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Meiling Shang, Victor J Chan, Dominic W S Wong, Hans Liao
Direct cloning of metagenomes has proven to be a powerful tool for the exploration of the diverse sequence space of a microbial community leading to gene discovery and biocatalyst development. The key to such approach is the development of rapid, sensitive, and reliable functional screening of libraries. The majority of library screen have relied on the use of agar plates in petri dishes incorporating the target enzyme substrate for activity detection of positive clones (Iqbal et al. [1], Knietsch et al. [2], Popovic et al...
2018: MethodsX
Leonardo M Pitombo, Juliana C Ramos, Helio D Quevedo, Karina P do Carmo, Jane M F Paiva, Elisabete A Pereira, Janaina B do Carmo
This methodology is proposed to measure the fluxes of trace gases among microcosms and the atmosphere. As microcosm respiration we include both aerobic and anaerobic respiration, which may results in CO2 , CH4 , NO, N2 O, N2 , H2 S and H2 fluxes. Its applicability includes the assessment of products biodegradability and toxicity, the effect of treatments and products on greenhouse gases fluxes, and the mineralization of organic fertilizers. A step by step procedure; the complementary parameters and good practices that might be taken into account to perform a microcosm experiment; and the tools nowadays available that could be useful in this respirometric methodology are presented...
2018: MethodsX
Jianhua Xu
Previous studies showed that hydro-climate processes are stochastic and complex systems, and it is difficult to discover the hidden patterns in the and non-stationary data and thoroughly understand the hydro-climate relationships. For the purpose to show multi-time scale responses of a hydrological variable to climate change, we developed an integrated approach by combining wavelet analysis and regression method, which is called wavelet regression (WR). The customization and the advantage of this approach over the existing methods are presented below: •The patterns in the data series of a hydrological variable and its related climatic factors are revealed by the wavelet analysis at different time scales...
2018: MethodsX
Leadin S Khudur, Andrew S Ball
Total Petroleum Hydrocarbons (TPH) represent major environmental contaminants which pose a significant risk to ecosystems and humans heath if left untreated. Bioremediation represents a simple, cheap and environmentally-safe approach to clean up TPH-contaminated sites. Traditional TPH analysis is expensive and time-consuming. Here we assess, for the first time, the potential of RemScan as a fast, accurate and cost-effective portable device to be used as a tool to monitor the bioremediation process. A variety of TPH-contaminated soils were subject to TPH quantitative analysis using RemScan...
2018: MethodsX
Carin A Huset, Kitrina M Barry
This data article includes details on the simple and efficient analytical methods used to measure perfluoroalkyl substances (PFASs) in water, soil, and produce from home gardens in Minnesota. PFASs in water were analyzed via direct injection. PFASs were extracted from homogenized soil using sonication, and from produce using dispersive solid phase extraction. Isotope dilution was used for quantitation in all methods. The method performance parameters and quality control measures are described. The methods described are applicable for a PFAS ranging from C4-C8 and the produce method was used on a wide variety of produce...
2018: MethodsX
Caitlin Walde, Roger Ristau, Danielle Cote
Metallic powders are commonly used in additive manufacturing processes. While their post-process consolidated properties are widely studied, there is little research on the properties of the powders prior to consolidation. Understanding the powder characteristics before use in additive manufacturing processes could lead to fine-tuning properties of additively manufactured materials. The three-dimensional grain structure of metals can be useful in predicting their properties and microstructure. Powder particles are much smaller and more difficult to fixture and polish than their bulk counterparts, hence typical protocols are difficult to use when serially sectioning them...
2018: MethodsX
Andie V Bleicher, Holger W Unger, Stephen J Rogerson, Elizabeth H Aitken
There is a lack of published enzyme linked immunosorbent assay (ELISA) protocols which use commercially available reagents for the measurement of ferritin in human plasma for research purposes. ELISA kits are often expensive and do not always provide detailed information about reagents included. A commercially available antibody pair was used to develop an in-house ELISA to measure ferritin in small (25 μl) volumes of human plasma. ELISA results were compared to ferritin levels measured using a commercial immune-assay system...
2018: MethodsX
Veerdhawal Kulkarni, John Awad, Adam Medlock, Paul Monis, Melody Lau, Barbara Drigo, John van Leeuwen
Drinking water distribution systems with long hydraulic retention times (HRTs) commonly encounter rapid microbiological-mediated monochloramine decay that results in microbial regrowth and nitrification with reduction in alkalinity. In this paper, we report the design and operation of a field-based pilot-scale distribution system (PDS) operated at flows that simulate long HRTs (∼10 days) to promote rapid microbiological monochloramine decay over long periods. The PDS is designed to enable the testing of chemical treatment for the control of nitrification and monochloramine decay...
2018: MethodsX
Leabaneng Tawe, Surbhi Grover, Mohan Narasimhamurthy, Sikhulile Moyo, Simani Gaseitsiwe, Ishmael Kasvosve, Giacomo M Paganotti
Archived Formalin-Fixed Paraffin-Embedded (FFPE) tissue specimens can be a valuable source of human papillomavirus (HPV) nucleic acids for molecular biological analyses in retrospective studies. Although successful amplification with polymerase chain reaction (PCR) is essential for analysis of HPV DNA extracted from cervical FFPE specimens, extensive DNA damage due to cross-linking and fragmentation results in poor yield. Therefore, techniques to improve the diagnostic rate and sensitivity from FFPE tissues through PCR is highly desired and of wider interest...
2018: MethodsX
Nikhil Bagalkot, Aly A Hamouda, Ole Morten Isdahl
The current method describes a simple modification to the dynamic and equilibrium interfacial tension (IFT) measurement in a multiphase system (gas-liquid/liquid-liquid) by the Axisymmetric Drop Shape Analysis (ADSA) pendant drop technique. The primary difficulty associated with dynamic IFT measurement by ADSA is providing the appropriate phase densities, especially in a system consisting of gas (CO2 , methane, and propane) and liquids (water and hydrocarbon). The density of the phases is calculated using a, considering the solubility og gases in liquids, as a function of time...
2018: MethodsX
Lee S Toni, Anastacia M Garcia, Danielle A Jeffrey, Xuan Jiang, Brian L Stauffer, Shelley D Miyamoto, Carmen C Sucharov
Accurate and reliable analysis of gene expression depends on the extraction of pure and high-quality RNA. However, while the conventional phenol-chloroform RNA extraction is preferable over silica-based columns, particularly when cost is a concern or higher RNA yield is desired, it can result in significant RNA contamination. Contaminants including excess phenol, chloroform, or salts, can have significant impacts on downstream applications, including RNA quantification and reverse transcription, that can skew data collection and interpretation...
2018: MethodsX
Julie A MacDonald, William H Fowle, Ellie Shin, Dori C Woods
Electron microscopy as a methodology for the study of mitochondria based on morphological features is a standard technique that has experienced little evolution over the course of several decades. This technology has identified heterogeneity of mitochondria populations across both whole tissues, as well between individual cells, using primarily ultrathin sections for transmission electron microscopy (TEM). However, this technique constrains the evaluation of a sample to a single two-dimensional plane. To overcome this limitation, scanning electron microscopy (SEM) has been successfully utilized to observe three-dimensional mitochondria structures within the complex microenvironment containing total cellular components...
2018: MethodsX
Frederik Naujoks, Katharina Wiedemann, Nadja Schömig, Oliver Jarosch, Christian Gold
Up to a level of full vehicle automation, drivers will have to be available as a fallback level and take back manual control of the vehicle in case of system limits or failures. Before introducing automated vehicles to the consumer market, the controllability of these control transitions has to be demonstrated. This paper presents a novel procedure for an expert-based controllability assessment of control transitions from automated to manual driving. A standardized rating scheme is developed that allows trained raters to integrate different aspects of driving performance during control transitions (e...
2018: MethodsX
Abdel-Naser A Zohri, Mohamed Abdelazim, Sara Ibrahim
3,5-dinitrosalicylic acid (DNS) reducing sugar assay is the most convenient method for quantification of total reducing sugar in biomass hydrolysate, fermentation samples, sugar industry and biotechnology laboratories. The dimeric proton transfer salt 2-aminoethanaminium 2-(ethoxycarbonyl)-4,6-dinitrophenolate (AED) is an intensely colored derivative of DNS and in turn its reduced form intense color showed a superior properties in reducing sugar quantification eliminating phenol and rochelle salt additives using the same practical methodology of DNS giving an overall methodology advantageous than using DNS assay as a greener route...
2018: MethodsX
Urvi Bhojoo, Kyle K Biggar
Characterization of protein- protein interactions is a vital aspect of molecular biology as multi-protein complexes are the functional units of cellular processes and defining their interactions provides valuable insights into their function based on a "guilt by association" concept. To identify the components in complexes, purification of the latter near homogeneity is required. The tandem affinity purification (i.e., TAP) method, coupled with mass spectrometry have been extensively used to define native protein complexes and transient protein-protein interactions under near physiological conditions (i...
2018: MethodsX
Diego Moya, Juan Paredes, Prasad Kaparaju
RETScreen presents a proven focused methodology on pre-feasibility studies. Although this tool has been used to carry out a number of pre-feasibility studies of solar, wind, and hydropower projects; that is not the case for geothermal developments. This method paper proposes a systematic methodology to cover all the necessary inputs of the RETScreen-International Geothermal Project Model. As case study, geothermal power plant developments in the Ecuadorian context were analysed by RETScreen-International Geothermal Project Model...
2018: MethodsX
Paola Lecca
We implement a Monte Carlo heuristic algorithm to model drug release from a solid dosage form. We show that with Monte Carlo simulations it is possible to identify and explain the causes of the unsatisfactory predictive power of current drug release models. It is well known that the power-law, the exponential models, as well as those derived from or inspired by them accurately reproduce only the first 60% of the release curve of a drug from a dosage form. In this study, by using Monte Carlo simulation approaches, we show that these models fit quite accurately almost the entire release profile when the release kinetics is not governed by the coexistence of different physico-chemical mechanisms...
2018: MethodsX
Maria Alvarado-Kristensson
When using fluorescence microscope techniques to study cells, it is essential that the cell structure and contents are preserved after preparation of the samples, and that the preparation method employed does not create artefacts that can be perceived as cellular structure/components. γ-Tubulin forms filaments that in some cases are immunostained with an anti-γ-tubulin antibody, but this immunostaining is not reproducible [[1], [2]]. In addition, the C terminal region of γ-tubulin (green fluorescence protein tagged [GFP]-γ-tubulin334--449 ) forms cytosolic GFP-labeled structures, which can easily be imaged in live cells but are not preserved in fixed cells [[1], [3]]...
2018: MethodsX
Tatiana M Minkina, Saglara S Mandzhieva, Marina V Burachevskaya, Tatiana V Bauer, Svetlana N Sushkova
Method of determination of heavy metals loosely bound compounds in the soil was developed using three separate extractions. The group of loosely bound compounds of metals includes exchangeable, complexed, and specifically adsorbed forms. This method is available, rapid and not expensive. Extraction takes less than 24 h. Sample procedure preparation is simple, and the analysis consists of only three steps, which can be performed simultaneously. The parallel extraction gives reliable and reproducible results and provides a relatively complete idea of the metals mobility in the soil, their availability to plants, migratory capacity, and transformation...
2018: MethodsX
Javier Valdes-Abellan, Yakov Pachepsky, Gonzalo Martinez
Data assimilation is becoming a promising technique in hydrologic modelling to update not only model states but also to infer model parameters, specifically to infer soil hydraulic properties in Richard-equation-based soil water models. The Ensemble Kalman Filter method is one of the most widely employed method among the different data assimilation alternatives. In this study the complete Matlab© code used to study soil data assimilation efficiency under different soil and climatic conditions is shown. The code shows the method how data assimilation through EnKF was implemented...
2018: MethodsX
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