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Rodrigo Montoro, Renee Dickie
The vascular system, the pipeline for oxygen and nutrient delivery to tissues, is essential for vertebrate development, growth, injury repair, and regeneration. With their capacity to regenerate entire appendages throughout their lifespan, axolotls are an unparalleled model for vertebrate regeneration, but they lack many of the molecular tools that facilitate vascular imaging in other animal models. The determination of vascular metrics requires high quality image data for the discrimination of vessels from background tissue...
2017: MethodsX
Stanislav Naryzhny, Victor Zgoda, Artur Kopylov, Elena Petrenko, Аlexander Archakov
A method for increasing the productivity of ESI LC-MS/MS (electrospray ionization-liquid chromatography-tandem mass spectrometry) was proposed and applied. After IF (isoelectric focusing) of the sample using IPG (immobilized pH gradient) strip, the strip was cut to sections, and every section was treated according to trypsinolysis protocol for MS/MS analysis. The peptides produced were further analyzed by ESI LC-MS/MS. The procedure allows to: •identify many more proteins and proteoforms compared to shotgun analysis of extracts...
2017: MethodsX
Mahin Basha Syed
High-performance liquid chromatography (HPLC) was used for the determination of compounds occurring during the production of biodiesel from karanja and jatropha oil. Methanol was used for fast monitoring of conversion of karanja and jatropha oil triacylglycerols to fatty acid methyl esters and for quantitation of residual triacylglycerols (TGs), in the final biodiesel product. The individual sample compounds were identified using HPLC. Analysis of fatty acid methyl esters (FAMES) in blends of biodiesel by HPLC using a refractive index and a UV detector at 238 nm...
2017: MethodsX
Leonid Livshits, Einav Gross
Cysteine catabolism by gut microbiota produces high levels of sulfide. Excessive sulfide can interfere with colon function, and therefore may be involved in the etiology and risk of relapse of ulcerative colitis, an inflammatory bowel disease affecting millions of people worldwide. Therefore, it is crucial to understand how cells/animals regulate the detoxification of sulfide generated by bacterial cysteine catabolism in the gut. Here we describe a simple and cost-effective way to explore the mechanism of sulfide toxicity in the nematode Caenorhabditis elegans (C...
2017: MethodsX
Mauro Holzman, Raúl Rivas, Facundo Carmona, Raquel Niclòs
Optimization of field techniques is crucial to ensure high quality soil moisture data. The aim of the work is to present a sampling method for undisturbed soil and soil water content to calibrated soil moisture probes, in a context of the SMOS (Soil Moisture and Ocean Salinity) mission MIRAS Level 2 soil moisture product validation in Pampean Region of Argentina. The method avoids soil alteration and is recommended to calibrated probes based on soil type under a freely drying process at ambient temperature...
2017: MethodsX
Mehdi Jalili, Mahmoud Nikkhah Shahmirzadi, Mahdi Kaseb Hazrati, Hamed Ahmadi
Liquids coming from different sources like wastewaters, agricultural and industrial activities and leakages of chemical substances often have high concentration of chemical compositions and the osmotic gradient generated around such sources causes a considerable transmission of the Contamination. The steam transmitted by non-polluted soils moves to polluted masses, causing an increase in the volume of pollution zone and movement of pollutants. Therefore, such physical and chemical processes should be taken into account in pollution transmission models...
2017: MethodsX
Chenlong Zhang, Sandra Cvetanovic, Joshua M Pearce
Recent advances in the use of plasmonic metamaterials to improve absorption of light in thin-film solar photovoltaic devices has created a demand for a scalable method of patterning large areas with metal nanostructures deposited in an ordered array. This article describes two methods of fabricating ordered 2D nanosphere colloidal films: spin coating and interface coating. The two methods are compared and parameter optimization discussed. The study reveals that: •For smaller nanosphere sizes, spin coating is more favorable, while for larger nanospheres, the angled interface coating provides more coverage and uniformity...
2017: MethodsX
Mario Plattes, Christian Koehler, Tom Gallé
Enzymes are important in biological wastewater treatment systems, since they are responsible for breakdown of macro- and micropollutants, thereby making the pollutants available for metabolism. Enzyme activity has been investigated in particular in activated sludge processes, since the activated sludge technology is the most important and widely spread wastewater treatment technology used today. Various methods have been used to extract enzymes from activated sludge in order to measure their activity, these include stirring with additives like detergents and cation exchange resins, ultrasonication (with probes) and combinations of the three [1], [2], [3]...
2017: MethodsX
Christina Thoisen, Benni Winding Hansen, Søren Laurentius Nielsen
The microalgal pigment phycoerythrin (PE) is of commercial interest as natural colorant in food and cosmetics, as well as fluoroprobes for laboratory analysis. Several methods for extraction and quantification of PE are available but they comprise typically various extraction buffers, repetitive freeze-thaw cycles and liquid nitrogen, making extraction procedures more complicated. A simple method for extraction of PE from cryptophytes is described using standard laboratory materials and equipment. The cryptophyte cells on the filters were disrupted at -80 °C and added phosphate buffer for extraction at 4 °C followed by absorbance measurement...
2017: MethodsX
Upendra M Sainju
Nitrogen balance in agroecosystems provides a quantitative framework of N inputs and outputs and retention in the soil that examines the sustainability of agricultural productivity and soil and environmental quality. Nitrogen inputs include N additions from manures and fertilizers, atmospheric depositions including wet and dry depositions, irrigation water, and biological N fixation. Nitrogen outputs include N removal in crop grain and biomass and N losses through leaching, denitrification, volatilization, surface runoff, erosion, gas emissions, and plant senescence...
2017: MethodsX
Aurélie Dufour, Christophe Migon
Several protocols using different treatments (various mixtures of acids at different temperatures for mineralisation) or using several analysis instrumentations were tested with the aim to define the method allowing the analysis of some groups of elements. This study proposes a protocol of sample treatment and analysis permitting in a single batch the determination of 16 elements (Al, As, Ba, Cd, Co, Cu, Fe, K, Mg, Mn, Na, Ni, Pb, Ti, V and Zn) with different chemical features such as volatile or refractory trace elements...
2017: MethodsX
Esmaeil Shahsavari, Jonathan Schmidt, Arturo Aburto-Medina, Basma Khallaf, Vivek Balakrishnan, Nicholas D Crosbie, Aravind Surapaneni, Andrew S Ball
Soil-transmitted helminths (STHs) pose a significant public health problem, infecting approximately 2 billion people globally. Despite relatively low prevalence in developed countries, the removal of STHs from wastewater remains crucial to allow the safe use of biosolids or recycled water for agriculture. Wastewater helminth egg count data can contribute to an assessment of the need for, or success of, a parasite management program. Although the World Health Organisation (WHO) has recommended a standard method for counting helminth eggs in raw sewage based on the method of Bailenger (Ayres et al...
2017: MethodsX
Omprakash Sahu
Sugar industry is an oldest accommodates industry in the world. It required and discharges a large amount of water for processing. Removal of chemical oxygen demand and color through the electrochemical process including hybrid iron and aluminum electrode was examined for the treatment of cane-based sugar industry wastewater. Most favorable condition at pH 6.5, inter-electrode gap 20 mm, current density 156 A m(-2), electrolyte concentration 0.5 M and reaction time 120 min, 90% COD and 93.5% color removal was achieved...
2017: MethodsX
Jared Schommer, Matthew Schrag, Alexander Nackenoff, Gurdeep Marwarha, Othman Ghribi
Organotypic slicing of brain tissue from young rodents has been used as a powerful model system for biomedical research [1], [2], [3]. Organotypic slicing complements cell culture and in vivo studies in multiple facets. This system can be useful for investigating manipulation of cellular signaling pathways without the hindrance of the blood-brain barrier while sacrificing fewer animals in the process. It also allows for preserved cellular connectivity and local intact circuitry which is a drawback of isolated cell cultures...
2017: MethodsX
Takaki Waritani, Jessica Chang, Bonnie McKinney, Kuniaki Terato
To assay serum antibodies by indirect ELISA, it is critical to eliminate a variety of false positive and negative reactions attributed to the principle. These include 1) the background (BG) noise reaction caused by hydrophobic binding of immunoglobulin components in sample specimens to solid surfaces, 2) false positive reaction caused by non-specific binding of immunoglobulins to target-antigens by protein-protein interactions, and 3) other false positive and negative reactions caused by buffer components. No current blocking agents can prevent these false positive and negative reactions, and antibody assay results vary significantly depending on the buffer system used...
2017: MethodsX
Jara Laso, María Margallo, Pére Fullana, Alba Bala, Cristina Gazulla, Ángel Irabien, Rubén Aldaco
To be able to fulfil high market expectations for a number of practical applications, Environmental Product Declarations (EPDs) have to meet and comply with specific and strict methodological prerequisites. These expectations include the possibility to add up Life Cycle Assessment (LCA)-based information in the supply chain and to compare different EPDs. To achieve this goal, common and harmonized calculation rules have to be established, the so-called Product Category Rules (PCRs), which set the overall LCA calculation rules to create EPDs...
2017: MethodsX
Jelmer J Nijp, Klaas Metselaar, Juul Limpens, Harm P A Gooren, Sjoerd E A T M van der Zee
The saturated hydraulic conductivity (Ks ) is a key characteristic of porous media, describing the rate of water flow through saturated porous media. It is an indispensable parameter in a broad range of simulation models that quantify saturated and/or unsaturated water flow. The constant-head permeameter test is a common laboratory method to determine Ks on undisturbed soil samples collected from the field. In this paper we show that the application of this conventional method may result in a biased Ks in the case of highly permeable media, such as the top layer of Sphagnum peat and gravel...
2017: MethodsX
Afroze Alam, Kamlesh Kumar Naik, Navneet Kumar Upadhaya, Shailendra Kumar, K L Dhar
The study was undertaken to develop a simplified procedure for the isolation of bioactive isoflavone from Iris kashmiriana, using a direct method of isolation, avoiding the use of chromatographic techniques. The compound was isolated by commercially viable procedure. The extraction of powdered drug (500 g) was done with petroleum ether (60-80) using a Soxhlet apparatus (24 h run). The petroleum ether extract (gums and resins 2.13 g) was obtained and the marc (400 g) was subjected to extraction with 95% methanol using a Soxhlet apparatus (24 h run)...
2017: MethodsX
Sumedha Liyanage, Rohan S Dassanayake, Amal Bouyanfif, Erandathi Rajakaruna, Latha Ramalingam, Naima Moustaid-Moussa, Noureddine Abidi
In Fourier transform infrared (FTIR) microspectrocopy, the tissue preparation method is crucial, especially how the tissue is cryo-sectioned prior to the imaging requires special consideration. Having a temperature difference between the cutting blade and the specimen holder of the cryostat greatly affects the quality of the sections. Therefore, we have developed an optimal protocol for cryo-sectioning of biological tissues by varying the temperature of both the cutting blade and the specimen holder. Using this protocol, we successfully cryo-sectioned four different difficult-to-section tissues including white adipose tissue (WAT), brown adipose tissue (BAT), lung, and liver...
2017: MethodsX
Zubairu Darma Umar, Nor Azwady Abd Aziz, Syaizwan Zahmir Zulkifli, Muskhazli Mustafa
Polycyclic Aromatic Hydrocarbons (PAHs) are complex and widely distributed environmental pollutants that can affect living ecosystems. This study was conducted to rapidly degrade phenanthrene and pyrene representing low and high molecular weight of PAHs, respectively. Cronobacter sakazakii MM045 (KT933253) was identified from used engine oil of contaminated soil. PAHs biodegradation was carried out using 2,6-dichlorophenol indophenol (DCPIP) assay. Biodegradation influencing factors including agitation, temperature, pH, inoculums volume and salinity were enhanced using Response Surface Methodology (RSM) by Central Composite Design (CCD)...
2017: MethodsX
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