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Marko Rožman, Mira Petrović
Quantitative target analysis by liquid chromatography coupled to mass spectrometry (LCMS) is ubiquitous in environmental, metabolomic and toxicological studies. Targeted LCMS methods are capable of the simultaneous determination of literally hundreds of analytes. Although acquiring of instrumental data is very fast, data post-processing i.e. quantification can be time consuming step (and)or dependent to various commercial software packages. In attempt to facilitate this drawback Wolfram Mathematica script for batch quantification of LCMS data was created...
2016: MethodsX
Ileana Frasier, Elke Noellemeyer, Romina Fernández, Alberto Quiroga
The present article describes a field auger sampling method for row-crop root measurements. In agroecosystems where crops are planted in a specific design (row crops), sampling procedures for root biomass quantification need to consider the spatial variability of the root system. This article explains in detail how to sample and calculate root biomass considering the sampling position in the field and the differential weight of the root biomass in the inter-row compared to the crop row when expressing data per area unit...
2016: MethodsX
Alejandro Cardoso Landaburu, María Pomares, Alfredo Avalos, Silvia Lapertosa, Gustavo Frechtel, Edgardo Poskus
The prevalence and high levels of anti-insulin antibodies (IA) have frequently been associated with brittle diabetes, lipodystrophy in the areas where the insulin is injected and/or poor metabolic control. When this happens the usual criterion adopted is the empirical change of insulin type and/or formulation intending to diminish the IA level and then to decrease the undesirable side-effects. Here, we present a rational two step radiometric method consisting in: A) a first-line radioligand binding assay (RBA) to assess IA in sera of these patients and detecting those with high levels...
2016: MethodsX
J Scholz, S Suppmann
Wave-mixed bioreactors have increasingly replaced stainless steel stirred tank reactors in seed inoculum productions and mammalian cell-based process developments. Pre-sterilized, single-use plastic bags are used for cultivation, eliminating the risk of cross-contamination and cleaning procedures. However, these advantages come with high consumable costs which is the main barrier to more uptakes of the technology by academic institutions. As an academic Core Facility that faces high demand in protein production from insect cells, we have therefore developed a cost-effective alternative to disposable wave bags...
2016: MethodsX
Russell F Cole, Graham A Mills, Adil Bakir, Ian Townsend, Anthony Gravell, Gary R Fones
Tributyltin (TBT) is a legacy pollutant in the aquatic environment, predominantly from its use in anti-foulant paints and is listed as a priority hazardous substance in the European Union's Water Framework Directive (WFD). Measuring low concentrations of TBT and other organotins (e.g. monobutyltin (MBT), dibutyltin (DBT), diphenyltin (DPhT) and triphenyltin (TPhT)) at sub ng/L concentrations in coastal waters using standard laboratory instrumentation is very challenging. Conventional, low injection volume gas chromatography/mass spectrometry (GC/MS) combined with liquid-liquid extraction typically achieves limits of detection for TBT ∼10 ng L(-1)...
2016: MethodsX
Sung Bae Kim, Takeaki Ozawa, Yoshio Umezawa
We introduce a method to evaluate the activities of cytokines based on the nuclear transport of NF-κB. A pair of bioluminescent indicators was made for conferring cytokine sensitivity to cervical carcinoma-derived HeLa cells. The principle is based on reconstitution of split fragments of Renilla reniformis luciferase (RLuc) by protein splicing with a DnaE intein from Synechocystis sp. PCC6803. The bioluminescence intensity of thus reconstituted RLuc in the HeLa cells was used as a measure of the activities for cytokines...
2016: MethodsX
Thomas E Gladwin, Matthijs Vink, Roger B Mars
Cluster-based analysis methods in neuroimaging provide control of whole-brain false positive rates without the need to conservatively correct for the number of voxels and the associated false negative results. The current method defines clusters based purely on shapes in the landscape of activation, instead of requiring the choice of a statistical threshold that may strongly affect results. Statistical significance is determined using permutation testing, combining both size and height of activation. A method is proposed for dealing with relatively small local peaks...
2016: MethodsX
Teresa Gazzotti, Andrea Barbarossa, Elisa Zironi, Paola Roncada, Marco Pietra, Giampiero Pagliuca
Although budesonide is frequently used in veterinary medicine for the treatment of canine respiratory and bowel inflammatory diseases, knowledge is lacking regarding its kinetics in this species. We developed and validated a liquid chromatography-tandem mass spectrometry method for the determination of budesonide and its metabolite 16α-hydroxyprednisolone in dog plasma. The analytes were extracted by solid phase extraction and analysis was performed by high performance liquid chromatography-tandem mass spectrometry, with positive electrospray ionization...
2016: MethodsX
Pirouz Nourian, Romulo Gonçalves, Sisi Zlatanova, Ken Arroyo Ohori, Anh Vu Vo
Voxel representations have been used for years in scientific computation and medical imaging. The main focus of our research is to provide easy access to methods for making large-scale voxel models of built environment for environmental modelling studies while ensuring they are spatially correct, meaning they correctly represent topological and semantic relations among objects. In this article, we present algorithms that generate voxels (volumetric pixels) out of point cloud, curve, or surface objects. The algorithms for voxelization of surfaces and curves are a customization of the topological voxelization approach [1]; we additionally provide an extension of this method for voxelization of point clouds...
2016: MethodsX
Stephanie R A Botelho, Thais P Martins, Macária F Duarte, Andreza V Barbosa, Douglas Lau, Fernanda R Fernandes, Marcio M Sanches
Seeds that contain large amounts of oil, starch, fibers and phenols are the most difficult tissues for RNA extraction. Currently, there are some reports of virus detection in seeds using commercial kits for RNA extraction. However, individual seeds were used, which may not be always suitable for analyses that deal with large amounts of seeds. Sangha [1] described a simple, quick and efficient protocol for RNA extraction and downstream applications in a group of seeds of jatropha (Jatropha curcas), mustard (Brassica sp...
2016: MethodsX
Eduardo Vitarelli de Queiroz, João Luiz Baptista de Carvalho
The curvature of the sea wave was tested as a parameter for estimating wave direction in the search for better results in estimates of wave direction in shallow waters, where waves of different sizes, frequencies and directions intersect and it is difficult to characterize. We used numerical simulations of the sea surface to determine wave direction calculated from the curvature of the waves. Using 1000 numerical simulations, the statistical variability of the wave direction was determined. The results showed good performance by the curvature parameter for estimating wave direction...
2016: MethodsX
Navid Ziaei-Darounkalaei, Mehrdad Ameri, Taghi Zahraei-Salehi, Omid Ziaei-Darounkalaei, Tahereh Mohajer-Tabrizi, Lotfollah Bornaei
The attempts via introducing many methods have been conducted to select the best antibiotic combination in the treatment of seriously ill patients. Operational or interpretational complexity or time-consuming along with sufficient accuracy led to postpone routine clinical use of these tests until today, despite the urgent need for them. By this study and proposed method, selection of the best double antibiotic synergistic combination against resistant pathogen is simply same as Kirby-Bauer antibiotic susceptibility test...
2016: MethodsX
Maria Chiara Fontanella, Gian Maria Beone
This work provides a method with application of valid techniques to extract and determinate inorganic species of antimony (Sb) for water. The procedure involves•the simultaneous accumulation of Sb(III) and Sb(V) on passive samplers like Diffusive Gradient in Thin Films (DGT) with iron (Fe) oxide gel, eliminating the risk of speciation changes due to transport and storage;•application of less concentrated acid (50 mM Na2EDTA) for elution and preservation of Sb species from DGT resin;•subsequent analytical determination of inorganic species with High Performance Liquid Chromatography-Isotopic Dilution-Inductively Coupled Plasma Mass Spectrometer (HPLC-ID-ICP MS) based on determination of the isotope ratio ((123)Sb/(121)Sb) of isotopes in the samples after spiking with 123Sb enriched standard solution, reducing the effect of signal drift and matrix effect on the final value...
2016: MethodsX
Wei Fu, Shui-Guang Huang, Zeng-Shun Li, Hao Shen, Jun-Shuai Li, Peng-Yuan Wang
In order to solve the issue which the fusion rules cannot be self-adaptively adjusted by using available fusion methods according to the subsequent processing requirements of Remote Sensing (RS) image, this paper puts forward GSDA (genetic-iterative self-organizing data analysis algorithm) by integrating the merit of genetic arithmetic together with the advantage of iterative self-organizing data analysis algorithm for multi-source RS image fusion. The proposed algorithm considers the wavelet transform of the translation invariance as the model operator, also regards the contrast pyramid conversion as the observed operator...
2016: MethodsX
Sai Kiran Aditha, Aditya Dileep Kurdekar, L A Avinash Chunduri, Sandeep Patnaik, Venkataramaniah Kamisetti
The aqueous based reflux method useful for the green synthesis of nanostructures is described in detail. In this method, the parameters: the order of addition of precursors, the time of the reflux and the cooling rate should be optimized in order to obtain the desired phase and morphology of the nanostructures. The application of this method is discussed with reference to the synthesis of CZTS nanoparticles which have great potential as an absorber material in the photovoltaic devices. The highlights of this method are:•Simple...
2016: MethodsX
Anastasia L Karpovich, Maria F Vlasova, Natalya I Sapronova, Valentin S Sukharev, Victor V Ivanov
A method for measurement of dimensions of platy particles of exfoliating, or delaminating, materials, such as clays, in aqueous suspensions in situ is proposed. Equivalent spherical diameter (esd), measured by many common methods, depends more on the major (lateral) dimension of a particle, while it is less sensitive to changes of the particle thickness. Addition of the second method, results of which are a function of the particle diameter and thickness too, would provide more accurate determination of the particle dimensions...
2016: MethodsX
Lucrezia Lamastra, Matteo Balderacchi, Marco Trevisan
Groundwater is essential for human life and its protection is a goal for the European policies. All the anthropogenic activities could impact on water quality. •Conventional pollutants and more than 700 emerging pollutants, resulting from point and diffuse source contamination, threat the aquatic ecosystem.•Policy-makers and scientists will have to cooperate to create an initial groundwater emerging pollutant priority list, to answer at consumer demands for safety and to the lack of conceptual models for emerging pollutants in groundwater...
2016: MethodsX
Suman Lee, Joomyeong Kim
We have developed an NGS-based deep bisulfite sequencing protocol for the DNA methylation analysis of genomes. This approach allows the rapid and efficient construction of NGS-ready libraries with a large number of PCR products that have been individually amplified from bisulfite-converted DNA. This approach also employs a bioinformatics strategy to sort the raw sequence reads generated from NGS platforms and subsequently to derive DNA methylation levels for individual loci. The results demonstrated that this NGS-based deep bisulfite sequencing approach provide not only DNA methylation levels but also informative DNA methylation patterns that have not been seen through other existing methods...
2016: MethodsX
Pau Calatayud-Vernich, Fernando Calatayud, Enrique Simó, Yolanda Picó
A comparison between QuEChERS and other pesticide extraction procedures for honey and honey bee matrices is discussed. Honey bee matrix was extracted by solvent based procedure whereas solid phase extraction was the protocol for the honey matrix. The citrate buffered QuEChERS method was used for both matrices. The methods were evaluated regarding cost (equipment and reagents), time, accuracy, precision, sensitivity and versatility. The results proved that the QuEChERS protocol was the most efficient method for the extraction of the selected pesticides in both matrices...
2016: MethodsX
Benet Gunsé, Charlotte Poschenrieder, Simone Rankl, Peter Schröeder, Ana Rodrigo-Moreno, Juan Barceló
In this study we present a highly versatile and easily configurable system for measuring plant electrophysiological parameters and ionic flow rates, connected to a computer-controlled highly accurate positioning device. The modular software used allows easy customizable configurations for the measurement of electrophysiological parameters. Both the operational tests and the experiments already performed have been fully successful and rendered a low noise and highly stable signal. Assembly, programming and configuration examples are discussed...
2016: MethodsX
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