scholarly journals Comparison of Five TRIzol-Based Protein Preparation Methods for 2-DE Production From Challenging Marine Dinoflagellate Samples: A Case Study on Two Benthic Prorocentrum Species

2020 ◽  
Vol 8 (5) ◽  
pp. 363
Author(s):  
Thomas Chun-Hung Lee ◽  
Kaze King-Yip Lai ◽  
Celia Sze-Nga Kwok ◽  
Steven Jing-Liang Xu ◽  
Fred Wang-Fat Lee
Keyword(s):  
Protein Extraction ◽  
Background Signal ◽  
High Quality ◽  
Two Dimensional Gel Electrophoresis ◽  
Protein Preparation ◽  
Preparation Methods ◽  
Complex Protein ◽  
Marine Dinoflagellates

Two-dimensional gel electrophoresis (2-DE) is a major element of conventional gel-based proteomics, which resolves complex protein mixtures. Protein extraction with the removal of interfering substances from the sample remains the key to producing high-quality 2-DE profiles. Marine dinoflagellates contain large endogenous amounts of salts, nucleic acids, polysaccharides, phenolic compounds, pigments, and other interfering compounds. These substances are detrimental to the quality of gel images. Protein preparation using TRIzol reagent is a promising method for producing high-quality 2-DE profiles for dinoflagellate samples. In addition to its remarkable performance, the TRIzol method’s several advantages have made it a popular and widely used method in the field of 2-DE sample preparation. Nonetheless, the quality of 2-DE of samples from certain dinoflagellate species is not as high as previously reported when the same TRIzol protocol is applied. Therefore, modifications to the original TRIzol method are required to remove interfering substances from those challenging dinoflagellate samples. In this study, the original TRIzol method and four modified methods, namely the aliquot TRIzol method, re-TRIzol method, TRIzol method with a commercial clean-up kit, and TRIzol method with trichloroacetic acid/acetone precipitation, were compared. Performance of these five methods in terms of protein yield, background signal, and resolution and number of protein spots was investigated on samples from two benthic Prorocentrum species: P. lima and P. hoffmannianum. Our results demonstrated that high-quality 2-DE could be achieved from P. lima samples prepared using both the original TRIzol method and the TRIzol method with a commercial clean-up kit. However, the original TRIzol method failed to produce high-quality 2-DE profiles for P. hoffmannianum samples. Among the four modified TRIzol methods, only the TRIzol method with a commercial clean-up kit could yield substantially improved high-quality 2-DE profiles for P. hoffmannianum samples. This combination of the conventional TRIzol method with a commercial clean-up kit potentially represents a promising protein extraction methodology for obtaining high-quality 2-DE profiles for difficult dinoflagellate samples.

scholarly journals Optimizing Human Bile Preparation for Two-Dimensional Gel Electrophoresis

2016 ◽  
Vol 2016 ◽  
pp. 1-6 ◽  
Author(s):  
Hao-Tsai Cheng ◽  
Sen-Yung Hsieh ◽  
Chang-Mu Sung ◽  
Betty Chien-Jung Pai ◽  
Nai-Jen Liu ◽  
...  
Keyword(s):  
Sample Preparation ◽  
Protein Extraction ◽  
Protein Profile ◽  
Two Dimensional Gel Electrophoresis ◽  
Protein Preparation ◽  
Preparation Methods ◽  
Human Bile ◽  
Acetone Precipitation ◽  
Exogenous Compounds ◽  
Dimensional Electrophoresis

Aims. Bile is an important body fluid which assists in the digestion of fat and excretion of endogenous and exogenous compounds. In the present study, an improved sample preparation for human bile was established.Methods and Material. The method involved acetone precipitation followed by protein extraction using commercially available 2D Clean-Up kit. The effectiveness was evaluated by 2-dimensional electrophoresis (2DE) profiling quality, including number of protein spots and spot distribution.Results. The total protein of bile fluid in benign biliary disorders was 0.797 ± 0.465 μg/μL. The sample preparation method using acetone precipitation first followed by 2D Clean-Up kit protein extraction resulted in better quality of 2DE gel images in terms of resolution as compared with other sample preparation methods. Using this protocol, we obtained approximately 558 protein spots on the gel images and with better protein spots presentation of haptoglobin, serum albumin, serotransferrin, and transthyretin.Conclusions. Protein samples of bile prepared using acetone precipitation followed by 2D Clean-Up kit exhibited high protein resolution and significant protein profile. This optimized protein preparation protocol can effectively concentrate bile proteins, remove abundant proteins and debris, and yield clear presentation of nonabundant proteins and its isoforms on 2-dimensional electrophoresis gel images.

scholarly journals Using the Google™ Search Engine for Health Information: Is There a Problem? Case Study: Supplements for Cancer

2021 ◽  
Vol 5 (2) ◽  
Author(s):  
Hannah C Cai ◽  
Leanne E King ◽  
Johanna T Dwyer
Keyword(s):  
Health Information ◽  
Search Engine ◽  
Information Quality ◽  
Nutrition Information ◽  
High Quality ◽  
Search Results ◽  
Health And Nutrition ◽  
Quality Rating

ABSTRACT We assessed the quality of online health and nutrition information using a Google™ search on “supplements for cancer”. Search results were scored using the Health Information Quality Index (HIQI), a quality-rating tool consisting of 12 objective criteria related to website domain, lack of commercial aspects, and authoritative nature of the health and nutrition information provided. Possible scores ranged from 0 (lowest) to 12 (“perfect” or highest quality). After eliminating irrelevant results, the remaining 160 search results had median and mean scores of 8. One-quarter of the results were of high quality (score of 10–12). There was no correlation between high-quality scores and early appearance in the sequence of search results, where results are presumably more visible. Also, 496 advertisements, over twice the number of search results, appeared. We conclude that the Google™ search engine may have shortcomings when used to obtain information on dietary supplements and cancer.

An open-source R-package and web application for high-quality probabilistic predictions in hydrology

2021 ◽  
Author(s):  
Jason Hunter ◽  
Mark Thyer ◽  
Dmitri Kavetski ◽  
David McInerney
Keyword(s):  
Open Source ◽  
Web Application ◽  
R Package ◽  
Error Model ◽  
Objective Functions ◽  
High Quality ◽  
Wide Range ◽  
Probabilistic Error

<p>Probabilistic predictions provide crucial information regarding the uncertainty of hydrological predictions, which are a key input for risk-based decision-making. However, they are often excluded from hydrological modelling applications because suitable probabilistic error models can be both challenging to construct and interpret, and the quality of results are often reliant on the objective function used to calibrate the hydrological model.</p><p>We present an open-source R-package and an online web application that achieves the following two aims. Firstly, these resources are easy-to-use and accessible, so that users need not have specialised knowledge in probabilistic modelling to apply them. Secondly, the probabilistic error model that we describe provides high-quality probabilistic predictions for a wide range of commonly-used hydrological objective functions, which it is only able to do by including a new innovation that resolves a long-standing issue relating to model assumptions that previously prevented this broad application.  </p><p>We demonstrate our methods by comparing our new probabilistic error model with an existing reference error model in an empirical case study that uses 54 perennial Australian catchments, the hydrological model GR4J, 8 common objective functions and 4 performance metrics (reliability, precision, volumetric bias and errors in the flow duration curve). The existing reference error model introduces additional flow dependencies into the residual error structure when it is used with most of the study objective functions, which in turn leads to poor-quality probabilistic predictions. In contrast, the new probabilistic error model achieves high-quality probabilistic predictions for all objective functions used in this case study.</p><p>The new probabilistic error model and the open-source software and web application aims to facilitate the adoption of probabilistic predictions in the hydrological modelling community, and to improve the quality of predictions and decisions that are made using those predictions. In particular, our methods can be used to achieve high-quality probabilistic predictions from hydrological models that are calibrated with a wide range of common objective functions.</p>

scholarly journals Facile, High Quality Sequencing of Bacterial Genomes from Small Amounts of DNA

2014 ◽  
Vol 2014 ◽  
pp. 1-8
Author(s):  
Momchilo Vuyisich ◽  
Ayesha Arefin ◽  
Karen Davenport ◽  
Shihai Feng ◽  
Cheryl Gleasner ◽  
...  
Keyword(s):  
Genomic Dna ◽  
De Novo ◽  
Gc Content ◽  
Library Preparation ◽  
Sequencing Data ◽  
Bacterial Genomes ◽  
Dna Amount ◽  
High Quality ◽  
Preparation Methods

Sequencing bacterial genomes has traditionally required large amounts of genomic DNA (~1 μg). There have been few studies to determine the effects of the input DNA amount or library preparation method on the quality of sequencing data. Several new commercially available library preparation methods enable shotgun sequencing from as little as 1 ng of input DNA. In this study, we evaluated the NEBNext Ultra library preparation reagents for sequencing bacterial genomes. We have evaluated the utility of NEBNext Ultra for resequencing andde novoassembly of four bacterial genomes and compared its performance with the TruSeq library preparation kit. The NEBNext Ultra reagents enable high quality resequencing andde novoassembly of a variety of bacterial genomes when using 100 ng of input genomic DNA. For the two most challenging genomes (Burkholderiaspp.), which have the highest GC content and are the longest, we also show that the quality of both resequencing andde novoassembly is not decreased when only 10 ng of input genomic DNA is used.

scholarly journals Using Multivariate Statistical Methods to Analyze High-Quality Bicycle Path Service Systems: A Case Study of Popular Bicycle Paths in Taiwan

2020 ◽  
Vol 12 (17) ◽  
pp. 7185
Author(s):  
Shinn-Jou Lin ◽  
Guey-Shin Shyu ◽  
Wei-Ta Fang ◽  
Bai-You Cheng
Keyword(s):  
Explanatory Power ◽  
Value Added ◽  
Service Systems ◽  
Image Management ◽  
High Quality ◽  
Multivariate Statistical ◽  
The Individual ◽  
Quantitative Indicators

Taiwan has promoted bicycle tourism for nearly 20 years, and the bicycle paths it has constructed throughout the island are diverse in design. In the present study, an evaluation scale for bicycle path sightseeing potential was devised with a focus on the overall service quality of the paths; 30 popular bicycle paths were analyzed using a field survey, with expert consultation on quantitative indicators, and a qualitative analysis entailing interviews with people regarding the bicycle paths. A multivariate statistical analysis was performed on the quality of the service systems for these paths. The results revealed that the quality of these service systems is influenced by four principal components, namely, landscape attractiveness, image management, bicycle-specific paths, and accessibility, for a total explanatory power of 76.21%; the individual explanatory power of these components was 25.89%, 21.49%, 16.81%, and 12.03%, respectively. Bicycle path conditions, service maintenance, and cleanliness and bicycle specificity are required for future high-quality bicycle paths; diverse bicycle rental services and bicycle types, entrance visibility, and ecological introduction boards along paths are value-added factors to bicycle path quality.

scholarly journals Soil Mapping Based on the Integration of the Similarity-Based Approach and Random Forests

Land ◽  
2020 ◽  
Vol 9 (6) ◽  
pp. 174
Author(s):  
Desheng Wang ◽  
A-Xing Zhu
Keyword(s):  
Random Forests ◽  
Cross Validation ◽  
Soil Mapping ◽  
High Quality ◽  
Integrated Method ◽  
Average Accuracy ◽  
Soil Information ◽  
Fold Cross Validation

Digital soil mapping (DSM) is currently the primary framework for predicting the spatial variation of soil information (soil type or soil properties). Random forests and similarity-based methods have been used widely in DSM. However, the accuracy of the similarity-based approach is limited, and the performance of random forests is affected by the quality of the feature set. The objective of this study was to present a method for soil mapping by integrating the similarity-based approach and the random forests method. The Heshan area (Heilongjiang province, China) was selected as the case study for mapping soil subgroups. The results of the regular validation samples showed that the overall accuracy of the integrated method (71.79%) is higher than that of a similarity-based approach (58.97%) and random forests (66.67%). The results of the 5-fold cross-validation showed that the overall accuracy of the integrated method, similarity-based approach, and random forests range from 55% to 72.73%, 43.48% to 69.57%, and 54.17% to 70.83%, with an average accuracy of 66.61%, 57.39%, and 59.62%, respectively. These results suggest that the proposed method can produce a high-quality covariate set and achieve a better performance than either the random forests or similarity-based approach alone.

scholarly journals Sports and Health as Cornerstones of Tourism Development: Case Study of Montenegro

2020 ◽  
Author(s):  
Anđela Jakšić-Stojanović ◽  
Neven Šerić
Keyword(s):  
Natural Resources ◽  
Driving Force ◽  
Tourism Development ◽  
International Market ◽  
The Other ◽  
Special Focus ◽  
Health Tourism ◽  
High Quality

The modern phenomenon of tourism is more focused on specific forms of tourism in which sports and health tourism play a very important role. That fact is not surprising having in mind that they represent interconnected activities that complement each other and give each other completely new dimension. On one side, sports and health represent very important content of tourist offer because of the fact they enable tourists to become active participants in various activities, and on the other side, they represent important driving force for visiting particular destination. The idea of this chapter is to provide a theoretical and practical framework of this issue with a special focus on case study of Montenegro. According to the results of the research that was carried out, the general conclusion is that Montenegro has extremely valuable natural resources and potentials for the development of sports and health tourism, but there are still a lot of challenges that should be faced in the future in order to improve the quality of tourist offer and the level of tourists’ satisfaction as well as to create completely new image of the destination and position it as high-quality sports and health tourist destination on international market.

scholarly journals Integrated Quality-Based Production-Distribution Planning in Two-Echelon Supply Chains

2021 ◽  
Vol 2021 ◽  
pp. 1-10
Author(s):  
Husein Pasha ◽  
Isa Nakhai Kamalabadi ◽  
Alireza Eydi
Keyword(s):  
Mixed Integer ◽  
High Quality ◽  
Swarm Optimization ◽  
Integrated Production ◽  
Quality Degradation ◽  
Production Distribution ◽  
Quality Of Products ◽  
Over Time

The integrated production-distribution (P-D) planning has turned into one of the most essential areas in supply chain (SC) management in recent years, especially in the case of perishable products in which the quality of products can change over time. Nonetheless, so far, the suggested models have focused on the P-D stages of the chain while the delivery of high-quality products to customers is of paramount significance in the perishable SC. In the present paper, a multiobjective, mixed-integer, and nonlinear programming (MOMINLP) mathematical model was developed for integrated P-D deteriorating items in a two-echelon SC that emphasizes quality degradation. Quality is monitored and calculated as a function of temperature and time throughout the SC, and the main purpose of the model is to first increase the quality of products delivered to customers and, second, minimize the SC costs. To optimize the problem, the particle swarm optimization (PSO) approach was also incorporated into the model. The obtained model was applied to a case study in Protein Gostar Sina Company in Iran, which resulted in decreased P-D costs as well as increased customer satisfaction.

scholarly journals Problems in the Implementation of the Lean Concept at a Steel Works - Case Study

2018 ◽  
Vol 183 ◽  
pp. 01014 ◽  
Author(s):  
Adrian Maszke ◽  
Renata Dwornicka ◽  
Robert Ulewicz
Keyword(s):  
Lean Management ◽  
Customer Requirements ◽  
Steel Mill ◽  
High Quality ◽  
Turbulent Environment ◽  
Management Concept ◽  
Steel Works

The paper presents the experience of implementing selected instruments of the Lean concept at a steel works. The functioning of an enterprises in the currently prevailing conditions, i.e. in a turbulent environment, results in increased customer requirements. They expect, among other things, high quality of steel products delivered on time at a low price. Many organizations decide to implement the lean management concept without proper preparation. The purpose of this paper is to present the limitations occurring during the implementation of the lean management concept in a steel mill.

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