12030284 DOI: 10.4315/0362-028x-65.5.752] [Citation(s) in RCA: 67] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
A study on the prevalence of Escherichia coli O157:H7 was conducted on 30 dairy farms in east Tennessee between May 2000 and April 2001. This pathogen was isolated from 8 of 30 (26.7%) dairy farms at various sampling times. A total of 415 fecal samples from cull dairy cows and 268 bulk tank milk samples were analyzed. Overall, 10 of 683 (1.46%) samples (2 of 268 [0.75%] milk samples and 8 of 415 [1.93%] fecal samples) tested positive for E. coli O157:H7. Food and Drug Administration Bacteriological Analytical Manual protocols were used for the conventional isolation and confirmation of E. coli O157:H7. Samples were shake cultured (150 rpm) at 42 degrees C for 24 h in tryptic soy broth containing 2 mg of novobiocin per liter. White colonies isolated on cefixime-tellurite sorbitol MacConkey agar plates were evaluated for fluorescence on sorbitol MacConkey agar supplemented with 0.025 g of methylumbelliferyl-beta-D-glucuronide per liter. Nonfluorescing white colonies were biochemically typed and serologically confirmed. Multiplex polymerase chain reaction profiles of E. coli O157:H7 isolates indicated the presence of common virulence factors (Shiga toxin, enterohemolysin, and intimin) of Shiga toxin-producing E. coli, suggesting the potential human pathogenicity of bacterial isolates. Pulsed-field gel electrophoresis profiles of SpeI and XbaI restriction enzyme-digested genomic DNA were used to establish relatedness among bacterial isolates. Data from this study indicate that both cull dairy cows and bulk tank milk pose a potential hazard with regard to human foodborne illness. It is therefore imperative to develop on-farm and preharvest pathogen reduction programs to control the carriage of E. coli O157:H7 pathogens.
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Affiliation(s)
- S E Murinda
- University of Tennessee Food Safety Center of Excellence, Knoxville 37996, USA
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Garza KM, Nguyen LT, Jones RG, Ohashi PS. Factors contributing to autoimmune disease. Adv Exp Med Biol 2002; 490:7-19. [PMID: 11505977 DOI: 10.1007/978-1-4615-1243-1_2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/21/2023]
Affiliation(s)
- K M Garza
- Ontario Cancer Institute, Department of Medical Biophysics, Toronto, Canada
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Abstract
We have already reported that the protein tyrosine kinase (PTK) activity in the dog prostate is distributed in cytosolic (75%) and particulate (Triton X-100-solubilized) fractions and that upon gel filtration, both PTKs migrate as entities of Mr 44,000 [(1991) Biochem. Cell. Biol. 69, 146-153]. Herein we demonstrate by immunoprecipitation with anti-phosphotyrosine antibodies that the soluble PTK has the ability to undergo self-phosphorylation. In addition, the polypeptide responsible for that enzymatic activity has been identified by 2 approaches: (1) a two-dimensional electrophoresis, in which the first dimension performed in non-denaturing conditions allowed the localization of the native enzyme, while the second dimension (SDS-PAGE) permitted the analysis of alkali-resistant phosphoproteins corresponding to the activity; (2) protein renaturation after SDS-PAGE followed by in situ phosphorylation (with [gamma-32P]ATP) of polyGT electrophoresed together with the enzyme preparation; the exclusive presence of the radiolabeled phosphotyrosine in the renatured protein confirmed its enzymatic nature. Using these methods, the major form of PTK in the dog prostate was shown to be expressed by a 50 kDa polypeptide which possesses autophosphorylation sites and which is present in the cytosol as an active monomer.
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Affiliation(s)
- L T Nguyen
- Department of Biochemistry, University of Montreal, Canada
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Folcher M, Gaillard H, Nguyen LT, Nguyen KT, Lacroix P, Bamas-Jacques N, Rinkel M, Thompson CJ. Pleiotropic functions of a Streptomyces pristinaespiralis autoregulator receptor in development, antibiotic biosynthesis, and expression of a superoxide dismutase. J Biol Chem 2001; 276:44297-306. [PMID: 11557748 DOI: 10.1074/jbc.m101109200] [Citation(s) in RCA: 105] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
In Streptomyces, a family of related butyrolactones and their corresponding receptor proteins serve as quorum-sensing systems that can activate morphological development and antibiotic biosynthesis. Streptomyces pristinaespiralis contains a gene cluster encoding enzymes and regulatory proteins for the biosynthesis of pristinamycin, a clinically important streptogramin antibiotic complex. One of these proteins, PapR1, belongs to a well known family of Streptomyces antibiotic regulatory proteins. Gel shift assays using crude cytoplasmic extracts detected SpbR, a developmentally regulated protein that bound to the papR1 promoter. SpbR was purified, and its gene was cloned using reverse genetics. spbR encoded a 25-kDa protein similar to Streptomyces autoregulatory proteins of the butyrolactone receptor family, including scbR from Streptomyces coelicolor. In Escherichia coli, purified SpbR and ScbR produced bound sequences immediately upstream of papR1, spbR, and scbR. SpbR DNA-binding activity was inhibited by an extracellular metabolite with chromatographic properties similar to those of the well known gamma-butyrolactone signaling compounds. DNase I protection assays mapped the SpbR-binding site in the papR1 promoter to a sequence homologous to other known butyrolactone autoregulatory elements. A nucleotide data base search showed that these binding motifs were primarily located upstream of genes encoding Streptomyces antibiotic regulatory proteins and butyrolactone receptors in various Streptomyces species. Disruption of the spbR gene in S. pristinaespiralis resulted in severe defects in growth, morphological differentiation, pristinamycin biosynthesis, and expression of a secreted superoxide dismutase.
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Affiliation(s)
- M Folcher
- Department of Molecular Microbiology, Biocenter, 70 Klingelbergstrasse, University of Basel, 4056 Basel, Switzerland
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Camara JG, Nguyen LT, Fernandez-Suntay JP, Nardin GF, Sua AS. The use of a computer-assisted image-guided system (InstaTrak) in orbital surgery. Ophthalmic Plast Reconstr Surg 2001; 17:447-51. [PMID: 11766027 DOI: 10.1097/00002341-200111000-00012] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
PURPOSE To assess the usefulness of a computer-assisted image-guided system (CAIGS) as an intraoperative anatomical guide in performing orbital surgery. METHODS Noncomparative interventional case series of 30 consecutive orbital procedures performed by one surgeon (J.G.C.) using the CAIGS (InstaTrak) for intraoperative anatomical guidance. RESULTS The series consisted of 8 cases of orbital decompression, 8 cases of orbital fracture, 11 cases of tumor excision, 2 cases of orbital reconstruction for severe enophthalmos, and 1 case of drainage of an orbital abscess. The CAIGS (InstaTrak) was useful in providing adjunctive intraoperative guidance in all 30 orbital cases. CONCLUSION The CAIGS (InstaTrak) system is a useful adjunctive tool in providing intraoperative anatomic guidance in a consecutive series of varied orbital operations.
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Affiliation(s)
- J G Camara
- Department of Ophthalmology, John A. Burns School of Medicine, University of Hawaii-St. Francis Medical Center, Honolulu 96817, USA.
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