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Giha HA, Joatar FE, AlDehaini DMB, Malalla ZHA, Ali ME, Al Qarni AA. Association of obesity in T2DM with differential polymorphism of ghrelin, growth hormone secretagogue receptor-1 and telomeres maintenance genes. Horm Mol Biol Clin Investig 2022; 43:297-306. [PMID: 35446515 DOI: 10.1515/hmbci-2021-0063] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2021] [Accepted: 03/12/2022] [Indexed: 11/15/2022]
Abstract
BACKGROUND Although obesity and T2DM comorbidity is too frequent, the molecular basis of diabetic obesity is largely unexplained and barely investigated. MATERIALS Cross-sectional studies were conducted in Kingdom of Saudi Arabia (KSA) in 2013 and Kuwait in 2019. Fasting blood samples were obtained from a total of 216 T2DM patients (104 from KSA) and 193 nondiabetic subjects (93 from KSA) after their consents. Eight SNPs in 5 genes known to be associated with both obesity and T2DM, ghrelin (GHRL) and growth hormone secretagogue receptor -GHSR (KSA) and telomeres maintenance genes (Kuwait) were genotyped by rtPCR. Both patients and controls were grouped into obese and non-obese and sub-grouped into 4-BMI- grades: normal, overweight (OW), obese (OBS) and severely obese (SOBS). RESULTS Showed that the only SNP which was distinguished between all groups/subgroups in all study subjects was the ACYP2 rs6713088G/C, where the common CC genotype was under-expressed in the obese compared to non-obese diabetics (17.8% vs. 40.4%, p 0.01) and between the 4-BMI-grade (p 0.025). Interestingly the same genotype was over-expressed in obese compared to non-obese non-diabetics (50% vs. 27.6%, p 0.04). Furthermore, the GHRL (rs27647C/T), GHSR (rs509030G/C) and TERC (rs12696304G/C) MAFs were significantly low in normal BMI patients; p= 0.034, 0.008 and 0.011, respectively. CONCLUSIONS This is the first report about the molecular distinction between the obese and non-obese diabetics, it showed the association of rs6713088G/C mutant allele with diabetic obesity, while the GHRL, GHSR and TERC SNPs were differentially expressed based on the BMI-grades.
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Affiliation(s)
- Hayder A Giha
- Medical Biochemistry and Molecular Biology, Khartoum, Sudan
| | - Faris E Joatar
- Clinical Biochemistry Laboratory, King Abdulaziz Hospital, Ministry of National Guard Health affairs, Al Ahsa, Saudi Arabia
| | | | - Zainab H A Malalla
- Medical Department of Biochemistry, College of Medicine and Medical Sciences (CMMS), Arabian Gulf University (AGU), Manama, Kingdom of Bahrain
| | - Muhalab E Ali
- Medical Department of Biochemistry, College of Medicine and Medical Sciences (CMMS), Arabian Gulf University (AGU), Manama, Kingdom of Bahrain
| | - Ali A Al Qarni
- Endocrinology and Metabolism Section, King Abdulaziz Hospital, Ministry of National Guard Health Affairs, King Abdullah Medical Research Center-Estern Region, Al Ahsa, Saudi Arabia
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Franzoni LT, Garcia EL, Motta SB, Ahner MM, Bertoletti OA, Saffi MAL, da Silveira AD, Pereira AA, Pereira AH, Danzmann LC, Stein R. Aerobic exercise and telomere length in patients with systolic heart failure: protocol study for a randomized controlled trial. Trials 2022; 23:283. [PMID: 35410445 PMCID: PMC8996601 DOI: 10.1186/s13063-022-06257-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2021] [Accepted: 03/29/2022] [Indexed: 11/23/2022] Open
Abstract
Background Heart failure (HF) with reduced ejection fraction (HFrEF) is a syndrome that leads to fatigue and reduced functional capacity due to disease-related pathophysiological mechanisms. Aerobic exercise (AERO) plays a key role in improving HF outcomes, such as an increase in peak oxygen uptake (VO2peak). In addition, HF promotes cell senescence, which involves reducing telomere length. Several studies have shown that patients with a worse prognosis (i.e., reduced VO2 peak) also have shorter telomeres. However, the effects of AERO on telomere length in patients with HFrEF are still unknown. In an attempt to fill this gap, we designed a study to determine the effects of 16 weeks of aerobic training (32 sessions) on telomere length in HFrEF patients. Methods In this single-center randomized controlled trial, men and women between 50 and 80 years old will be allocated into two different groups: a moderate-intensity aerobic training and a control grouTelomere length, functional capacity, echocardiographic variables, endothelial function, and walking ability will be assessed before and after the 16-week intervention period. Discussion Understanding the role of physical exercise in biological aging in HFrEF patients is relevant. Due to cell senescence, these individuals have shown a shorter telomere length. AERO can delay biological aging according to a balance in oxidative stress through antioxidant action. Positive telomere length results are expected for the aerobic training group. Trial registration ClinicalTrials.gov NCT03856736. Registered on February 27, 2019
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Identification of the principal transcriptional regulators for low-fat and high-fat meal responsive genes in small intestine. Nutr Metab (Lond) 2017; 14:66. [PMID: 29075307 PMCID: PMC5654052 DOI: 10.1186/s12986-017-0221-3] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2017] [Accepted: 10/16/2017] [Indexed: 12/31/2022] Open
Abstract
BACKGROUND High-fat (HF) diet is a well-known cause of obesity. To identify principle transcriptional regulators that could be therapeutic targets of obesity, we investigated transcriptomic modulation in the duodenal mucosa following low-fat (LF) and HF meal ingestion. METHODS Whereas one group of mice was sacrificed after fasting, the others were fed ad libitum with LF or HF meal, and sacrificed 30 min, 1 h and 3 h after the beginning of the meal. A transcriptome analysis of the duodenal mucosa of the 7 groups was conducted using both microarray and serial analysis of gene expression (SAGE) method followed by an Ingenuity Pathways Analysis (IPA). RESULTS SAGE and microarray showed that the modulation of a total of 896 transcripts in the duodenal mucosa after LF and/or HF meal, compared to the fasting condition. The IPA identified lipid metabolism, molecular transport, and small molecule biochemistry as top three molecular and cellular functions for the HF-responsive, HF-specific, HF-delay, and LF-HF different genes. Moreover, the top transcriptional regulator for the HF-responsive and HF-specific genes was peroxisome proliferator-activated receptor alpha (PPARα). On the other hand, the LF-responsive and LF-specific genes were related to carbohydrate metabolism, cellular function and maintenance, and cell death/cellular growth and proliferation, and the top transcriptional regulators were forkhead box protein O1 (FOXO1) and cAMP response element binding protein 1 (CREB1), respectively. CONCLUSIONS These results will help to understand the molecular mechanisms of intestinal response after LF and HF ingestions, and contribute to identify therapeutic targets for obesity and obesity-related diseases.
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Sharifi-Sanjani M, Meeker AK, Mourkioti F. Evaluation of telomere length in human cardiac tissues using cardiac quantitative FISH. Nat Protoc 2017; 12:1855-1870. [PMID: 28817123 DOI: 10.1038/nprot.2017.082] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Telomere length has been correlated with various diseases, including cardiovascular disease and cancer. The use of currently available telomere-length measurement techniques is often restricted by the requirement of a large amount of cells (Southern-based techniques) or the lack of information on individual cells or telomeres (PCR-based methods). Although several methods have been used to measure telomere length in tissues as a whole, the assessment of cell-type-specific telomere length provides valuable information on individual cell types. The development of fluorescence in situ hybridization (FISH) technologies enables the quantification of telomeres in individual chromosomes, but the use of these methods is dependent on the availability of isolated cells, which prevents their use with fixed archival samples. Here we describe an optimized quantitative FISH (Q-FISH) protocol for measuring telomere length that bypasses the previous limitations by avoiding contributions from undesired cell types. We have used this protocol on small paraffin-embedded cardiac-tissue samples. This protocol describes step-by-step procedures for tissue preparation, permeabilization, cardiac-tissue pretreatment and hybridization with a Cy3-labeled telomeric repeat complementing (CCCTAA)3 peptide nucleic acid (PNA) probe coupled with cardiac-specific antibody staining. We also describe how to quantify telomere length by means of the fluorescence intensity and area of each telomere within individual nuclei. This protocol provides comparative cell-type-specific telomere-length measurements in relatively small human cardiac samples and offers an attractive technique to test hypotheses implicating telomere length in various cardiac pathologies. The current protocol (from tissue collection to image procurement) takes ∼28 h along with three overnight incubations. We anticipate that the protocol could be easily adapted for use on different tissue types.
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Affiliation(s)
- Maryam Sharifi-Sanjani
- Department of Orthopaedic Surgery, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Alan K Meeker
- Departments of Pathology, Oncology and Urology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Foteini Mourkioti
- Department of Orthopaedic Surgery, University of Pennsylvania, Philadelphia, Pennsylvania, USA.,Cardiovascular Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA.,Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
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Abstract
BACKGROUND The exciting discovery that telomere shortening is associated with many health conditions and that telomere lengths can be altered in response to social and environmental exposures has underscored the need for methods to accurately and consistently quantify telomere length. OBJECTIVES The purpose of this article is to provide a comprehensive summary that compares and contrasts the current technologies used to assess telomere length. DISCUSSION Multiple methods have been developed for the study of telomeres. These techniques include quantification of telomere length by terminal restriction fragmentation-which was one of the earliest tools used for length assessment-making it the gold standard in telomere biology. Quantitative polymerase chain reaction provides the advantage of being able to use smaller amounts of DNA, thereby making it amenable to epidemiology studies involving large numbers of people. An alternative method uses fluorescent probes to quantify not only mean telomere lengths but also chromosome-specific telomere lengths; however, the downside of this approach is that it can only be used on mitotically active cells. Additional methods that permit assessment of the length of a subset of chromosome-specific telomeres or the subset of telomeres that demonstrate shortening are also reviewed. CONCLUSION Given the increased utility for telomere assessments as a biomarker in physiological, psychological, and biobehavioral research, it is important that investigators become familiar with the methodological nuances of the various procedures used for measuring telomere length. This will ensure that they are empowered to select an optimal assessment approach to meet the needs of their study designs. Gaining a better understanding of the benefits and drawbacks of various measurement techniques is important not only in individual studies, but also to further establish the science of telomere associations with biobehavioral phenomena.
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Skibsted S, Bhasin MK, Aird WC, Shapiro NI. Bench-to-bedside review: future novel diagnostics for sepsis - a systems biology approach. Crit Care 2013; 17:231. [PMID: 24093155 PMCID: PMC4057467 DOI: 10.1186/cc12693] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
The early, accurate diagnosis and risk stratification of sepsis remains an important challenge in the critically ill. Since traditional biomarker strategies have not yielded a gold standard marker for sepsis, focus is shifting towards novel strategies that improve assessment capabilities. The combination of technological advancements and information generated through the human genome project positions systems biology at the forefront of biomarker discovery. While previously available, developments in the technologies focusing on DNA, gene expression, gene regulatory mechanisms, protein and metabolite discovery have made these tools more feasible to implement and less costly, and they have taken on an enhanced capacity such that they are ripe for utilization as tools to advance our knowledge and clinical research. Medicine is in a genome-level era that can leverage the assessment of thousands of molecular signals beyond simply measuring selected circulating proteins. Genomics is the study of the entire complement of genetic material of an individual. Epigenetics is the regulation of gene activity by reversible modifications of the DNA. Transcriptomics is the quantification of the relative levels of messenger RNA for a large number of genes in specific cells or tissues to measure differences in the expression levels of different genes, and the utilization of patterns of differential gene expression to characterize different biological states of a tissue. Proteomics is the large-scale study of proteins. Metabolomics is the study of the small molecule profiles that are the terminal downstream products of the genome and consists of the total complement of all low-molecular-weight molecules that cellular processes leave behind. Taken together, these individual fields of study may be linked during a systems biology approach. There remains a valuable opportunity to deploy these technologies further in human research. The techniques described in this paper not only have the potential to increase the spectrum of diagnostic and prognostic biomarkers in sepsis, but they may also enable the discovery of new disease pathways. This may in turn lead us to improved therapeutic targets. The objective of this paper is to provide an overview and basic framework for clinicians and clinical researchers to better understand the 'omics technologies' to enhance further use of these valuable tools.
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Affiliation(s)
- Simon Skibsted
- Department of Emergency Medicine and Center for Vascular Biology Research, Beth Israel Deaconess Medical Center and Harvard Medical School, 330 Brookline Avenue, Boston, MA 02215, USA
- Center for Vascular Biology Research, Beth Israel Deaconess Medical Center, 99 Brookline Street, Boston, MA 02215, USA
| | - Manoj K Bhasin
- Beth Israel Deaconess Medical Center Genomics and Core, 99 Brookline Avenue, Boston, MA 02115, USA
| | - William C Aird
- Center for Vascular Biology Research, Beth Israel Deaconess Medical Center, 99 Brookline Street, Boston, MA 02215, USA
| | - Nathan I Shapiro
- Department of Emergency Medicine and Center for Vascular Biology Research, Beth Israel Deaconess Medical Center and Harvard Medical School, 330 Brookline Avenue, Boston, MA 02215, USA
- Center for Vascular Biology Research, Beth Israel Deaconess Medical Center, 99 Brookline Street, Boston, MA 02215, USA
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Jamil M, Altaf AA, Badshah A, Ahmad I, Zubair M, Kemal S, Ali MI. Naked Eye DNA detection: synthesis, characterization and DNA binding studies of a novel azo-guanidine. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2013; 105:165-170. [PMID: 23299023 DOI: 10.1016/j.saa.2012.12.020] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/16/2012] [Revised: 11/29/2012] [Accepted: 12/06/2012] [Indexed: 06/01/2023]
Abstract
A novel class of azo-guanidine compounds is introduced in this article. The novel compound 2-(2-hydroxyphenyl)-1-(phenylamino)-3-(phenylimino)guanidine (AG) was synthesized and well characterized by using different analytical instrumental techniques like elemental analysis, FTIR, (1)H and (13)C NMR, UV-Visible spectroscopy and cyclic voltammetry. The new compound was found interacting with DNA and shows clear color change in the solution. The AG-DNA complex was qualitatively and quantitatively characterized with UV-Visible spectroscopy and cyclic voltammetry. Electrostatic mode of interaction, clear color change and moderate binding constant (K(b)=10(4)) indicate its potential use as DNA staining agent.
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Affiliation(s)
- Muhammad Jamil
- Department of Chemistry, Govt. College University Faisalabad, Pakistan
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Spring KJ, Pham S, Zufall RA. Chromosome copy number variation and control in the ciliate Chilodonella uncinata. PLoS One 2013; 8:e56413. [PMID: 23437129 PMCID: PMC3577910 DOI: 10.1371/journal.pone.0056413] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2012] [Accepted: 01/09/2013] [Indexed: 12/02/2022] Open
Abstract
Copy number variations are widespread in eukaryotes. The unusual genome architecture of ciliates, in particular, with its process of amitosis in macronuclear division, provides a valuable model in which to study copy number variation. The current model of amitosis envisions stochastic distribution of macronuclear chromosomes during asexual reproduction. This suggests that amitosis is likely to result in high levels of copy number variation in ciliates, as dividing daughter cells can have variable copy numbers of chromosomes if chromosomal distribution during amitosis is a stochastic process. We examined chromosomal distribution during amitosis in Chilodonella uncinata, a ciliate with gene-size macronuclear chromosomes. We quantified 4 chromosomes in evolving populations of C. uncinata and modeled the amitotic distribution process. We found that macronuclear chromosomes differ in copy number from one another but that copy number does not change as expected under a stochastic process. The chromosome carrying SSU increased in copy number, which is consistent with selection to increase abundance; however, two other studied chromosomes displayed much lower than expected among-line variance. Our models suggest that balancing selection is sufficient to explain the observed maintenance of chromosome copy during asexual reproduction.
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Affiliation(s)
- Kevin J Spring
- Department of Biology and Biochemistry, University of Houston, Houston, Texas, USA.
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Mendes GA, Pereira-Lima JFS, Kohek MB, Trott G, Di Domenico M, Ferreira NP, Oliveira MDC. Prolactin gene expression in primary central nervous system tumors. J Negat Results Biomed 2013; 12:4. [PMID: 23317095 PMCID: PMC3552985 DOI: 10.1186/1477-5751-12-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2012] [Accepted: 01/03/2013] [Indexed: 02/06/2023] Open
Abstract
Background Prolactin (PRL) is a hormone synthesized in both the pituitary gland and extrapituitary sites. It has been associated with the occurrence of neoplasms and, more recently, with central nervous system (CNS) neoplasms. The aim of this study was to evaluate prolactin expression in primary central nervous system tumors through quantitative real-time PCR and immunohistochemistry (IH). Results Patient mean age was 49.1 years (SD 15.43), and females accounted for 70% of the sample. The most frequent subtype of histological tumor was meningioma (61.5%), followed by glioblastoma (22.9%). Twenty cases (28.6%) showed prolactin expression by immunohistochemistry, most of them females (18 cases, 90%). Quantitative real-time PCR did not show any prolactin expression. Conclusions Despite the presence of prolactin expression by IH, the lack of its expression by quantitative real-time PCR indicates that its presence in primary tumors in CNS is not a reflex of local production.
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Affiliation(s)
- Graziella Alebrant Mendes
- Postgraduate Program in Pathology, Universidade Federal de Ciências da Saúde de Porto Alegre, Porto Alegre, Brazil.
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Guertler P, Brandl C, Meyer HHD, Tichopad A. Feeding genetically modified maize (MON810) to dairy cows: comparison of gene expression pattern of markers for apoptosis, inflammation and cell cycle. J Verbrauch Lebensm 2012. [DOI: 10.1007/s00003-012-0778-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
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Etiologic diagnosis of lower respiratory tract bacterial infections using sputum samples and quantitative loop-mediated isothermal amplification. PLoS One 2012; 7:e38743. [PMID: 22719933 PMCID: PMC3375278 DOI: 10.1371/journal.pone.0038743] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2011] [Accepted: 05/10/2012] [Indexed: 11/19/2022] Open
Abstract
UNLABELLED Etiologic diagnoses of lower respiratory tract infections (LRTI) have been relying primarily on bacterial cultures that often fail to return useful results in time. Although DNA-based assays are more sensitive than bacterial cultures in detecting pathogens, the molecular results are often inconsistent and challenged by doubts on false positives, such as those due to system- and environment-derived contaminations. Here we report a nationwide cohort study on 2986 suspected LRTI patients across P. R. China. We compared the performance of a DNA-based assay qLAMP (quantitative Loop-mediated isothermal AMPlification) with that of standard bacterial cultures in detecting a panel of eight common respiratory bacterial pathogens from sputum samples. Our qLAMP assay detects the panel of pathogens in 1047(69.28%) patients from 1533 qualified patients at the end. We found that the bacterial titer quantified based on qLAMP is a predictor of probability that the bacterium in the sample can be detected in culture assay. The relatedness of the two assays fits a logistic regression curve. We used a piecewise linear function to define breakpoints where latent pathogen abruptly change its competitive relationship with others in the panel. These breakpoints, where pathogens start to propagate abnormally, are used as cutoffs to eliminate the influence of contaminations from normal flora. With help of the cutoffs derived from statistical analysis, we are able to identify causative pathogens in 750 (48.92%) patients from qualified patients. In conclusion, qLAMP is a reliable method in quantifying bacterial titer. Despite the fact that there are always latent bacteria contaminated in sputum samples, we can identify causative pathogens based on cutoffs derived from statistical analysis of competitive relationship. TRIAL REGISTRATION ClinicalTrials.gov NCT00567827.
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Abstract
Quantitative measurement of the levels of mRNA expression using real-time reverse transcription polymerase chain reaction (RT-PCR) has long been used for analyzing expression differences in tissue or cell lines of interest. This method has been used somewhat less frequently to measure the changes in gene expression due to perturbagens such as small molecules or siRNA. The availability of new instrumentation for liquid handling and real-time PCR analysis as well as the commercial availability of start-to-finish kits for RT-PCR has enabled the use of this method for high-throughput small-molecule screening on a scale comparable to traditional high-throughput screening (HTS) assays. This protocol focuses on the special considerations necessary for using quantitative RT-PCR as a primary small-molecule screening assay, including the different methods available for mRNA isolation and analysis.
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Affiliation(s)
- Joshua A Bittker
- Chemical Biology Platform, Broad Institute of MIT and Harvard, Cambridge, MA 617-714-7373
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Bhaduri AM, Fulekar MH. Assessment of arbuscular mycorrhizal fungi on the phytoremediation potential of Ipomoea aquatica on cadmium uptake. 3 Biotech 2012. [PMCID: PMC3433885 DOI: 10.1007/s13205-012-0046-8] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
Abstract
The phytoremedial potential of Ipomoea aquatica and role of arbuscular mycorrhizal fungi (AMF) during Cadmium uptake was studied under two different soils i.e., soil inoculated with and without AMF. The plants were treated with different concentrations of Cd(NO)3 starting from 0, 5, 10, 25, 50, and 100 ppm in three replicate design in soil with and without AMF inoculation. Results showed that AMF enhanced accumulation of cadmium in plant tissues at all concentrations. Plants in AMF exhibited tolerance for Cd up to 100 mg/l and accumulated 88.07% in its tissues with no visual symptoms of toxicity, whereas those in non-AMF showed marked growth reduction at the same concentration with a metal accumulation of 73.2%. A significant variation of antioxidant enzymes under different environments evaluated the defense pathways of plants during uptake of Cd. Physiological changes and nutrient uptake showed that plants inoculated in AMF were more unwavering during stress conditions. The study established that phytoremedial potential of I. aquatica depends on rhizospheric conditions which enhanced Cd uptake. Finally, it was established that AMF was able to maintain an efficient symbiosis with I. aquatica in soil moderately contaminated by Cd, viable due to relation between fungus and plant.
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Affiliation(s)
- Anwesha M. Bhaduri
- Environmental Biotechnology Laboratory, Department of Life Sciences, University of Mumbai, Santacruz (E), Mumbai, 400098 India
| | - M. H. Fulekar
- Environmental Biotechnology Laboratory, Department of Life Sciences, University of Mumbai, Santacruz (E), Mumbai, 400098 India
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Xu H, Sung WK. Identifying differential histone modification sites from ChIP-seq data. Methods Mol Biol 2012; 802:293-303. [PMID: 22130888 DOI: 10.1007/978-1-61779-400-1_19] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Epigenetic modifications are critical to gene regulations and genome functions. Among different epigenetic modifications, it is of great interest to study the differential histone modification sites (DHMSs), which contribute to the epigenetic dynamics and the gene regulations among various cell-types or environmental responses. ChIP-seq is a robust and comprehensive approach to capture the histone modifications at the whole genome scale. By comparing two histone modification ChIP-seq libraries, the DHMSs are potentially identifiable. With this aim, we proposed an approach called ChIPDiff for the genome-wide comparison of histone modification sites identified by ChIP-seq (Xu, Wei, Lin et al., Bioinformatics 24:2344-2349, 2008). The approach employs a hidden Markov model (HMM) to infer the states of histone modification changes at each genomic location. We evaluated the performance of ChIPDiff by comparing the H3K27me3 modification sites between mouse embryonic stem cell (ESC) and neural progenitor cell (NPC). We demonstrated that the H3K27me3 DHMSs identified by our approach are of high sensitivity, specificity, and technical reproducibility. ChIPDiff was further applied to uncover the differential H3K4me3 and H3K36me3 sites between different cell states. The result showed significant correlation between the histone modification states and the gene expression levels.
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Affiliation(s)
- Han Xu
- Department of Computational and Mathematical Biology, Genome Institute of Singapore, Singapore, Singapore
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Development of salt-tolerance interface for an high performance liquid chromatography/inductively coupled plasma mass spectrometry system and its application to accurate quantification of DNA samples. Anal Chim Acta 2011; 713:23-9. [PMID: 22200303 DOI: 10.1016/j.aca.2011.11.039] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2011] [Revised: 11/13/2011] [Accepted: 11/17/2011] [Indexed: 11/22/2022]
Abstract
Accurate quantification of DNA is highly important in various fields. Determination of phosphorus by ICP-MS is one of the most effective methods for accurate quantification of DNA due to the fixed stoichiometry of phosphate to this molecule. In this paper, a smart and reliable method for accurate quantification of DNA fragments and oligodeoxythymidilic acids by hyphenated HPLC/ICP-MS equipped with a highly efficient interface device is presented. The interface was constructed of a home-made capillary-attached micronebulizer and temperature-controllable cyclonic spray chamber (IsoMist). As a separation column for DNA samples, home-made methacrylate-based weak anion-exchange monolith was employed. Some parameters, which include composition of mobile phase, gradient program, inner and outer diameters of capillary, temperature of spray chamber etc., were optimized to find the best performance for separation and accurate quantification of DNA samples. The proposed system could achieve many advantages, such as total consumption for small amount sample analysis, salt-tolerance for hyphenated analysis, high accuracy and precision for quantitative analysis. Using this proposed system, the samples of 20 bp DNA ladder (20, 40, 60, 80, 100, 120, 140, 160, 180, 200, 300, 400, 500 base pairs) and oligodeoxythymidilic acids (dT(12-18)) were rapidly separated and accurately quantified.
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Relevant spatial scales of chemical variation in Aplysina aerophoba. Mar Drugs 2011; 9:2499-2513. [PMID: 22363236 PMCID: PMC3280577 DOI: 10.3390/md9122499] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2011] [Revised: 11/14/2011] [Accepted: 11/16/2011] [Indexed: 11/17/2022] Open
Abstract
Understanding the scale at which natural products vary the most is critical because it sheds light on the type of factors that regulate their production. The sponge Aplysina aerophoba is a common Mediterranean sponge inhabiting shallow waters in the Mediterranean and its area of influence in Atlantic Ocean. This species contains large concentrations of brominated alkaloids (BAs) that play a number of ecological roles in nature. Our research investigates the ecological variation in BAs of A. aerophoba from a scale of hundred of meters to thousand kilometers. We used a nested design to sample sponges from two geographically distinct regions (Canary Islands and Mediterranean, over 2500 km), with two zones within each region (less than 50 km), two locations within each zone (less than 5 km), and two sites within each location (less than 500 m). We used high-performance liquid chromatography to quantify multiple BAs and a spectrophotometer to quantify chlorophyll a (Chl a). Our results show a striking degree of variation in both natural products and Chl a content. Significant variation in Chl a content occurred at the largest and smallest geographic scales. The variation patterns of BAs also occurred at the largest and smallest scales, but varied depending on which BA was analyzed. Concentrations of Chl a and isofistularin-3 were negatively correlated, suggesting that symbionts may impact the concentration of some of these compounds. Our results underline the complex control of the production of secondary metabolites, with factors acting at both small and large geographic scales affecting the production of multiple secondary metabolites.
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Condori J, Nopo-Olazabal C, Medrano G, Medina-Bolivar F. Selection of reference genes for qPCR in hairy root cultures of peanut. BMC Res Notes 2011; 4:392. [PMID: 21985172 PMCID: PMC3199266 DOI: 10.1186/1756-0500-4-392] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2011] [Accepted: 10/10/2011] [Indexed: 11/10/2022] Open
Abstract
Background Hairy root cultures produced via Agrobacterium rhizogenes-mediated transformation have emerged as practical biological models to elucidate the biosynthesis of specialized metabolites. To effectively understand the expression patterns of the genes involved in the metabolic pathways of these compounds, reference genes need to be systematically validated under specific experimental conditions as established by the MIQE (Minimum Information for Publication of Quantitative Real-Time PCR Experiments) guidelines. In the present report we describe the first validation of reference genes for RT-qPCR in hairy root cultures of peanut which produce stilbenoids upon elicitor treatments. Results A total of 21 candidate reference genes were evaluated. Nineteen genes were selected based on previous qPCR studies in plants and two were from the T-DNAs transferred from A. rhizogenes. Nucleotide sequences of peanut candidate genes were obtained using their homologous sequences in Arabidopsis. To identify the suitable primers, calibration curves were obtained for each candidate reference gene. After data analysis, 12 candidate genes meeting standard efficiency criteria were selected. The expression stability of these genes was analyzed using geNorm and NormFinder algorithms and a ranking was established based on expression stability of the genes. Candidate reference gene expression was shown to have less variation in methyl jasmonate (MeJA) treated root cultures than those treated with sodium acetate (NaOAc). Conclusions This work constitutes the first effort to validate reference genes for RT-qPCR in hairy roots. While these genes were selected under conditions of NaOAc and MeJA treatment, we anticipate these genes to provide good targets for reference genes for hairy roots under a variety of stress conditions. The lead reference genes were a gene encoding for a TATA box binding protein (TBP2) and a gene encoding a ribosomal protein (RPL8C). A commonly used reference gene GAPDH showed low stability of expression suggesting that its use may lead to inaccurate gene expression profiles when used for data normalization in stress-stimulated hairy roots. Likewise the A. rhizogenes transgene rolC showed less expression stability than GAPDH. This study proposes that a minimum of two reference genes should be used for a normalization procedure in gene expression profiling using elicited hairy roots.
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Affiliation(s)
- Jose Condori
- Arkansas Biosciences Institute, Arkansas State University, P,O, Box 639, State University, AR 72467, USA.
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18
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Simpson JE, Ince PG, Shaw PJ, Heath PR, Raman R, Garwood CJ, Gelsthorpe C, Baxter L, Forster G, Matthews FE, Brayne C, Wharton SB. Microarray analysis of the astrocyte transcriptome in the aging brain: relationship to Alzheimer's pathology and APOE genotype. Neurobiol Aging 2011; 32:1795-807. [PMID: 21705112 DOI: 10.1016/j.neurobiolaging.2011.04.013] [Citation(s) in RCA: 135] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2010] [Revised: 03/21/2011] [Accepted: 04/20/2011] [Indexed: 12/31/2022]
Abstract
Astrocytes contribute to a variety of functions in the brain, including homeostasis, synapse formation, plasticity, and metabolism. Astrocyte dysfunction may disrupt their normal role, including neuronal support, thereby contributing to neurodegenerative pathologies, including Alzheimer's disease (AD). To understand the role of astrocytes in the pathogenesis of age-related disorders, we isolated astrocytes by laser capture microdissection, using glial fibrillary acidic protein (GFAP) as a marker, and characterized the astrocyte transcriptome at different Braak neurofibrillary tangle stages in postmortem temporal cortex samples derived from the Medical Research Council Cognitive Function and Ageing Study (MRC CFAS) cohort, using microarray analysis. The largest number of significant, differentially expressed genes were identified when the expression profile of astrocytes from isocortical stages of neurofibrillary tangle pathology (Braak stages V-VI) were compared with entorhinal stages (Braak stages I-II). Dysregulation of genes associated with the actin cytoskeleton, proliferation, apoptosis, and ubiquitin-mediated proteolysis occurred at low Braak stages, while altered regulation of intracellular signaling pathways, including insulin, phosphatidylinositol 3-kinase (PI3K)/Akt, and mitogen-activated protein kinase (MAPK) pathways were primarily associated with high levels of Alzheimer-type pathology, and occurred at lower Braak stages in individuals with the APOEε4 allele. Our findings implicate astrocyte dysfunction in the pathogenesis of neurodegenerative pathology in the aging brain, and provide a basis for future candidate studies based on specific pathways.
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Affiliation(s)
- Julie E Simpson
- Department of Neuroscience, Sheffield Institute for Translational Neuroscience, University of Sheffield, Sheffield, UK
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Exploring the links between natural products and bacterial assemblages in the sponge Aplysina aerophoba. Appl Environ Microbiol 2010; 77:862-70. [PMID: 21115701 DOI: 10.1128/aem.00100-10] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
The sponge Aplysina aerophoba produces a large diversity of brominated alkaloids (BAs) and hosts a complex microbial assemblage. Although BAs are located within sponge cells, the enzymes that bind halogen elements to organic compounds have been exclusively described in algae, fungi, and bacteria. Bacterial communities within A. aerophoba could therefore be involved in the biosynthesis of these compounds. This study investigates whether changes in both the concentration of BAs and the bacterial assemblages are correlated in A. aerophoba. To do so, we quantified major natural products using high-performance liquid chromatography and analyzed bacterial assemblages using denaturing gradient gel electrophoresis on the 16S rRNA gene. We identified multiple associations between bacteria and natural products, including a strong relationship between a Chloroflexi phylotype and aplysinamisin-1 and between an unidentified bacterium and aerophobin-2 and isofistularin-3. Our results suggest that these bacteria could either be involved in the production of BAs or be directly affected by them. To our knowledge, this is one of the first reports that find a significant correlation between natural products and bacterial populations in any benthic organism. Further investigating these associations will shed light on the organization and functioning of host-endobiont systems such as Aplysina aerophoba.
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Liu JM, Huang XM, Liu ZB, Li FM, Lin LP, Wang XX, Lin CQ, Huang YH, Li ZM, Lin SQ. Determination of trace deoxyribonucleic acid by using fluorescein isothiocyanate-phenosafranine as a double-luminescent phosphorescence probe. J Fluoresc 2010; 21:195-202. [PMID: 20665096 PMCID: PMC3032200 DOI: 10.1007/s10895-010-0705-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2010] [Accepted: 07/19/2010] [Indexed: 11/29/2022]
Abstract
Using Pb(2+) as ion perturber, phenosafranine (PF) and fluorescein isothiocyanate (FITC) could emit strong and stable room temperature phosphorescence (RTP) signal on the filter paper, respectively. When they were mixed, the phenomenon that the RTP signal of PF and FITC enhanced significantly was found. And 1.12 ag DNA spot(-1) (sample volume was 0.40 μL, corresponding concentration was 2.8 × 10(-15) g mL(-1)) could cause the RTP signal of both PF and FITC to enhance sharply. The content of DNA was proportional to the ΔI(p) of PF and FITC in the system at 634 and 659 nm. Thus, a new solid substrate room temperature phosphorimetry (SSRTP) for the determination of trace DNA was established by using FITC-PF as double-luminescent phosphorescence probe. The detection limit (LD) of this method calculated by 3S(b)/k was 14 zg DNA spot(-1) for PF and 18 zg DNA spot(-1) for FITC, respectively, showing high sensitivity. It has been applied to the determination of trace DNA in practical samples and the analysis results were in accordance with those of fluorescence probe. The reaction mechanism of SSRTP for the determination of trace DNA was also discussed.
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Affiliation(s)
- Jia-Ming Liu
- Department of Chemistry and Environmental Science, Zhangzhou Normal College, Zhangzhou, People's Republic of China.
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21
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22
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Wang YY, Smith P, Murphy M, Cook M. Global expression profiling in epileptogenesis: does it add to the confusion? Brain Pathol 2010; 20:1-16. [PMID: 19243383 PMCID: PMC2805866 DOI: 10.1111/j.1750-3639.2008.00254.x] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2008] [Revised: 10/23/2008] [Accepted: 10/28/2008] [Indexed: 12/14/2022] Open
Abstract
Since the inception of global gene expression profiling platforms in the mid-1990s, there has been a significant increase in publications of differentially expressed genes in the process of epileptogenesis. In particular for mesial temporal lobe epilepsy, the presence of a latency period between the first manifestation of seizures to chronic epilepsy provides the opportunity for therapeutic interventions at the molecular biology level. Using global expression profiling techniques, approximately 2000 genes have been published demonstrating differential expression in mesial temporal epilepsy. The majority of these changes, however, are specific to laboratory or experimental conditions with only 53 genes demonstrating changes in more than two publications. To this end, we review the current status of gene expression profiling in epileptogenesis and suggest standard guidelines to be followed for greater accuracy and reproducibility of results.
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Affiliation(s)
- Yi Yuen Wang
- Centre for Clinical Neuroscience and Neurological Research, St Vincent's Hospital, Melbourne, Australia.
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23
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Tsaftaris SA, Katsaggelos AK. Retrieval efficiency of DNA-based databases of digital signals. IEEE Trans Nanobioscience 2009; 8:259-70. [PMID: 19596640 DOI: 10.1109/tnb.2009.2026371] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
Using DNA to store digital signals, or data in general, offers significant advantages when compared to other media. The DNA molecule, especially in its double-stranded form, is very stable, compact, and inexpensive. In the past, we have shown that DNA can be used to store and retrieve digital signals encoded and stored in DNA. We have also shown that DNA hybridization can be used as a similarity criterion for retrieving digital signals encoded and stored in a DNA database. Retrieval is achieved through hybridization of "query" and "data" DNA molecules. In this paper, we present a mathematical framework to simulate single-query and parallel-query scenarios, and to estimate hybridization efficiency. Our framework allows for exact numerical solutions as well as closed-form approximations under certain conditions. Similarly to the digital domain, we define a DNA SNR measure to assess the performance of the DNA-based retrieval scheme in terms of database size and source statistics. With approximations, we show that the SNR of any finite-sized DNA-based database is upper bounded by the SNR of an infinitely large DNA-based database that has the same source distribution. Computer simulations are presented to validate our results.
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Affiliation(s)
- Sotirios A Tsaftaris
- Department of Electrical Engineering and Computer Science, Northwestern University, Evanston, IL 60208, USA.
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24
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Seliger B, Dressler SP, Wang E, Kellner R, Recktenwald CV, Lottspeich F, Marincola FM, Baumgärtner M, Atkins D, Lichtenfels R. Combined analysis of transcriptome and proteome data as a tool for the identification of candidate biomarkers in renal cell carcinoma. Proteomics 2009; 9:1567-81. [PMID: 19235166 DOI: 10.1002/pmic.200700288] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Results obtained from expression profilings of renal cell carcinoma using different "ome"-based approaches and comprehensive data analysis demonstrated that proteome-based technologies and cDNA microarray analyses complement each other during the discovery phase for disease-related candidate biomarkers. The integration of the respective data revealed the uniqueness and complementarities of the different technologies. While comparative cDNA microarray analyses though restricted to up-regulated targets largely revealed genes involved in controlling gene/protein expression (19%) and signal transduction processes (13%), proteomics/PROTEOMEX-defined candidate biomarkers include enzymes of the cellular metabolism (36%), transport proteins (12%), and cell motility/structural molecules (10%). Candidate biomarkers defined by proteomics and PROTEOMEX are frequently shared, whereas the sharing rate between cDNA microarray and proteome-based profilings is limited. Putative candidate biomarkers provide insights into their cellular (dys)function and their diagnostic/prognostic value but still warrant further validation in larger patient numbers. Based on the fact that merely three candidate biomarkers were shared by all applied technologies, namely annexin A4, tubulin alpha-1A chain, and ubiquitin carboxyl-terminal hydrolase L1, the analysis at a single hierarchical level of biological regulation seems to provide only limited results thus emphasizing the importance and benefit of performing rather combinatorial screenings which can complement the standard clinical predictors.
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Affiliation(s)
- Barbara Seliger
- Martin-Luther-University Halle-Wittenberg, Institute of Medical Immunology, Halle, Germany.
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25
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Robust detection and identification of multiple oomycetes and fungi in environmental samples by using a novel cleavable padlock probe-based ligation detection assay. Appl Environ Microbiol 2009; 75:4185-93. [PMID: 19395562 DOI: 10.1128/aem.00071-09] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Simultaneous detection and identification of multiple pathogenic microorganisms in complex environmental samples are required in numerous diagnostic fields. Here, we describe the development of a novel, background-free ligation detection (LD) system using a single compound detector probe per target. The detector probes used, referred to as padlock probes (PLPs), are long oligonucleotides containing asymmetric target complementary regions at both their 5' and 3' ends which confer extremely specific target detection. Probes also incorporate a desthiobiotin moiety and an internal endonuclease IV cleavage site. DNA samples are PCR amplified, and the resulting products serve as potential targets for PLP ligation. Upon perfect target hybridization, the PLPs are circularized via enzymatic ligation, captured, and cleaved, allowing only the originally ligated PLPs to be visualized on a universal microarray. Unlike previous procedures, the probes themselves are not amplified, thereby allowing a simple PLP cleavage to yield a background-free assay. We designed and tested nine PLPs targeting several oomycetes and fungi. All of the probes specifically detected their corresponding targets and provided perfect discrimination against closely related nontarget organisms, yielding an assay sensitivity of 1 pg genomic DNA and a dynamic detection range of 10(4). A practical demonstration with samples collected from horticultural water circulation systems was performed to test the robustness of the newly developed multiplex assay. This novel LD system enables highly specific detection and identification of multiple pathogens over a wide range of target concentrations and should be easily adaptable to a variety of applications in environmental microbiology.
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26
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Vares G, Wang B, Shang Y, Ohyama H, Tanaka K, Nakajima T, Nenoi M, Hayata I. Adaptive response in embryogenesis: vi. Comparative microarray analysis of gene expressions in mouse fetuses. Int J Radiat Biol 2009; 85:70-86. [PMID: 19205986 DOI: 10.1080/09553000802635039] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
PURPOSE Exposure of sublethal doses of ionizing radiation can induce protective mechanisms against a subsequent higher dose irradiation. This phenomenon, called radiation-induced adaptive response (AR), has been described in a wide range of biological models. We previously demonstrated the existence of AR in mice during late organogenesis. In this study, we investigated molecular mechanisms underlying AR in this model. MATERIALS AND METHODS Using DNA microarrays, we performed a global analysis of transcriptome regulations in adapted and non-adapted cells collected from whole mouse fetuses, after in utero exposure to priming irradiation. RESULTS We identified AR-specific gene modulations. Our results suggested the involvement of signal transduction and Tumor protein (p53)-related pathways in the induction of AR. CONCLUSIONS Our results are in agreement with previous investigations showing that AR could be dependant on p53 activity. The observed gene modulations may also have possible consequences for subsequent developmental process of the fetus. This is the first report of AR-specific modulations at the molecular level in utero, which could serve as a basis for subsequent studies aimed at understanding AR in this model and possible long-term effects.
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Affiliation(s)
- G Vares
- National Institute of Radiological Sciences, Anagawa, Inage-ku, Chiba, Japan
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27
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Xi D, Keeler B, Zhang W, Houle JD, Gao WJ. NMDA receptor subunit expression in GABAergic interneurons in the prefrontal cortex: application of laser microdissection technique. J Neurosci Methods 2009; 176:172-81. [PMID: 18845188 PMCID: PMC2740488 DOI: 10.1016/j.jneumeth.2008.09.013] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2008] [Revised: 08/28/2008] [Accepted: 09/09/2008] [Indexed: 11/16/2022]
Abstract
The selective involvement of a subset of neurons in many psychiatric disorders, such as gamma-aminobutyric acid (GABA)-ergic interneurons in schizophrenia, creates a significant need for in-depth analysis of these cells. Here we introduce a combination of techniques to examine the relative gene expression of N-methyl-d-aspartic acid (NMDA) receptor subtypes in GABAergic interneurons from the rat prefrontal cortex. Neurons were identified by immunostaining, isolated by laser microdissection and RNA was prepared for reverse transcription polymerase chain reaction (RT-PCR) and real-time PCR. These experimental procedures have been described individually; however, we found that this combination of techniques is powerful for the analysis of gene expression in individual identified neurons. This approach provides the means to analyze relevant molecular mechanisms that are involved in the neuropathological process of a devastating brain disorder.
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Affiliation(s)
- Dong Xi
- Department of Neurobiology and Anatomy, Drexel University College of Medicine, 2900 Queen Lane, Philadelphia, PA 19129, United States
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28
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Comparison and evaluation of RNA quantification methods using viral, prokaryotic, and eukaryotic RNA over a 10(4) concentration range. Anal Biochem 2009; 387:122-7. [PMID: 19454255 DOI: 10.1016/j.ab.2009.01.003] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2008] [Revised: 01/08/2009] [Accepted: 01/09/2009] [Indexed: 11/21/2022]
Abstract
Quantification of RNA is essential for various molecular biology studies. In this work, three quantification methods were evaluated: ultraviolet (UV) absorbance, microcapillary electrophoresis (MCE), and fluorescence-based quantification. Viral, bacterial, and eukaryotic RNA were measured in the 500 to 0.05-ng microl(-1) range via an ND-1000 spectrophotometer (UV), Agilent RNA 6000 kits (MCE), and Quant-iT RiboGreen assay (fluorescence). The precision and accuracy of each method were assessed and compared with a concentration derived independently using inductively coupled plasma-optical emission spectroscopy (ICP-OES). Cost, operator time and skill, and required sample volumes were also considered in the evaluation. Results indicate an ideal concentration range for each quantification technique to optimize accuracy and precision. The ND-1000 spectrophotometer exhibits high precision and accurately quantifies a 1-microl sample in the 500 to 5-ng microl(-1) range. The Quant-iT RiboGreen assay demonstrates high precision in the 1 to 0.05-ng microl(-1) range but is limited to lower RNA concentrations and is more costly than the ND-1000 spectrophotometer. The Agilent kits exhibit less precision than the ND-1000 spectrophotometer and Quant-iT RiboGreen assays in the 500 to 0.05-ng microl(-1) range. However, the Agilent kits require 1 microl of sample and can determine the integrity of the RNA, a useful feature for verifying whether the isolation process was successful.
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Riley RS, Williams D, Ross M, Zhao S, Chesney A, Clark BD, Ben-Ezra JM. Bone marrow aspirate and biopsy: a pathologist's perspective. II. interpretation of the bone marrow aspirate and biopsy. J Clin Lab Anal 2009; 23:259-307. [PMID: 19774631 PMCID: PMC6648980 DOI: 10.1002/jcla.20305] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2008] [Accepted: 02/19/2009] [Indexed: 12/11/2022] Open
Abstract
Bone marrow examination has become increasingly important for the diagnosis and treatment of hematologic and other illnesses. Morphologic evaluation of the bone marrow aspirate and biopsy has recently been supplemented by increasingly sophisticated ancillary assays, including immunocytochemistry, cytogenetic analysis, flow cytometry, and molecular assays. With our rapidly expanding knowledge of the clinical and biologic diversity of leukemia and other hematologic neoplasms, and an increasing variety of therapeutic options, the bone marrow examination has became more critical for therapeutic monitoring and planning optimal therapy. Sensitive molecular techniques, in vitro drug sensitivity testing, and a number of other special assays are available to provide valuable data to assist these endeavors. Fortunately, improvements in bone marrow aspirate and needle technology has made the procurement of adequate specimens more reliable and efficient, while the use of conscious sedation has improved patient comfort. The procurement of bone marrow specimens was reviewed in the first part of this series. This paper specifically addresses the diagnostic interpretation of bone marrow specimens and the use of ancillary techniques.
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Affiliation(s)
- Roger S Riley
- Medical College of Virginia Hospitals of Virginia Commonwealth University, Richmond, Virginia, USA.
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30
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Pinzani P, Lind K, Malentacchi F, Nesi G, Salvianti F, Villari D, Kubista M, Pazzagli M, Orlando C. Prostate-specific antigen mRNA and protein levels in laser microdissected cells of human prostate measured by real-time reverse transcriptase–quantitative polymerase chain reaction and immuno–quantitative polymerase chain reaction. Hum Pathol 2008; 39:1474-82. [DOI: 10.1016/j.humpath.2008.02.012] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/01/2007] [Revised: 02/20/2008] [Accepted: 02/20/2008] [Indexed: 01/15/2023]
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Yoo WG, Kim TI, Li S, Kwon OS, Cho PY, Kim TS, Kim K, Hong SJ. Reference genes for quantitative analysis on Clonorchis sinensis gene expression by real-time PCR. Parasitol Res 2008; 104:321-8. [PMID: 18815810 DOI: 10.1007/s00436-008-1195-x] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2008] [Accepted: 09/09/2008] [Indexed: 02/06/2023]
Abstract
The accuracies of relative gene expressions as determined by quantitative real-time polymerase chain reaction are largely dependent on the variabilities of the reference genes used. Validation of the stabilities of reference genes under experimental conditions is an essential initial step for comparative studies on the expression levels of target genes in experimental groups. Using three total RNA samples extracted independently from Clonorchis sinensis metacercariae and adults, we determined the gene expression stabilities of eight reference gene candidates and the relative transcript levels of three target genes using the geNorm program. The reference genes found to be stably expressed in metacercariae and adults were phosphoglycerate kinase, beta-actin, and calcyphosine; reference genes found to be stably expressed under gamma-irradiated and non-irradiated conditions were succinate dehydrogenase, small nuclear ribonucleoprotein, and beta-actin; and those stably expressed regardless of bile treatment were small nuclear ribonucleoprotein, phosphoglycerate kinase, and succinate dehydrogenase. According to our data, the expression levels of target genes are dependent on normalization factors, such as the C (T) values of single reference genes and the geometric mean of the C (T) values of three reference genes. When comparing C. sinensis gene expressions, we propose to employ the geometric mean of the C (T) values of more than three reference genes validated in the same experimental setting.
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Affiliation(s)
- Won Gi Yoo
- Department of Medical Environmental Biology, Chung-Ang University College of Medicine, Tongjak-gu, Seoul 156-756, Republic of Korea
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Misra A, Kim S. Microbead device for isolating biotinylated oligonucleotides for use in mass spectrometric analysis. Anal Biochem 2008; 384:96-100. [PMID: 18823931 DOI: 10.1016/j.ab.2008.09.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2008] [Revised: 08/26/2008] [Accepted: 09/02/2008] [Indexed: 10/21/2022]
Abstract
We describe a prototypical device for isolating biotinylated oligonucleotides for use in mass spectrometric analysis. It consists of monomeric avidin-coated microbeads trapped in a pipette tip and has been used for genotyping single nucleotide polymorphisms (SNPs) with the previously developed solid phase capture-single base extension (SPC-SBE) method. The device reduces processing time for genotyping by SPC-SBE and allows direct spotting of sample for rapid analysis by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS). In addition, it allows simultaneous processing of multiple samples and can be reused after regeneration of beads with no carryover effects. These results indicate that the microbead device is a low-cost tool that enhances sample cleanup prior to MS for SNP genotyping.
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Affiliation(s)
- Ashish Misra
- Department of Chemical and Biochemical Engineering, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
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Bessaud M, Autret A, Jegouic S, Balanant J, Joffret ML, Delpeyroux F. Development of a Taqman RT-PCR assay for the detection and quantification of negatively stranded RNA of human enteroviruses: evidence for false-priming and improvement by tagged RT-PCR. J Virol Methods 2008; 153:182-9. [PMID: 18706930 DOI: 10.1016/j.jviromet.2008.07.010] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2008] [Revised: 07/09/2008] [Accepted: 07/17/2008] [Indexed: 11/28/2022]
Abstract
Human enteroviruses are among the most common viruses infecting humans. These viruses are known to be able to infect a wide range of tissues and are believed to establish persistent infections. Enteroviruses are positive-sense single-stranded RNA viruses whose replication involves the synthesis of negative strand intermediates. Therefore, the specific detection of negatively stranded viral RNA in tissues or cells is a reliable marker of active enteroviral replication. The present report presents the development of a real-time RT-PCR allowing the specific detection and quantification of negatively stranded viral RNA. Since it was known that specific amplification of single-stranded RNA can be made difficult by false-priming events leading to false-positive or overestimated results, the assay was developed by using a tagged RT primer. This tagged RT-PCR was shown to be able to amplify specifically negative RNA of enteroviruses grown in cell cultures by preventing the amplification of cDNAs generated by false-priming.
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Affiliation(s)
- Maël Bessaud
- Unité postulante de biologie des virus entériques, Institut Pasteur, 25 rue du Dr Roux, 75 015 Paris, France.
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Hansen RR, Avens HJ, Shenoy R, Bowman CN. Quantitative evaluation of oligonucleotide surface concentrations using polymerization-based amplification. Anal Bioanal Chem 2008; 392:167-75. [PMID: 18661123 PMCID: PMC2517095 DOI: 10.1007/s00216-008-2259-6] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2008] [Revised: 06/17/2008] [Accepted: 06/18/2008] [Indexed: 01/10/2023]
Abstract
Quantitative evaluation of minimal polynucleotide concentrations has become a critical analysis among a myriad of applications found in molecular diagnostic technology. Development of high-throughput, nonenzymatic assays that are sensitive, quantitative and yet feasible for point-of-care testing are thus beneficial for routine implementation. Here, we develop a nonenzymatic method for quantifying surface concentrations of labeled DNA targets by coupling regulated amounts of polymer growth to complementary biomolecular binding on array-based biochips. Polymer film thickness measurements in the 20–220 nm range vary logarithmically with labeled DNA surface concentrations over two orders of magnitude with a lower limit of quantitation at 60 molecules/μm2 (∼106 target molecules). In an effort to develop this amplification method towards compatibility with fluorescence-based methods of characterization, incorporation of fluorescent nanoparticles into the polymer films is also evaluated. The resulting gains in fluorescent signal enable quantification using detection instrumentation amenable to point-of-care settings. Polymerization-based amplification for quantitative evaluation of 3’ biotinylated oligonucleotide surface concentrations ![]()
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Affiliation(s)
- Ryan R Hansen
- Department of Chemical and Biological Engineering, ECCH 111 CB 424, University of Colorado, Boulder, CO 80309, USA
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Affiliation(s)
- Zoltan P. Arany
- Cardiovascular Institute, Beth Israel Deaconess Medical Center and Harvard Medical School Boston Massachusetts
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36
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Burns M, Valdivia H. A simulation approach to assess the minimal number of real-time PCR replicates for GM quantification. Eur Food Res Technol 2008. [DOI: 10.1007/s00217-008-0899-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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Serrano E, Carnicer MJ, Lasa A, Orantes V, Pena J, Brunet S, Aventín A, Sierra J, Nomdedéu JF. Epigenetic-based treatments emphasize the biologic differences of core-binding factor acute myeloid leukemias. Leuk Res 2008; 32:944-53. [DOI: 10.1016/j.leukres.2007.11.038] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2007] [Revised: 11/14/2007] [Accepted: 11/24/2007] [Indexed: 10/22/2022]
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Dutil S, Veillette M, Mériaux A, Lazure L, Barbeau J, Duchaine C. Aerosolization of mycobacteria and legionellae during dental treatment: low exposure despite dental unit contamination. Environ Microbiol 2008; 9:2836-43. [PMID: 17922766 DOI: 10.1111/j.1462-2920.2007.01395.x] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Dental unit waterlines (DUWL) support growth of a dense microbial population that includes pathogens and hypersensitivity-inducing bacteria, such as Legionella spp. and non-tuberculous mycobacteria (NTM). Dynamic dental instruments connected to DUWL generate aerosols in the work environment, which could allow waterborne pathogens to be aerosolized. The use of the real-time quantitative polymerase chain reaction (qPCR) provides a more accurate estimation of exposure levels compared with the traditional culture approach. Bioaerosol sampling was performed 13 times in an isolated dental treatment room according to a standardized protocol that included four dental prophylaxis treatments. Inhalable dust samples were taken at the breathing zone of both the hygienist and patient and outside the treatment room (control). Total bacteria as well as Legionella spp. and NTM were quantified by qPCR in bioaerosol and DUWL water samples. Dental staff and patients are exposed to bacteria generated during dental treatments (up to 4.3 E + 05 bacteria per m(3) of air). Because DUWL water studied was weakly contaminated by Legionella spp. and NTM, their aerosolization during dental treatment was not significant. As a result, infectious and sensitization risks associated with legionellae and NTM should be minimal.
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Affiliation(s)
- Steve Dutil
- Institut universitaire de cardiologie et de pneumologie de l'Université Laval, Hôpital Laval, Québec, Québec, Canada
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Hashimoto T, Arion D, Unger T, Maldonado-Avilés JG, Morris HM, Volk DW, Mirnics K, Lewis DA. Alterations in GABA-related transcriptome in the dorsolateral prefrontal cortex of subjects with schizophrenia. Mol Psychiatry 2008; 13:147-61. [PMID: 17471287 PMCID: PMC2882638 DOI: 10.1038/sj.mp.4002011] [Citation(s) in RCA: 388] [Impact Index Per Article: 24.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/11/2006] [Revised: 03/07/2007] [Accepted: 03/19/2007] [Indexed: 12/23/2022]
Abstract
In subjects with schizophrenia, impairments in working memory are associated with dysfunction of the dorsolateral prefrontal cortex (DLPFC). This dysfunction appears to be due, at least in part, to abnormalities in gamma-aminobutyric acid (GABA)-mediated inhibitory circuitry. To test the hypothesis that altered GABA-mediated circuitry in the DLPFC of subjects with schizophrenia reflects expression changes of genes that encode selective presynaptic and postsynaptic components of GABA neurotransmission, we conducted a systematic expression analysis of GABA-related transcripts in the DLPFC of 14 pairs of schizophrenia and age-, sex- and post-mortem interval-matched control subjects using a customized DNA microarray with enhanced sensitivity and specificity. Subjects with schizophrenia exhibited expression deficits in GABA-related transcripts encoding (1) presynaptic regulators of GABA neurotransmission (67 kDa isoform of glutamic acid decarboxylase (GAD(67)) and GABA transporter 1), (2) neuropeptides (somatostatin (SST), neuropeptide Y (NPY) and cholecystokinin (CCK)) and (3) GABA(A) receptor subunits (alpha1, alpha4, beta3, gamma2 and delta). Real-time qPCR and/or in situ hybridization confirmed the deficits for six representative transcripts tested in the same pairs and in an extended cohort, respectively. In contrast, GAD(67), SST and alpha1 subunit mRNA levels, as assessed by in situ hybridization, were not altered in the DLPFC of monkeys chronically exposed to antipsychotic medications. These findings suggest that schizophrenia is associated with alterations in inhibitory inputs from SST/NPY-containing and CCK-containing subpopulations of GABA neurons and in the signaling via certain GABA(A) receptors that mediate synaptic (phasic) or extrasynaptic (tonic) inhibition. In concert with previous findings, these data suggest that working memory dysfunction in schizophrenia is mediated by altered GABA neurotransmission in certain DLPFC microcircuits.
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Affiliation(s)
- T Hashimoto
- Department of Psychiatry, Western Psychiatric Institute and Clinic, University of Pittsburgh, Pittsburgh, PA 15213, USA
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Piña B, Casado M, Quirós L. Analysis of gene expression as a new tool in ecotoxicology and environmental monitoring. Trends Analyt Chem 2007. [DOI: 10.1016/j.trac.2007.09.009] [Citation(s) in RCA: 57] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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Tani H, Kanagawa T, Morita N, Kurata S, Nakamura K, Tsuneda S, Noda N. Calibration-curve-free quantitative PCR: A quantitative method for specific nucleic acid sequences without using calibration curves. Anal Biochem 2007; 369:105-11. [PMID: 17679100 DOI: 10.1016/j.ab.2007.06.047] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2007] [Revised: 06/29/2007] [Accepted: 06/30/2007] [Indexed: 10/23/2022]
Abstract
We have developed a simple quantitative method for specific nucleic acid sequences without using calibration curves. This method is based on the combined use of competitive polymerase chain reaction (PCR) and fluorescence quenching. We amplified a gene of interest (target) from DNA samples and an internal standard (competitor) with a sequence-specific fluorescent probe using PCR and measured the fluorescence intensities before and after PCR. The fluorescence of the probe is quenched on hybridization with the target by guanine bases, whereas the fluorescence is not quenched on hybridization with the competitor. Therefore, quench rate (i.e., fluorescence intensity after PCR divided by fluorescence intensity before PCR) is always proportional to the ratio of the target to the competitor. Consequently, we can calculate the ratio from quench rate without using a calibration curve and then calculate the initial copy number of the target from the ratio and the initial copy number of the competitor. We successfully quantified the copy number of a recombinant DNA of genetically modified (GM) soybean and estimated the GM soybean contents. This method will be particularly useful for rapid field tests of the specific gene contamination in samples.
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Affiliation(s)
- Hidenori Tani
- Department of Chemical Engineering, Waseda University, Shinjuku-ku, Tokyo 169-8555, Japan
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du Plessis E, Theron J, Berger E, Louw M. Evaluation of the Staphylococcus aureus class C nonspecific acid phosphatase (SapS) as a reporter for gene expression and protein secretion in gram-negative and gram-positive bacteria. Appl Environ Microbiol 2007; 73:7232-9. [PMID: 17905879 PMCID: PMC2168221 DOI: 10.1128/aem.01030-07] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
A phosphatase secreted by Staphylococcus aureus strain 154 has previously been characterized and classified as a new member of the bacterial class C family of nonspecific acid phosphatases. As the acid phosphatase activity can be easily detected with a cost-effective plate screen assay, quantitatively measured by a simple enzyme assay, and detected by zymography, its potential use as a reporter system was investigated. The S. aureus acid phosphatase (sapS) gene has been cloned and expressed from its own regulatory sequences in Escherichia coli, Bacillus subtilis, and Bacillus halodurans. Transcriptional and translational fusions of the sapS gene with selected heterologous promoters and signal sequences were constructed and expressed in all three of the host strains. From the range of promoters evaluated, the strongest promoter for heterologous protein production in each of the host strains was identified, i.e., the E. coli lacZ promoter in E. coli, the B. halodurans alkaline protease promoter in B. subtilis, and the B. halodurans sigma(D) promoter in B. halodurans. This is the first report on the development of a class C acid phosphatase gene as a reporter gene with the advantage of being able to function in both gram-positive and gram-negative host strains.
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Turakulov R, Nontachaiyapoom S, Mitchelson KR, Gresshoff PM, Men AE. Ultrasensitive determination of absolute mRNA amounts at attomole levels of nearly identical plant genes with high-throughput mass spectrometry (MassARRAY). PLANT & CELL PHYSIOLOGY 2007; 48:1379-84. [PMID: 17686807 DOI: 10.1093/pcp/pcm103] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2023]
Abstract
Detection of very small amounts of RNA based on microdissection of plant tissue is essential for modern plant biology. Mass spectroscopy technology (MassARRAY) based on Sequenomtrade mark instrumentation was adapted to determine quickly and in a high-throughput fashion (by multiplexing) the absolute amounts of mRNA of closely related soybean genes. A sensitivity of 0.1 amol (10(-19)) was achieved, representing as few as 1,000 mRNA molecules. This methodology eliminates the use of housekeeping genes as reference standards and has multiple applications for plant functional genomics, such as the monitoring of individual expression of paralogous genes at ultra-low expression levels and/or in extremely small tissue samples.
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Affiliation(s)
- Rust Turakulov
- Australian Genome Research Facility, Level 5, Gehrmann Laboratories, University of Queensland, St Lucia, Brisbane, Australia
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van Doorn R, Szemes M, Bonants P, Kowalchuk GA, Salles JF, Ortenberg E, Schoen CD. Quantitative multiplex detection of plant pathogens using a novel ligation probe-based system coupled with universal, high-throughput real-time PCR on OpenArrays. BMC Genomics 2007; 8:276. [PMID: 17697351 PMCID: PMC2064939 DOI: 10.1186/1471-2164-8-276] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2007] [Accepted: 08/14/2007] [Indexed: 11/10/2022] Open
Abstract
Background Diagnostics and disease-management strategies require technologies to enable the simultaneous detection and quantification of a wide range of pathogenic microorganisms. Most multiplex, quantitative detection methods available suffer from compromises between the level of multiplexing, throughput and accuracy of quantification. Here, we demonstrate the efficacy of a novel, high-throughput, ligation-based assay for simultaneous quantitative detection of multiple plant pathogens. The ligation probes, designated Plant Research International-lock probes (PRI-lock probes), are long oligonucleotides with target complementary regions at their 5' and 3' ends. Upon perfect target hybridization, the PRI-lock probes are circularized via enzymatic ligation, subsequently serving as template for individual, standardized amplification via unique probe-specific primers. Adaptation to OpenArrays™, which can accommodate up to 3072 33 nl PCR amplifications, allowed high-throughput real-time quantification. The assay combines the multiplex capabilities and specificity of ligation reactions with high-throughput real-time PCR in the OpenArray™, resulting in a flexible, quantitative multiplex diagnostic system. Results The performance of the PRI-lock detection system was demonstrated using 13 probes targeting several significant plant pathogens at different taxonomic levels. All probes specifically detected their corresponding targets and provided perfect discrimination against non-target organisms with very similar ligation target sites. The nucleic acid targets could be reliably quantified over 5 orders of magnitude with a dynamic detection range of more than 104. Pathogen quantification was equally robust in single target versus mixed target assays. Conclusion This novel assay enables very specific, high-throughput, quantitative detection of multiple pathogens over a wide range of target concentrations and should be easily adaptable for versatile diagnostic purposes.
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Affiliation(s)
- Ronald van Doorn
- Plant Research International B.V., Droevendaalsesteeg 1, 6708 PB, Wageningen, the Netherlands
- NIOO-Centre for Terrestrial Ecology, P.O. Box 40, 6666 ZG, Heteren, the Netherlands
| | - Marianna Szemes
- Plant Research International B.V., Droevendaalsesteeg 1, 6708 PB, Wageningen, the Netherlands
- University of Bristol, Department of Cellular and Molecular Medicine, University Walk, Bristol, BS8 1TD, UK
| | - Peter Bonants
- Plant Research International B.V., Droevendaalsesteeg 1, 6708 PB, Wageningen, the Netherlands
| | - George A Kowalchuk
- NIOO-Centre for Terrestrial Ecology, P.O. Box 40, 6666 ZG, Heteren, the Netherlands
- Free University of Amsterdam, Institute of Ecological Science, De Boelelaan 1085, 1081 HV, Amsterdam, the Netherlands
| | - Joana F Salles
- Plant Research International B.V., Droevendaalsesteeg 1, 6708 PB, Wageningen, the Netherlands
- UMR CNRS 5557- Université Lyon 1, USC INRA 1193, Microbial Ecology Centre, F-69622 Villeurbanne, France
| | - Elen Ortenberg
- BioTrove, Inc. 12 Gill Street, Woburn, MA 01801-1728, USA
| | - Cor D Schoen
- Plant Research International B.V., Droevendaalsesteeg 1, 6708 PB, Wageningen, the Netherlands
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Characterization of the genomic region containing the Shadow of Prion Protein (SPRN) gene in sheep. BMC Genomics 2007; 8:138. [PMID: 17537256 PMCID: PMC1899180 DOI: 10.1186/1471-2164-8-138] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2007] [Accepted: 05/30/2007] [Indexed: 01/23/2023] Open
Abstract
Background TSEs are a group of fatal neurodegenerative diseases occurring in man and animals. They are caused by prions, alternatively folded forms of the endogenous prion protein, encoded by PRNP. Since differences in the sequence of PRNP can not explain all variation in TSE susceptibility, there is growing interest in other genes that might have an influence on this susceptibility. One of these genes is SPRN, a gene coding for a protein showing remarkable similarities with the prion protein. Until now, SPRN has not been described in sheep, a highly relevant species in prion matters. Results In order to characterize the genomic region containing SPRN in sheep, a BAC mini-contig was built, covering approximately 200,000 bp and containing the genes ECHS1, PAOX, MTG1, SPRN, LOC619207, CYP2E1 and at least partially SYCE1. FISH mapping of the two most exterior BAC clones of the contig positioned this contig on Oari22q24. A fragment of 4,544 bp was also sequenced, covering the entire SPRN gene and 1206 bp of the promoter region. In addition, the transcription profile of SPRN in 21 tissues was determined by RT-PCR, showing high levels in cerebrum and cerebellum, and low levels in testis, lymph node, jejunum, ileum, colon and rectum. Conclusion Annotation of a mini-contig including SPRN suggests conserved linkage between Oari22q24 and Hsap10q26. The ovine SPRN sequence, described for the first time, shows a high level of homology with the bovine, and to a lesser extent with the human SPRN sequence. In addition, transcription profiling in sheep reveals main expression of SPRN in brain tissue, as in rat, cow, man and mouse.
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Ouakad M, Bahi-Jaber N, Chenik M, Dellagi K, Louzir H. Selection of endogenous reference genes for gene expression analysis in Leishmania major developmental stages. Parasitol Res 2007; 101:473-7. [PMID: 17318579 DOI: 10.1007/s00436-007-0491-1] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2006] [Accepted: 02/01/2007] [Indexed: 10/23/2022]
Abstract
At the era of post-genomics, gene expression analysis constitutes an important step for understanding the biological functions of genes. For this, reverse transcription and real-time polymerase chain reaction (RT-PCR) is one of the most accurate techniques available to date. Normalization with a proper internal control is critical for the generation of reliable results with biological significance. This is particularly true for pathogens, like Leishmania (L.) parasites, that alternate between different stages during their life cycle. In this study, we evaluate six different sequences for their potential as suitable internal control for the study of gene expression in three different developmental stages (procyclic and metacyclic promastigotes and amastigotes) of the parasite Leishmania major. Experiments were performed on RNA purified from three L. major isolates using the RT-PCR technique. Data analysis was performed using GeNorm and NormFinder programs. We could determine that a sequence encoding rRNA45 is the most stable in the three developmental stages of the parasite and can thus be used as a reference gene in gene expression studies in L. major.
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Affiliation(s)
- Meriam Ouakad
- Laboratory of Immunopathology, Vaccinology and Molecular Genetics (LIVGM), Institut Pasteur de Tunis, BP 74, 13, Place Pasteur, 1002, Tunis-Belvedere, Tunisia
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Ouakad M, Chenik M, Ben Achour-Chenik Y, Louzir H, Dellagi K. Gene expression analysis of wild Leishmania major isolates: identification of genes preferentially expressed in amastigotes. Parasitol Res 2006; 100:255-64. [PMID: 17016728 DOI: 10.1007/s00436-006-0277-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2006] [Accepted: 07/03/2006] [Indexed: 10/24/2022]
Abstract
Trying to identify virulence genes of wild Leishmania (L.) major parasites, the species responsible for zoonotic cutaneous leishmaniasis, we compared, using differential display technique, gene expression in two L. major isolates obtained from human lesions and characterized by their contrasting pathogenicity in the BALB/c mouse model. The analysis was performed on amastigotes derived from BALB/c mice lesions. A total of 13 different clones were identified, but the use of reverse transcription and real-time polymerase chain reaction technique did not allow us to confirm any of these clones as differentially expressed. However, the fact that we used the amastigote stage of the parasite led us the identification of amastigote-specific genes, essentially (8 among 13). They are overexpressed, two to seven times, in amastigotes relative to promastigotes. Sequence analysis revealed that two of them namely LPG3 and the ATP dependent RNA helicase correspond to previously described amastigote-specific genes. The others correspond to genes involved in important biological process. Their better characterization could help the development of new drugs targeting the processes in which these molecules are involved.
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Affiliation(s)
- Meriem Ouakad
- Laboratoire d'Immunopathologie, Vaccinologie et Génétique Moléculaire, Institut Pasteur de Tunis, 13, Place Pasteur 1002, Tunis-Belvédère, Tunisia
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Schefe JH, Lehmann KE, Buschmann IR, Unger T, Funke-Kaiser H. Quantitative real-time RT-PCR data analysis: current concepts and the novel "gene expression's CT difference" formula. J Mol Med (Berl) 2006; 84:901-10. [PMID: 16972087 DOI: 10.1007/s00109-006-0097-6] [Citation(s) in RCA: 607] [Impact Index Per Article: 33.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2006] [Accepted: 07/20/2006] [Indexed: 01/02/2023]
Abstract
For quantification of gene-specific mRNA, quantitative real-time RT-PCR has become one of the most frequently used methods over the last few years. This article focuses on the issue of real-time PCR data analysis and its mathematical background, offering a general concept for efficient, fast and precise data analysis superior to the commonly used comparative CT (DeltaDeltaCT) and the standard curve method, as it considers individual amplification efficiencies for every PCR. This concept is based on a novel formula for the calculation of relative gene expression ratios, termed GED (Gene Expression's CT Difference) formula. Prerequisites for this formula, such as real-time PCR kinetics, the concept of PCR efficiency and its determination, are discussed. Additionally, this article offers some technical considerations and information on statistical analysis of real-time PCR data.
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Affiliation(s)
- Jan H Schefe
- Center for Cardiovascular Research (CCR)/Institute of Pharmacology and Toxicology, Charité-Universitätsmedizin Berlin, Hessische Strasse 3-4, 10115, Berlin, Germany
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Canevari S, Gariboldi M, Reid JF, Bongarzone I, Pierotti MA. Molecular predictors of response and outcome in ovarian cancer. Crit Rev Oncol Hematol 2006; 60:19-37. [PMID: 16829123 DOI: 10.1016/j.critrevonc.2006.03.003] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2005] [Revised: 03/30/2006] [Accepted: 03/30/2006] [Indexed: 02/03/2023] Open
Abstract
A major problem in clinical management of patients with epithelial ovarian cancer (EOC) is the largely unpredictable response to first-line treatment and the occurrence of relapse after complete initial response, associated with broad cross-resistance to even structurally dissimilar drugs. During tumor development and progression, multiple genic alterations take place that might contribute specifically to the treatment response and eventually impact on disease outcome. One area of intense research is the identification of molecular markers to accurately assess the prognosis of EOC patients and to define innovative therapeutic strategies. A large survey of recent published data indicates the need to revisit traditional molecular markers with respect to their contribution to the assessment of overall survival in selected populations. Furthermore, recent technological developments that enable simultaneous measurement of many parameters ("omic" approaches) hold the promise of identifying new molecular prognostic and predictive markers.
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Affiliation(s)
- Silvana Canevari
- Unit of Molecular Therapies, Department of Experimental Oncology, Istituto Nazionale Tumori, 20133-Milan, Italy.
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Ralser M, Querfurth R, Warnatz HJ, Lehrach H, Yaspo ML, Krobitsch S. An efficient and economic enhancer mix for PCR. Biochem Biophys Res Commun 2006; 347:747-51. [PMID: 16842759 DOI: 10.1016/j.bbrc.2006.06.151] [Citation(s) in RCA: 155] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2006] [Accepted: 06/27/2006] [Indexed: 11/19/2022]
Abstract
Polymerase chain reaction (PCR) has become a fundamental technique in molecular biology. Nonetheless, further improvements of the existing protocols are required to broaden the applicability of PCR for routine diagnostic purposes, to enhance the specificity and the yield of PCRs as well as to reduce the costs for high-throughput applications. One known problem typically reported in PCR experiments is the poor amplification of GC-rich DNA sequences. Here we designed and tested a novel effective and low-cost PCR enhancer, a concentration-dependent combination of betaine, dithiothreitol, and dimethyl sulfoxide that broadly enhanced the quantitative and/or qualitative output of PCRs. Additionally, we showed that the performances of this enhancer mix are comparable to those of commercially available PCR additives and highly effective with different DNA polymerases. Thus, we propose the routine application of this PCR enhancer mix for low- and high-throughput experiments.
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Affiliation(s)
- Markus Ralser
- Max Planck Institute for Molecular Genetics, Berlin, Germany
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