scholarly journals Ultra Low-cost DNA Miniprep Spin-Columns for Rapid Filter-Trapped Proteomics Sample Preparation

2021 ◽  
Author(s):  
Campbell Mousseau ◽  
Camille Pierre ◽  
Matthew Champion
Keyword(s):  
Sample Preparation ◽  
Proteomic Analysis ◽  
Low Cost ◽  
Dna Purification ◽  
Ionic Interactions ◽  
Spectrometric Analysis ◽  
Label Free ◽  
Proteolytic Digestion ◽  
Spin Filters ◽  
The Cost

Complete proteolytic digestion in the preparation of proteins for bottom-up proteomic analysis is substantially improved by the use of detergents for complete denaturation. This however is incompatible with many proteases, and highly detrimental to LC-MS/MS data collection. Recently, filter-based methods such as FASP (Filter-Aided Sample Prep) have seen wide use due to their ability to remove detergents and other harmful reagents prior to digestion and mass spectrometric analysis. Unfortunately, these techniques can be variable and time consuming. Suspension trapping (S-Trapping) is a newer method that utilizes a depth-filter to trap flocculated proteins, and has proven to be a faster approach for proteomic analysis. Sample preparation by these methods requires careful control of protein concentrations in order to flocculate the sample for collection, and the cost of commercial solutions can be high. We hypothesized that protein suspensions also retain on silica-based filters due to ionic interactions mediated by the presence of sodium (Na+), SO42- and PO43-. As such, we sought to investigate if very low-cost DNA purification spin-filters, so called ‘minipreps’ could efficiently and reproducibly trap proteins for digest and LC-MS/MS analysis. Using model proteins and whole-cell lysates we compared digestion efficiencies, capacities, recovery and identification rates from samples prepared using DNA-minipreps and FASP-based protocols. Samples were analyzed using nano uHPLC MS-MS/MS and Label-Free-Quantitative (LFQ) proteomics. DNA-filters show low variability, excellent recovery, sensitivity, and proteome depth from a commercially obtainable device which costs < $0.25 (US) per sample.

A comparative study of qualitative immunochemical screening assays for the combined measurement of T-2/HT-2 in cereals and cereal-based products

2011 ◽  
Vol 4 (4) ◽  
pp. 385-394 ◽  
Author(s):  
J. Meneely ◽  
F. Ricci ◽  
S. Vesco ◽  
M. Abouzied ◽  
M. Sulyok ◽  
...  
Keyword(s):  
Sample Preparation ◽  
Low Cost ◽  
Ease Of Use ◽  
The Other ◽  
Accuracy And Precision ◽  
Cost Implications ◽  
Electrochemical Array ◽  
The Cost ◽  
Preparation Techniques ◽  
Speed Of Analysis

Many different immunochemical platforms exist for the screening of naturally occurring contaminants in food from the low cost enzyme linked immunosorbent assays (ELISA) to the expensive instruments such as optical biosensors based on the phenomenon of surface plasmon resonance (SPR). The primary aim of this study was to evaluate and compare a number of these platforms to assess their accuracy and precision when applied to naturally contaminated samples containing HT-2/T-2 mycotoxins. Other important factors considered were the speed of analysis, ease of use (sample preparation techniques and use of the equipment) and ultimately the cost implications. The three screening procedures compared included an SPR biosensor assay, a commercially available ELISA and an enzymelinked immunomagnetic electrochemical array (ELIME array). The qualitative data for all methods demonstrated very good overall agreements with each other, however on comparison with mass spectrometry confirmatory results, the ELISA and SPR assay performed slightly better than the ELIME array, exhibiting an overall agreement of 95.8% compared to 91.7%. Currently, SPR is more costly than the other two platforms and can only be used in the laboratory whereas in theory both the ELISA and ELIME array are portable and can be used in the field, but ultimately this is dependent on the sample preparation techniques employed. Sample preparative techniques varied for all methods evaluated, the ELISA was the most simple to perform followed by that of the SPR method. The ELIME array involved an additional clean-up step thereby increasing both the time and cost of analysis. Therefore in the current format, field use would not be an option for the ELIME array. In relation to speed of analysis, the ELISA outperformed the other methods.

scholarly journals Molecular Dynamics Simulation-assisted Ionic Liquid Screening for Deep Coverage Proteome Analysis

2020 ◽  
Vol 19 (10) ◽  
pp. 1724-1737
Author(s):  
Fei Fang ◽  
Qun Zhao ◽  
Huiying Chu ◽  
Mingwei Liu ◽  
Baofeng Zhao ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Ionic Liquid ◽  
Molecular Dynamics Simulation ◽  
Membrane Proteins ◽  
Sample Preparation ◽  
Proteomic Analysis ◽  
Dynamics Simulation ◽  
Dominant Factor ◽  
Label Free ◽  
Compound Libraries

In-depth coverage of proteomic analysis could enhance our understanding to the mechanism of the protein functions. Unfortunately, many highly hydrophobic proteins and low-abundance proteins, which play critical roles in signaling networks, are easily lost during sample preparation, mainly attributed to the fact that very few extractants can simultaneously satisfy the requirements on strong solubilizing ability to membrane proteins and good enzyme compatibility. Thus, it is urgent to screen out ideal extractant from the huge compound libraries in a fast and effective way. Herein, by investigating the interior mechanism of extractants on the membrane proteins solubilization and trypsin compatibility, a molecular dynamics simulation system was established as complement to the experimental procedure to narrow down the scope of candidates for proteomics analysis. The simulation data shows that the van der Waals interaction between cation group of ionic liquid and membrane protein is the dominant factor in determining protein solubilization. In combination with the experimental data, 1-dodecyl-3-methylimidazolium chloride (C12Im-Cl) is on the shortlist for the suitable candidates from comprehensive aspects. Inspired by the advantages of C12Im-Cl, an ionic liquid-based filter-aided sample preparation (i-FASP) method was developed. Using this strategy, over 3,300 proteins were confidently identified from 103 HeLa cells (∼100 ng proteins) in a single run, an improvement of 53% over the conventional FASP method. Then the i-FASP method was further successfully applied to the label-free relative quantitation of human liver cancer and para-carcinoma tissues with obviously improved accuracy, reproducibility and coverage than the commonly used urea-based FASP method. The above results demonstrated that the i-FASP method could be performed as a versatile tool for the in-depth coverage proteomic analysis of biological samples.

Advance Protection for Three Phase Induction Motor using Microcontroller Atmega32

2018 ◽  
Vol 8 (1) ◽  
pp. 172
Author(s):  
Karan S Belsare ◽  
Gajanan D Patil
Keyword(s):  
Induction Motor ◽  
Low Cost ◽  
Short Circuit ◽  
Cost Factor ◽  
Protection Scheme ◽  
Three Phase ◽  
The Cost

A low cost and reliable protection scheme has been designed for a three phase induction motor against unbalance voltages, under voltage, over voltage, short circuit and overheating protection. Taking the cost factor into consideration the design has been proposed using microcontroller Atmega32, MOSFETs, relays, small CTs and PTs. However the sensitivity of the protection scheme has been not compromised. The design has been tested online in the laboratory for small motors and the same can be implemented for larger motors by replacing the i-v converters and relays of suitable ratings.

Janus – A New Approach to Air Combat Pilot Training

2019 ◽  
Vol 2019 (4) ◽  
pp. 7-22
Author(s):  
Georges Bridel ◽  
Zdobyslaw Goraj ◽  
Lukasz Kiszkowiak ◽  
Jean-Georges Brévot ◽  
Jean-Pierre Devaux ◽  
...  
Keyword(s):  
Low Cost ◽  
Cost Effective ◽  
High Energy ◽  
Training System ◽  
Embedded Sensors ◽  
Pilot Training ◽  
New Approach ◽  
Combat Aircraft ◽  
Air Combat ◽  
The Cost

Abstract Advanced jet training still relies on old concepts and solutions that are no longer efficient when considering the current and forthcoming changes in air combat. The cost of those old solutions to develop and maintain combat pilot skills are important, adding even more constraints to the training limitations. The requirement of having a trainer aircraft able to perform also light combat aircraft operational mission is adding unnecessary complexity and cost without any real operational advantages to air combat mission training. Thanks to emerging technologies, the JANUS project will study the feasibility of a brand-new concept of agile manoeuvrable training aircraft and an integrated training system, able to provide a live, virtual and constructive environment. The JANUS concept is based on a lightweight, low-cost, high energy aircraft associated to a ground based Integrated Training System providing simulated and emulated signals, simulated and real opponents, combined with real-time feedback on pilot’s physiological characteristics: traditionally embedded sensors are replaced with emulated signals, simulated opponents are proposed to the pilot, enabling out of sight engagement. JANUS is also providing new cost effective and more realistic solutions for “Red air aircraft” missions, organised in so-called “Aggressor Squadrons”.

To Eliminate Curtain Effect of FIB TEM Samples by a Combination of Sample Dicing and Backside Milling

2014 ◽  
Author(s):  
Jian-Shing Luo ◽  
Hsiu Ting Lee
Keyword(s):  
Sample Preparation ◽  
Focused Ion Beam ◽  
Preparation Method ◽  
Low Cost ◽  
Ion Beam ◽  
Sample Preparation Method ◽  
Site Specific ◽  
Dual Beam ◽  
Transmission Electron

Abstract Several methods are used to invert samples 180 deg in a dual beam focused ion beam (FIB) system for backside milling by a specific in-situ lift out system or stages. However, most of those methods occupied too much time on FIB systems or requires a specific in-situ lift out system. This paper provides a novel transmission electron microscopy (TEM) sample preparation method to eliminate the curtain effect completely by a combination of backside milling and sample dicing with low cost and less FIB time. The procedures of the TEM pre-thinned sample preparation method using a combination of sample dicing and backside milling are described step by step. From the analysis results, the method has applied successfully to eliminate the curtain effect of dual beam FIB TEM samples for both random and site specific addresses.

scholarly journals Label-free quantitative proteomic analysis of the inhibition effect of Lactobacillus rhamnosus GG on Escherichia coli biofilm formation in co-culture

2021 ◽  
Vol 19 (1) ◽  
Author(s):  
Huiyi Song ◽  
Ni Lou ◽  
Jianjun Liu ◽  
Hong Xiang ◽  
Dong Shang
Keyword(s):  
Escherichia Coli ◽  
Proteomic Analysis ◽  
Biofilm Formation ◽  
Lactobacillus Rhamnosus ◽  
Differentially Expressed ◽  
Differentially Expressed Proteins ◽  
Label Free ◽  
Quantitative Proteomic Analysis ◽  
E Coli ◽  
Protein Ubiquitination

Abstract Background Escherichia coli (E. coli) is the principal pathogen that causes biofilm formation. Biofilms are associated with infectious diseases and antibiotic resistance. This study employed proteomic analysis to identify differentially expressed proteins after coculture of E. coli with Lactobacillus rhamnosus GG (LGG) microcapsules. Methods To explore the relevant protein abundance changes after E. coli and LGG coculture, label-free quantitative proteomic analysis and qRT-PCR were applied to E. coli and LGG microcapsule groups before and after coculture, respectively. Results The proteomic analysis characterised a total of 1655 proteins in E. coli K12MG1655 and 1431 proteins in the LGG. After coculture treatment, there were 262 differentially expressed proteins in E. coli and 291 in LGG. Gene ontology analysis showed that the differentially expressed proteins were mainly related to cellular metabolism, the stress response, transcription and the cell membrane. A protein interaction network and Kyoto Encyclopaedia of Genes and Genomes (KEGG) pathway analysis indicated that the differentiated proteins were mainly involved in the protein ubiquitination pathway and mitochondrial dysfunction. Conclusions These findings indicated that LGG microcapsules may inhibit E. coli biofilm formation by disrupting metabolic processes, particularly in relation to energy metabolism and stimulus responses, both of which are critical for the growth of LGG. Together, these findings increase our understanding of the interactions between bacteria under coculture conditions.

Label-free proteomic analysis revealed the mechanisms of protein oxidation induced by hydroxyl radicals in whiteleg shrimp (Litopenaeus vannamei) muscle

2021 ◽  
Author(s):  
Hui-min Lin ◽  
Xue-er Qi ◽  
Shan-shan Shui ◽  
Soottawat Benjakul ◽  
Santiago P. Aubourg ◽  
...  
Keyword(s):  
Ascorbic Acid ◽  
Hydroxyl Radicals ◽  
Litopenaeus Vannamei ◽  
Protein Oxidation ◽  
Proteomic Analysis ◽  
Muscle Proteins ◽  
Label Free ◽  
Whiteleg Shrimp ◽  
The Stability ◽  
Oxidative Effects

The oxidative effects of hydroxyl radicals derived from a FeCl3/ascorbic acid/H2O2 system on the stability of muscle proteins in peeled shrimp (Litopenaeus vannamei) were investigated.

scholarly journals Demonstration of a Label-Free and Low-Cost Optical Cavity-Based Biosensor Using Streptavidin and C-Reactive Protein

Biosensors ◽  
2020 ◽  
Vol 11 (1) ◽  
pp. 4
Author(s):  
Donggee Rho ◽  
Seunghyun Kim
Keyword(s):  
Limit Of Detection ◽  
Point Of Care ◽  
Low Cost ◽  
Optical Cavity ◽  
Sample Volume ◽  
Small Sample ◽  
Label Free ◽  
C Reactive Protein ◽  
Reactive Protein ◽  
Cavity Structure

An optical cavity-based biosensor (OCB) has been developed for point-of-care (POC) applications. This label-free biosensor employs low-cost components and simple fabrication processes to lower the overall cost while achieving high sensitivity using a differential detection method. To experimentally demonstrate its limit of detection (LOD), we conducted biosensing experiments with streptavidin and C-reactive protein (CRP). The optical cavity structure was optimized further for better sensitivity and easier fluid control. We utilized the polymer swelling property to fine-tune the optical cavity width, which significantly improved the success rate to produce measurable samples. Four different concentrations of streptavidin were tested in triplicate, and the LOD of the OCB was determined to be 1.35 nM. The OCB also successfully detected three different concentrations of human CRP using biotinylated CRP antibody. The LOD for CRP detection was 377 pM. All measurements were done using a small sample volume of 15 µL within 30 min. By reducing the sensing area, improving the functionalization and passivation processes, and increasing the sample volume, the LOD of the OCB are estimated to be reduced further to the femto-molar range. Overall, the demonstrated capability of the OCB in the present work shows great potential to be used as a promising POC biosensor.

scholarly journals A low-cost wireless endoscope camera: a preliminary report

2021 ◽  
Vol 27 (1) ◽  
Author(s):  
J. M. Lazarus ◽  
M. Ncube
Keyword(s):  
Minimally Invasive Surgery ◽  
Minimally Invasive ◽  
Video Transmission ◽  
Low Cost ◽  
Battery Life ◽  
Resource Constrained ◽  
High Definition ◽  
Industry Standard ◽  
Constrained Environments ◽  
The Cost

Abstract Background Technology currently used for surgical endoscopy was developed and is manufactured in high-income economies. The cost of this equipment makes technology transfer to resource constrained environments difficult. We aimed to design an affordable wireless endoscope to aid visualisation during rigid endoscopy and minimally invasive surgery (MIS). The initial prototype aimed to replicate a 4-mm lens used in rigid cystoscopy. Methods Focus was placed on using open-source resources to develop the wireless endoscope to significantly lower the cost and make the device accessible for resource-constrained settings. An off the shelf miniature single-board computer module was used because of its low cost (US$10) and its ability to handle high-definition (720p) video. Open-source Linux software made monitor mode (“hotspot”) wireless video transmission possible. A 1280 × 720 pixel high-definition tube camera was used to generate the video signal. Video is transmitted to a standard laptop computer for display. Bench testing included latency of wireless digital video transmission. Comparison to industry standard wired cameras was made including weight and cost. The battery life was also assessed. Results In comparison with industry standard cystoscope lens, wired camera, video processing unit and light source, the prototype costs substantially less. (US$ 230 vs 28 000). The prototype is light weight (184 g), has no cables tethering and has acceptable battery life (of over 2 h, using a 1200 mAh battery). The camera transmits video wirelessly in near real time with only imperceptible latency of < 200 ms. Image quality is high definition at 30 frames per second. Colour rendering is good, and white balancing is possible. Limitations include the lack of a zoom. Conclusion The novel wireless endoscope camera described here offers equivalent high-definition video at a markedly reduced cost to contemporary industry wired units and could contribute to making minimally invasive surgery possible in resource-constrained environments.

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