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Kim S, Lee YM, Kim DH, Ha JJ, Yi JK, Kim DH, Oh D, Han K. Investigation of high correlation with carcass traits of SNPs of the PLCB1, C/EBPα, and TDRKH genes and the combinations of SNPs using the MDR method in the Hanwoo. Genes Genomics 2021; 43:961-973. [PMID: 34129193 DOI: 10.1007/s13258-021-01122-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2021] [Accepted: 06/08/2021] [Indexed: 11/28/2022]
Abstract
BACKGROUND Recently, many researchers focus on the best way to produce high-quality meat, as the trend in food consumption today is to focus on quality. In general, consumers' preferences in beef differ depending on taste and meatiness. Therefore, researchers are interested in how the marbling score affects the flavors of meat or the various factors that make up the meatiness to captivate the consumers' tastes. OBJECTIVE This study identifies single nucleotide polymorphisms (SNPs) or gene combinations that affect the carcass traits of Korean cattle (Hanwoo) by using the multifactor dimensionality reduction (MDR) method. METHODS We collected the candidate SNPs to identify SNPs related to marbling scores from whole-exome sequencing and bovine SNP genotyping data. Using 96 Hanwoo samples, we performed PCR amplification to investigate the polymorphism status. In addition, we investigated genetic relationships between carcass traits and SNPs using 612 Hanwoo samples. Furthermore, each candidate SNP genotype and the combinations of SNP genotypes were verified to improve the accuracy of genetic relationships using MDR method. RESULTS Twenty-four candidate SNPs associated with carcass trait and marbling scores were identified from SNP genotyping and whole-exome sequencing. Among them, three SNP markers (c.459 T > C of the PLCB1 gene, c.271 A > C of the C/EBPα gene, and g.17257 A > G of the TDRKH gene) were showed statistically significant differences between intramuscular fat and genotypes. Especially, two candidate SNPs, including c.459 T > C located in the PLCB1 gene and c.271 A > C located in the C/EBPα gene, could be highly associated with the intramuscular fat of Hanwoo quality grade. In addition, the combination of SNP genotypes is showed higher significant differences with carcass weight, backfat thickness, and longissimus dorsi muscle area. CONCLUSION Three SNP genotypes and the combination of SNP genotypes in the PLCB1, C/EBPα, and TDRKH genes may be useful genetic markers for improving beef quality.
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Affiliation(s)
- Songmi Kim
- Center for Bio-Medical Engineering Core Facility, Dankook University, Cheonan-si, 31116, Republic of Korea.,Department of Microbiology, Dankook University, Cheonan-si, 31116, Republic of Korea
| | - Yong-Moon Lee
- Department of Pathology, Dankook University College of Medicine, Cheonan-si, 31116, Republic of Korea
| | - Dong Hee Kim
- Department of Anesthesiology and Pain Management, Dankook University Hospital, Cheonan-si, 31116, Republic of Korea
| | - Jae Jung Ha
- Livestock Research Institute, Yeongju-si, Gyeongsangbuk-do, 36052, Republic of Korea
| | - Jun Koo Yi
- Livestock Research Institute, Yeongju-si, Gyeongsangbuk-do, 36052, Republic of Korea
| | - Dae Hyun Kim
- Livestock Research Institute, Yeongju-si, Gyeongsangbuk-do, 36052, Republic of Korea
| | - Dongyep Oh
- Livestock Research Institute, Yeongju-si, Gyeongsangbuk-do, 36052, Republic of Korea.
| | - Kyudong Han
- Center for Bio-Medical Engineering Core Facility, Dankook University, Cheonan-si, 31116, Republic of Korea. .,Department of Microbiology, Dankook University, Cheonan-si, 31116, Republic of Korea.
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Masterson AN, Liyanage T, Kaimakliotis H, Gholami Derami H, Deiss F, Sardar R. Bottom-Up Fabrication of Plasmonic Nanoantenna-Based High-throughput Multiplexing Biosensors for Ultrasensitive Detection of microRNAs Directly from Cancer Patients' Plasma. Anal Chem 2020; 92:9295-9304. [PMID: 32469524 DOI: 10.1021/acs.analchem.0c01639] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
There is an unmet need in clinical point-of-care (POC) cancer diagnostics for early state disease detection, which would greatly increase patient survival rates. Currently available analytical techniques for early stage cancer diagnosis do not meet the requirements for POC of a clinical setting. They are unable to provide the high demand of multiplexing, high-throughput, and ultrasensitive detection of biomarkers directly from low volume patient samples ("liquid biopsy"). To overcome these current technological bottle-necks, herein we present, for the first time, a bottom-up fabrication strategy to develop plasmonic nanoantenna-based sensors that utilize the unique localized surface plasmon resonance (LSPR) properties of chemically synthesized gold nanostructures, gold triangular nanoprisms (Au TNPs), gold nanorods (Au NRs), and gold spherical nanoparticles (Au SNPs). Our Au TNPs, NRs, and SNPs display refractive index unit (RIU) sensitivities of 318, 225, and 135 nm/RIU respectively. Based on the RIU results, we developed plasmonic nanoantenna-based multiplexing and high-throughput biosensors for the ultrasensitive assay of microRNAs. MicroRNAs are directly linked with cancer development, progression, and metastasis, thus they hold promise as next generation biomarkers for cancer diagnosis and prognosis. The developed biosensors are capable of assaying five different types of microRNAs at an attomolar detection limit. These sets of microRNAs include both oncogenic and tumor suppressor microRNAs. To demonstrate the efficiency as a POC cancer diagnostic tool, we analyzed the plasma of 20-bladder cancer patients without any sample processing steps. Importantly, our liquid biopsy-based biosensing approach is capable of differentiating healthy from early ("non-metastatic") and late ("metastatic") stage cancer with a p value <0.0001. Further, receiver operating characteristic analysis shows that our biosensing approach is highly specific, with an area under the curve of 1.0. Additionally, our plasmonic nanoantenna-based biosensors are regenerative, allowing multiple measurements using the same biosensors, which is essential in low- and middle-income countries. Taken together, our multiplexing and high-throughput biosensors have the unmatched potential to advance POC diagnostics and meet global needs for early stage detection of cancer and other diseases (e.g., infectious, autoimmune, and neurogenerative diseases).
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Affiliation(s)
- Adrianna N Masterson
- Department of Chemistry and Chemical Biology, Indiana University-Purdue University Indianapolis, 402 N Blackford Street, Indianapolis, Indiana 46202, United States
| | - Thakshila Liyanage
- Department of Chemistry and Chemical Biology, Indiana University-Purdue University Indianapolis, 402 N Blackford Street, Indianapolis, Indiana 46202, United States
| | - Hristos Kaimakliotis
- Department of Urology, Indiana University School of Medicine, 535 N. Barnhill Dr. Indianapolis, Indiana 46202, United States
| | - Hamed Gholami Derami
- Department of Mechanical Engineering and Materials Science, Institute of Materials Science and Engineering, Washington University in St. Louis, Saint Louis, Missouri 63130, United States
| | - Frédérique Deiss
- Department of Chemistry and Chemical Biology, Indiana University-Purdue University Indianapolis, 402 N Blackford Street, Indianapolis, Indiana 46202, United States
| | - Rajesh Sardar
- Department of Chemistry and Chemical Biology, Indiana University-Purdue University Indianapolis, 402 N Blackford Street, Indianapolis, Indiana 46202, United States.,Integrated Nanosystems Development Institute, Indiana University-Purdue University Indianapolis, 723 W. Michigan Street, Indianapolis, Indiana 46202, United States
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Lee JY, Ha J, Yi J, Jang J, Lee W, Lee Y, Oh DY, Han K. Superior single nucleotide polymorphisms that contribute to two main routes of the fatty acid synthesis pathway in Korean cattle. Genes Genomics 2018; 40:945-954. [PMID: 30155709 DOI: 10.1007/s13258-018-0704-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2018] [Accepted: 04/30/2018] [Indexed: 11/28/2022]
Abstract
The fatty acid composition of adipose tissue in livestock has been recognized as an important carcass trait that affects meat quality. To determine the overall positive effect on fatty acid synthesis, we investigated PPARγ, SREBPs, FABP4, SCD, and FASN genes because SNP and/or SNP combinations were strongly affecting each fatty acid synthesis pathway. We screened their SNPs, SNP combinations, and genotype. Furthermore, we studied the economic traits C18:1, monounsaturated fatty acid (MUFA), and marbling score (MS). To enhance the accuracy of the predictive genetic effect, we applied a statistical adjustment model excluding environmental factors. We also selected superior genes, gene combinations, and genotypes for each economic trait by using multifactor dimensionality reduction. Based on the results, g.3977-325 T>C (CC) was selected as the best genotype of the SNP and the combination (g.10153 A>G, g.3977-325 T>C) (AACC, AGCC, GGCC), (g.3690 G>A, g.3977-325 T>C) (GGCC, GACC), (g.3977-325 T>C, g.25670 C>T) (CCCC, CCCT, CCTT) (genotypes of the best SNP combination) was selected as the best gene combination for C18:1 and MUFA. In addition, g.3977-325 T>C (CC) was selected as the best genotype of the SNP and the combination (g.3977-325 T>C, g.6974 G>A) (TTAA, CTAA, CCAA, CCGA, CCGG) as the best SNP combination for MS. We integrated genes that were selected as excellent SNP and SNP combinations affecting two main routes of the fatty acid synthesis pathway and identified the best and final SNP, SNP combination, and superior genotype.
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Affiliation(s)
- Jea-Young Lee
- Department of Statistics, Yeungnam University, Gyeongsan-si, Gyeongbuk, 38541, Republic of Korea
| | - Jaejung Ha
- Livestock Research Institute, Gyeongsangbuk-Do, Yeongju, Gyeongbuk, 36052, Republic of Korea
| | - Junkoo Yi
- Livestock Research Institute, Gyeongsangbuk-Do, Yeongju, Gyeongbuk, 36052, Republic of Korea
| | - Jieun Jang
- Department of Statistics, Yeungnam University, Gyeongsan-si, Gyeongbuk, 38541, Republic of Korea
| | - Wooseok Lee
- Department of Nanobiomedical Science & BK21 PLUS NBM Global Research Center for Regenerative Medicine, Dankook University, Cheonan, 31116, Republic of Korea
| | - Yoonseok Lee
- Department of Biotechnology, College of Agriculture & Life Science, Hankyong National University, Anseong, Gyeonggi, 17579, Republic of Korea
| | - Dong-Yep Oh
- Livestock Research Institute, Gyeongsangbuk-Do, Yeongju, Gyeongbuk, 36052, Republic of Korea.
| | - Kyudong Han
- Department of Nanobiomedical Science & BK21 PLUS NBM Global Research Center for Regenerative Medicine, Dankook University, Cheonan, 31116, Republic of Korea.
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Cui X, Liu Y, Hu D, Qian W, Tin C, Sun D, Chen W, Lam RHW. A fluorescent microbead-based microfluidic immunoassay chip for immune cell cytokine secretion quantification. LAB ON A CHIP 2018; 18:522-531. [PMID: 29326990 DOI: 10.1039/c7lc01183k] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Quantitative and dynamic analyses of immune cell secretory cytokines are essential for precise determination and characterization of the "immune phenotype" of patients for clinical diagnosis and treatment of immune-related diseases. Although multiple methods including the enzyme-linked immunosorbent assay (ELISA) have been applied for cytokine detection, such measurements remain very challenging in real-time, high-throughput, and high-sensitivity immune cell analysis. In this paper, we report a highly integrated microfluidic device that allows for on-chip isolation, culture, and stimulation, as well as sensitive and dynamic cytokine profiling of immune cells. Such a microfluidic sensing chip is integrated with cytometric fluorescent microbeads for real-time and multiplexed monitoring of immune cell cytokine secretion dynamics, consuming a relatively small extracted sample volume (160 nl) without interrupting the immune cell culture. Furthermore, it is integrated with a Taylor dispersion-based mixing unit in each detection chamber that shortens the immunoassay period down to less than 30 minutes. We demonstrate the profiling of multiple pro-inflammatory cytokine secretions (e.g. interleukin-6, interleukin-8, and tumor necrosis factors) of human peripheral blood mononuclear cells (PBMCs) with a sensitivity of 20 pg ml-1 and a sample volume of 160 nl per detection. Further applications of this automated, rapid, and high-throughput microfluidic immunophenotyping platform can help unleash the mechanisms of systemic immune responses, and enable efficient assessments of the pathologic immune status for clinical diagnosis and immune therapy.
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Affiliation(s)
- Xin Cui
- Department of Mechanical and Biomedical Engineering, City University of Hong Kong, Hong Kong.
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Oh DY, Lee JY, Jang JE, Lee SU. Genetic effects of sterol regulatory element binding proteins and fatty acid-binding protein4 on the fatty acid composition of Korean cattle (Hanwoo). ASIAN-AUSTRALASIAN JOURNAL OF ANIMAL SCIENCES 2016; 30:160-166. [PMID: 27492349 PMCID: PMC5205601 DOI: 10.5713/ajas.16.0262] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/04/2016] [Revised: 05/25/2016] [Accepted: 08/03/2016] [Indexed: 11/27/2022]
Abstract
Objective This study identifies single-nucleotide polymorphisms (SNP) or gene combinations that affect the flavor and quality of Korean cattle (Hanwoo) by using the SNP Harvester method. Methods Four economic traits (oleic acid [C18:1], saturated fatty acids), monounsaturated fatty acids, and marbling score) were adjusted for environmental factors in order to focus solely on genetic effects. The SNP Harvester method was used to investigate gene combinations (two-way gene interactions) associated with these economic traits. Further, a multifactor dimensionality reduction method was used to identify superior genotypes in gene combinations. Results Table 3 to 4 show the analysis results for differences between superior genotypes and others for selected major gene combinations using the multifactor dimensionality reduction method. Environmental factors were adjusted for in order to evaluate only the genetic effect. Table 5 shows the adjustment effect by comparing the accuracy before and after correction in two-way gene interactions. Conclusion The g.3977-325 T>C and (g.2988 A>G, g.3977-325 T>C) combinations of fatty acid-binding protein4 were the superior gene, and the superior genotype combinations across all economic traits were the CC genotype at g.3977-325 T>C and the AACC, GACC, GGCC genotypes of (g.2988 A>G, g.3977-325 T>C).
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Affiliation(s)
- Dong-Yep Oh
- Livestock Research institute, Yeongju 750-871, Korea
| | - Jea-Young Lee
- Department of Statistics, Yeungnam University, Gyeongsan 712-749, Korea
| | - Ji-Eun Jang
- Department of Statistics, Yeungnam University, Gyeongsan 712-749, Korea
| | - Seung-Uk Lee
- Department of Civil and Environmental Engineering, National University of Singapore, Singapore 117576, Singapore
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Lee JY, Ha JJ, Park YS, Yi JK, Lee S, Mun S, Han K, Kim JJ, Kim HJ, Oh DY. Relationship between Single Nucleotide Polymorphisms in the Peroxisome Proliferator-Activated Receptor Gamma Gene and Fatty Acid Composition in Korean Native Cattle. ASIAN-AUSTRALASIAN JOURNAL OF ANIMAL SCIENCES 2016; 29:184-94. [PMID: 26732443 PMCID: PMC4698698 DOI: 10.5713/ajas.15.0502] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/10/2015] [Revised: 08/03/2015] [Accepted: 08/24/2015] [Indexed: 12/18/2022]
Abstract
The peroxisome proliferator-activated receptor gamma (PPARγ) gene plays an important role in the biosynthesis process controlled by a number of fatty acid transcription factors. This study investigates the relationships between 130 single-nucleotide polymorphisms (SNPs) in the PPARγ gene and the fatty acid composition of muscle fat in the commercial population of Korean native cattle. We identified 38 SNPs and verified relationships between 3 SNPs (g.1159-71208 A>G, g.42555-29812 G>A, and g.72362 G>T) and the fatty acid composition of commercial Korean native cattle (n = 513). Cattle with the AA genotype of g.1159-71208 A>G and the GG genotype of g.42555-29812 G>A and g.72362 G>T had higher levels of monounsaturated fatty acids and carcass traits (p<0.05). The results revealed that the 3 identified SNPs in the PPARγ gene affected fatty acid composition and carcass traits, suggesting that these 3 SNPs may improve the flavor and quality of beef in commercial Korean native cattle.
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Affiliation(s)
- Jea-Young Lee
- Livestock Research institute, Yeongju 750-871, Korea
| | - Jae-Jung Ha
- Livestock Research institute, Yeongju 750-871, Korea
| | - Yong-Soo Park
- Department of Equine Industry, Korea National College of Agriculture and Fisheries, Hwaseong 445-760, Korea
| | - Jun-Koo Yi
- Livestock Research institute, Yeongju 750-871, Korea
| | - Seunguk Lee
- Biotechnology Research Center, The University of Tokyo, Bunkyo 113-8657, Tokyo
| | - Seyoung Mun
- Department of Nanobiomedical Science & BK21 PLUS NBM Global Research Center for Regenerative Medicine, Dankook University, Cheonan 330-714, Korea; DKU-Theragen institute for NGS analysis (DTiNa), Cheonan 330-714, Korea
| | - Kyudong Han
- Department of Nanobiomedical Science & BK21 PLUS NBM Global Research Center for Regenerative Medicine, Dankook University, Cheonan 330-714, Korea; DKU-Theragen institute for NGS analysis (DTiNa), Cheonan 330-714, Korea
| | - J-J Kim
- School of Biotechnology, Yeungnam University, Gyeongsan 712-749, Korea
| | - Hyun-Ji Kim
- Livestock Research institute, Yeongju 750-871, Korea
| | - Dong-Yep Oh
- Livestock Research institute, Yeongju 750-871, Korea
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Label-free cytokine micro- and nano-biosensing towards personalized medicine of systemic inflammatory disorders. Adv Drug Deliv Rev 2015; 95:90-103. [PMID: 26408791 DOI: 10.1016/j.addr.2015.09.005] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2015] [Revised: 08/17/2015] [Accepted: 09/10/2015] [Indexed: 01/31/2023]
Abstract
Systemic inflammatory disorders resulting from infection, trauma, surgery, and severe disease conditions pose serious threats to human health leading to organ dysfunction, organ failure, and mortality. The highly complex and dynamic nature of the immune system experiencing acute inflammation makes immunomodulatory therapy blocking pro-inflammatory cytokines very challenging. Successful therapy requires the ability to determine appropriate anti-cytokine drugs to be delivered at a right dose in a timely manner. Label-free micro- and nano-biosensors hold the potential to overcome the current challenges, enabling cytokine-targeted treatments to be tailored according to the immune status of an individual host with their unique cytokine biomarker detection capabilities. This review studies the recent progress in label-free cytokine biosensors, summarizes their performances and potential merits, and discusses future directions for their advancements to meet challenges towards personalized anti-cytokine drug delivery.
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Istivan SB, Bishop DK, Jones AL, Grosser ST, Schneider JW. A 502-Base Free-Solution Electrophoretic DNA Sequencing Method Using End-Attached Wormlike Micelles. Anal Chem 2015; 87:11433-40. [PMID: 26455271 DOI: 10.1021/acs.analchem.5b02931] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We demonstrate that the use of wormlike nonionic micelles as drag-tags in end-labeled free-solution electrophoresis ("micelle-ELFSE") provides single-base resolution of Sanger sequencing products up to 502 bases in length, a nearly 2-fold improvement over reported ELFSE separations. "CiEj" running buffers containing 48 mM C12E5, 6 mM C10E5, and 3 M urea (32.5 °C) form wormlike micelles that provide a drag equivalent to an uncharged DNA fragment with a length (α) of 509 bases (effective Rh = 27 nm). Runtime in a 40 cm capillary (30 kV) was 35 min for elution of all products down to the 26-base primer. We also show that smaller Triton X-100 micelles give a read length of 103 bases in a 4 min run, so that a combined analysis of the Sanger products using the two buffers in separate capillaries could be completed in 14 min for the full range of lengths. A van Deemter analysis shows that resolution is limited by diffusion-based peak broadening and wall adsorption. Effects of drag-tag polydispersity are not observed, despite the inherent polydispersity of the wormlike micelles. We ascribe this to a stochastic size-sampling process that occurs as micelle size fluctuates rapidly during the runtime. A theoretical model of the process suggests that fluctuations occur with a time scale less than 10 ms, consistent with the monomer exchange process in nonionic micelles. The CiEj buffer has a low viscosity (2.7 cP) and appears to be semidilute in micelle concentration. The large drag-tag size of the CiEj buffers leads to steric segregation of the DNA and tag for short fragments and attendant mobility shifts.
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Affiliation(s)
- Stephen B Istivan
- Department of Chemical Engineering and ‡Department of Biomedical Engineering, Carnegie Mellon University , Pittsburgh, Pennsylvania 15213, United States
| | - Daniel K Bishop
- Department of Chemical Engineering and ‡Department of Biomedical Engineering, Carnegie Mellon University , Pittsburgh, Pennsylvania 15213, United States
| | - Angela L Jones
- Department of Chemical Engineering and ‡Department of Biomedical Engineering, Carnegie Mellon University , Pittsburgh, Pennsylvania 15213, United States
| | - Shane T Grosser
- Department of Chemical Engineering and ‡Department of Biomedical Engineering, Carnegie Mellon University , Pittsburgh, Pennsylvania 15213, United States
| | - James W Schneider
- Department of Chemical Engineering and ‡Department of Biomedical Engineering, Carnegie Mellon University , Pittsburgh, Pennsylvania 15213, United States
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Fujishima K, Yamamoto S, Tsukagoshi K, Hashimoto M. A Microbead-based Single Base Extension Assay for the Detection of Known Single-base Changes in Genomic DNA. CHEM LETT 2015. [DOI: 10.1246/cl.150014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Kohei Fujishima
- Department of Chemical Engineering and Materials Science, Doshisha University
| | - Shunsuke Yamamoto
- Department of Chemical Engineering and Materials Science, Doshisha University
| | - Kazuhiko Tsukagoshi
- Department of Chemical Engineering and Materials Science, Doshisha University
| | - Masahiko Hashimoto
- Department of Chemical Engineering and Materials Science, Doshisha University
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Zhu X, Li J, He H, Huang M, Zhang X, Wang S. Application of nanomaterials in the bioanalytical detection of disease-related genes. Biosens Bioelectron 2015; 74:113-33. [PMID: 26134290 DOI: 10.1016/j.bios.2015.04.069] [Citation(s) in RCA: 48] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2015] [Revised: 04/09/2015] [Accepted: 04/21/2015] [Indexed: 12/15/2022]
Abstract
In the diagnosis of genetic diseases and disorders, nanomaterials-based gene detection systems have significant advantages over conventional diagnostic systems in terms of simplicity, sensitivity, specificity, and portability. In this review, we describe the application of nanomaterials for disease-related genes detection in different methods excluding PCR-related method, such as colorimetry, fluorescence-based methods, electrochemistry, microarray methods, surface-enhanced Raman spectroscopy (SERS), quartz crystal microbalance (QCM) methods, and dynamic light scattering (DLS). The most commonly used nanomaterials are gold, silver, carbon and semiconducting nanoparticles. Various nanomaterials-based gene detection methods are introduced, their respective advantages are discussed, and selected examples are provided to illustrate the properties of these nanomaterials and their emerging applications for the detection of specific nucleic acid sequences.
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Affiliation(s)
- Xiaoqian Zhu
- Ministry-of-Education Key Laboratory for the Green Preparation and Application of Functional Materials, College of Materials Science and Engineering, Hubei University, Youyi Road 368, Wuchang, Wuhan, Hubei 430062, PR China
| | - Jiao Li
- Ministry-of-Education Key Laboratory for the Green Preparation and Application of Functional Materials, College of Materials Science and Engineering, Hubei University, Youyi Road 368, Wuchang, Wuhan, Hubei 430062, PR China
| | - Hanping He
- Hubei Collaborative Innovation Center for Advanced Organic Chemical Materials, Ministry of Education Key Laboratory for the Synthesis and Application of Organic Functional Molecules, College of Chemistry and Chemical Engineering, Hubei University, Youyi Road 368, Wuchang, Wuhan, Hubei 430062, PR China; Ministry-of-Education Key Laboratory for the Green Preparation and Application of Functional Materials, College of Materials Science and Engineering, Hubei University, Youyi Road 368, Wuchang, Wuhan, Hubei 430062, PR China.
| | - Min Huang
- Ministry-of-Education Key Laboratory for the Green Preparation and Application of Functional Materials, College of Materials Science and Engineering, Hubei University, Youyi Road 368, Wuchang, Wuhan, Hubei 430062, PR China
| | - Xiuhua Zhang
- Hubei Collaborative Innovation Center for Advanced Organic Chemical Materials, Ministry of Education Key Laboratory for the Synthesis and Application of Organic Functional Molecules, College of Chemistry and Chemical Engineering, Hubei University, Youyi Road 368, Wuchang, Wuhan, Hubei 430062, PR China; Ministry-of-Education Key Laboratory for the Green Preparation and Application of Functional Materials, College of Materials Science and Engineering, Hubei University, Youyi Road 368, Wuchang, Wuhan, Hubei 430062, PR China
| | - Shengfu Wang
- Hubei Collaborative Innovation Center for Advanced Organic Chemical Materials, Ministry of Education Key Laboratory for the Synthesis and Application of Organic Functional Molecules, College of Chemistry and Chemical Engineering, Hubei University, Youyi Road 368, Wuchang, Wuhan, Hubei 430062, PR China; Ministry-of-Education Key Laboratory for the Green Preparation and Application of Functional Materials, College of Materials Science and Engineering, Hubei University, Youyi Road 368, Wuchang, Wuhan, Hubei 430062, PR China
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Oh DY, Jin MH, Lee YS, Ha JJ, Kim BK, Yeo JS, Lee JY. Identification of Stearoyl-CoA Desaturase (SCD) Gene Interactions in Korean Native Cattle Based on the Multifactor-dimensionality Reduction Method. ASIAN-AUSTRALASIAN JOURNAL OF ANIMAL SCIENCES 2014; 26:1218-28. [PMID: 25049903 PMCID: PMC4093401 DOI: 10.5713/ajas.2013.13058] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 01/22/2013] [Revised: 05/26/2013] [Accepted: 04/27/2013] [Indexed: 11/27/2022]
Abstract
Fat quality is determined by the composition of fatty acids. Genetic relationships between this composition and single nucleotide polymorphisms (SNPs) in the stearoyl-CoA desaturase1 (SCD1) gene were examined using 513 Korean native cattle. Single and epistatic effects of 7 SNP genetic variations were investigated, and the multifactor dimensionality reduction (MDR) method was used to investigate gene interactions in terms of oleic acid (C18:1), mono-unsaturated fatty acids (MUFAs) and marbling score (MS). The g.6850+77 A>G and g.14047 C>T SNP interactions were identified as the statistically optimal combination (C18:1, MUFAs and MS permutation p-values were 0.000, 0.000 and 0.001 respectively) of two-way gene interactions. The interaction effects of g.6850+77 A>G, g.10213 T>C and g.14047 C>T reflected the highest training-balanced accuracy (63.76%, 64.70% and 61.85% respectively) and was better than the individual effects for C18:1, MUFAs and MS. In addition, the superior genotype groups were AATTCC, AGTTCC, GGTCCC, AGTCCT, GGCCCT and AGCCTT. These results suggest that the selected SNP combination of the SCD1 gene and superior genotype groups can provide useful inferences for the improvement of the fatty acid composition in Korean native cattle.
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Affiliation(s)
- Dong-Yep Oh
- Livestock Research institute, Gyeongsangbuk-Do, Yeongju, Gyeongbuk, 750-871, Korea
| | - Me-Hyun Jin
- Livestock Research institute, Gyeongsangbuk-Do, Yeongju, Gyeongbuk, 750-871, Korea
| | - Yoon-Seok Lee
- Livestock Research institute, Gyeongsangbuk-Do, Yeongju, Gyeongbuk, 750-871, Korea
| | - Jae-Jung Ha
- Livestock Research institute, Gyeongsangbuk-Do, Yeongju, Gyeongbuk, 750-871, Korea
| | - Byung-Ki Kim
- Livestock Research institute, Gyeongsangbuk-Do, Yeongju, Gyeongbuk, 750-871, Korea
| | - Jung-Sou Yeo
- Livestock Research institute, Gyeongsangbuk-Do, Yeongju, Gyeongbuk, 750-871, Korea
| | - Jea-Young Lee
- Livestock Research institute, Gyeongsangbuk-Do, Yeongju, Gyeongbuk, 750-871, Korea
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Lee JY, Lee JH, Yeo JS, Kim JJ. A SNP Harvester Analysis to Better Detect SNPs of CCDC158 Gene That Are Associated with Carcass Quality Traits in Hanwoo. ASIAN-AUSTRALASIAN JOURNAL OF ANIMAL SCIENCES 2014; 26:766-71. [PMID: 25049848 PMCID: PMC4093242 DOI: 10.5713/ajas.2012.12715] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/26/2012] [Revised: 02/22/2013] [Accepted: 02/16/2013] [Indexed: 11/27/2022]
Abstract
The purpose of this study was to investigate interaction effects of genes using a Harvester method. A sample of Korean cattle, Hanwoo (n = 476) was chosen from the National Livestock Research Institute of Korea that were sired by 50 Korean proven bulls. The steers were born between the spring of 1998 and the autumn of 2002 and reared under a progeny-testing program at the Daekwanryeong and Namwon branches of NLRI. The steers were slaughtered at approximately 24 months of age and carcass quality traits were measured. A SNP Harvester method was applied with a support vector machine (SVM) to detect significant SNPs in the CCDC158 gene and interaction effects between the SNPs that were associated with average daily gains, cold carcass weight, longissimus dorsi muscle area, and marbling scores. The statistical significance of the major SNP combinations was evaluated with x (2)-statistics. The genotype combinations of three SNPs, g.34425+102 A>T(AA), g.4102636T>G(GT), and g.11614+19G>T(GG) had a greater effect than the rest of SNP combinations, e.g. 0.82 vs. 0.75 kg, 343 vs. 314 kg, 80.4 vs 74.7 cm(2), and 7.35 vs. 5.01, for the four respective traits (p<0.001). Also, the estimates were greater compared with single SNPs analyzed (the greatest estimates were 0.76 kg, 320 kg, 75.5 cm(2), and 5.31, respectively). This result suggests that the SNP Harvester method is a good option when multiple SNPs and interaction effects are tested. The significant SNPs could be applied to improve meat quality of Hanwoo via marker-assisted selection.
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Affiliation(s)
- Jea-Young Lee
- School of Biotechnology, Yeungnam University, Gyeongsan, 712-749, Korea
| | - Jong-Hyeong Lee
- School of Biotechnology, Yeungnam University, Gyeongsan, 712-749, Korea
| | - Jung-Sou Yeo
- School of Biotechnology, Yeungnam University, Gyeongsan, 712-749, Korea
| | - Jong-Joo Kim
- School of Biotechnology, Yeungnam University, Gyeongsan, 712-749, Korea
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Oh DY, Lee YS, La BM, Yeo JS. Identification of the SNP (Single Nucleotide Polymorphism) for Fatty Acid Composition Associated with Beef Flavor-related FABP4 (Fatty Acid Binding Protein 4) in Korean Cattle. ASIAN-AUSTRALASIAN JOURNAL OF ANIMAL SCIENCES 2014; 25:913-20. [PMID: 25049644 PMCID: PMC4092985 DOI: 10.5713/ajas.2012.12078] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/10/2012] [Revised: 03/31/2012] [Accepted: 03/15/2012] [Indexed: 11/27/2022]
Abstract
In this study, we investigated the relationship between unsaturated fatty acids influencing beef flavor and four types of SNPs (c.280A>G, c.388G>A, c.408G>C and c.456A>G) located at exon 2, 3 and 4 of the FABP4 gene, which is a fatty acid binding protein 4 in Korean cattle (n = 513). When analyzing the relationship between single genotype, fatty acids and carcass trait, individuals of GG, GG, CC and GG genotypes that are homozygotes, had a higher content of unsaturated fatty acids and marbling scores than other genotypes (p<0.05). Then, haplotype block showed strong significant relationships not only with unsaturated fatty acids (54.73%), but also with marbling scores (5.82) in ht1×ht1 group (p<0.05). This ht1×ht1 group showed significant differences with unsaturated fatty acids and marbling scores that affected beef flavor in Korean cattle. Therefore, it can be inferred that the ht1×ht1 types might be valuable new markers for use in the improvement of Korean cattle.
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Affiliation(s)
- Dong-Yep Oh
- Charmpoom Hanwoo Research Institution, Charmpoom Hanwoo Co., Ltd., Chilgok-gun, Gyeongsangbuk-do 718-913, Korea
| | - Yoon-Seok Lee
- Charmpoom Hanwoo Research Institution, Charmpoom Hanwoo Co., Ltd., Chilgok-gun, Gyeongsangbuk-do 718-913, Korea
| | - Boo-Mi La
- Charmpoom Hanwoo Research Institution, Charmpoom Hanwoo Co., Ltd., Chilgok-gun, Gyeongsangbuk-do 718-913, Korea
| | - Jung-Sou Yeo
- Charmpoom Hanwoo Research Institution, Charmpoom Hanwoo Co., Ltd., Chilgok-gun, Gyeongsangbuk-do 718-913, Korea
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Detection of exonic variants within the melanocortin 1 receptor (MC1R) gene in Black Silky, White Leghorn and Golden duckwing Araucana chicken. Mol Biol Rep 2014; 41:4843-6. [PMID: 24830563 DOI: 10.1007/s11033-014-3394-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2014] [Accepted: 05/02/2014] [Indexed: 10/25/2022]
Abstract
The melanocortin 1 receptor (MC1R) gene can be considered a candidate functional gene for the pigmentation of plumage color. The aim of this study was to investigate the association between the genotype frequencies of g.69 T>C, g.376 G>A and g.427 A>G SNPs within the MC1R gene in Black silky (O), Golden duckwing Araucana (GA) and White Leghorn (W). The CC and AA genotype frequencies of g.69 T>C and g.427 A>G SNPs in White Leghorn (W) were both 1.000, and the TT genotype frequency of the g.69 T>C SNP in Golden duckwing Araucana (GA) was also 1.000. The GG and AA genotype frequencies of g.376 G>A and g.427 A>G SNPs in Black silky (O) were both 0.100. When a haplotype is observed using a combination of markers, a Golden duckwing Araucana (GA) can especially be distinguished when it is a TAG, TGG and TAA type in the SNP combination of the MC1R gene. In case of the CAA types, only White Leghorn (W) could specifically be distinguished. Therefore, three SNPs in MC1R may provide identification in chicken breeds.
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Lee J, Jin M, Lee Y, Ha J, Yeo J, Oh D. Gene–gene interactions of fatty acid synthase (FASN) using multifactor-dimensionality reduction method in Korean cattle. Mol Biol Rep 2014; 41:2021-7. [PMID: 24413995 DOI: 10.1007/s11033-014-3050-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2013] [Accepted: 01/04/2014] [Indexed: 10/25/2022]
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16
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Ham HO, Park SH, Kurutz JW, Szleifer IG, Messersmith PB. Antifouling glycocalyx-mimetic peptoids. J Am Chem Soc 2013; 135:13015-22. [PMID: 23919653 DOI: 10.1021/ja404681x] [Citation(s) in RCA: 86] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
The glycocalyx of the cell is composed of highly hydrated saccharidic groups conjugated to protein and lipid cores. Although components of the glycocalyx are important in cell-cell interactions and other specific biological recognition events, a fundamental role of the glycocalyx is the inhibition of nonspecific interactions at the cell surface. Inspired by glycoproteins present in the glycocalyx, we describe a new class of synthetic antifouling polymer composed of saccharide containing N-substituted polypeptide (glycopeptoid). Grafting of glycopeptoids to a solid surface resulted in a biomimetic shielding layer that dramatically reduced nonspecific protein, fibroblast, and bacterial cell attachment. All-atom molecular dynamics simulation of grafted glycopeptoids revealed an aqueous interface enriched in highly hydrated saccharide residues. In comparison to saccharide-free peptoids, the interfacial saccharide residues of glycopeptoids formed a higher number of hydrogen bonds with water molecules. Moreover, these hydrogen bonds displayed a longer persistence time, which we believe contributed to fouling resistance by impeding interactions with biomolecules. Our findings suggest that the fouling resistance of glycopeptoids can be explained by the presence of both a 'water barrier' effect associated with the hydrated saccharide residues as well as steric hindrance from the polymer backbone.
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Affiliation(s)
- Hyun Ok Ham
- Biomedical Engineering Department, Northwestern University, Evanston, Illinois 60208, United States
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Albrecht JC, Kotani A, Lin JS, Soper SA, Barron AE. Simultaneous detection of 19 K-ras mutations by free-solution conjugate electrophoresis of ligase detection reaction products on glass microchips. Electrophoresis 2013; 34:590-7. [PMID: 23192597 PMCID: PMC4361093 DOI: 10.1002/elps.201200462] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2012] [Revised: 10/19/2012] [Accepted: 10/23/2012] [Indexed: 01/08/2023]
Abstract
We demonstrate here the power and flexibility of free-solution conjugate electrophoresis (FSCE) as a method of separating DNA fragments by electrophoresis with no sieving polymer network. Previous work introduced the coupling of FSCE with ligase detection reaction (LDR) to detect point mutations, even at low abundance compared to the wild-type DNA. Here, four large drag-tags are used to achieve free-solution electrophoretic separation of 19 LDR products ranging in size from 42 to 66 nt that correspond to mutations in the K-ras oncogene. LDR-FSCE enabled electrophoretic resolution of these 19 LDR-FSCE products by CE in 13.5 min (E = 310 V/cm) and by microchip electrophoresis in 140 s (E = 350 V/cm). The power of FSCE is demonstrated in the unique characteristic of free-solution separations where the separation resolution is constant no matter the electric field strength. By microchip electrophoresis, the electric field was increased to the maximum of the power supply (E = 700 V/cm), and the 19 LDR-FSCE products were separated in less than 70 s with almost identical resolution to the separation at E = 350 V/cm. These results will aid the goal of screening K-ras mutations on integrated "sample-in/answer-out" devices with amplification, LDR, and detection all on one platform.
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Affiliation(s)
| | - Akira Kotani
- Department of Chemistry, Louisiana State University, Baton Rouge, Louisiana, USA
- School of Pharmacy, Tokyo University of Pharmacy and Life Sciences, Tokyo, Japan
| | - Jennifer S. Lin
- Department of Bioengineering, Stanford University, Stanford, California, USA
| | - Steven A. Soper
- Department of Chemistry, Louisiana State University, Baton Rouge, Louisiana, USA
| | - Annelise E. Barron
- Department of Bioengineering, Stanford University, Stanford, California, USA
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Kim KS, Kim SW, Raney NE, Ernst CW. Evaluation of BTA1 and BTA5 QTL Regions for Growth and Carcass Traits in American and Korean Cattle. ASIAN-AUSTRALASIAN JOURNAL OF ANIMAL SCIENCES 2012; 25:1521-8. [PMID: 25049512 PMCID: PMC4093042 DOI: 10.5713/ajas.2012.12218] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 04/23/2012] [Revised: 08/17/2012] [Accepted: 06/07/2012] [Indexed: 11/30/2022]
Abstract
Previously identified QTL regions on BTA1 and BTA5 were investigated to validate the QTL regions and to identify candidate genes for growth and carcass traits in commercial cattle populations from the USA and Korea. Initially, a total of 8 polymorphic microsatellite (MS) markers in the BTA1 and 5 QTL regions were used for Chi-square tests to compare the frequencies of individual alleles between high and low phenotypic groups for the US (Michigan Cattleman’s Association/Michigan State University; MCA/MSU) cattle. For a subsequent study, 24 candidate genes containing missense mutations and located within the QTL regions based on bovine genome sequence data were analyzed for genotyping in the two commercial cattle populations. Re-sequencing analyses confirmed 18 public missense SNPs and identified 9 new SNPs. Seventeen of these SNPs were used for genotyping of the MCA/MSU cattle (n = 98) and Korean native cattle (n = 323). On BTA1, UPK1B, HRG, and MAGEF1 polymorphisms residing between BM1312 and BMS4048 were significantly associated with growth and carcass traits in one or both of the MCA/MSU and Korean populations. On BTA5, ABCD2, IL22 and SNRPF polymorphisms residing between BL4 and BR2936 were associated with marbling and backfat traits in one or both of the MCA/MSU and Korean cattle populations. These results suggested that BTA 1 and 5 QTL regions may be segregating in both Korean Hanwoo and USA commercial cattle populations and DNA markers tested in this study may contribute to the identification of positional candidate genes for marker-assisted selection programs.
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Affiliation(s)
- K S Kim
- Department of Animal Science, Michigan State University, East Lansing, MI 48824, USA
| | - S W Kim
- Department of Animal Science, Michigan State University, East Lansing, MI 48824, USA
| | - N E Raney
- Department of Animal Science, Michigan State University, East Lansing, MI 48824, USA
| | - C W Ernst
- Department of Animal Science, Michigan State University, East Lansing, MI 48824, USA
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Lee Y, Oh D, Lee J, La B, Yeo J. Novel single nucleotide polymorphisms of bovine SREBP1 gene is association with fatty acid composition and marbling score in commercial Korean cattle (Hanwoo). Mol Biol Rep 2012; 40:247-54. [DOI: 10.1007/s11033-012-2055-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2012] [Accepted: 10/02/2012] [Indexed: 11/30/2022]
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Esteves F, Gaspar J, de Sousa B, Antunes F, Mansinho K, Matos O. Pneumocystis jirovecii multilocus genotyping in pooled DNA samples: a new approach for clinical and epidemiological studies. Clin Microbiol Infect 2012; 18:E177-84. [DOI: 10.1111/j.1469-0691.2012.03828.x] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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21
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Determination of RNA degradation by capillary electrophoresis with cyan light-emitted diode-induced fluorescence. J Chromatogr A 2012; 1239:78-84. [DOI: 10.1016/j.chroma.2012.03.070] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2012] [Revised: 03/10/2012] [Accepted: 03/21/2012] [Indexed: 11/18/2022]
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Association analysis of formyl peptide receptor 2 (FPR2) polymorphisms and aspirin exacerbated respiratory diseases. J Hum Genet 2012; 57:247-53. [PMID: 22377711 DOI: 10.1038/jhg.2012.12] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Aspirin-exacerbated respiratory diseases (AERD) are associated with the metabolism of arachidonic acid. FPR2 (formyl peptide receptor2) is a high-affinity ligand receptor for potent anti-inflammatory lipid metabolites: lipoxins. Thus, functional alterations of the FPR2 may contribute to AERD. We investigated the relationship between single-nucleotide polymorphisms (SNPs) in the FPR2 and AERD. Asthmatics were categorized into AERD <15% decreases in forced expiratory volume in one second (FEV(1)), and/or naso-ocular reactions after oral aspirin challenge (n=170) and aspirin-tolerant asthma (ATA, n=268). In all, 11 SNPs were genotyped. FPR2 protein expressions on CD14-positive monocytes in peripheral blood were measured using flow cytometric analysis. We performed RT-PCR of the FPR2 mRNA expressed by peripheral blood mononuclear cells. Logistic regression analysis showed that the minor allele frequency of FPR2 -4209T>G (rs1769490) in intron 2 was significantly lower in the AERD group (n=170) than in the ATA group (n=268) (P=0.006, P(corr)=0.04, recessive model). The decline of FEV(1) after aspirin challenge was significantly lower in the subjects with GG homozygotes of FPR2 -4209T>G than those with the other genotypes (P=0.0002). Asthmatic homozygotes for FPR2 -4209T>G minor allele exhibited significantly higher FPR2 protein expression in CD14-positive monocytes than did those with the common allele of FPR2 -4209T>G allele (P=0.01). There was no difference in the expression of the wild form and the exon 2 deleted variant form of FPR2 gene according to the genotypes of FPR2 -4209T>G. The minor allele at FPR2 -4209T>G may have a protective role against the development of AERD, via increase of FPR2 protein expression in inflammatory cells.
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Jiao A, Zheng J, Hu Y, Zhu G, Li J, Li H, Yang R, Tan W. Hybridization-triggered isothermal signal amplification coupled with MutS for label-free and sensitive fluorescent assay of SNPs. Chem Commun (Camb) 2012; 48:5659-61. [DOI: 10.1039/c2cc30882g] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
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Oh SH, Kim YH, Park SM, Cho SH, Park JS, Jang AS, Park SW, Uh ST, Lee YM, Kim MK, Choi IS, Cho SH, Hong CS, Lee YW, Lee JY, Choi BW, Park BL, Shin HD, Park CS. Association analysis of thromboxane A synthase 1 gene polymorphisms with aspirin intolerance in asthmatic patients. Pharmacogenomics 2011; 12:351-63. [PMID: 21449675 DOI: 10.2217/pgs.10.181] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
AIM Thromboxane A synthase (TBXAS1) converts prostaglandin H to thromboxane A, a potent constrictor of smooth respiratory muscle. Thus, functional alterations of the TBXAS1 gene may contribute to aspirin-intolerant asthma (AIA). MATERIALS & METHODS We investigated the relationship between SNPs in the TBXAS1 gene and AIA. Asthmatics (n = 470) were categorized into AIA (20% or greater decreases in forced expiratory volume in 1 s [FEV(1)], or 15% to 19% decreases in FEV(1) with naso-ocular or cutaneous reactions) and aspirin-tolerant asthma (ATA). A total of 101 SNPs were genotyped. mRNA expression of the TBXAS1 gene by peripheral blood mononuclear cells and plasma thromboxane B2 (TXB2) concentrations were measured by reverse transcriptase (RT)-PCR and ELISA. RESULTS Logistic regression analysis showed that the rare allele frequency of rs6962291 in intron 9 was significantly lower in the AIA group (n = 115) than in the ATA group (n = 270) (p(corr) = 0.04). The linear regression analysis revealed a strong association of rs6962291 with the aspirin challenge-induced FEV(1) fall (p = 0.003). RT-PCR revealed an exon-12-deleted splice variant. We measured TBXAS1 mRNA levels in peripheral blood mononuclear cells. The mRNA levels of the full-length wild-type and splice variant were significantly higher in the TT homozygotes than in the AA homozygotes of rs6962291 (1.00 ± 0.18 vs 0.57 ± 0.03 and 1.00 ± 0.18 vs 0.21 ± 0.05, p = 0.047 and 0.001, respectively). The plasma TXB2 level was significantly lower in rs6962291 AA carriers than in rs6962291 TT (p = 0.016) carriers. CONCLUSION The rare allele of rs6962291 may play a protective role against aspirin hypersensitivity via a lower catalytic activity of the TBXAS1 gene, attributed to the increase of a nonfunctioning isoform of TBXAS1.
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Affiliation(s)
- Sun-Hee Oh
- Genome Research Center for Allergy & Respiratory Disease, Soonchunhyang University Bucheon Hospital, 1174 Jung-dong, Wonmi-gu, Bucheon, Gyeonggi-do, 420-767, Republic of Korea
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Oh D, Lee Y, La B, Yeo J, Chung E, Kim Y, Lee C. Fatty acid composition of beef is associated with exonic nucleotide variants of the gene encoding FASN. Mol Biol Rep 2011; 39:4083-90. [PMID: 21773945 DOI: 10.1007/s11033-011-1190-7] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2011] [Accepted: 07/11/2011] [Indexed: 10/18/2022]
Abstract
Genetic associations of fatty acid composition with exonic single nucleotide polymorphisms (SNPs) in the gene encoding fatty acid synthase (FASN) were examined using 513 Korean cattle. All five individual SNPs of g.12870 T>C, g.13126 T>C, g.15532 C>A, g.16907 T>C and g.17924 G>A were associated with a variety of fatty acid compositions and further with marbling score (P < 0.05). Their genotypes of CC, TT, AA, TT, and GG were associated with increased monounsaturated fatty acids and with decreased saturated fatty acids (P < 0.05). The genotypes at all the SNPs also increased marbling score (P < 0.05). Further genetic associations with fatty acid composition suggested that homozygous genotype with the haplotype of ATG at g.15532, g.16907, and g.17924 in a linkage disequilibrium block increased monounsaturated fatty acids and marbling score (P < 0.05). We concluded that the five exonic SNPs of g.12870, g.13126, g.15532, g.16907, and g.17924 in the FASN gene could change fatty acid contents. Their genotypes of CC, TT, AA, TT, and GG and haplotype of ATG at g.15532, g.16907, and g.17924 were recommended for genetic improvement of beef quality.
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Affiliation(s)
- Dongyep Oh
- School of Biotechnology, Yeungnam University, Gyeongsan, Gyeongbuk, 712-749, South Korea
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Giestas L, Lima JC, Baptista PV. Coupling single base extension to a spectral codification tool for increased throughput screening. J Biotechnol 2011; 154:199-204. [DOI: 10.1016/j.jbiotec.2011.05.012] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2011] [Revised: 05/09/2011] [Accepted: 05/25/2011] [Indexed: 10/18/2022]
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Clinical relevance of multiple single-nucleotide polymorphisms in Pneumocystis jirovecii Pneumonia: development of a multiplex PCR-single-base-extension methodology. J Clin Microbiol 2011; 49:1810-5. [PMID: 21389160 DOI: 10.1128/jcm.02303-10] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Pneumocystis jirovecii pneumonia (PcP) is a major cause of respiratory illness in patients with AIDS. The identification of multiple single-nucleotide polymorphisms (SNPs) at three distinct P. jirovecii loci encoding dihydrofolate reductase (DHFR), mitochondrial large-subunit rRNA (mtLSU rRNA), and superoxide dismutase (SOD) was achieved using multiplex-PCR (MPCR) followed by direct sequencing and two single-base extension (SBE) techniques. Four SNPs (DHFR312, mt85, SOD215, and SOD110), correlated previously with parameters of disease, were amplified and genotyped simultaneously. The concordance of results between the standard sequencing technique (direct sequencing) and SBE analysis was 96.9% for the acrylamide gel electrophoresis and 98.4% for the capillary electrophoresis. The cross-genetic analysis established several statistical associations among the SNPs studied: mt85C-SOD110T, SOD110T-SOD215C, and SOD110C-SOD215T. These results were confirmed by cluster analysis. Data showed that among the isolates with low to moderate parasite burden, the highest percentages of DHFR312C, mt85C, SOD110T, and SOD215C were detected, whereas for high parasite burden cases the highest frequencies were observed among isolates with DHFR312T, mt85T, SOD110C, and SOD215T. The polymorphisms studied were shown to be suitable genetic targets potentially correlated with PcP clinical data that can be used as predictors of outcome in further studies to help clinical decision-making in the management of PcP. The MPCR/SBE protocol described for the first time in the present study was shown to be a rapid, highly accurate method for genotyping P. jirovecii SNPs encoded by different loci that could be used for epidemiological studies and as an additional procedure for the prognostic classification and diagnosis of PcP.
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Kim JM, Park BL, Park SM, Lee SH, Kim MO, Jung S, Lee EH, Uh ST, Park JS, Choi JS, Kim YH, Kim MK, Choi IS, Cho SH, Choi BW, Park HS, Chang HS, Shin HD, Park CS. Association analysis of N-acetyl transferase-2 polymorphisms with aspirin intolerance among asthmatics. Pharmacogenomics 2011; 11:951-8. [PMID: 20602614 DOI: 10.2217/pgs.10.65] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
AIMS Cysteinyl leukotrienes are inactivated by acetyl coenzyme A-dependent N-acetyltransferase (NAT). Thus, functional alterations of the NAT gene may contribute to the risk of aspirin-intolerant asthma. MATERIALS & METHODS Asthmatics (n = 438) were categorized into aspirin-intolerant asthma (15% or greater decrease in the forced expiratory volume in 1 s or cutaneous reactions, n = 170) or aspirin-tolerant asthma (n = 268) groups. In total, 14 polymorphisms of the NAT2 gene were genotyped by a single-base extension method. RESULTS The distributions of all loci of the 14 SNPs were in Hardy-Weinberg equilibrium (p > 0.05). Among the 14 SNPs, six common SNPs (minor allele frequency >5%) in a Korean population were used for haplotype construction and further statistical analysis. The logistic regression analysis demonstrated that NAT2 -9246G>C and haplotype 2 (TCACGG) were significantly associated with the risk of aspirin-intolerant asthma. The rare allele frequencies of the SNP and Ht2 were significantly higher in the aspirin-intolerant asthma group than in the aspirin-tolerant asthma group (p(corr) = 0.03 and p(corr) = 0.02 in codominant model). CONCLUSION In a large genetic epidemiology study of aspirin-intolerant asthma in a Korean population, genetic polymorphisms of NAT2 were found to be related to a risk of aspirin hypersensitivity among asthmatics.
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Affiliation(s)
- Jin-Moo Kim
- Genome Research Center for Allergy & Respiratory Disease, Soonchunhyang University Bucheon Hospital, 1174 Jung-dong, Wonmi-gu, Bucheon, Gyeonggi-do 420-767, Republic of Korea
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Li J, Deng T, Chu X, Yang R, Jiang J, Shen G, Yu R. Rolling circle amplification combined with gold nanoparticle aggregates for highly sensitive identification of single-nucleotide polymorphisms. Anal Chem 2010; 82:2811-6. [PMID: 20192245 DOI: 10.1021/ac100336n] [Citation(s) in RCA: 166] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
A highly sensitive and specific colorimetry-based rolling circle amplification (RCA) assay method for single-nucleotide polymorphism genotyping has been developed. A circular template is generated by ligation upon the recognition of a point mutation on DNA targets. An RCA amplification is then initiated using the circular template in the presence of Phi29 polymerase. The RCA product can be digested by a restricting endonuclease, and the cleaved DNA fragments can mediate the aggregation of gold nanoparticle-tagged DNA probes. This causes a colorimetric change of the solution as the indicator of the mutation occurrence, which can be detected using UV-vis spectroscopy or viewed by naked eyes. On the basis of the high amplification efficiency of Phi29 polymerase, a mutated target of approximately 70 fM can be detected in this assay. In addition, the protection of the circle template using phosphorothioated nucleotides allows the digestion reaction to be performed simultaneously in RCA. Moreover, DNA ligase offers high fidelity in distinguishing the mismatched bases at the ligation site, resulting in positive detection of mutant targets even when the ratio of the wild-type to the mutant is 10,000:1. The developed RCA-based colorimetric detection scheme was demonstrated for SNP typing of beta-thalassemia gene at position -28 in genomic DNA.
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Affiliation(s)
- Jishan Li
- State Key Laboratory of Chem/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, 410082, China
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Li G, Ge S, Ni X, Wang Q, He P, Fang Y. Multiplexed p53 Mutation Detection by Microchip Electro-phoresis with Laser-Induced Fluorescence Detector. CHINESE J CHEM 2010. [DOI: 10.1002/cjoc.201090149] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
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Kanayama N, Shibata H, Kimura A, Miyamoto D, Takarada T, Maeda M. RAFT-generated polyacrylamide-DNA block copolymers for single-nucleotide polymorphism genotyping by affinity capillary electrophoresis. Biomacromolecules 2010; 10:805-13. [PMID: 19249847 DOI: 10.1021/bm801301b] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Capillary electrophoretic separation of a mixture of 5'-fluorescein isothiocyanate-labeled single-stranded DNA (normal ssDNA) and its single-base-substituted one (mutant ssDNA) was achieved by using a RAFT-generated polyacrylamide-oligodeoxyribonucleotide block copolymer (PAAm-b-ODN) as an affinity polymeric probe. PAAm-b-ODN was synthesized through the Michael addition of thiol-terminated PAAm (PAAm-SH) to 5'-maleimide-modified ODN. PAAm-SH was derived from dithiobenzoate-terminated PAAm prepared via RAFT polymerization. The number-averaged molecular weight (M(n)) and the molecular weight distribution were determined by aqueous size exclusion chromatography. After a capillary tube was filled with the running buffer solution of PAAm-b-ODN, a mixture of normal and mutant ssDNA was subjected to electrophoresis and detected by a laser-induced fluorescent detector. Because the base sequence of PAAm-b-ODN was complementary to part of the mutant ssDNA, including a single-base substitution site, the electrophoretic migration of mutant ssDNA was retarded due to the formation of the equilibrium complex with PAAm-b-ODN. Increasing M(n) of the PAAm segment enhanced this retardation. On the other hand, normal ssDNA was unable to form the complex owing to a single-base mismatch, which was proved by melting curve measurements. The Lineweaver-Burk-type analysis of the mobility of mutant ssDNA revealed that the binding constants for the complexes with different PAAm-b-ODN probes were almost identical to each other. The analysis also demonstrated that the ratio of the hydrodynamic radius of the complex to that of the free mutant ssDNA increased with increasing M(n) of the affinity polymeric probe's PAAm segment. This means that the PAAm segment indirectly provides mutant ssDNA with an additional hydrodynamic friction force via the affinity interaction of the ODN segment. Optimization of the salt concentration of the running buffer and the capillary temperature improved the resolution of the separation. This affinity polymeric probe will be useful for developing a simple and highly reliable single-nucleotide polymorphism genotyping method.
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Affiliation(s)
- Naoki Kanayama
- Bioengineering Laboratory, RIKEN Advanced Science Institute, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
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Li T, Zhang D, Luo W, Lu M, Wang Z, Song Y, Wang H. Metal Cation Mediated-Capillary Electrophoresis of Nucleic Acids. Anal Chem 2009; 82:487-90. [DOI: 10.1021/ac9025708] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Affiliation(s)
- Tao Li
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center For Eco-Environmental Sciences, Chinese Academy of Sciences, Shuangqing Road 18, Beijing 100085, China
| | - Dapeng Zhang
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center For Eco-Environmental Sciences, Chinese Academy of Sciences, Shuangqing Road 18, Beijing 100085, China
| | - Wenru Luo
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center For Eco-Environmental Sciences, Chinese Academy of Sciences, Shuangqing Road 18, Beijing 100085, China
| | - Meiling Lu
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center For Eco-Environmental Sciences, Chinese Academy of Sciences, Shuangqing Road 18, Beijing 100085, China
| | - Zhixin Wang
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center For Eco-Environmental Sciences, Chinese Academy of Sciences, Shuangqing Road 18, Beijing 100085, China
| | - Yuling Song
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center For Eco-Environmental Sciences, Chinese Academy of Sciences, Shuangqing Road 18, Beijing 100085, China
| | - Hailin Wang
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center For Eco-Environmental Sciences, Chinese Academy of Sciences, Shuangqing Road 18, Beijing 100085, China
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Cheong HS, Yoon DH, Bae JS, Kim LH, Kim EM, Kim JO, Hong J, Kim N, Shin HD. ADFP promoter polymorphism associated with marbling score in Korean cattle. BMB Rep 2009; 42:529-34. [PMID: 19712591 DOI: 10.5483/bmbrep.2009.42.8.529] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Marbling score (MS) is the major trait that affects carcass quality in beef cattle. In this study, we investigated the association between genetic polymorphisms of the adipose differentiation-related protein gene (ADFP) and carcass traits in Korean cattle (also known as Hanwoo). Using direct DNA sequencing in 24 unrelated Korean cattle, 25 novel polymorphisms were identified within all exons and their flanking regions of ADFP, including the promoter region (1.5 kb). Among them, 21 polymorphic sites were selected for genotyping in the beef cattle (n = 425). Statistical analyses revealed that one promoter polymorphism (c.-56-18A > G) was associated with MS (P = 0.009). The "A" allele of c.-56-18A > G exerted a lowering effect on MS, e.g., the lowest MS was found in "A/A" (MS = 2.09 +/- 1.23), intermediate in "A/G" (MS = 2.11 +/- 1.31), and the highest in "G/G" (MS = 2.47 +/- 1.47). Our findings suggest that these polymorphisms in ADFP might be important genetic factors involved in carcass quality in beef cattle.
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Affiliation(s)
- Hyun Sub Cheong
- Department of Life Science, Sogang University, Seoul 121-742, Korea
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36
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Quantitative effects of position and type of single mismatch on single base primer extension. J Microbiol Methods 2009; 77:267-75. [PMID: 19285527 DOI: 10.1016/j.mimet.2009.03.001] [Citation(s) in RCA: 106] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2008] [Revised: 02/26/2009] [Accepted: 03/01/2009] [Indexed: 11/21/2022]
Abstract
Single mismatch (MM) present at the region where primer binds onto the template strand can greatly affect the PCR efficacy. Earlier studies revealed that PCR or primer extension is hindered by a single MM at the primer 3' end. The MMs located at other positions within a primer also have similar performance, but to what extent they can decrease the efficiency is not clear. In this study, a modified single base extension assay was used to systematically compare the extension efficiencies between a perfect-matched (PM) primer and its single-MM primers with all possible MM types. The extension efficiencies of single-MM primers, which were generally lower or equivalent to that of the PM primer, were observed to strongly depend on the MM location and/or type. Due to the enzymatic activity, single MMs present at the last 3-4 positions from the primer 3' end exhibited zero or minimal (<3.9%) extension efficiencies. For those MMs at positions 5 onward from primer 3' end where was affected mainly by the primer-target binding stability, an increasing trend in extension efficiency with the highest (i.e., 69.3%) occurring at the primer 5' end was observed to significantly correlate in an inverse relationship with the duplex stability (i.e., difference of melting temperature) under a empirically polynomial equation, y=-0.0731 x(3) + 2.2519 x(2) - 22.617 x + 76.691 (R(2)=0.5318). It was further shown that the extension efficiencies of these MM types could be improved with a factor of 3.25 on average in relation to the decrease in the annealing temperature by 7 degrees C. On the other hand, substitution of a less selective inosine nucleotide did not convincingly improve the extension efficiency. Overall findings obtained could further improve the rational design of oligonucleotide primers in various microbiological studies that involve the use of PCR techniques.
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37
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Sinville R, Coyne J, Meagher RJ, Cheng YW, Barany F, Barron A, Soper SA. Ligase detection reaction for the analysis of point mutations using free-solution conjugate electrophoresis in a polymer microfluidic device. Electrophoresis 2009; 29:4751-60. [PMID: 19053073 DOI: 10.1002/elps.200800197] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
We have developed a new method for the analysis of low abundant point mutations in genomic DNA using a combination of an allele-specific ligase detection reaction (LDR) with free-solution conjugate electrophoresis (FSCE) to generate and analyze the genetic products. FSCE eliminates the need for a polymer sieving matrix by conjugating chemically synthesized polyamide "drag-tags" onto the LDR primers. The additional drag of the charge-neutral drag-tag breaks the linear scaling of the charge-to-friction ratio of DNA and enables size-based separations of DNA in free solution using electrophoresis with no sieving matrix. We successfully demonstrate the conjugation of polyamide drag-tags onto a set of four LDR primers designed to probe the K-ras oncogene for mutations highly associated with colorectal cancer, the simultaneous generation of fluorescently labeled LDR/drag-tag conjugate (LDR-dt) products in a multiplexed, single-tube format with mutant:WT ratios as low as 1:100, respectively, and the single-base, high-resolution separation of all four LDR-dt products. Separations were conducted in free solution with no polymer network using both a commercial capillary array electrophoresis (CAE) system and a PMMA microchip replicated via hot-embossing with only a Tris-based running buffer containing additives to suppress the EOF. Typical analysis times for LDR-dt were 11 min using the CAE system and as low as 85 s for the PMMA microchips. With resolution comparable to traditional gel-based CAE, FSCE along with microchip electrophoresis decreased the separation time by more than a factor of 40.
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Affiliation(s)
- Rondedrick Sinville
- Center for BioModular Multi-Scale Microsystems, Department of Chemistry, Louisiana State University, Baton Rouge, LA 70803, USA
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38
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Kim I, Hur NW, Shin HD, Park BL, Cheong HS, Bae SC. Associations of DNase IV polymorphisms with autoantibodies in patients with systemic lupus erythematosus. Rheumatology (Oxford) 2008; 47:996-9. [DOI: 10.1093/rheumatology/ken125] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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Cheong HS, Yoon DH, Park BL, Kim LH, Bae JS, Namgoong S, Lee HW, Han CS, Kim JO, Cheong IC, Shin HD. A single nucleotide polymorphism in CAPN1 associated with marbling score in Korean cattle. BMC Genet 2008; 9:33. [PMID: 18423040 PMCID: PMC2386817 DOI: 10.1186/1471-2156-9-33] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2007] [Accepted: 04/19/2008] [Indexed: 11/10/2022] Open
Abstract
Background Marbling score (MS) is the major quantitative trait that affects carcass quality in beef cattle. In this study, we examined the association between genetic polymorphisms of the micromolar calcium-activated neutral protease gene (micro-calpain, CAPN1) and carcass traits in Korean cattle (also known as Hanwoo). Results By direct DNA sequencing in 24 unrelated Korean cattle, we identified 39 sequence variants within exons and their flanking regions in CAPN1. Among them, 12 common polymorphic sites were selected for genotyping in the beef cattle (n = 421). Statistical analysis revealed that a polymorphism in the 3'UTR (c.2151*479C>T) showed significant association with MS (Pcor. = 0.02). Conclusion Our findings suggest that polymorphisms in CAPN1 might be one of the important genetic factors involved in carcass quality in beef cattle, although it could be false positive association.
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Affiliation(s)
- Hyun Sub Cheong
- Department of Genetic Epidemiology, SNP Genetics, Inc., Rm 1407, Complex B, WooLim Lion's Valley, 371-28, Gasan-Dong, Geumcheon-Gu, Seoul, 153-803, Korea.
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40
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Galbiati S, Chiari M, Macellari M, Ferrari M, Cremonesi L, Cretich M. High-throughput mutational screening for beta-thalassemia by single-nucleotide extension. Electrophoresis 2008; 28:4289-94. [PMID: 18040987 DOI: 10.1002/elps.200700181] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
In this work a high-throughput method based on the single-nucleotide extension (SNE) reaction and multicolour detection in a DNA sequencer was developed to screen for eight mutations in the human beta-globin gene: IVSI.110, cd39, IVSI.1, IVSI.6, IVSII.745, HbC, HbS and cd6. The method has been validated on a large number of samples for the two most common mutations causing beta-thalassemia in the Mediterranean area (IVSI.110 and cd39). The development of a high-throughput, fast and reliable method to assay beta-thalassemia mutations represents a significant improvement in molecular diagnosis of this disease. The multicolour detection and the use of multiple injections further enhances the throughput of mutational screening by the DNA sequencer and facilitates automated genotyping for routine molecular diagnostics.
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Affiliation(s)
- Silvia Galbiati
- Genomic Unit for the Diagnosis of Human Pathologies, San Raffaele Scientific Institute, Milano, Italy
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41
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Cho SA, Park TS, Yoon DH, Cheong HS, Namgoong S, Park BL, Lee HW, Han CS, Kim EM, Cheong IC, Kim HB, Shin HD. Identification of genetic polymorphisms in FABP3 and FABP4 and putative association with back fat thickness in Korean native cattle. BMB Rep 2008; 41:29-34. [DOI: 10.5483/bmbrep.2008.41.1.029] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
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42
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Li J, Jiang JH, Xu XM, Chu X, Jiang C, Shen G, Yu RQ. Simultaneous identification of point mutations via DNA ligase-mediated gold nanoparticle assembly. Analyst 2008; 133:939-45. [DOI: 10.1039/b717853k] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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43
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Li J, Zhong W. Typing of multiple single-nucleotide polymorphisms by a microsphere-based rolling circle amplification assay. Anal Chem 2007; 79:9030-8. [PMID: 17973502 DOI: 10.1021/ac701702t] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The combination of suspension array with rolling circle amplification can lead to a sensitive and specific assay for single-nucleotide polymorphisms (SNPs) detection, as demonstrated in this study. A circular template generated by ligation upon the recognition of a point mutation on DNA targets was amplified isothermally by the Phi29 polymerase on microspheres. The elongation products were labeled with fluorochrome-tagged probes and detected in a flow cytometer, indicating the mutation occurrence. As low as 10 amol of mutated strands was detected by this assay, and positive mutation detection was achieved with a wild-type to mutant ratio of 10 000:1, which could be attributed to the high amplification efficiency of Phi29, the high binding capacity of the microspheres, and the remarkable precision of DNA ligase in distinguishing mismatched bases at the ligation site. A novel design of using two differently labeled detection probes on the same microsphere to target both the wild-type and mutant samples allowed parallel determination of the heterozygosity for two SNPs (K-ras G12C and TP53 R273H) in PCR amplicons prepared from human genomic DNA extracts. This ability lays the groundwork for further enhancing the assay throughput by using multiple fluorophores and microspheres with distinct properties.
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Affiliation(s)
- Jishan Li
- Department of Chemistry, University of California, Riverside, California 92521, USA
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44
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Affiliation(s)
- Karel Klepárník
- Institute of Analytical Chemistry, Academy of Sciences of the Czech Republic, Veveří 97, CZ-602 00 Brno, Czech Republic
| | - Petr Boček
- Institute of Analytical Chemistry, Academy of Sciences of the Czech Republic, Veveří 97, CZ-602 00 Brno, Czech Republic
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45
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Abstract
Planar microfluidic devices have emerged as effective tools for the electrophoretic separation of a variety of different DNA inputs. The advancement of this miniaturized platform was inspired initially by demands placed on electrophoretic performance metrics by the human genome project and has provided a viable alternative to slab gel and even capillary formats due to its ability to offer high resolution separations of nucleic acid materials in a fraction of the time associated with its predecessors, consumption of substantially less sample and reagents while maintaining the ability to perform many separations in parallel for realizing ultra-high throughputs. Another compelling advantage of this separation platform is that it offers the potential for integrating front-end sample preprocessing steps onto the separation device eliminating the need for manual sample handling. This review aims to compile a recent survey of various electrophoretic separations using either glass or polymer-based microchips in the areas of genotyping and DNA sequencing as well as those involving the growing field of DNA-based forensics.
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Affiliation(s)
- Rondedrick Sinville
- Department of Chemistry, Louisiana State University, Baton Rouge, LA 70803, USA
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46
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Pennathur S, Baldessari F, Santiago JG, Kattah MG, Steinman JB, Utz PJ. Free-solution oligonucleotide separation in nanoscale channels. Anal Chem 2007; 79:8316-22. [PMID: 17883279 DOI: 10.1021/ac0710580] [Citation(s) in RCA: 69] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
In this paper, we report an experimental study of electrokinetic transport and separation of double-stranded deoxyribonucleic acid (dsDNA) oligonucleotides in custom-fabricated fused-silica nanochannels filled with a gel-free sodium borate aqueous buffer. Mixtures of fluorescently labeled dsDNA molecules in the range of 10-100 base pair (bp), fluorescein, and fluorescein-12-UTP (UTP) were separated in less than 120 s in channels of depth ranging from 40 to 1560 nm. We varied the channel depth and background buffer concentration to achieve a 0.006-0.2 range of Debye length-to-channel-half-depth ratio (lambdaD/h), and a 0.004-1.7 range of the ratio of length of dsDNA molecule to channel half-depth (l/h). We find observed oligonucleotide migration times depend on both l/h and lambdaD/h. Electrophoretic mobility estimates agree well with published (micrometer-scale channel) values for background electrolyte (BGE) concentrations greater than approximately 10 mM. At BGE concentrations of 1 and 5 mM, mobility estimates in our nanochannels are higher than published values. Of the cases studied, the highest separation sensitivities were achieved in 100 nm channels with 1-10 mM ion density buffers. Potential applications of this technology include rapid small-scale sequencing and other fluorescence-based oligonucleotide separation and detection assays.
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Affiliation(s)
- Sumita Pennathur
- Mechanical Engineering Department, Stanford University, Stanford, California 94305, USA
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47
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Joo KW, Hwang YH, Kim JH, Oh KH, Kim H, Shin HD, Chung WK, Yang J, Park KS, Ahn C. MCP-1 and RANTES polymorphisms in Korean diabetic end-stage renal disease. J Korean Med Sci 2007; 22:611-5. [PMID: 17728497 PMCID: PMC2693807 DOI: 10.3346/jkms.2007.22.4.611] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Macrophage infiltration has been observed in the renal biopsy specimens of diabetic nephropathy (DN), and hyperglycemic state stimulates the renal expression of RANTES (regulated upon activation, normal T-cell expressed and secreted) and MCP- 1 (monocyte chemoattractant protein-1). Upregulation of RANTES and MCP-1 with infiltrating macrophages may play a crucial role in the development and progression of DN. Genetic polymorphisms of RANTES and its receptors were reported to be independent risk factors for DN. We genotyped single nucleotide polymorphism (SNPs) in the MCP-1 G-2518A, CCR2 G46295A, RANTES C-28G and G-403A in 177 diabetic end-stage renal disease (ESRD) patients and 184 patients without renal involvement (controls) in order to investigate the effects of these SNPs on DN in Korean patients with type 2 DM. There were no differences in the frequencies of SNPs and the distribution of haplotypes of RANTES promoter SNPs between two groups. In conclusion, there were no associations of MCP-1, CCR2 and RANTES promoter SNPs with diabetic ESRD in Korean population. Prospective studies with clearly-defined, homogenous cohorts are needed to confirm the effect of these genetic polymorphisms on DN.
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Affiliation(s)
- Kwon Wook Joo
- Department of Internal Medicine, Seoul National University College of Medicine, Seoul, Korea
| | - Young-Hwan Hwang
- Department of Internal Medicine, Eulji General Hospital, Eulji University, Seoul, Korea
| | - Jae Hyeon Kim
- Department of Internal Medicine, Seoul National University Boramae Hospital, Seoul, Korea
- Genome Research Center for Diabetes and Endocrine Disease, Clinical Research Institute, Seoul National University Hospital, Seoul, Korea
| | - Kook-Hwan Oh
- Department of Internal Medicine, Seoul National University College of Medicine, Seoul, Korea
| | - Hyunho Kim
- Department of Internal Medicine, Seoul National University College of Medicine, Seoul, Korea
- Cancer Research Institute, Seoul National University, Seoul, Korea
| | - Hyoung Doo Shin
- Department of Genetic Epidemiology, SNP genetics, Inc., Seoul, Korea
| | - Woo-Kyung Chung
- Department of Internal Medicine, Gil Medical Center, Gachon University, Incheon, Korea
| | - Jaeseok Yang
- Department of Internal Medicine, Gil Medical Center, Gachon University, Incheon, Korea
| | - Kyong Soo Park
- Department of Internal Medicine, Seoul National University College of Medicine, Seoul, Korea
- Genome Research Center for Diabetes and Endocrine Disease, Clinical Research Institute, Seoul National University Hospital, Seoul, Korea
| | - Curie Ahn
- Department of Internal Medicine, Seoul National University College of Medicine, Seoul, Korea
- Transplantation Research Institute, Seoul National University, Seoul, Korea
- Cancer Research Institute, Seoul National University, Seoul, Korea
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48
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Cheong HS, Yoon D, Kim LH, Park BL, Lee HW, Han CS, Kim EM, Cho H, Chung ER, Cheong I, Shin HD. Titin-cap (TCAP) polymorphisms associated with marbling score of beef. Meat Sci 2007; 77:257-63. [PMID: 22061598 DOI: 10.1016/j.meatsci.2007.03.014] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2006] [Revised: 03/13/2007] [Accepted: 03/14/2007] [Indexed: 10/23/2022]
Abstract
Marbling score (MS) is the major qualitative trait that affects carcass quality in beef cattle. In this study, we examined the association between genetic polymorphisms of the titin-cap gene (TCAP) and carcass traits in Korean native cattle (also known as Hanwoo). By direct DNA sequencing in 24 unrelated Korean cattle, we identified five sequence variants in 1.2kb of TCAP. Among them, four common polymorphic sites were selected for genotyping in the beef cattle (n=437). Pair-wise linkage analysis with four polymorphisms showed strong linkage disequilibrium (LD), and three major haplotypes (freq.>0.1) were constructed. Statistical analysis revealed that polymorphisms in intron1 (g.346G>A) and exon2 (g.592-597CTGCAG[Leu-Gln]insdel) showed significant association with marbling score (P(cor.)=0.003 and 0.02, respectively). One haplotype, ht2[C-G-G-del], also showed significant association with MS (P(cor.)=0.0004). Our findings suggest that polymorphisms in TCAP might be among the important genetic factors involved in carcass quality in beef cattle.
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Affiliation(s)
- H S Cheong
- Department of Genetic Epidemiology, SNP Genetics, Inc., Rm 1407, Complex B, WooLim Lion's Valley, 371-28, Gasan-Dong, Geumcheon-Gu, Seoul, 153-803, Republic of Korea
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49
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Meagher RJ, Coyne JA, Hestekin CN, Chiesl TN, Haynes RD, Won JI, Barron AE. Multiplexed p53 mutation detection by free-solution conjugate microchannel electrophoresis with polyamide drag-tags. Anal Chem 2007; 79:1848-54. [PMID: 17256875 DOI: 10.1021/ac061903z] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We report a new, bioconjugate approach to performing highly multiplexed single-base extension (SBE) assays, which we demonstrate by genotyping a large panel of point mutants in exons 5-9 of the p53 gene. A series of monodisperse polyamide "drag-tags" was created using both chemical and biological synthesis and used to achieve the high-resolution separation of genotyping reaction products by microchannel electrophoresis without a polymeric sieving matrix. A highly multiplexed SBE reaction was performed in which 16 unique drag-tagged primers simultaneously probe 16 p53 gene loci, with an abbreviated thermal cycling protocol of only 9 min. The drag-tagged SBE products were rapidly separated by free-solution conjugate electrophoresis (FSCE) in both capillaries and microfluidic chips with genotyping accuracy in excess of 96%. The separation requires less than 70 s in a glass microfluidic chip, or about 20 min in a commercial capillary array sequencing instrument. Compared to gel electrophoresis, FSCE offers greater freedom in the design of SBE primers by essentially decoupling the length of the primer and the electrophoretic mobility of the genotyping products. FSCE also presents new possibilities for the facile implementation of SBE on integrated microfluidic electrophoresis devices for rapid, high-throughput genetic mutation detection or SNP scoring.
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Affiliation(s)
- Robert J Meagher
- Department of Chemical and Biological Engineering and Department of Chemistry, Northwestern University, Evanston, Illinois 60208, USA
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50
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Cheong HS, Yoon DH, Kim LH, Park BL, Choi YH, Chung ER, Cho YM, Park EW, Cheong IC, Oh SJ, Yi SG, Park T, Shin HD. Growth hormone-releasing hormone (GHRH) polymorphisms associated with carcass traits of meat in Korean cattle. BMC Genet 2006; 7:35. [PMID: 16749938 PMCID: PMC1524984 DOI: 10.1186/1471-2156-7-35] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2005] [Accepted: 06/03/2006] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Cold carcass weight (CW) and longissimus muscle area (EMA) are the major quantitative traits in beef cattle. In this study, we found several polymorphisms of growth hormone-releasing hormone (GHRH) gene and examined the association of polymorphisms with carcass traits (CW and EMA) in Korean native cattle (Hanwoo). RESULTS By direct DNA sequencing in 24 unrelated Korean cattle, we identified 12 single nucleotide polymorphisms within the 9 kb full gene region, including the 1.5 kb promoter region. Among them, six polymorphic sites were selected for genotyping in our beef cattle (n = 428) and five marker haplotypes (frequency > 0.1) were identified. Statistical analysis revealed that -4241A>T showed significant associations with CW and EMA. CONCLUSION Our findings suggest that polymorphisms in GHRH might be one of the important genetic factors that influence carcass yield in beef cattle. Sequence variation/haplotype information identified in this study would provide valuable information for the production of a commercial line of beef cattle.
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Affiliation(s)
- Hyun Sub Cheong
- Department of Genetic Epidemiology, SNP Genetics, Inc., Seoul, 153-803, Korea
| | - Du-Hak Yoon
- National Livestock Research Institute, RDA, 441-706, Korea
| | - Lyoung Hyo Kim
- Department of Genetic Epidemiology, SNP Genetics, Inc., Seoul, 153-803, Korea
| | - Byung Lae Park
- Department of Genetic Epidemiology, SNP Genetics, Inc., Seoul, 153-803, Korea
| | - Yoo Hyun Choi
- Department of Genetic Epidemiology, SNP Genetics, Inc., Seoul, 153-803, Korea
| | - Eui Ryong Chung
- Department of Biotechnology, Sangi University, Wonju, Kangwon Do, 220-702, Korea
| | - Yong Min Cho
- National Livestock Research Institute, RDA, 441-706, Korea
| | - Eng Woo Park
- National Livestock Research Institute, RDA, 441-706, Korea
| | | | - Sung-Jong Oh
- National Livestock Research Institute, RDA, 441-706, Korea
| | - Sung-Gon Yi
- Department of Statistics, Seoul National University, Seoul, 151-747, Korea
| | - Taesung Park
- Department of Statistics, Seoul National University, Seoul, 151-747, Korea
| | - Hyoung Doo Shin
- Department of Genetic Epidemiology, SNP Genetics, Inc., Seoul, 153-803, Korea
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