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Search Results: 1 - 10 of 3021 matches for " Nicole Regier "
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Experimental comparison of relative RT-qPCR quantification approaches for gene expression studies in poplar
Nicole Regier, Beat Frey
BMC Molecular Biology , 2010, DOI: 10.1186/1471-2199-11-57
Abstract: We quantified gene expression of superoxide dismutase (SOD) and ascorbate peroxidase (APX) in the roots of two black poplar clones, 58-861 and Poli, which were subjected to drought stress. After proving the chosen reference genes actin (ACT), elongation factor 1 (EF1) and ubiquitin (UBQ) to be constantly expressed in the different watering regimes, we applied different approaches for relative quantification to the same raw fluorescence data. The results obtained using the comparative Cq method, LinRegPCR, qBase software and the Pfaffl model showed a good correlation, whereas calculation according to the Liu and Saint method produced highly variable results. However, it has been shown that the most reliable approach for calculation of the amplification efficiency is using the mean increase in fluorescence during PCR in each individual reaction. Accordingly, we could improve the quality of our results by applying the mean amplification efficiencies for each amplicon to the Liu and Saint method.As we could show that gene expression results can vary depending on the approach used for quantification, we recommend to carefully evaluate different quantification approaches before using them in studies analysing gene expression.RT-qPCR is a widely used method for analysing gene expression. It has been developed by combining PCR with fluorescent techniques [1,2]. It depends on collecting data throughout the PCR amplification, which is achieved by monitoring the increase in fluorescence intensity of a specific fluorescence dye, which correlates to the increase in PCR product concentration. The major progress of qPCR is that quantification does not have to be done in the plateau phase of amplification, which is a disadvantage of previous quantification methods [1].PCR can be divided into four major phases: linear ground phase, early exponential phase, log-linear phase and plateau phase [3]. During the linear ground phase, only background fluorescence is detected. The early expo
Effect of Elodea nuttallii Roots on Bacterial Communities and MMHg Proportion in a Hg Polluted Sediment
Nicole Regier, Beat Frey, Brandon Converse, Eric Roden, Alexander Grosse-Honebrink, Andrea Garcia Bravo, Claudia Cosio
PLOS ONE , 2012, DOI: 10.1371/journal.pone.0045565
Abstract: The objective of this study was to assess the effect of a rooted macrophyte Elodea nuttallii on rhizosphere bacterial communities in Hg contaminated sediments. Specimens of E. nuttallii were exposed to sediments from the Hg contaminated Babeni reservoir (Olt River, Romania) in our microcosm. Plants were allowed to grow for two months until they occupied the entirety of the sediments. Total Hg and MMHg were analysed in sediments where an increased MMHg percentage of the total Hg in pore water of rhizosphere sediments was found. E. nuttallii roots also significantly changed the bacterial community structure in rhizosphere sediments compared to bulk sediments. Deltaproteobacteria dominated the rhizosphere bacterial community where members of Geobacteraceae within the Desulfuromonadales and Desulfobacteraceae were identified. Two bacterial operational taxonomic units (OTUs) which were phylogenetically related to sulfate-reducing bacteria (SRB) became abundant in the rhizosphere. We suggest that these phylotypes could be potentially methylating bacteria and might be responsible for the higher MMHg percentage of the total Hg in rhizosphere sediments. However, SRB were not significantly favoured in rhizosphere sediments as shown by qPCR. Our findings support the hypothesis that rooted macrophytes created a microenvironment favorable for Hg methylation. The presence of E. nuttallii in Hg contaminated sediments should therefore not be overlooked.
Earthways: Opportunity, Community and Meaning in the Personal Garden
Renate Sander-Regier
The Brock Review , 2008,
Abstract: The hybrid space of the personal garden offers valuable opportunities for individuals to express themselves personally in an outdoor setting, to develop meaningful relationships with green spaces, and to connect with the greater natural environment and urban community, as demonstrated in the works of contemporary gardener-authors Marjorie Harris, Sara Stein, and Leon Whiteson. These opportunities are particularly significant in urban environments where access to nature and green space is limited, and where gardening activities can contribute to the health of the natural environment, the wellbeing of people involved in the space, and the vitality of the community at large.
Sources of Signal in 62 Protein-Coding Nuclear Genes for Higher-Level Phylogenetics of Arthropods
Jerome C. Regier,Andreas Zwick
PLOS ONE , 2012, DOI: 10.1371/journal.pone.0023408
Abstract: This study aims to investigate the strength of various sources of phylogenetic information that led to recent seemingly robust conclusions about higher-level arthropod phylogeny and to assess the role of excluding or downweighting synonymous change for arriving at those conclusions.
From Sméagol to Gollum: Mechanical Stress and Bone Remodelling  [PDF]
Nicole Pace
Open Journal of Orthopedics (OJO) , 2018, DOI: 10.4236/ojo.2018.84018
Abstract: This imaginary transformation from Sméagol to Gollum is a dramatization of the illusive repercussions of mechanical stress affecting bone. This paper presents the main ideas of mechanical stress and bone remodelling from a novel’s perspective. The object of this study is to provide evidence for new ways to explore bone’s functional adaptation to mechanical stress made through the copious interpretation and integration of new and existing literature. It tackles the underlying biology of bone cells and how they detect and react to strain stimuli. The different types of mechanical demands in daily activities are sifted through and any misconceptions found fallible in literature are refined. A personal experience of a stress fracture is reviewed to parallel the implications that lead to the incident with the findings on the link between mechanical stress and bone remodelling. Some factors regarding age, gender and ethnicity and the interplay with mechanical stress influencing bone remodelling are considered. Brief overviews of three new medical novelties in bone healing are outlined, hoping that these interventions of proper medical techniques can be a change for the better: one from Gollum to Sméagol rather than vice versa.
Mini-Minimax Uncertainty Quantification for Emulators
Jeffrey C. Regier,Philip B. Stark
Statistics , 2013, DOI: 10.1137/130917909
Abstract: Consider approximating a "black box" function $f$ by an emulator $\hat{f}$ based on $n$ noiseless observations of $f$. Let $w$ be a point in the domain of $f$. How big might the error $|\hat{f}(w) - f(w)|$ be? If $f$ could be arbitrarily rough, this error could be arbitrarily large: we need some constraint on $f$ besides the data. Suppose $f$ is Lipschitz with known constant. We find a lower bound on the number of observations required to ensure that for the best emulator $\hat{f}$ based on the $n$ data, $|\hat{f}(w) - f(w)| \le \epsilon$. But in general, we will not know whether $f$ is Lipschitz, much less know its Lipschitz constant. Assume optimistically that $f$ is Lipschitz-continuous with the smallest constant consistent with the $n$ data. We find the maximum (over such regular $f$) of $|\hat{f}(w) - f(w)|$ for the best possible emulator $\hat{f}$; we call this the "mini-minimax uncertainty" at $w$. In reality, $f$ might not be Lipschitz or---if it is---it might not attain its Lipschitz constant on the data. Hence, the mini-minimax uncertainty at $w$ could be much smaller than $|\hat{f}(w) - f(w)|$. But if the mini-minimax uncertainty is large, then---even if $f$ satisfies the optimistic regularity assumption---$|\hat{f}(w) - f(w)|$ could be large, no matter how cleverly we choose $\hat{f}$. For the Community Atmosphere Model, the maximum (over $w$) of the mini-minimax uncertainty based on a set of 1154~observations of $f$ is no smaller than it would be for a single observation of $f$ at the centroid of the 21-dimensional parameter space. We also find lower confidence bounds for quantiles of the mini-minimax uncertainty and its mean over the domain of $f$. For the Community Atmosphere Model, these lower confidence bounds are an appreciable fraction of the maximum.
The Influence of Implicit Achievement Motive and Graphological Variables on Learning Variables  [PDF]
Nicole Gruber, Ludwig Kreuzpointner
Psychology (PSYCH) , 2015, DOI: 10.4236/psych.2015.612145
Abstract: There are several methods of implicit measurement. A very valid and wide spread assessment of motives by using the technique of projection is picture story exercises (PSE). Graphology, as theory of inferences on personality and motives by analyzing handwriting, is another one. The presented study examines the commons of the both measurement methods and their prediction of achievement behaviour. So, the achievement motive of 189 students was assessed using the PSE of Heckhausen (1963) and afterwards their handwriting was scored by a categorical system of Ploog (2013). Achievement related behaviour was operatively analyzed with self-reported learning time, learning behaviour and task-choice performance. It is shown that implicit motives measured by PSE are related with the criteria of task-choice performance. It is shown that both implicit motives measured by PSE and graphological variables deliver information about learning variables.
The Use of Low Molecular Weight Heparin for Venous Thromboembolism Prophylaxis in Medical Patients: How Much Are We Adherent to the Guidelines?  [PDF]
Lamia AlHajri, Nicole Gebran
Open Journal of Internal Medicine (OJIM) , 2015, DOI: 10.4236/ojim.2015.54012
Abstract: Background: Venous thromboembolism (VTE) is a common complication seen during or after hospitalization that manifests as deep venous thrombosis (DVT) and/or pulmonary embolism (PE). PE is considered the commonest preventable cause of death during and/or after hospitalization. Thus, pharmacological and mechanical methods are used to prevent VTE in hospitalized patients. Despite the availability of guidelines for VTE prophylaxis, it is crucial to assess the adherence and adaptation of the institution to these guidelines. Purpose: This study aimed to investigate adherence to the American College of Chest Physicians (ACCP) 2012 VTE prophylaxis guidelines in hospitalized medical patients in a tertiary care hospital in the United Arab Emirates. Methods: An observational prospective design was utilized in this study. To achieve the purpose, primary and secondary end points were identified to be the core of the investigation. The primary end points were: the incidence of bleeding, VTE, and cardiovascular events. While the secondary end points were: dose and indication validity for prophylaxis, VTE and bleeding risk assessments, adverse drug events (ADE) other than bleeding, appropriate monitoring when on low molecular weight heparin (LMWH) and the presence of contraindication at the time of prescribing LMWH. Results: 16 patients (20%) out of the total 80 met one or more of the primary end points. The vast majority of patients (81.25%) developed bleeding, while VTE was seen in one case only during hospitalization. 11 patients (13.75%) received LMWH while a contraindication was present. 15 patients (18.75%) who were prescribed LMWH had an International Medical Prevention Registry on Venous Thromboembolism (IMPROVE) bleeding risk score of ≥7. However, 5 out of 13 patients (38.46%) who developed bleeding had a bleeding score of ≥7, and the relationship between bleeding score of ≥7 and the development of bleeding was statistically significant (p = 0.047). When investigating the doses that were utilized, 40% were prescribed an inappropriate dose. Conclusion: Various factors played a role in the inappropriateness of VTE prophylaxis such as; poor adherence to VTE guidelines, inappropriate dosing and monitoring, and not evaluating the bleeding risk. Hence, to be able to achieve effective VTE prophylaxis, these factors need to be addressed through adherence to and adaptation of the ACCP 2012 VTE prophylaxis guidelines.
Resolving Discrepancy between Nucleotides and Amino Acids in Deep-Level Arthropod Phylogenomics: Differentiating Serine Codons in 21-Amino-Acid Models
Andreas Zwick, Jerome C. Regier, Derrick J. Zwickl
PLOS ONE , 2012, DOI: 10.1371/journal.pone.0047450
Abstract: Background In a previous study of higher-level arthropod phylogeny, analyses of nucleotide sequences from 62 protein-coding nuclear genes for 80 panarthopod species yielded significantly higher bootstrap support for selected nodes than did amino acids. This study investigates the cause of that discrepancy. Methodology/Principal Findings The hypothesis is tested that failure to distinguish the serine residues encoded by two disjunct clusters of codons (TCN, AGY) in amino acid analyses leads to this discrepancy. In one test, the two clusters of serine codons (Ser1, Ser2) are conceptually translated as separate amino acids. Analysis of the resulting 21-amino-acid data matrix shows striking increases in bootstrap support, in some cases matching that in nucleotide analyses. In a second approach, nucleotide and 20-amino-acid data sets are artificially altered through targeted deletions, modifications, and replacements, revealing the pivotal contributions of distinct Ser1 and Ser2 codons. We confirm that previous methods of coding nonsynonymous nucleotide change are robust and computationally efficient by introducing two new degeneracy coding methods. We demonstrate for degeneracy coding that neither compositional heterogeneity at the level of nucleotides nor codon usage bias between Ser1 and Ser2 clusters of codons (or their separately coded amino acids) is a major source of non-phylogenetic signal. Conclusions The incongruity in support between amino-acid and nucleotide analyses of the forementioned arthropod data set is resolved by showing that “standard” 20-amino-acid analyses yield lower node support specifically when serine provides crucial signal. Separate coding of Ser1 and Ser2 residues yields support commensurate with that found by degenerated nucleotides, without introducing phylogenetic artifacts. While exclusion of all serine data leads to reduced support for serine-sensitive nodes, these nodes are still recovered in the ML topology, indicating that the enhanced signal from Ser1 and Ser2 is not qualitatively different from that of the other amino acids.
Looking for biomarkers of Hg exposure by transcriptome analysis in the aquatic plant Elodea nuttallii
Regier N.,Baerlocher L.,Münsterk?tter M.,Farinelli L.
E3S Web of Conferences , 2013, DOI: 10.1051/e3sconf/20130129004
Abstract: Recently developed genomics tools have a promising potential to identify early biomarkers of exposure to toxicants. In the present work we used transcriptome analysis (RNA-seq) of Elodea nuttallii –an invasive rooted macrophyte that is able to accumulate large amounts of metals- to identify biomarkers of Hg exposure. RNA-seq allowed identification of genes affected by Hg exposure and also unraveled plant response to the toxic metal: a change in energy/reserve metabolism caused by the inhibition of photosynthesis, and an adaptation of homeostasis networks to control accumulation of Hg. Data were validated by RT-qPCR and selected genes were further tested as biomarkers. Samples exposed in the field and to natural contaminated sediments clustered well with samples exposed to low metal concentrations under laboratory conditions. Our data suggest that this plant and/or this approach could be useful to develop new tests for water and sediment quality assessment.
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