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Michael George Zaki Ghali
Tracheostomy is used to obtain airway access to allow for mechanical ventilation in experimental animal models. We present a microsurgical atlas of our technique for tracheostomy in the adult rat.
2018: MethodsX
Elyn M Rowe, Kyle K Biggar
While a number of post-translational modifications (PTM), such as phosphorylation and ubiquitination, have been extensively studied, lysine methylation is emerging as an important PTM with implications in a growing number of diverse cellular processes. To date, there are approximately 5000 identified methylation sites on non-histone proteins, and as the methyllysine proteome expands it becomes important to identify the lysine methyltransferase enzymes responsible for each methylation event. The use of peptide SPOT methylation assay has proven to be a useful in the identification and validation of novel substrates for lysine methyltransferase enzymes as it uses a weak beta emitter coupled with fluorography to detect methylation events...
2018: MethodsX
E S Joel, O Maxwell, O O Adewoyin, C O Ehi-Eromosele, Z Embong, F Oyawoye
In this study, we evaluated the activity concentration of natural radionuclides (226Ra, 232Th and 40K) for fifteen (15) different brands of tile samples used for building purposes in Nigeria. The tile samples were analyzed using High purity Germanium gamma detector. The mean activity concentrations of 226Ra, 232Th, and 40K were observed to be 61.1 ± 5.5 Bq/kg, 70.2 ± 6.08 Bq/kg and 514.7 ± 59.8 Bq/kg respectively. Various hazard indices such as absorbed dose rate, external and internal hazard index, annual effective dose rate, Gamma activity Index (Iγ) and Alpha Index (Iα) were calculated...
2018: MethodsX
Samer Salameh, Dominique Nouel, Cecilia Flores, Daniel Hoops
Netrin-1, an axon guidance protein, is difficult to detect using immunohistochemistry. We performed a multi-step, blinded, and controlled protocol optimization procedure to establish an efficient and effective fluorescent immunohistochemistry protocol for characterizing Netrin-1 expression. Coronal mouse brain sections were used to test numerous antigen retrieval methods and combinations thereof in order to optimize the stain quality of a commercially available Netrin-1 antibody. Stain quality was evaluated by experienced neuroanatomists for two criteria: signal intensity and signal-to-noise ratio...
2018: MethodsX
Elisabeth Mohammed, Terry Mohammed, Azad Mohammed
A simple, efficient and cost effective method was developed and optimized for the digestion of fish tissue for the determination of Lead, Cadmium, Mercury, Antimony, Arsenic and Selenium by FAAS, CVAAS and HGAAS. Three of the more common classical open tubed acid digestion procedures were explored with the purpose of optimizing the variables and selecting the single most efficient, convenient and inexpensive digestion method. The effect of parameters such as digestion media, digestion time and digestion temperature on the efficiency of extraction of heavy metals from fish tissue was examined...
2017: MethodsX
Negar Motayagheni
Oscar Langendorff introduced the first method for isolating a heart with contractile activity in 1895. Since then, the Langendorff method has remained a powerful technique in cardiac research and has led to major advances in medicine. The primary goal of the Langendorff method is to provide an isolated heart with oxygen and metabolites via a cannula inserted into the aorta. The Langendorff heart is a complex in vitro technique used primarily in pharmacological and physiological research that allows the evaluation of multiple cardiac hemodynamic parameters including, but not limited to, contractility and heart rate...
2017: MethodsX
Pavel Trtik
Pilot attempt of the neutron microtomography of voids in gold carried out using the Neutron Microscope instrument is presented in the paper. The paper demonstrates that neutron microtomography provides viable alternative to X-ray imaging for the assessment of porosity in high atomic number materials. The model sample based on gold with artificially induced void system reveals segmented porosity with 5.4 micrometres voxel size and the spatial resolution close to 10 micrometres.
2017: MethodsX
Norhayati Abu Bakar, Muhamad Mat Salleh, Akrajas Ali Umar, Joseph George Shapter
Silver nanoparticles deposited on quartz substrates are widely used as SERS substrates. The nanoparticles can be deposited directly from colloidal solution by dipping technique. However, the adhesion of the particles on the quartz surface is very poor. Normally the substrate is pre-treated with hydroxylation or silanisation process. In this paper, we have demonstrated that the application of the sequence pre-treatment hydroxylation and silanisation have improved the density of silver nanoplates desposited on the quartz surface...
2017: MethodsX
Heather A Hintz, Courtney Weihing, Rachel Bayer, David Lonzarich, Winnifred Bryant
In various species of fishes, the importance of visual cues in the determination of environmental threat and subsequent predator avoidance is clear. Chemical cues also play an essential role facilitating predator avoidance. Among fish in the superorder Ostariophysi, club cells in the epidermis produce an alarm substance. Damage to the skin during a predation event releases an alarm substance (AS), which diffuses through the water column and binds to olfactory receptors of conspecifics. Fish then engage in a number of anti-predator behaviors that may include darting, schooling, or hiding...
2017: MethodsX
T V S Udaya Bhaskar, R Venkat Shesu, Timothy P Boyer, E Pattabhi Rama Rao
A new method of identifying anomalous oceanic temperature and salinity (T/S) data from Argo profiling floats is proposed. The proposed method uses World Ocean Database 2013 climatology to classify good against anomalous data by using convex hulls. An n-sided polygon (convex hull) with least area encompassing all the climatological points is constructed using Jarvis March algorithm. Subsequently Points In Polygon (PIP) principle implemented using ray casting algorithm is used to classify the T/S data as within or without acceptable bounds...
2017: MethodsX
Ileana F Márquez, Marisela Vélez
We describe a simple way of fusing E. coli lipid vesicles onto a gold surface. Supported lipid bilayers on metal surfaces are interesting for several reasons: transducing a biological signal to an electric readout, using surface analytical tools such as Surface Plasmon Resonance (SPR), Infrared Reflection Absorption Spectroscopy, Neutron Reflectivity or Electrochemistry. The most widely used method to prepare supported lipid membranes is fusion of preexisting liposomes. It is quite efficient on hydrophilic surfaces such as glass, mica or SiO2 , but vesicle fusion on metals and metal oxide surfaces (as gold, titanium oxide or indium tin oxide), remains a challenge, particularly for vesicles containing charged lipids, as is the case of bacterial lipids...
2017: MethodsX
Prathap Moothamadathil Baby, Sanu Susan Jacob, Rajesh Kumar, Pramod Kumar
Serial injection into marginal vein and blood collection through auricular artery in New Zealand white Rabbit (Oryctolagus cuniculus) is an important procedure for various types of experimental studies. Limitations of the existing methods for serial injection and blood collection includes complex procedures, causes considerable discomfort to rabbits, whole blood samples obtained are highly prone to hemolysis and lastly detailed protocol is not available in the literature. Approximately 10 min before commencement of the experiment, a local anesthetic cream was applied over the right and left ear lobes...
2017: MethodsX
Tariq J Al-Musawi, Ibrahim A Mohammed, Huda M Atiea
The present study aims to manage and determine the most economical efficiency of five wastewater treatment plants discharging wastewater into the Tigris River in Iraq. The management system was based on ensuring the five-day biological oxygen demand concentration in the river is <30 mg/L according to the Iraqi standards. In many cases, the determined optimized efficiencies were found to be lower than the present working efficiencies. Although this was good for the environment, it was not cost-effective...
2017: MethodsX
Alexander A Loshkarev, Maria F Vlasova, Natalya I Sapronova, Yuri M Tokunov, Ivan A Volkov, Victor V Ivanov, Thomas Maeder
A method for determining the critical values of the flow speed and the flow constriction degree characteristic of the alignment of cylindrical nano-objects in a flowing suspension is proposed. Previously, the alignment process of cylindrical nano-objects in suspensions was investigated by using birefringence of the polarized light and the small-angle X-ray scattering. While both methods are suitable for measuring the alignment degree of cylindrical nano-objects in suspensions diluted down to low concentrations, they are restricted for the application to undiluted concentrated suspensions because of non-transparency and multiple scattering of X-rays...
2017: MethodsX
Khalil Ur Rehman, Abid Ali Khan, M Y Malik, Usman Ali
We have found that few attempts are reported on Williamson fluid flow yields by an inclined cylindrical surface. To be more specific, Williamson fluid flow regime characteristics under stagnation point region especially when it is manifested with mutual interaction of double stratification and mixed convection effects are not proposed as yet. Therefore, we have considered stagnation point mixed convection Williamson fluid flow brought by an inclined cylinder in the presence of temperature and concentration stratification phenomena...
2017: MethodsX
Christoph Bauer, Eugenia Niculescu-Morzsa, Stefan Nehrer
RNA isolation from human or animal cartilage tissue is necessary when performing mechanical or biotribological applications. Despite no influence on the cells and no alterations in gene expression patterns, enzymatic digestion of tissues should be avoided as it's known that the expression of collagen 2 can be effected (Hayman et al., 2006 [1]). After mechanical or biotribological tests alternative options with an immediate disruption of the tissue should be contemplated. To obtain RNA, different tissue homogenization and disruption methods are available on the market (Yu et al...
2017: MethodsX
Liam J Hawkins, Kenneth B Storey
Common Western-blot imaging systems have previously been adapted to measure signals from luminescent microplate assays. This can be a cost saving measure as Western-blot imaging systems are common laboratory equipment and could substitute a dedicated luminometer if one is not otherwise available. One previously unrecognized limitation is that the signals captured by the cameras in these systems are not equal for all wells. Signals are dependent on the angle of incidence to the camera, and thus the location of the well on the microplate...
2017: MethodsX
Katie L Hill, Timo Hamers, Jorke H Kamstra, William G Willmore, Robert J Letcher
Thyroid hormones (THs) are involved in the regulation of many physiological processes in vertebrates. Competition for TH binding sites on serum transport proteins can interfere with delivery of THs to target tissues, and this is a potential mechanism of action of exogenous thyroidogenic substances. To date, detailed accounts of in vitro methods for competitive binding with THs on TH transport proteins (human or wildlife) are sparse. In the limited number of published studies on in vitro radio-labelled TH-TH transport protein interactions, method descriptions were brief and with insufficient details for successful replication...
2017: MethodsX
Tesfay Berhe, Omprakash Sahu
Bioethanol is one of the most important alternative renewable energy sources that substitute the fossil fuels. Sugarcane bagasse has a content of cellulose and hemicelluloses, which make it suitable as fermentation substrate when hydrolyzed. The objective of work is ethanol production from sugarcane bagasse (SCB) by the fermentation process. Eight laboratory experiments were conducted to produce bioethanol from sugarcane bagasse. By using Design Expert, it was formulated the dilute acid hydrolysis step to investigate the effects of hydrolysis parameters on a yield of ethanol and optimum condition...
2017: MethodsX
Seyed Ali Sajjadi, Ghasem Zolfaghari, Hamed Adab, Ahmad Allahabadi, Mehri Delsouz
This paper presented the levels of PM2.5 and PM10 in different stations at the city of Sabzevar, Iran. Furthermore, this study was an attempt to evaluate spatial interpolation methods for determining the PM2.5 and PM10 concentrations in the city of Sabzevar. Particulate matters were measured by Haz-Dust EPAM at 48 stations. Then, four interpolating models, including Radial Basis Functions (RBF), Inverse Distance Weighting (IDW), Ordinary Kriging (OK), and Universal Kriging (UK) were used to investigate the status of air pollution in the city...
2017: MethodsX
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