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Abstract
Here we report one of the smallest real-time polymerase chain reaction (PCR) systems to date with an approximate size of 100 mm × 60 mm × 33 mm. The system is an autonomous unit requiring an external 12 V power supply. Four simultaneous reactions are performed in the form of virtual reaction chambers (VRCs) where a ≈200 nL sample is covered with mineral oil and placed on a glass cover slip. Fast, 40 cycle amplification of an amplicon from the H7N9 gene was used to demonstrate the PCR performance. The standard curve slope was -3.02 ± 0.16 cycles at threshold per decade (mean ± standard deviation) corresponding to an amplification efficiency of 0.91 ± 0.05 per cycle (mean ± standard deviation). The PCR device was capable of detecting a single deoxyribonucleic acid (DNA) copy. These results further suggest that our handheld PCR device may have broad, technologically-relevant applications extending to rapid detection of infectious diseases in small clinics.
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Affiliation(s)
| | - Bojan Robert Ilic
- National Institute of Standard and Technology (NIST), Center for Nanoscale Science and Technology, 100 Bureau Drive, MS 6201, Gaithersburg, MD 20899-6201, USA
| | - Andreas Manz
- KIST-Europe, Microfluidics Group, Campus E7.1, 66111 Saarbrücken, Germany.
| | - Pavel Neužil
- KIST-Europe, Microfluidics Group, Campus E7.1, 66111 Saarbrücken, Germany. and Brno University of Technology (BUT), Central European Institute of Technology (CEITEC), Technická 3058/10, CZ-616 00 Brno, Czech Republic
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152
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Jiang M, Lee JN, Bionaz M, Deng XY, Wang Y. Evaluation of Suitable Internal Control Genes for RT-qPCR in Yak Mammary Tissue during the Lactation Cycle. PLoS One 2016; 11:e0147705. [PMID: 26808329 PMCID: PMC4726593 DOI: 10.1371/journal.pone.0147705] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2015] [Accepted: 01/07/2016] [Indexed: 11/18/2022] Open
Abstract
The yak is primarily found throughout the Tibetan high plateau and the surrounding mountainous area of south central Asia; among its others attributes, its milk is very important for the local population. A key concern in the field of yak research is the better understanding of which genes control the production and composition of milk. The most accurate and sensitive method for gene expression analysis is quantitative reverse transcription polymerase chain reaction (RT-qPCR). It is essential for reliable RT-qPCR to be able to the normalize the data using internal control genes (ICGs). However, it is critical to assess the reliability of the normalization by testing multiple ICGs. Our objective was to uncover a reliable normalization for RT-qPCR data obtained from yak mammary tissue during the lactation cycle. We assessed the reliability of 10 ICGs (ACTB, EIF6, GAPDH, LRP10, MRPL39, MRPS15, MTG1, RPS8, RPS23, and UXT) using geNorm. The analysis revealed that all of the tested ICGs can be considered to be reliable, but the use of the 6 most stable ICGs should be applied to yield a reliable normalization factor (NF). We compared the results of 3 target genes (CSN1S1, ESR1, and MYC) normalized using 6, 3, or 1 of the best ICGs. We did not observe overall differences between the 3 normalization strategies with the exception of 1 time point in MYC. The use of only a single ICG is not recommended; thus, we concluded that the calculation of the NF using the 3 best ICGs, MRPS15, RPS23, and UXT, is a reliable normalization strategy for RT-qPCR data obtained from yak mammary tissue during pregnancy and lactation. A dilution effect of the ICGs due to a large increase in the mRNA of abundantly expressed genes in bovine and porcine mammary tissue during the lactation cycle was previously observed. To test for the presence of a dilution effect in our study, we evaluated the pattern of non-normalized RT-qPCR data of ICGs from pregnancy to lactation and compared them with the total RNA concentration, milk yield, and non-normalized RT-qPCR data of 3 target genes. With a few exceptions, the non- normalized RT-qPCR data for the tested ICGs was significantly increased by lactation and had a positive correlation with total RNA and the non-normalized RT-qPCR data of CSN1S1. These data clearly indicated the presence of a “concentration effect” of single mRNA that remains unexplained but needs to be accounted for during the normalization of RT-qPCR data. Based on our findings, we recommend that the NF of the MRPS15, RPS23, and UXT genes should be used in the normalization of RT-qPCR data obtained from mammary tissue of lactating yaks during pregnancy and lactation.
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Affiliation(s)
- MingFeng Jiang
- College of Life Science and Technology, Southwest University for Nationalities, Chengdu, China
- * E-mail: (MFJ); (MB)
| | - Jung Nam Lee
- College of Life Science and Technology, Southwest University for Nationalities, Chengdu, China
- National Research Foundation of Korea, Seoul, Korea
| | - Massimo Bionaz
- College of Agricultural Sciences, Oregon State University, Oregon, United States of America
- * E-mail: (MFJ); (MB)
| | - Xiao Yu Deng
- College of Life Science and Technology, Southwest University for Nationalities, Chengdu, China
| | - Yong Wang
- Sichuan Key Laboratory of Conservation and Utilization of Animal Genetic Resources in Tibetan Plateau, Southwest University for Nationalities, Chengdu, China
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153
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Jatav P, Sodhi M, Sharma A, Mann S, Kishore A, Shandilya UK, Mohanty AK, Kataria RS, Yadav P, Verma P, Kumar S, Malakar D, Mukesh M. Identification of internal control genes in milk-derived mammary epithelial cells during lactation cycle of Indian zebu cow. Anim Sci J 2016; 87:344-53. [DOI: 10.1111/asj.12384] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2014] [Accepted: 12/11/2014] [Indexed: 12/29/2022]
Affiliation(s)
- Pradeep Jatav
- National Bureau of Animal Genetic Resources; Haryana India
| | - Monika Sodhi
- National Bureau of Animal Genetic Resources; Haryana India
| | - Ankita Sharma
- National Bureau of Animal Genetic Resources; Haryana India
| | - Sandeep Mann
- National Bureau of Animal Genetic Resources; Haryana India
| | - Amit Kishore
- National Bureau of Animal Genetic Resources; Haryana India
| | | | | | | | - Poonam Yadav
- National Bureau of Animal Genetic Resources; Haryana India
| | - Preeti Verma
- National Bureau of Animal Genetic Resources; Haryana India
| | | | | | - Manishi Mukesh
- National Bureau of Animal Genetic Resources; Haryana India
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154
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Abstract
One of the major challenges in plant molecular biology is to generate transgenic plants that express transgenes stably over generations. Here, we describe some routine methods to study transgene locus structure and to analyze transgene expression in plants: Southern hybridization using DIG chemiluminescent technology for characterization of transgenic locus, SYBR Green-based real-time RT-PCR to measure transgene transcript level, and protein immunoblot analysis to evaluate accumulation and stability of transgenic protein product in the target tissue.
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155
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Sudhakar Reddy P, Srinivas Reddy D, Sivasakthi K, Bhatnagar-Mathur P, Vadez V, Sharma KK. Evaluation of Sorghum [Sorghum bicolor (L.)] Reference Genes in Various Tissues and under Abiotic Stress Conditions for Quantitative Real-Time PCR Data Normalization. FRONTIERS IN PLANT SCIENCE 2016; 7:529. [PMID: 27200008 PMCID: PMC4843019 DOI: 10.3389/fpls.2016.00529] [Citation(s) in RCA: 79] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/20/2015] [Accepted: 04/04/2016] [Indexed: 05/20/2023]
Abstract
Accurate and reliable gene expression data from qPCR depends on stable reference gene expression for potential gene functional analyses. In this study, 15 reference genes were selected and analyzed in various sample sets including abiotic stress treatments (salt, cold, water stress, heat, and abscisic acid) and tissues (leaves, roots, seedlings, panicle, and mature seeds). Statistical tools, including geNorm, NormFinder and RefFinder, were utilized to assess the suitability of reference genes based on their stability rankings for various sample groups. For abiotic stress, PP2A and CYP were identified as the most stable genes. In contrast, EIF4α was the most stable in the tissue sample set, followed by PP2A; PP2A was the most stable in all the sample set, followed by EIF4α. GAPDH, and UBC1 were the least stably expressed in the tissue and all the sample sets. These results also indicated that the use of two candidate reference genes would be sufficient for the optimization of normalization studies. To further verify the suitability of these genes for use as reference genes, SbHSF5 and SbHSF13 gene expression levels were normalized using the most and least stable sorghum reference genes in root and water stressed-leaf tissues of five sorghum varieties. This is the first systematic study of the selection of the most stable reference genes for qPCR-related assays in Sorghum bicolor that will potentially benefit future gene expression studies in sorghum and other closely related species.
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156
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Dam V, Sikder T, Santosa S. From neutrophils to macrophages: differences in regional adipose tissue depots. Obes Rev 2016; 17:1-17. [PMID: 26667065 DOI: 10.1111/obr.12335] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/26/2015] [Revised: 09/01/2015] [Accepted: 09/23/2015] [Indexed: 12/27/2022]
Abstract
Currently, we do not fully understand the underlying mechanisms of how regional adiposity promotes metabolic dysregulation. As adipose tissue expands, there is an increase in chronic systemic low-grade inflammation due to greater infiltration of immune cells and production of cytokines. This chronic inflammation is thought to play a major role in the development of metabolic complications and disease such as insulin resistance and diabetes. We know that different adipose tissue depots contribute differently to the risk of metabolic disease. People who have an upper body fat distribution around the abdomen are at greater risk of disease than those who tend to store fat in their lower body around the hips and thighs. Thus, it is conceivable that adipose tissue depots contribute differently to the inflammatory milieu as a result of varied infiltration of immune cell types. In this review, we describe the role and function of major resident immune cells in the development of adipose tissue inflammation and discuss their regional differences in the context of metabolic disease risk. We find that although initial studies have found regional differences, a more comprehensive understanding of how immune cells interrupt adipose tissue homeostasis is needed.
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Affiliation(s)
- V Dam
- Department of Exercise Science, Concordia University, Montreal, QC, Canada.,Nutrition, Obesity, and Metabolism Lab, PERFORM Centre, Concordia University, Montreal, QC, Canada
| | - T Sikder
- Department of Exercise Science, Concordia University, Montreal, QC, Canada.,Nutrition, Obesity, and Metabolism Lab, PERFORM Centre, Concordia University, Montreal, QC, Canada
| | - S Santosa
- Department of Exercise Science, Concordia University, Montreal, QC, Canada.,Nutrition, Obesity, and Metabolism Lab, PERFORM Centre, Concordia University, Montreal, QC, Canada
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157
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Using Real-Time PCR as a tool for monitoring the authenticity of commercial coffees. Food Chem 2015; 199:433-8. [PMID: 26775992 DOI: 10.1016/j.foodchem.2015.12.045] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2014] [Revised: 09/12/2015] [Accepted: 12/09/2015] [Indexed: 11/23/2022]
Abstract
Coffee is one of the main food products commercialized in the world. Its considerable market value among food products makes it susceptible to adulteration, especially with cereals. Therefore, the objective of this study was to develop a method based on Real-Time Polymerase Chain Reaction (PCR) for detection of cereals in commercial ground roast and soluble coffees. After comparison with standard curves obtained by serial dilution of DNA extracted from barley, corn and rice, the method was sensitive and specific to quantify down to 0.6 pg, 14 pg and 16 pg of barley, corn and rice DNA, respectively. To verify the applicability of the method, 30 commercial samples obtained in different countries were evaluated and those classified as gourmets or superior did not present the tested cereals DNA. However, barley was detected in various traditional (cheaper) samples from South America. In addition, corn and rice were also detected in different samples. Real-Time PCR showed to be suitable for detection of food adulterants in commercial ground roast and soluble coffees.
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158
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Scientific Symposium “Small Solution for Big Water-Related Problems: Innovative Microarrays and Small Sensors to Cope with Water Quality and Food Security”. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2015. [PMCID: PMC4690928 DOI: 10.3390/ijerph121214992] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
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159
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Bejrowska A, Kudłak B, Owczarek K, Szczepańska N, Namieśnik J, Mazerska Z. New generation of analytical tests based on the assessment of enzymatic and nuclear receptor activity changes induced by environmental pollutants. Trends Analyt Chem 2015. [DOI: 10.1016/j.trac.2015.05.009] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
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160
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Javar S, Mohamed R, Sajap AS, Lau WH. Expression profiles of lysozyme- and prophenoloxidase-encoding genes inSpodopteraspecies challenged with entomopathogenic fungus,Metarhizium anisopliae(Metchnikoff) Sorokin using qRT-PCR. INVERTEBR REPROD DEV 2015. [DOI: 10.1080/07924259.2015.1108934] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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161
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Lopez AM, Chuang JC, Posey KS, Ohshiro T, Tomoda H, Rudel LL, Turley SD. PRD125, a potent and selective inhibitor of sterol O-acyltransferase 2 markedly reduces hepatic cholesteryl ester accumulation and improves liver function in lysosomal acid lipase-deficient mice. J Pharmacol Exp Ther 2015; 355:159-67. [PMID: 26283692 PMCID: PMC4613965 DOI: 10.1124/jpet.115.227207] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2015] [Accepted: 08/14/2015] [Indexed: 11/22/2022] Open
Abstract
In most organs, the bulk of cholesterol is unesterified, although nearly all possess a varying capability of esterifying cholesterol through the action of either sterol O-acyltransferase (SOAT) 1 or, in the case of hepatocytes and enterocytes, SOAT2. Esterified cholesterol (EC) carried in plasma lipoproteins is hydrolyzed by lysosomal acid lipase (LAL) when they are cleared from the circulation. Loss-of-function mutations in LIPA, the gene that encodes LAL, result in Wolman disease or cholesteryl ester storage disease (CESD). Hepatomegaly and a massive increase in tissue EC levels are hallmark features of both disorders. While these conditions can be corrected with enzyme replacement therapy, the question arose as to whether pharmacological inhibition of SOAT2 might reduce tissue EC accretion in CESD. When weaned at 21 days, Lal(-/-) mice, of either gender, had a whole liver cholesterol content that was 12- to 13-fold more than that of matching Lal(+/+) littermates (23 versus 1.8 mg, respectively). In Lal(-/-) males given the selective SOAT2 inhibitor PRD125 1,11-O-o-methylbenzylidene-7-O-p-cyanobenzoyl-1,7,11-trideacetylpyripyropene A in their diet (∼10 mg/day per kg body weight) from 21 to 53 days, whole liver cholesterol content was 48.6 versus 153.7 mg in untreated 53-day-old Lal(-/-) mice. This difference reflected a 59% reduction in hepatic EC concentration (mg/g), combined with a 28% fall in liver mass. The treated mice also showed a 63% reduction in plasma alanine aminotransferase activity, in parallel with decisive falls in hepatic mRNA expression levels for multiple proteins that reflect macrophage presence and inflammation. These data implicate SOAT2 as a potential target in CESD management.
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Affiliation(s)
- Adam M Lopez
- Department of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, Texas (A.M.L., J-C.C., K.S.P., S.D.T.); Graduate School of Pharmaceutical Science, Kitasato University, Tokyo, Japan (T.O., H.T.); and Department of Pathology, Wake Forest University School of Medicine, Winston-Salem, North Carolina (T.O., L.L.R.)
| | - Jen-Chieh Chuang
- Department of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, Texas (A.M.L., J-C.C., K.S.P., S.D.T.); Graduate School of Pharmaceutical Science, Kitasato University, Tokyo, Japan (T.O., H.T.); and Department of Pathology, Wake Forest University School of Medicine, Winston-Salem, North Carolina (T.O., L.L.R.)
| | - Kenneth S Posey
- Department of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, Texas (A.M.L., J-C.C., K.S.P., S.D.T.); Graduate School of Pharmaceutical Science, Kitasato University, Tokyo, Japan (T.O., H.T.); and Department of Pathology, Wake Forest University School of Medicine, Winston-Salem, North Carolina (T.O., L.L.R.)
| | - Taichi Ohshiro
- Department of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, Texas (A.M.L., J-C.C., K.S.P., S.D.T.); Graduate School of Pharmaceutical Science, Kitasato University, Tokyo, Japan (T.O., H.T.); and Department of Pathology, Wake Forest University School of Medicine, Winston-Salem, North Carolina (T.O., L.L.R.)
| | - Hiroshi Tomoda
- Department of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, Texas (A.M.L., J-C.C., K.S.P., S.D.T.); Graduate School of Pharmaceutical Science, Kitasato University, Tokyo, Japan (T.O., H.T.); and Department of Pathology, Wake Forest University School of Medicine, Winston-Salem, North Carolina (T.O., L.L.R.)
| | - Lawrence L Rudel
- Department of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, Texas (A.M.L., J-C.C., K.S.P., S.D.T.); Graduate School of Pharmaceutical Science, Kitasato University, Tokyo, Japan (T.O., H.T.); and Department of Pathology, Wake Forest University School of Medicine, Winston-Salem, North Carolina (T.O., L.L.R.)
| | - Stephen D Turley
- Department of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, Texas (A.M.L., J-C.C., K.S.P., S.D.T.); Graduate School of Pharmaceutical Science, Kitasato University, Tokyo, Japan (T.O., H.T.); and Department of Pathology, Wake Forest University School of Medicine, Winston-Salem, North Carolina (T.O., L.L.R.)
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162
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Caballero-Gallardo K, Guerrero-Castilla A, Johnson-Restrepo B, de la Rosa J, Olivero-Verbel J. Chemical and toxicological characterization of sediments along a Colombian shoreline impacted by coal export terminals. CHEMOSPHERE 2015; 138:837-46. [PMID: 26298075 DOI: 10.1016/j.chemosphere.2015.07.062] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/17/2015] [Revised: 07/20/2015] [Accepted: 07/21/2015] [Indexed: 05/18/2023]
Abstract
Extraction, transport and utilization of coal spread out coal dust. Nowadays, Colombia is an important producer of this mineral in South America, being the Santa Marta area one of the largest coal exporting ports in the country. The aim of this work was to assess the pollutants levels and toxicity of shoreline sediments from this place. 16 PAHs and 46 elements were measured in nine locations during dry and rainy seasons. HepG2 cells were exposed to 1% sediment extracts and mRNA expression evaluated for selected genes. PAHs levels were greater during the rainy season. The highest ∑PAHs (89.9 ng g(-1)) appeared at a site located around 300 m far from the coast line at close proximity to the area where coal is loaded into cargo vessels for international shipments, being naphthalene the most abundant PAH. At Santa Marta Bay port, ∑PAHs were 62.8 ng g(-1) and 72.8 ng g(-1) for dry and rainy seasons, respectively, with greatest levels for fluoranthene. Based on sediment standards, most stations have poor condition regarding Cr, but moderate contamination on Cu, Pb and Zn. Sediments from the port and coal transport sites, the most polluted by PAHs and metals, induced CYP1A1 and NQO1 during the dry season. Data showed the sediments from this shoreline have bioactive chemicals that determine their toxicological profile.
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Affiliation(s)
- Karina Caballero-Gallardo
- Environmental and Computational Chemistry Group, School of Pharmaceutical Sciences, Zaragocilla Campus, University of Cartagena, Cartagena 130015, Colombia
| | - Angelica Guerrero-Castilla
- Environmental and Computational Chemistry Group, School of Pharmaceutical Sciences, Zaragocilla Campus, University of Cartagena, Cartagena 130015, Colombia
| | - Boris Johnson-Restrepo
- Environmental Chemistry Research Group, School of Sciences, San Pablo Campus, University of Cartagena, Cartagena 130015, Colombia
| | - Jesus de la Rosa
- Associate Unit CSIC - University of Huelva "Atmospheric Pollution", Center for Research in Sustainable Chemistry (CIQSO), University of Huelva, E21071 Huelva, Spain
| | - Jesus Olivero-Verbel
- Environmental and Computational Chemistry Group, School of Pharmaceutical Sciences, Zaragocilla Campus, University of Cartagena, Cartagena 130015, Colombia.
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163
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Lund HS, Skogtun G, Sørum H, Eggertsdóttir AV. Absence of bacterial DNA in culture-negative urine from cats with and without lower urinary tract disease. J Feline Med Surg 2015; 17:909-14. [PMID: 25535211 PMCID: PMC11112191 DOI: 10.1177/1098612x14563098] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/10/2024]
Abstract
A diagnosis of bacterial cystitis commonly relies on a positive microbiological culture demonstrating the presence of a significant number of colony-forming units/ml urine, as urine within the upper urinary tract, bladder and proximal urethra generally is considered sterile. Recent studies from human and veterinary medicine indicate the presence of non-culturable bacteria in culture-negative urine samples. The aim of the present study was to determine the occurrence of bacterial DNA in culture-negative urine samples from cats with signs of feline lower urinary tract disease (FLUTD) and healthy control cats by 16S ribosomal DNA PCR and subsequent sequencing. The study sample included 38 culture-negative urine samples from cats with FLUTD and 43 culture-negative samples from control cats. Eight culture-positive urine samples from cats with FLUTD were included as external positive controls in addition to negative reaction controls. Of possible methodological limitations, degradation of DNA due to storage, the use of non-sedimented urine for DNA isolation and lack of internal positive reaction controls should be mentioned. The positive controls were recognised, but occurrence of bacterial DNA in culture-negative urine from cats with or without signs of lower urinary tract disease was not demonstrated. However, considering the possible methodological limitations, the presence of bacterial DNA in the urine of culture-negative FLUTD cats cannot be excluded based on the present results alone. Therefore, a prospective study reducing the possibility of degradation of DNA due to storage, in combination with modifications enhancing the chance of detecting even lower levels of bacterial DNA in culture-negative samples, seems warranted.
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Affiliation(s)
- Heidi Sjetne Lund
- Department of Companion Animal Clinical Sciences, Norwegian University of Life Sciences, Oslo, Norway
| | - Gaute Skogtun
- Department of Food Safety and Infection Biology, Norwegian University of Life Sciences, Oslo, Norway
| | - Henning Sørum
- Department of Food Safety and Infection Biology, Norwegian University of Life Sciences, Oslo, Norway
| | - Anna Vigdís Eggertsdóttir
- Department of Companion Animal Clinical Sciences, Norwegian University of Life Sciences, Oslo, Norway
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164
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Iser I, de Campos R, Bertoni A, Wink M. Identification of valid endogenous control genes for determining gene expression in C6 glioma cell line treated with conditioned medium from adipose-derived stem cell. Biomed Pharmacother 2015; 75:75-82. [DOI: 10.1016/j.biopha.2015.08.035] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2015] [Accepted: 08/23/2015] [Indexed: 12/12/2022] Open
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165
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Huang X, Gao Y, Jiang B, Zhou Z, Zhan A. Reference gene selection for quantitative gene expression studies during biological invasions: A test on multiple genes and tissues in a model ascidian Ciona savignyi. Gene 2015; 576:79-87. [PMID: 26428313 DOI: 10.1016/j.gene.2015.09.066] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2015] [Revised: 09/16/2015] [Accepted: 09/25/2015] [Indexed: 12/20/2022]
Abstract
As invasive species have successfully colonized a wide range of dramatically different local environments, they offer a good opportunity to study interactions between species and rapidly changing environments. Gene expression represents one of the primary and crucial mechanisms for rapid adaptation to local environments. Here, we aim to select reference genes for quantitative gene expression analysis based on quantitative Real-Time PCR (qRT-PCR) for a model invasive ascidian, Ciona savignyi. We analyzed the stability of ten candidate reference genes in three tissues (siphon, pharynx and intestine) under two key environmental stresses (temperature and salinity) in the marine realm based on three programs (geNorm, NormFinder and delta Ct method). Our results demonstrated only minor difference for stability rankings among the three methods. The use of different single reference gene might influence the data interpretation, while multiple reference genes could minimize possible errors. Therefore, reference gene combinations were recommended for different tissues - the optimal reference gene combination for siphon was RPS15 and RPL17 under temperature stress, and RPL17, UBQ and TubA under salinity treatment; for pharynx, TubB, TubA and RPL17 were the most stable genes under temperature stress, while TubB, TubA and UBQ were the best under salinity stress; for intestine, UBQ, RPS15 and RPL17 were the most reliable reference genes under both treatments. Our results suggest that the necessity of selection and test of reference genes for different tissues under varying environmental stresses. The results obtained here are expected to reveal mechanisms of gene expression-mediated invasion success using C. savignyi as a model species.
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Affiliation(s)
- Xuena Huang
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China
| | - Yangchun Gao
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China
| | - Bei Jiang
- Liaoning Key Lab of Marine Fishery Molecular Biology, Liaoning Ocean and Fishery Science Research Institute, Dalian, Liaoning, China
| | - Zunchun Zhou
- Liaoning Key Lab of Marine Fishery Molecular Biology, Liaoning Ocean and Fishery Science Research Institute, Dalian, Liaoning, China
| | - Aibin Zhan
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China.
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166
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Cava C, Bertoli G, Castiglioni I. Integrating genetics and epigenetics in breast cancer: biological insights, experimental, computational methods and therapeutic potential. BMC SYSTEMS BIOLOGY 2015; 9:62. [PMID: 26391647 PMCID: PMC4578257 DOI: 10.1186/s12918-015-0211-x] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/14/2015] [Accepted: 09/15/2015] [Indexed: 12/11/2022]
Abstract
BACKGROUND Development of human cancer can proceed through the accumulation of different genetic changes affecting the structure and function of the genome. Combined analyses of molecular data at multiple levels, such as DNA copy-number alteration, mRNA and miRNA expression, can clarify biological functions and pathways deregulated in cancer. The integrative methods that are used to investigate these data involve different fields, including biology, bioinformatics, and statistics. RESULTS These methodologies are presented in this review, and their implementation in breast cancer is discussed with a focus on integration strategies. We report current applications, recent studies and interesting results leading to the identification of candidate biomarkers for diagnosis, prognosis, and therapy in breast cancer by using both individual and combined analyses. CONCLUSION This review presents a state of art of the role of different technologies in breast cancer based on the integration of genetics and epigenetics, and shares some issues related to the new opportunities and challenges offered by the application of such integrative approaches.
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Affiliation(s)
- Claudia Cava
- Institute of Molecular Bioimaging and Physiology (IBFM), National Research Council (CNR), Milan, Italy.
| | - Gloria Bertoli
- Institute of Molecular Bioimaging and Physiology (IBFM), National Research Council (CNR), Milan, Italy.
| | - Isabella Castiglioni
- Institute of Molecular Bioimaging and Physiology (IBFM), National Research Council (CNR), Milan, Italy.
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167
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Jiang H, Qian Z, Lu W, Ding H, Yu H, Wang H, Li J. Identification and Characterization of Reference Genes for Normalizing Expression Data from Red Swamp Crawfish Procambarus clarkii. Int J Mol Sci 2015; 16:21591-605. [PMID: 26370979 PMCID: PMC4613269 DOI: 10.3390/ijms160921591] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2015] [Revised: 08/23/2015] [Accepted: 08/28/2015] [Indexed: 01/12/2023] Open
Abstract
qRT-PCR is a widely used technique for rapid and accurate quantification of gene expression data. The use of reference genes for normalization of the expression levels is crucial for accuracy. Several studies have shown that there is no perfect reference gene that is appropriate for use in all experimental conditions, and research on suitable reference genes in red swamp crawfish (Procambarus clarkii) is particularly scarce. In this study, eight commonly used crustacean reference genes were chosen from P. clarkii transcriptome data and investigated as potential candidates for normalization of qRT-PCR data. Expression of these genes under different experimental conditions was examined by qRT-PCR, and the stability of their expression was evaluated using three commonly used statistical algorithms, geNorm, NormFinder and BestKeeper. A final comprehensive ranking determined that EIF and 18S were the optimal reference genes for expression data from different tissues, while TBP and EIF were optimal for expression data from different ovarian developmental stages. To our knowledge, this is the first systematic analysis of reference genes for normalization of qRT-PCR data in P. clarkii. These results will facilitate more accurate and reliable expression studies of this and other crustacean species.
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Affiliation(s)
- Hucheng Jiang
- Key Laboratory of Freshwater Fishery Germplasm Resources, Ministry of Agriculture, Shanghai Ocean University, Shanghai 201306, China.
| | - Zhaojun Qian
- Key Laboratory of Freshwater Fishery Germplasm Resources, Ministry of Agriculture, Shanghai Ocean University, Shanghai 201306, China.
| | - Wei Lu
- Jiangsu Xuyi Riverred Crawfish Eco-Park Co., Ltd., Xuyi 211700, China.
| | - Huaiyu Ding
- Jiangsu Key Laboratory for Eco-Agricultural Biotechnoology Around Hongze Lake, Huaiyin Normal University, Huaian 223300, China.
| | - Hongwei Yu
- Jiangsu Xuyi Riverred Crawfish Eco-Park Co., Ltd., Xuyi 211700, China.
| | - Hui Wang
- Jiangsu Key Laboratory for Eco-Agricultural Biotechnoology Around Hongze Lake, Huaiyin Normal University, Huaian 223300, China.
| | - Jiale Li
- Key Laboratory of Freshwater Fishery Germplasm Resources, Ministry of Agriculture, Shanghai Ocean University, Shanghai 201306, China.
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168
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Kim YN, Kim KM, Choi HN, Lee JH, Park HS, Jang KY, Moon WS, Kang MJ, Lee DG, Chung MJ. Clinical Usefulness of PCR for Differential Diagnosis of Tuberculosis and Nontuberculous Mycobacterial Infection in Paraffin-Embedded Lung Tissues. J Mol Diagn 2015; 17:597-604. [DOI: 10.1016/j.jmoldx.2015.04.005] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2014] [Revised: 03/29/2015] [Accepted: 04/02/2015] [Indexed: 10/23/2022] Open
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169
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Luekasemsuk T, Panvisavas N, Chaturongakul S. TaqMan qPCR for detection and quantification of mitochondrial DNA from toxic pufferfish species. Toxicon 2015; 102:43-7. [DOI: 10.1016/j.toxicon.2015.05.016] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2015] [Revised: 05/23/2015] [Accepted: 05/26/2015] [Indexed: 12/20/2022]
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170
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Validation of candidate reference genes for qRT-PCR studies in symbiotic and non-symbiotic Casuarina glauca Sieb. ex Spreng. under salinity conditions. Symbiosis 2015. [DOI: 10.1007/s13199-015-0330-6] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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171
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Ramírez-Castillo FY, Loera-Muro A, Jacques M, Garneau P, Avelar-González FJ, Harel J, Guerrero-Barrera AL. Waterborne pathogens: detection methods and challenges. Pathogens 2015; 4:307-34. [PMID: 26011827 PMCID: PMC4493476 DOI: 10.3390/pathogens4020307] [Citation(s) in RCA: 209] [Impact Index Per Article: 20.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2015] [Revised: 05/08/2015] [Accepted: 05/13/2015] [Indexed: 12/13/2022] Open
Abstract
Waterborne pathogens and related diseases are a major public health concern worldwide, not only by the morbidity and mortality that they cause, but by the high cost that represents their prevention and treatment. These diseases are directly related to environmental deterioration and pollution. Despite the continued efforts to maintain water safety, waterborne outbreaks are still reported globally. Proper assessment of pathogens on water and water quality monitoring are key factors for decision-making regarding water distribution systems’ infrastructure, the choice of best water treatment and prevention waterborne outbreaks. Powerful, sensitive and reproducible diagnostic tools are developed to monitor pathogen contamination in water and be able to detect not only cultivable pathogens but also to detect the occurrence of viable but non-culturable microorganisms as well as the presence of pathogens on biofilms. Quantitative microbial risk assessment (QMRA) is a helpful tool to evaluate the scenarios for pathogen contamination that involve surveillance, detection methods, analysis and decision-making. This review aims to present a research outlook on waterborne outbreaks that have occurred in recent years. This review also focuses in the main molecular techniques for detection of waterborne pathogens and the use of QMRA approach to protect public health.
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Affiliation(s)
- Flor Yazmín Ramírez-Castillo
- Laboratorio de Biología Celular y Tisular, Departamento de Morfología, Centro de Ciencias Básicas, Universidad Autónoma de Aguascalientes, Aguascalientes, Aguascalientes 20131, Mexico.
- Laboratorio de Ciencias Ambientales, Departamento de Fisiología y Farmacología, Centro de Ciencias Básicas, Universidad Autónoma de Aguascalientes, Aguascalientes, Aguascalientes 20131, Mexico.
| | - Abraham Loera-Muro
- Laboratorio de Biología Celular y Tisular, Departamento de Morfología, Centro de Ciencias Básicas, Universidad Autónoma de Aguascalientes, Aguascalientes, Aguascalientes 20131, Mexico.
| | - Mario Jacques
- Centre de Recherche en Infectiologie Porcine et Avicole, Faculté de Médecine Vétérinaire, Université de Montréal, St-Hyacinthe, QC J2S 7C6, Canada.
| | - Philippe Garneau
- Centre de Recherche en Infectiologie Porcine et Avicole, Faculté de Médecine Vétérinaire, Université de Montréal, St-Hyacinthe, QC J2S 7C6, Canada.
| | - Francisco Javier Avelar-González
- Laboratorio de Ciencias Ambientales, Departamento de Fisiología y Farmacología, Centro de Ciencias Básicas, Universidad Autónoma de Aguascalientes, Aguascalientes, Aguascalientes 20131, Mexico.
| | - Josée Harel
- Centre de Recherche en Infectiologie Porcine et Avicole, Faculté de Médecine Vétérinaire, Université de Montréal, St-Hyacinthe, QC J2S 7C6, Canada.
| | - Alma Lilián Guerrero-Barrera
- Laboratorio de Biología Celular y Tisular, Departamento de Morfología, Centro de Ciencias Básicas, Universidad Autónoma de Aguascalientes, Aguascalientes, Aguascalientes 20131, Mexico.
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172
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Lal SV, Brahma B, Gohain M, Mohanta D, De BC, Chopra M, Dass G, Vats A, Upadhyay RC, Datta TK, De S. Splice variants and seasonal expression of buffalo HSF genes. Cell Stress Chaperones 2015; 20:545-54. [PMID: 25655489 PMCID: PMC4406941 DOI: 10.1007/s12192-014-0563-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2014] [Revised: 12/11/2014] [Accepted: 12/12/2014] [Indexed: 01/09/2023] Open
Abstract
In eukaryotes, the heat shock factors (HSFs) are recognized as the master regulator of the heat shock response. In this respect, the genes encoding the heat shock factors seem to be important for adaptation to thermal stress in organisms. Despite this, only few mammalian HSFs has been characterized. In this study, four major heat shock factor genes viz. HSF-1, 2, 4, and 5 were studied. The main objective of the present study was to characterize the cDNA encoding using conserved gene specific primers and to investigate the expression status of these buffalo HSF genes. Our RT-PCR analysis uncovered two distinct variants of buffalo HSF-1 and HSF-2 gene transcripts. In addition, we identified a variant of the HSF5 transcript in buffalo lacking a DNA-binding domain. In silico analysis of deduced amino acid sequences for buffalo HSF genes showed domain architecture similar to other mammalian species. Changes in the gene expression profile were noted by quantitative real-time PCR (qRT-PCR) analysis. We detected the transcript of buffalo HSF genes in different tissues. We also evaluated the seasonal changes in the expression of HSF genes. Interestingly, the transcript level of HSF-1 gene was found upregulated in months of high and low ambient temperatures. In contrast, the expression of the HSF-4 and 5 genes was found to be downregulated in months of high ambient temperature. This suggests that the intricate balance of different HSFs is adjusted to minimize the effect of seasonal changes in environmental conditions. These findings advance our understanding of the complex, context-dependent regulation of HSF gene expression under normal and stressful conditions.
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Affiliation(s)
- Shardul Vikram Lal
- />Animal Genomics Lab, Animal Biotechnology Centre, National Dairy Research Institute, Karnal, 132001 Haryana India
| | - Biswajit Brahma
- />Animal Genomics Lab, Animal Biotechnology Centre, National Dairy Research Institute, Karnal, 132001 Haryana India
| | - Moloya Gohain
- />Animal Genomics Lab, Animal Biotechnology Centre, National Dairy Research Institute, Karnal, 132001 Haryana India
| | - Debashish Mohanta
- />Animal Genomics Lab, Animal Biotechnology Centre, National Dairy Research Institute, Karnal, 132001 Haryana India
| | - Bidan Chandra De
- />Animal Genomics Lab, Animal Biotechnology Centre, National Dairy Research Institute, Karnal, 132001 Haryana India
| | - Meenu Chopra
- />Animal Genomics Lab, Animal Biotechnology Centre, National Dairy Research Institute, Karnal, 132001 Haryana India
| | - Gulshan Dass
- />Animal Genomics Lab, Animal Biotechnology Centre, National Dairy Research Institute, Karnal, 132001 Haryana India
| | - Ashutosh Vats
- />Animal Genomics Lab, Animal Biotechnology Centre, National Dairy Research Institute, Karnal, 132001 Haryana India
| | | | - T. K. Datta
- />Animal Genomics Lab, Animal Biotechnology Centre, National Dairy Research Institute, Karnal, 132001 Haryana India
| | - Sachinandan De
- />Animal Genomics Lab, Animal Biotechnology Centre, National Dairy Research Institute, Karnal, 132001 Haryana India
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173
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Azizishirazi A, Dew WA, Bougas B, Bernatchez L, Pyle GG. Dietary sodium protects fish against copper-induced olfactory impairment. AQUATIC TOXICOLOGY (AMSTERDAM, NETHERLANDS) 2015; 161:1-9. [PMID: 25646894 DOI: 10.1016/j.aquatox.2015.01.017] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/21/2014] [Revised: 01/19/2015] [Accepted: 01/21/2015] [Indexed: 06/04/2023]
Abstract
Exposure to low concentrations of copper impairs olfaction in fish. To determine the transcriptional changes in the olfactory epithelium induced by copper exposure, wild yellow perch (Perca flavescens) were exposed to 20 μg/L of copper for 3 and 24h. A novel yellow perch microarray with 1000 candidate genes was used to measure differential gene transcription in the olfactory epithelium. While three hours of exposure to copper changed the transcription of only one gene, the transcriptions of 70 genes were changed after 24h of exposure to copper. Real-time PCR was utilized to determine the effect of exposure duration on two specific genes of interest, two sub-units of Na/K-ATPase. At 24 and 48 h, Na/K-ATPase transcription was down-regulated by copper at olfactory rosettes. As copper-induced impairment of Na/K-ATPase activity in gills can be ameliorated by increased dietary sodium, rainbow trout (Oncorhynchus mykiss) were used to determine if elevated dietary sodium was also protective against copper-induced olfactory impairment. Measurement of the olfactory response of rainbow trout using electro-olfactography demonstrated that sodium was protective of copper-induced olfactory dysfunction. This work demonstrates that the transcriptions of both subunits of Na/K-ATPase in the olfactory epithelium of fish are affected by Cu exposure, and that dietary Na protects against Cu-induced olfactory dysfunction.
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Affiliation(s)
- Ali Azizishirazi
- Department of Biology, Lakehead University, Thunder Bay, Ontario P7B 5E1, Canada
| | - William A Dew
- Department of Biology, Brandon University, Brandon, Manitoba R7A 6A9, Canada; Department of Biological Sciences, University of Lethbridge, Lethbridge, Alberta T1K 3M4, Canada
| | - Berenice Bougas
- Institut National de la Recherche Scientifique, Centre INRS Eau Terre et Environnement, 490, rue de la Couronne, Québec City, Québec G1K 9A9, Canada
| | - Louis Bernatchez
- Département de biologie, Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec City, Québec G1V 0A6, Canada
| | - Greg G Pyle
- Department of Biology, Lakehead University, Thunder Bay, Ontario P7B 5E1, Canada; Department of Biological Sciences, University of Lethbridge, Lethbridge, Alberta T1K 3M4, Canada.
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174
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Cloning and validation of reference genes for normalization of gene expression studies in pearl millet [Pennisetum glaucum (L.) R. Br.] by quantitative real-time PCR. ACTA ACUST UNITED AC 2015. [DOI: 10.1016/j.plgene.2015.02.001] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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175
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Ndlovu T, Le Roux M, Khan W, Khan S. Co-detection of virulent Escherichia coli genes in surface water sources. PLoS One 2015; 10:e0116808. [PMID: 25659126 PMCID: PMC4320055 DOI: 10.1371/journal.pone.0116808] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2014] [Accepted: 12/15/2014] [Indexed: 11/28/2022] Open
Abstract
McNemar’s test and the Pearson Chi-square were used to assess the co-detection and observed frequency, respectively, for potentially virulent E. coli genes in river water. Conventional multiplex Polymerase Chain Reaction (PCR) assays confirmed the presence of the aggR gene (69%), ipaH gene (23%) and the stx gene (15%) carried by Enteroaggregative E. coli (EAEC), Enteroinvasive E. coli (EIEC) and Enterohermorrhagic E. coli (EHEC), respectively, in river water samples collected from the Berg River (Paarl, South Africa). Only the aggR gene was present in 23% of samples collected from the Plankenburg River system (Stellenbosch, South Africa). In a comparative study, real-time multiplex PCR assays confirmed the presence of aggR (EAEC) in 69%, stx (EHEC) in 15%, ipaH (EIEC) in 31% and eae (EPEC) in 8% of the river water samples collected from the Berg River. In the Plankenburg River, aggR (EAEC) was detected in 46% of the samples, while eae (EPEC) was present in 15% of the water samples analyzed using real-time multiplex PCR in the Plankenburg River. Pearson Chi-square showed that there was no statistical difference (p > 0.05) between the conventional and real-time multiplex PCRs for the detection of virulent E. coli genes in water samples. However, the McNemar’s test showed some variation in the co-detection of virulent E. coli genes, for example, there was no statistical difference in the misclassification of the discordant results for stx versus ipaH, which implies that the ipaH gene was frequently detected with the stx gene. This study thus highlights the presence of virulent E. coli genes in river water and while early detection is crucial, quantitative microbial risk analysis has to be performed to identify and estimate the risk to human health.
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Affiliation(s)
- Thando Ndlovu
- Department of Biomedical Sciences, Faculty of Health and Wellness Sciences, Cape Peninsula University of Technology, PO Box 1906, Bellville, 7535, South Africa
| | - Marcellous Le Roux
- Department of Biomedical Sciences, Faculty of Health and Wellness Sciences, Cape Peninsula University of Technology, PO Box 1906, Bellville, 7535, South Africa
| | - Wesaal Khan
- Department of Microbiology, Faculty of Science, Stellenbosch University, Private Bag X1, Stellenbosch, 7602, South Africa
| | - Sehaam Khan
- Department of Biomedical Sciences, Faculty of Health and Wellness Sciences, Cape Peninsula University of Technology, PO Box 1906, Bellville, 7535, South Africa
- * E-mail:
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176
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Laurie MT, Bertout JA, Taylor SD, Burton JN, Shendure JA, Bielas JH. Simultaneous digital quantification and fluorescence-based size characterization of massively parallel sequencing libraries. Biotechniques 2015; 55:61-7. [PMID: 23931593 DOI: 10.2144/000114063] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2013] [Accepted: 07/01/2013] [Indexed: 12/12/2022] Open
Abstract
Due to the high cost of failed runs and suboptimal data yields, quantification and determination of fragment size range are crucial steps in the library preparation process for massively parallel sequencing (or next-generation sequencing). Current library quality control methods commonly involve quantification using real-time quantitative PCR and size determination using gel or capillary electrophoresis. These methods are laborious and subject to a number of significant limitations that can make library calibration unreliable. Herein, we propose and test an alternative method for quality control of sequencing libraries using droplet digital PCR (ddPCR). By exploiting a correlation we have discovered between droplet fluorescence and amplicon size, we achieve the joint quantification and size determination of target DNA with a single ddPCR assay. We demonstrate the accuracy and precision of applying this method to the preparation of sequencing libraries.
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Affiliation(s)
- Matthew T Laurie
- Translational Research Program, Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
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177
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Dogi CA, Pellegrino M, Poloni V, Poloni L, Pereyra CM, Sanabria A, Pianzzola MJ, Dalcero A, Cavaglieri L. Efficacy of corn silage inoculants on the fermentation quality under farm conditions and their influence onAspergillus parasitucus, A. flavus and A. fumigatusdetermined by q-PCR. Food Addit Contam Part A Chem Anal Control Expo Risk Assess 2015; 32:229-35. [DOI: 10.1080/19440049.2014.986223] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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178
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Unamba CIN, Nag A, Sharma RK. Next Generation Sequencing Technologies: The Doorway to the Unexplored Genomics of Non-Model Plants. FRONTIERS IN PLANT SCIENCE 2015; 6:1074. [PMID: 26734016 PMCID: PMC4679907 DOI: 10.3389/fpls.2015.01074] [Citation(s) in RCA: 98] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/06/2015] [Accepted: 11/16/2015] [Indexed: 05/04/2023]
Abstract
Non-model plants i.e., the species which have one or all of the characters such as long life cycle, difficulty to grow in the laboratory or poor fecundity, have been schemed out of sequencing projects earlier, due to high running cost of Sanger sequencing. Consequently, the information about their genomics and key biological processes are inadequate. However, the advent of fast and cost effective next generation sequencing (NGS) platforms in the recent past has enabled the unearthing of certain characteristic gene structures unique to these species. It has also aided in gaining insight about mechanisms underlying processes of gene expression and secondary metabolism as well as facilitated development of genomic resources for diversity characterization, evolutionary analysis and marker assisted breeding even without prior availability of genomic sequence information. In this review we explore how different Next Gen Sequencing platforms, as well as recent advances in NGS based high throughput genotyping technologies are rewarding efforts on de-novo whole genome/transcriptome sequencing, development of genome wide sequence based markers resources for improvement of non-model crops that are less costly than phenotyping.
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Affiliation(s)
- Chibuikem I. N. Unamba
- Biotechnology Division, CSIR-Institute of Himalayan Bioresource TechnologyPalampur, India
- Department of Plant Science and Biotechnology, Imo State UniversityOwerri, Nigeria
| | - Akshay Nag
- Biotechnology Division, CSIR-Institute of Himalayan Bioresource TechnologyPalampur, India
| | - Ram K. Sharma
- Biotechnology Division, CSIR-Institute of Himalayan Bioresource TechnologyPalampur, India
- *Correspondence: Ram K. Sharma ;
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179
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Huang S, Xu Y, Yan X, Shang Y, Zhu P, Tian W, Xu W. Development and application of a quantitative loop-mediated isothermal amplification method for detecting genetically modified maize MON863. JOURNAL OF THE SCIENCE OF FOOD AND AGRICULTURE 2015; 95:253-259. [PMID: 24771525 DOI: 10.1002/jsfa.6707] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/13/2013] [Revised: 03/04/2014] [Accepted: 04/20/2014] [Indexed: 06/03/2023]
Abstract
BACKGROUND A SYBR Green I-based quantitative loop-mediated isothermal amplification (LAMP) assay was developed for the rapid detection of genetically modified maize MON863. A set of primers was designed based on the integration region of the Cry3Bb1 and tahsp17 genes. RESULTS The qualitative and quantitative reaction conditions (dNTPs, betaine, primers, Mg(2+), Bst polymerase, temperature, reaction time) were optimized. The concentrations of Mg(2+) and betaine were found to be important to the LAMP assay. The detection limits of both qualitative and quantitative LAMP for MON863 were as low as 4 haploid genomic DNA, and the LAMP reactions can be completed within 1 h at an isothermal temperature of 65 °C. CONCLUSION The results of this study demonstrate that this new SYBR Green I-based quantitative LAMP assay system is reliable, sensitive and accurate.
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Affiliation(s)
- Sicong Huang
- High School attached to Tsinghua University, Beijing, 100084, China
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180
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The Lactobacillus plantarum Eno A1 Enolase Is Involved in Immunostimulation of Caco-2 Cells and in Biofilm Development. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2015; 897:33-44. [PMID: 26577529 DOI: 10.1007/5584_2015_5009] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
The role of probiotics in prevention and treatment of a variety of diseases is now well assessed. The presence of adhesive molecules on the cell surface of probiotics has been related to the ability to confer health benefit to the host. We have previously shown that the enolase EnoA1 of Lactobacillus plantarum, one of the most predominant species in the gut microbiota of healthy individuals, is cell surface-expressed and is involved in binding with human fibronectin and plasminogen. By means of comparative analysis between L. plantarum LM3 (wild type) and its isogenic LM3-CC1 (ΔenoA1) mutant strain, here we show that EnoA1 affects the ability of this bacterium to modulate immune response as determined by analysis of expression of immune system molecules in Caco-2 cells. Indeed, we observed induction of TLR2 expression in cells exposed to L. plantarum LM3, while no induction was detectable in cells exposed to LM3-CC1. This difference was much less consistent when expression of TLR4 was determined in cells exposed to the two strains. Pro-inflammatory (IL-6) and anti-inflammatory cytokines (IL-10, TGF-β), and the antimicrobial peptide HBD-2 were induced in Caco-2 cells exposed to L. plantarum LM3, while lower levels of induction were detected in cells exposed to LM3-CC1. We also analyzed the ability to develop biofilm of the two strains, and observed a decrease of about 65 % in the development of mature biofilm in LM3-CC1 compared to the wild type.
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181
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Mascelli S. A reliable assay for rapidly defining transplacental metastasis using quantitative PCR. Methods Mol Biol 2014; 1160:125-31. [PMID: 24740227 DOI: 10.1007/978-1-4939-0733-5_12] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
To choose the most appropriate treatment for children affected by a transplacental metastasis, it is crucial to ascertain the maternal origin of the tumor. Up-to-date conclusive diagnosis is generally achieved through fluorescence in situ hybridization or karyotyping analysis. Herein, we report an alternative, reliable assay for rapidly defining vertical cancer transmission to the fetus by using quantitative polymerase chain reaction. Our assay indicates that quantification of the copy number of the sex chromosomes by specific short tandem repeats markers, in genomic DNA purified from the tumor biopsy cells, could be used to correctly evaluate transplacental metastasis events.
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Affiliation(s)
- Samantha Mascelli
- UOC Neurochirurgia, Istituto Giannina Gaslini, VIA G. Gaslini 5, Genova, 16147, Italy,
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182
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Luo J, Vogel RF, Niessen L. Rapid detection of aflatoxin producing fungi in food by real-time quantitative loop-mediated isothermal amplification. Food Microbiol 2014; 44:142-8. [DOI: 10.1016/j.fm.2014.06.004] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2013] [Revised: 04/10/2014] [Accepted: 06/06/2014] [Indexed: 11/30/2022]
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183
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Yu L, Chen H, Sun J, Li L. PtrKOR1 is required for secondary cell wall cellulose biosynthesis in Populus. TREE PHYSIOLOGY 2014; 34:1289-300. [PMID: 24728296 DOI: 10.1093/treephys/tpu020] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/19/2023]
Abstract
KORRIGAN (KOR), encoding an endo-1,4-β-glucanase, plays a critical role in the cellulose synthesis of plant cell wall formation. KOR sequence orthologs are duplicated in the Populus genome relative to Arabidopsis. This study reports an expression analysis of the KOR genes in Populus. The five PtrKOR genes displayed different expression patterns, suggesting that they play roles in different developmental processes. Through RNAi suppression, results demonstrated that PtrKOR1 is required for secondary cell wall cellulose formation in Populus. Together, the results suggest that the PtrKOR genes may play distinct roles in association with cell wall formation in different tissues.
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Affiliation(s)
- Liangliang Yu
- National Key Laboratory of Plant Molecular Genetics/CAS Key Laboratory of Synthetic Biology, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 300 Fenglin Road, Shanghai 200032, China
| | - Hongpeng Chen
- National Key Laboratory of Plant Molecular Genetics/CAS Key Laboratory of Synthetic Biology, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 300 Fenglin Road, Shanghai 200032, China Present address: China Eucalyptus Research Center, 30 Middle Renmin Ave, Zhanjiang, Guangdong 524022, China
| | - Jiayan Sun
- National Key Laboratory of Plant Molecular Genetics/CAS Key Laboratory of Synthetic Biology, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 300 Fenglin Road, Shanghai 200032, China
| | - Laigeng Li
- National Key Laboratory of Plant Molecular Genetics/CAS Key Laboratory of Synthetic Biology, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 300 Fenglin Road, Shanghai 200032, China
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184
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Guerrero-Castilla A, Olivero-Verbel J. Altered gene expression in HepG2 cells exposed to a methanolic coal dust extract. ENVIRONMENTAL TOXICOLOGY AND PHARMACOLOGY 2014; 38:742-750. [PMID: 25305735 DOI: 10.1016/j.etap.2014.09.003] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/16/2014] [Revised: 09/01/2014] [Accepted: 09/03/2014] [Indexed: 06/04/2023]
Abstract
Exposure to coal dust has been associated with different chronic diseases and mortality risk. This airborne pollutant is produced during coal mining and transport activities, generating environmental and human toxicity. The aim of this study was to determine the effects of a coal dust methanolic extract on HepG2, a human liver hepatocellular carcinoma cell line. Cells were exposed to 5-100ppm methanolic coal extract for 12h, using DMSO as control. MTT and comet assays were used for the evaluation of cytotoxicity and genotoxicity, respectively. Real time PCR was utilized to quantify relative expression of genes related to oxidative stress, xenobiotic metabolism and DNA damage. Coal extract concentrations did not induce significant changes in HepG2 cell viability after 12h exposure; however, 50 and 100ppm of the coal extract produced a significant increase in genetic damage index with respect to negative control. Compared to vehicle control, mRNA CYP1A1 (up to 163-fold), NQO1 (up to 4.7-fold), and GADD45B (up to 4.7-fold) were up regulated, whereas PRDX1, SOD, CAT, GPX1, XPA, ERCC1 and APEX1 remained unaltered. This expression profile suggests that cells exposed to coal dust extract shows aryl hydrocarbon receptor-mediated alterations, changes in cellular oxidative status, and genotoxic effects. These findings share some similarities with those observed in liver of mice captured near coal mining areas, and add evidence that living around these industrial operations may be negatively impacting the biota and human health.
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Affiliation(s)
- Angelica Guerrero-Castilla
- Environmental and Computational Chemistry Group, School of Pharmaceutical Sciences, University of Cartagena, Cartagena, Colombia
| | - Jesus Olivero-Verbel
- Environmental and Computational Chemistry Group, School of Pharmaceutical Sciences, University of Cartagena, Cartagena, Colombia.
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185
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Liu YK, Li HP, Huang T, Cheng W, Gao CS, Zuo DY, Zhao ZX, Liao YC. Wheat-specific gene, ribosomal protein l21, used as the endogenous reference gene for qualitative and real-time quantitative polymerase chain reaction detection of transgenes. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2014; 62:10405-10413. [PMID: 25325387 DOI: 10.1021/jf503559b] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Wheat-specific ribosomal protein L21 (RPL21) is an endogenous reference gene suitable for genetically modified (GM) wheat identification. This taxon-specific RPL21 sequence displayed high homogeneity in different wheat varieties. Southern blots revealed 1 or 3 copies, and sequence analyses showed one amplicon in common wheat. Combined analyses with sequences from common wheat (AABBDD) and three diploid ancestral species, Triticum urartu (AA), Aegilops speltoides (BB), and Aegilops tauschii (DD), demonstrated the presence of this amplicon in the AA genome. Using conventional qualitative polymerase chain reaction (PCR), the limit of detection was 2 copies of wheat haploid genome per reaction. In the quantitative real-time PCR assay, limits of detection and quantification were about 2 and 8 haploid genome copies, respectively, the latter of which is 2.5-4-fold lower than other reported wheat endogenous reference genes. Construct-specific PCR assays were developed using RPL21 as an endogenous reference gene, and as little as 0.5% of GM wheat contents containing Arabidopsis NPR1 were properly quantified.
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Affiliation(s)
- Yi-Ke Liu
- Molecular Biotechnology Laboratory of Triticeae Crops, ‡College of Life Science and Technology, §College of Plant Science and Technology, and ∥National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University , Wuhan, Hubei 430070, People's Republic of China
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186
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Hindra, Huang T, Yang D, Rudolf JD, Xie P, Xie G, Teng Q, Lohman J, Zhu X, Huang Y, Zhao LX, Jiang Y, Duan Y, Shen B. Strain prioritization for natural product discovery by a high-throughput real-time PCR method. JOURNAL OF NATURAL PRODUCTS 2014; 77:2296-2303. [PMID: 25238028 PMCID: PMC4208669 DOI: 10.1021/np5006168] [Citation(s) in RCA: 65] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/01/2014] [Indexed: 08/31/2023]
Abstract
Natural products offer unmatched chemical and structural diversity compared to other small-molecule libraries, but traditional natural product discovery programs are not sustainable, demanding too much time, effort, and resources. Here we report a strain prioritization method for natural product discovery. Central to the method is the application of real-time PCR, targeting genes characteristic to the biosynthetic machinery of natural products with distinct scaffolds in a high-throughput format. The practicality and effectiveness of the method were showcased by prioritizing 1911 actinomycete strains for diterpenoid discovery. A total of 488 potential diterpenoid producers were identified, among which six were confirmed as platensimycin and platencin dual producers and one as a viguiepinol and oxaloterpin producer. While the method as described is most appropriate to prioritize strains for discovering specific natural products, variations of this method should be applicable to the discovery of other classes of natural products. Applications of genome sequencing and genome mining to the high-priority strains could essentially eliminate the chance elements from traditional discovery programs and fundamentally change how natural products are discovered.
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Affiliation(s)
- Hindra
- Department of Chemistry, Department of Molecular Therapeutics, and Natural Products Library
Initiative, The Scripps Research Institute, Jupiter, Florida 33458, United States
| | - Tingting Huang
- Department of Chemistry, Department of Molecular Therapeutics, and Natural Products Library
Initiative, The Scripps Research Institute, Jupiter, Florida 33458, United States
| | - Dong Yang
- Department of Chemistry, Department of Molecular Therapeutics, and Natural Products Library
Initiative, The Scripps Research Institute, Jupiter, Florida 33458, United States
| | - Jeffrey D. Rudolf
- Department of Chemistry, Department of Molecular Therapeutics, and Natural Products Library
Initiative, The Scripps Research Institute, Jupiter, Florida 33458, United States
| | - Pengfei Xie
- Department of Chemistry, Department of Molecular Therapeutics, and Natural Products Library
Initiative, The Scripps Research Institute, Jupiter, Florida 33458, United States
| | - Guangbo Xie
- Department of Chemistry, Department of Molecular Therapeutics, and Natural Products Library
Initiative, The Scripps Research Institute, Jupiter, Florida 33458, United States
| | - Qihui Teng
- Department of Chemistry, Department of Molecular Therapeutics, and Natural Products Library
Initiative, The Scripps Research Institute, Jupiter, Florida 33458, United States
| | - Jeremy
R. Lohman
- Department of Chemistry, Department of Molecular Therapeutics, and Natural Products Library
Initiative, The Scripps Research Institute, Jupiter, Florida 33458, United States
| | - Xiangcheng Zhu
- Xiangya
International Academy of Translational Medicine, Central South University, Changsha, Hunan 410013, People’s Republic of China
- Hunan
Engineering Research Center of Combinatorial Biosynthesis and Natural
Product Drug Discovery, Changsha, Hunan 410329, People’s Republic of China
| | - Yong Huang
- Xiangya
International Academy of Translational Medicine, Central South University, Changsha, Hunan 410013, People’s Republic of China
| | - Li-Xing Zhao
- Yunnan
Institute of Microbiology, Yunnan University, Kunming, Yunnan 650091, People’s Republic
of China
| | - Yi Jiang
- Yunnan
Institute of Microbiology, Yunnan University, Kunming, Yunnan 650091, People’s Republic
of China
| | - Yanwen Duan
- Xiangya
International Academy of Translational Medicine, Central South University, Changsha, Hunan 410013, People’s Republic of China
- Hunan
Engineering Research Center of Combinatorial Biosynthesis and Natural
Product Drug Discovery, Changsha, Hunan 410329, People’s Republic of China
| | - Ben Shen
- Department of Chemistry, Department of Molecular Therapeutics, and Natural Products Library
Initiative, The Scripps Research Institute, Jupiter, Florida 33458, United States
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187
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Navarro E, Serrano-Heras G, Castaño MJ, Solera J. Real-time PCR detection chemistry. Clin Chim Acta 2014; 439:231-50. [PMID: 25451956 DOI: 10.1016/j.cca.2014.10.017] [Citation(s) in RCA: 244] [Impact Index Per Article: 22.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2014] [Revised: 10/09/2014] [Accepted: 10/11/2014] [Indexed: 12/28/2022]
Abstract
Real-time PCR is the method of choice in many laboratories for diagnostic and food applications. This technology merges the polymerase chain reaction chemistry with the use of fluorescent reporter molecules in order to monitor the production of amplification products during each cycle of the PCR reaction. Thus, the combination of excellent sensitivity and specificity, reproducible data, low contamination risk and reduced hand-on time, which make it a post-PCR analysis unnecessary, has made real-time PCR technology an appealing alternative to conventional PCR. The present paper attempts to provide a rigorous overview of fluorescent-based methods for nucleic acid analysis in real-time PCR described in the literature so far. Herein, different real-time PCR chemistries have been classified into two main groups; the first group comprises double-stranded DNA intercalating molecules, such as SYBR Green I and EvaGreen, whereas the second includes fluorophore-labeled oligonucleotides. The latter, in turn, has been divided into three subgroups according to the type of fluorescent molecules used in the PCR reaction: (i) primer-probes (Scorpions, Amplifluor, LUX, Cyclicons, Angler); (ii) probes; hydrolysis (TaqMan, MGB-TaqMan, Snake assay) and hybridization (Hybprobe or FRET, Molecular Beacons, HyBeacon, MGB-Pleiades, MGB-Eclipse, ResonSense, Yin-Yang or displacing); and (iii) analogues of nucleic acids (PNA, LNA, ZNA, non-natural bases: Plexor primer, Tiny-Molecular Beacon). In addition, structures, mechanisms of action, advantages and applications of such real-time PCR probes and analogues are depicted in this review.
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Affiliation(s)
- E Navarro
- Research Unit, General University Hospital, Laurel s/n, 02006 Albacete, Spain.
| | - G Serrano-Heras
- Research Unit, General University Hospital, Laurel s/n, 02006 Albacete, Spain.
| | - M J Castaño
- Research Unit, General University Hospital, Laurel s/n, 02006 Albacete, Spain.
| | - J Solera
- Internal Medicine Department, General University Hospital, Hermanos Falcó 37, 02006 Albacete, Spain.
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188
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Aqul A, Lopez AM, Posey KS, Taylor AM, Repa JJ, Burns DK, Turley SD. Hepatic entrapment of esterified cholesterol drives continual expansion of whole body sterol pool in lysosomal acid lipase-deficient mice. Am J Physiol Gastrointest Liver Physiol 2014; 307:G836-47. [PMID: 25147230 PMCID: PMC4200320 DOI: 10.1152/ajpgi.00243.2014] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
Cholesteryl ester storage disease (CESD) results from loss-of-function mutations in LIPA, the gene that encodes lysosomal acid lipase (LAL). Hepatomegaly and deposition of esterified cholesterol (EC) in multiple organs ensue. The present studies quantitated rates of synthesis, absorption, and disposition of cholesterol, and whole body cholesterol pool size in a mouse model of CESD. In 50-day-old lal(-/-) and matching lal(+/+) mice fed a low-cholesterol diet, whole animal cholesterol content equalled 210 and 50 mg, respectively, indicating that since birth the lal(-/-) mice sequestered cholesterol at an average rate of 3.2 mg·day(-1)·animal(-1). The proportion of the body sterol pool contained in the liver of the lal(-/-) mice was 64 vs. 6.3% in their lal(+/+) controls. EC concentrations in the liver, spleen, small intestine, and lungs of the lal(-/-) mice were elevated 100-, 35-, 15-, and 6-fold, respectively. In the lal(-/-) mice, whole liver cholesterol synthesis increased 10.2-fold, resulting in a 3.2-fold greater rate of whole animal sterol synthesis compared with their lal(+/+) controls. The rate of cholesterol synthesis in the lal(-/-) mice exceeded that in the lal(+/+) controls by 3.7 mg·day(-1)·animal(-1). Fractional cholesterol absorption and fecal bile acid excretion were unchanged in the lal(-/-) mice, but their rate of neutral sterol excretion was 59% higher than in their lal(+/+) controls. Thus, in this model, the continual expansion of the body sterol pool is driven by the synthesis of excess cholesterol, primarily in the liver. Despite the severity of their disease, the median life span of the lal(-/-) mice was 355 days.
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Affiliation(s)
- Amal Aqul
- 2Department of Pediatrics, University of Texas Southwestern Medical Center, Dallas, Texas;
| | - Adam M. Lopez
- 1Department of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, Texas;
| | - Kenneth S. Posey
- 1Department of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, Texas;
| | - Anna M. Taylor
- 3Department of Physiology, University of Texas Southwestern Medical Center, Dallas, Texas; and
| | - Joyce J. Repa
- 1Department of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, Texas; ,3Department of Physiology, University of Texas Southwestern Medical Center, Dallas, Texas; and
| | - Dennis K. Burns
- 4Department of Pathology, University of Texas Southwestern Medical Center, Dallas, Texas
| | - Stephen D. Turley
- 1Department of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, Texas;
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189
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Karam M, Bièche I, Legay C, Vacher S, Auclair C, Ricort JM. Protein kinase D1 regulates ERα-positive breast cancer cell growth response to 17β-estradiol and contributes to poor prognosis in patients. J Cell Mol Med 2014; 18:2536-52. [PMID: 25287328 PMCID: PMC4302658 DOI: 10.1111/jcmm.12322] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2013] [Accepted: 04/07/2014] [Indexed: 12/21/2022] Open
Abstract
About 70% of human breast cancers express and are dependent for growth on estrogen receptor α (ERα), and therefore are sensitive to antiestrogen therapies. However, progression to an advanced, more aggressive phenotype is associated with acquisition of resistance to antiestrogens and/or invasive potential. In this study, we highlight the role of the serine/threonine-protein kinase D1 (PKD1) in ERα-positive breast cancers. Growth of ERα-positive MCF-7 and MDA-MB-415 human breast cancer cells was assayed in adherent or anchorage-independent conditions in cells overexpressing or depleted for PKD1. PKD1 induces cell growth through both an ERα-dependent manner, by increasing ERα expression and cell sensitivity to 17β-estradiol, and an ERα-independent manner, by reducing cell dependence to estrogens and conferring partial resistance to antiestrogen ICI 182,780. PKD1 knockdown in MDA-MB-415 cells strongly reduced estrogen-dependent and independent invasion. Quantification of PKD1 mRNA levels in 38 cancerous and non-cancerous breast cell lines and in 152 ERα-positive breast tumours from patients treated with adjuvant tamoxifen showed an association between PKD1 and ERα expression in 76.3% (29/38) of the breast cell lines tested and a strong correlation between PKD1 expression and invasiveness (P < 0.0001). In tamoxifen-treated patients, tumours with high PKD1 mRNA levels (n = 77, 50.66%) were significantly associated with less metastasis-free survival than tumours with low PKD1 mRNA expression (n = 75, 49.34%; P = 0.031). Moreover, PKD1 mRNA levels are strongly positively associated with EGFR and vimentin levels (P < 0.0000001). Thus, our study defines PKD1 as a novel attractive prognostic factor and a potential therapeutic target in breast cancer.
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Affiliation(s)
- Manale Karam
- Laboratoire de Biologie et de Pharmacologie Appliquée, UMR 8113 CNRS, Ecole Normale Supérieure de Cachan, Cachan, France
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190
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Preliminary investigation into the use of a real-time PCR method for the quantification of an oligonucleotide in human plasma and the development of novel acceptance criteria. Bioanalysis 2014; 6:127-36. [PMID: 24423591 DOI: 10.4155/bio.13.284] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
BACKGROUND The aim of the work was to evaluate the sensitivity and reproducibility of real-time reverse transcriptase PCR for quantitative analysis of an oligonucleotide in a biological matrix. A novel approach for the identification of outliers when assessing the suitability of calibration standards and QC samples is investigated. RESULTS A suitable assay was established for the determination of the oligonucleotide in human plasma over a range of 0.5-100 ng/ml. CONCLUSION In these preliminary investigations, the precision and accuracy of the method was established for the quantification of the oligonucleotide in human plasma. It was established that the method was precise and accurate for quantification of the oligonucleotide in human plasma. The acceptability of the data was assessed using a novel three-step process to identify any outliers, involving the use of the Grubbs' test. The analytical method only requires a small sample volume (<0.01 ml), so would be applicable in analysis of low-volume samples.
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191
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Wu Q, Prager KC, Goldstein T, Alt DP, Galloway RL, Zuerner RL, Lloyd-Smith JO, Schwacke L. Development of a real-time PCR for the detection of pathogenic Leptospira spp. in California sea lions. DISEASES OF AQUATIC ORGANISMS 2014; 110:165-172. [PMID: 25114040 PMCID: PMC6423441 DOI: 10.3354/dao02752] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
Several real-time PCR assays are currently used for detection of pathogenic Leptospira spp.; however, few methods have been described for the successful evaluation of clinical urine samples. This study reports a rapid assay for the detection of pathogenic Leptospira spp. in California sea lions Zalophus californianus using real-time PCR with primers and a probe targeting the lipL32 gene. The PCR assay had high analytic sensitivity-the limit of detection was 3 genome copies per PCR volume using L. interrogans serovar Pomona DNA and 100% analytic specificity; it detected all pathogenic leptospiral serovars tested and none of the non-pathogenic Leptospira species (L. biflexa and L. meyeri serovar Semaranga), the intermediate species L. inadai, or the non-Leptospira pathogens tested. Our assay had an amplification efficiency of 1.00. Comparisons between the real-time PCR assay and culture isolation for detection of pathogenic Leptospira spp. in urine and kidney tissue samples from California sea lions showed that samples were more often positive by real-time PCR than by culture methods. Inclusion of an internal amplification control in the real-time PCR assay showed no inhibitory effects in PCR negative samples. These studies indicated that our real-time PCR assay has high analytic sensitivity and specificity for the rapid detection of pathogenic Leptospira species in urine and kidney tissue samples.
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Affiliation(s)
- Qingzhong Wu
- Hollings Marine Laboratory, National Centers for Coastal Ocean Science, National Ocean Service, National Oceanic Atmospheric Administration, Charleston, South Carolina 29412, USA
| | - Katherine C. Prager
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, California 90095, USA
- Fogarty International Center, National Institutes of Health, Bethesda, Maryland 20892, USA
- The Marine Mammal Center, Sausalito, California 94965, USA
| | - Tracey Goldstein
- One Health Institute, School of Veterinary Medicine, University of California, Davis, California 95616, USA
| | - David P. Alt
- Infectious Bacterial Diseases Research Unit, National Animal Disease Center, Ames, Iowa 50010, USA
| | - Renee L. Galloway
- Centers for Disease Control and Prevention, Atlanta, Georgia 30333, USA
| | - Richard L. Zuerner
- Infectious Bacterial Diseases Research Unit, National Animal Disease Center, Ames, Iowa 50010, USA
| | - James O. Lloyd-Smith
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, California 90095, USA
- Fogarty International Center, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Lori Schwacke
- Hollings Marine Laboratory, National Centers for Coastal Ocean Science, National Ocean Service, National Oceanic Atmospheric Administration, Charleston, South Carolina 29412, USA
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192
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Robins HS, Ericson NG, Guenthoer J, O'Briant KC, Tewari M, Drescher CW, Bielas JH. Digital genomic quantification of tumor-infiltrating lymphocytes. Sci Transl Med 2014; 5:214ra169. [PMID: 24307693 DOI: 10.1126/scitranslmed.3007247] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Infiltrating T lymphocytes are frequently found in malignant tumors and are suggestive of a host cancer immune response. Multiple independent studies have documented that the presence and quantity of tumor-infiltrating lymphocytes (TILs) are strongly correlated with increased survival. However, because of methodological factors, the exact effect of TILs on prognosis has remained enigmatic, and inclusion of TILs in standard prognostic panels has been limited. For example, some reports enumerate all CD3(+) cells, some count only cytotoxic CD8(+) T cells, and the criteria used to score tumors as TIL-positive or TIL-negative are inconsistent among studies. To address this limitation, we introduce a robust digital DNA-based assay, termed QuanTILfy, to count TILs and assess T cell clonality in tissue samples, including tumors. We demonstrate the clonal specificity of this approach by the diagnosis of T cell acute lymphoblastic leukemia and the accurate, sensitive, and highly reproducible measurement of TILs in primary and metastatic ovarian cancer. Our experiments demonstrate an association between higher TIL counts and improved survival among women with ovarian cancer, and are consistent with previous observations that the immune response against ovarian cancer is a meaningful and independent prognostic factor. Surprisingly, the TIL repertoire is diverse for all tumors in the study with no notable oligoclonal expansions. Furthermore, because variability in the measurement and characterization of TILs has limited their clinical utility as biomarkers, these results highlight the significant translational potential of a robust, standardizable DNA-based assay to assess TILs in a variety of cancer types.
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Affiliation(s)
- Harlan S Robins
- Herbold Computational Biology Program, Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
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193
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Nagarajan K, Loh KC. Molecular biology-based methods for quantification of bacteria in mixed culture: perspectives and limitations. Appl Microbiol Biotechnol 2014; 98:6907-19. [DOI: 10.1007/s00253-014-5870-9] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2014] [Revised: 05/30/2014] [Accepted: 05/31/2014] [Indexed: 02/07/2023]
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194
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Paten AM, Pain SJ, Peterson SW, Blair HT, Kenyon PR, Dearden PK, Duncan EJ. Identification of reference genes for RT-qPCR in ovine mammary tissue during late pregnancy and lactation and in response to maternal nutritional programming. Physiol Genomics 2014; 46:560-70. [PMID: 24893875 DOI: 10.1152/physiolgenomics.00030.2014] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
The mammary gland is a complex tissue consisting of multiple cell types which, over the lifetime of an animal, go through repeated cycles of development associated with pregnancy, lactation and involution. The mammary gland is also known to be sensitive to maternal programming by environmental stimuli such as nutrition. The molecular basis of these adaptations is of significant interest, but requires robust methods to measure gene expression. Reverse-transcription quantitative PCR (RT-qPCR) is commonly used to measure gene expression, and is currently the method of choice for validating genome-wide expression studies. RT-qPCR requires the selection of reference genes that are stably expressed over physiological states and treatments. In this study we identify suitable reference genes to normalize RT-qPCR data for the ovine mammary gland in two physiological states; late pregnancy and lactation. Biopsies were collected from offspring of ewes that had been subjected to different nutritional paradigms during pregnancy to examine effects of maternal programming on the mammary gland of the offspring. We evaluated eight candidate reference genes and found that two reference genes (PRPF3 and CUL1) are required for normalising RT-qPCR data from pooled RNA samples, but five reference genes are required for analyzing gene expression in individual animals (SENP2, EIF6, MRPL39, ATP1A1, CUL1). Using these stable reference genes, we showed that TET1, a key regulator of DNA methylation, is responsive to maternal programming and physiological state. The identification of these novel reference genes will be of utility to future studies of gene expression in the ovine mammary gland.
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Affiliation(s)
- A M Paten
- Laboratory for Evolution and Development, Genetics Otago, Department of Biochemistry, University of Otago, Dunedin, Aotearoa-New Zealand; International Sheep Research Centre, Institute of Veterinary, Animal and Biomedical Sciences, Massey University, Palmerston North, Aotearoa-New Zealand; and Gravida: National Centre for Growth and Development, Aukland, New Zealand
| | - S J Pain
- International Sheep Research Centre, Institute of Veterinary, Animal and Biomedical Sciences, Massey University, Palmerston North, Aotearoa-New Zealand; and Gravida: National Centre for Growth and Development, Aukland, New Zealand
| | - S W Peterson
- International Sheep Research Centre, Institute of Veterinary, Animal and Biomedical Sciences, Massey University, Palmerston North, Aotearoa-New Zealand; and Gravida: National Centre for Growth and Development, Aukland, New Zealand
| | - H T Blair
- International Sheep Research Centre, Institute of Veterinary, Animal and Biomedical Sciences, Massey University, Palmerston North, Aotearoa-New Zealand; and Gravida: National Centre for Growth and Development, Aukland, New Zealand
| | - P R Kenyon
- International Sheep Research Centre, Institute of Veterinary, Animal and Biomedical Sciences, Massey University, Palmerston North, Aotearoa-New Zealand; and Gravida: National Centre for Growth and Development, Aukland, New Zealand
| | - P K Dearden
- Laboratory for Evolution and Development, Genetics Otago, Department of Biochemistry, University of Otago, Dunedin, Aotearoa-New Zealand; Gravida: National Centre for Growth and Development, Aukland, New Zealand
| | - E J Duncan
- Laboratory for Evolution and Development, Genetics Otago, Department of Biochemistry, University of Otago, Dunedin, Aotearoa-New Zealand; Gravida: National Centre for Growth and Development, Aukland, New Zealand
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195
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Galata M, Sarker LS, Mahmoud SS. Transcriptome profiling, and cloning and characterization of the main monoterpene synthases of Coriandrum sativum L. PHYTOCHEMISTRY 2014; 102:64-73. [PMID: 24636455 DOI: 10.1016/j.phytochem.2014.02.016] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/10/2013] [Revised: 12/23/2013] [Accepted: 02/18/2014] [Indexed: 05/06/2023]
Abstract
Terpenoids are a large and diverse class of specialized metabolites that are essential for the growth and development of plants, and have tremendous industrial applications. The mericarps of Coriandrum sativum L. (coriander) produce an essential oil (EO) rich in monoterpenes, volatile C10 terpenoids. To investigate EO metabolism, the transcriptome of coriander mericarps, at three developmental stages (early, mid, late) was sequenced via Illumina technology and a transcript library was produced. To validate the usability of the transcriptome sequences, two terpene synthase candidate genes, CsγTRPS and CsLINS, encoding 558 and 562 amino acid proteins were expressed in bacteria, and the recombinant proteins purified by Ni-NTA affinity chromatography. The 65.16 (CsγTRPS) and 65.91 (CsLINS)kDa recombinant proteins catalyzed the conversion of geranyl diphosphate, the precursor to monoterpenes, to γ-terpinene and (S)-linalool, respectively, with apparent Vmax and Km values of 2.24±0.16 (CsγTRPS); 19.63±1.05 (CsLINS)pkat/mg and 66.25±13 (CsγTRPS); 2.5±0.6 (CsLINS)μM, respectively. Together, CsγTRPS and CsLINS account for the majority of EO constituents in coriander mericarps. Investigation of the coriander transcriptome, and knowledge gained from these experiments will facilitate future studies concerning essential and fatty acid oil production in coriander. They also enable efforts to improve the coriander oils through metabolic engineering or plant breeding.
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Affiliation(s)
- Mariana Galata
- Department of Biology, University of British Columbia Okanagan Campus, 3333 University Way, Kelowna, BC V1V 1V7, Canada
| | - Lukman S Sarker
- Department of Biology, University of British Columbia Okanagan Campus, 3333 University Way, Kelowna, BC V1V 1V7, Canada
| | - Soheil S Mahmoud
- Department of Biology, University of British Columbia Okanagan Campus, 3333 University Way, Kelowna, BC V1V 1V7, Canada.
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Sanders R, Mason DJ, Foy CA, Huggett JF. Considerations for accurate gene expression measurement by reverse transcription quantitative PCR when analysing clinical samples. Anal Bioanal Chem 2014; 406:6471-83. [PMID: 24858468 PMCID: PMC4182594 DOI: 10.1007/s00216-014-7857-x] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2014] [Revised: 04/17/2014] [Accepted: 04/24/2014] [Indexed: 01/04/2023]
Abstract
Reverse transcription quantitative PCR is an established, simple and effective method for RNA measurement. However, technical standardisation challenges combined with frequent insufficient experimental detail render replication of many published findings challenging. Consequently, without adequate consideration of experimental standardisation, such findings may be sufficient for a given publication but cannot be translated to wider clinical application. This article builds on earlier standardisation work and the MIQE guidelines, discussing processes that need consideration for accurate, reproducible analysis when dealing with patient samples. By applying considerations common to the science of measurement (metrology), one can maximise the impact of gene expression studies, increasing the likelihood of their translation to clinical tools.
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Affiliation(s)
- Rebecca Sanders
- Molecular & Cell Biology, LGC, Queens Road, Teddington, TW11 0LY, UK,
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197
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Izagirre U, Errasti A, Bilbao E, Múgica M, Marigómez I. Combined effects of thermal stress and Cd on lysosomal biomarkers and transcription of genes encoding lysosomal enzymes and HSP70 in mussels, Mytilus galloprovincialis. AQUATIC TOXICOLOGY (AMSTERDAM, NETHERLANDS) 2014; 149:145-156. [PMID: 24656323 DOI: 10.1016/j.aquatox.2014.01.013] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/29/2013] [Revised: 01/02/2014] [Accepted: 01/16/2014] [Indexed: 06/03/2023]
Abstract
In estuaries and coastal areas, intertidal organisms may be subject to thermal stress resulting from global warming, together with pollution. In the present study, the combined effects of thermal stress and exposure to Cd were investigated in the endo-lysosomal system of digestive cells in mussels, Mytilus galloprovincialis. Mussels were maintained for 24h at 18°C and 26°C seawater temperature in absence and presence of 50 μg Cd/L seawater. Cadmium accumulation in digestive gland tissue, lysosomal structural changes and membrane stability were determined. Semi-quantitative PCR was applied to reveal the changes elicited by the different experimental conditions in hexosaminidase (hex), β-glucuronidase (gusb), cathepsin L (ctsl) and heat shock protein 70 (hsp70) gene transcription levels. Thermal stress provoked lysosomal enlargement whilst Cd-exposure led to fusion of lysosomes. Both thermal stress and Cd-exposure caused lysosomal membrane destabilisation. hex, gusb and ctsl genes but not hsp70 gene were transcriptionally up-regulated as a result of thermal stress. In contrast, all the studied genes were transcriptionally down-regulated in response to Cd-exposure. Cd bioaccumulation was comparable at 18°C and 26°C seawater temperatures but interactions between thermal stress and Cd-exposure were remarkable both in lysosomal biomarkers and in gene transcription. hex, gusb and ctsl genes, reacted to elevated temperature in absence of Cd but not in Cd-exposed mussels. Therefore, thermal stress resulting from global warming might influence the use and interpretation of lysosomal biomarkers in marine pollution monitoring programmes and, vice versa, the presence of pollutants may condition the capacity of mussels to respond against thermal stress in a climate change scenario.
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Affiliation(s)
- Urtzi Izagirre
- CBET Research Group, Research Centre for Experimental Marine Biology and Biotechnology (PIE-UPV/EHU), University of the Basque Country UPV/EHU, Areatza, 48620 Plentzia-Bizkaia, Basque Country, Spain
| | - Aitzpea Errasti
- CBET Research Group, Research Centre for Experimental Marine Biology and Biotechnology (PIE-UPV/EHU), University of the Basque Country UPV/EHU, Areatza, 48620 Plentzia-Bizkaia, Basque Country, Spain
| | - Eider Bilbao
- CBET Research Group, Research Centre for Experimental Marine Biology and Biotechnology (PIE-UPV/EHU), University of the Basque Country UPV/EHU, Areatza, 48620 Plentzia-Bizkaia, Basque Country, Spain
| | - María Múgica
- CBET Research Group, Research Centre for Experimental Marine Biology and Biotechnology (PIE-UPV/EHU), University of the Basque Country UPV/EHU, Areatza, 48620 Plentzia-Bizkaia, Basque Country, Spain
| | - Ionan Marigómez
- CBET Research Group, Research Centre for Experimental Marine Biology and Biotechnology (PIE-UPV/EHU), University of the Basque Country UPV/EHU, Areatza, 48620 Plentzia-Bizkaia, Basque Country, Spain.
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198
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Asynchronous Magnetic Bead Rotation (AMBR) Microviscometer for Label-Free DNA Analysis. BIOSENSORS-BASEL 2014; 4:76-89. [PMID: 25587411 PMCID: PMC4264372 DOI: 10.3390/bios4010076] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/17/2014] [Revised: 02/27/2014] [Accepted: 03/17/2014] [Indexed: 11/17/2022]
Abstract
We have developed a label-free viscosity-based DNA detection system, using paramagnetic beads as an asynchronous magnetic bead rotation (AMBR) microviscometer. We have demonstrated experimentally that the bead rotation period is linearly proportional to the viscosity of a DNA solution surrounding the paramagnetic bead, as expected theoretically. Simple optical measurement of asynchronous microbead motion determines solution viscosity precisely in microscale volumes, thus allowing an estimate of DNA concentration or average fragment length. The response of the AMBR microviscometer yields reproducible measurement of DNA solutions, enzymatic digestion reactions, and PCR systems at template concentrations across a 5000-fold range. The results demonstrate the feasibility of viscosity-based DNA detection using AMBR in microscale aqueous volumes.
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199
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Guerrero-Castilla A, Olivero-Verbel J, Marrugo-Negrete J. Heavy metals in wild house mice from coal-mining areas of Colombia and expression of genes related to oxidative stress, DNA damage and exposure to metals. MUTATION RESEARCH-GENETIC TOXICOLOGY AND ENVIRONMENTAL MUTAGENESIS 2014; 762:24-9. [DOI: 10.1016/j.mrgentox.2013.12.005] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/24/2013] [Revised: 07/31/2013] [Accepted: 12/28/2013] [Indexed: 10/25/2022]
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200
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Tajadini M, Panjehpour M, Javanmard SH. Comparison of SYBR Green and TaqMan methods in quantitative real-time polymerase chain reaction analysis of four adenosine receptor subtypes. Adv Biomed Res 2014; 3:85. [PMID: 24761393 PMCID: PMC3988599 DOI: 10.4103/2277-9175.127998] [Citation(s) in RCA: 107] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2013] [Accepted: 05/22/2013] [Indexed: 12/14/2022] Open
Abstract
Background: Real-time polymerase chain reaction (PCR) is based on the revolutionary method of PCR. This technique is the result of PCR enormous sensitivity and real-time monitoring combination. In quantitative gene expression analysis, two methods have more popularity, SYBR Green and TaqMan, SYBR Green is relatively cost benefit and easy to use and technically based on binding the fluorescent dye to double-stranded deoxyribonucleic acid (dsDNA) where TaqMan method has more expensive and based on dual labeled oligonucleotide and exonuclease activity of Taq polymerase enzyme. Specificity is the most important concern with the usage of any non-specific dsDNA-binding Dyes such as SYBR Green whiles more specificity showed by labeled oligonucleotide method such as TaqMan. In this study, we compared two common RT PCR methods, TaqMan and SYBR Green in measurement gene expression profile of adenosine receptors. Materials and Methods: Gene expression profiles of A1, A2A, A2B and A3 Adenosine receptors were analyzed by optimized TaqMan and SYBR Green quantitative RT PCR in breast cancer tissues. Primary expression data was normalizing by B. actin reference gene. Results: Efficiencies were calculated more than 95% for TaqMan and SYBR Green methods in all genes. The correlations between means of normalized data of each gene in two methods were positive and significant (P < 0.05). Conclusion: Data analysis showed that with the use of high performance primer and by use proper protocols and material we can make precise data by SYBR Green as TaqMan method. In other word by optimization of SYBR Green method, its performance and quality could be comparable to TaqMan method.
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Affiliation(s)
- Mohamadhasan Tajadini
- Department of Clinical Biochemistry, School of Pharmacy and Pharmaceutical Research Center, Isfahan University of Medical Sciences, Isfahan, Iran ; Physiology Research Center, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Mojtaba Panjehpour
- Department of Clinical Biochemistry, School of Pharmacy and Pharmaceutical Research Center, Isfahan University of Medical Sciences, Isfahan, Iran
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