scholarly journals A simple serum depletion method for proteomics analysis

BioTechniques ◽  
2020 ◽  
Vol 69 (2) ◽  
pp. 148-151
Author(s):  
Alexandre Zougman ◽  
John P Wilson ◽  
Rosamonde E Banks
Keyword(s):  
Sample Preparation ◽  
Serum Protein ◽  
Body Fluid ◽  
Biomarker Discovery ◽  
The Body ◽  
Protein Digestion ◽  
Proteomics Analysis ◽  
Serum Proteome ◽  
Serum Fractions

Serum is the body fluid most often used in biomarker discovery. Albumin, the most abundant serum protein, contributes approximately 50% of the serum protein content, with an additional dozen abundant proteins dominating the rest of the serum proteome. To profile this challenging protein mixture by proteomics, the abundant proteins must be depleted to allow for detection of the low-abundant proteins, the primary biomarker targets. Current serum depletion approaches for proteomics are costly and relatively complex to couple with protein digestion. We demonstrate a simple, affordable serum depletion methodology that, within a few minutes of processing, results in two captured serum fractions – albumin-depleted and albumin-rich – which are digested in situ. We believe our method is a useful addition to the biomarker sample preparation toolbox.

scholarly journals Human body-fluid proteome: quantitative profiling and computational prediction

2020 ◽  
Author(s):  
Lan Huang ◽  
Dan Shao ◽  
Yan Wang ◽  
Xueteng Cui ◽  
Yufei Li ◽  
...  
Keyword(s):  
High Throughput ◽  
Human Body ◽  
Body Fluid ◽  
Biomarker Discovery ◽  
Interaction Network ◽  
Computational Prediction ◽  
Computational Effort ◽  
The Body ◽  
Support Vector ◽  
Learning Approaches

Abstract Empowered by the advancement of high-throughput bio technologies, recent research on body-fluid proteomes has led to the discoveries of numerous novel disease biomarkers and therapeutic drugs. In the meantime, a tremendous progress in disclosing the body-fluid proteomes was made, resulting in a collection of over 15 000 different proteins detected in major human body fluids. However, common challenges remain with current proteomics technologies about how to effectively handle the large variety of protein modifications in those fluids. To this end, computational effort utilizing statistical and machine-learning approaches has shown early successes in identifying biomarker proteins in specific human diseases. In this article, we first summarized the experimental progresses using a combination of conventional and high-throughput technologies, along with the major discoveries, and focused on current research status of 16 types of body-fluid proteins. Next, the emerging computational work on protein prediction based on support vector machine, ranking algorithm, and protein–protein interaction network were also surveyed, followed by algorithm and application discussion. At last, we discuss additional critical concerns about these topics and close the review by providing future perspectives especially toward the realization of clinical disease biomarker discovery.

scholarly journals Optimisation of urine sample preparation for shotgun proteomics

2020 ◽  
Vol 18 (1) ◽  
pp. 850-856
Author(s):  
Soňa Tkáčiková ◽  
Ivan Talian ◽  
Ján Sabo
Keyword(s):  
Sample Preparation ◽  
Biomarker Discovery ◽  
Shotgun Proteomics ◽  
The Body ◽  
Sequence Coverage ◽  
Prognostic Information ◽  
Laboratory Equipment ◽  
Non Invasive ◽  
Sample Preparation Procedure ◽  
Urine Biomarker

AbstractUrine reflects the renal function and urinary and kidney systems, but it may also reflect the presence of cancer in other parts of the body. Urine also has potential for providing prognostic information during therapeutic treatments thanks to non-invasive monitoring. A quick and reproducible protein purification procedure is essential to allow data comparison between proteomic studies in urine biomarker discovery. The article describes a simple, reproducible and cheap sample preparation procedure with a maximum protein yield (400 µg) obtained from only 10 mL of urine utilising cut-off filter desalting and digestion. The reported procedure removes yellowish background coloration residues and thus prevents the errors in spectrophotometric protein concentration determination. Different extraction solvents used in the presented procedure point to the possibility of partial elimination of abundant proteins (albumin and keratin family), as well as to the improvement of the sequence coverage of proteins identified, which helps to reveal changes in the urinary proteome. With this workflow, proteins can be easily obtained on standard laboratory equipment within 3 h. Data are available via ProteomeXchange with identifier PXD019738.

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.

In-Situ Mechanical Sample Preparation of Selected Sites and Components on Large Modules and Boards

2016 ◽  
Author(s):  
Jim Colvin ◽  
Timothy Hazeldine ◽  
Heenal Patel
Keyword(s):  
Sample Preparation ◽  
Printed Circuit Board ◽  
Circuit Board ◽  
Tilt Table ◽  
Standard Requirement ◽  
Open Design ◽  
Bga Packages ◽  
Silicon Thickness ◽  
Board Level

Abstract The standard requirement for FA Engineers needing to remove components from a board, prior to decapsulation or sample preparation, is shown to be greatly reduced, by the methods discussed here. By using a mechanical selected area preparation system with an open-design it is possible to reach all required areas of a large printed circuit board (PCB) or module to prepare a single component ‘in situ’. This makes subsequent optical or electrical testing faster and often more convenient to accomplish. Electronic End-pointing and 3D curvature compensation methods can often be used in parallel with sample prep techniques to further improve the consistency and efficacy of the decapsulation and thinning uniformity and final remaining silicon thickness (RST). Board level prep eliminates the worry of rework removal of BGA packages and the subsequent risk of damage to the device. Since the entire board is mounted, the contamination is restricted to the die surface and can be kept from the underside ball connections unlike current liquid immersion methods of package thinning or delayering. Since the camera is in line with the abrasion interface, imaging is real time during the entire milling and thinning process. Recent advances in automated tilt-table design have meant that a specific component’s angular orientation can be optimized for sample preparation. Improved tilt table technology also allows for improved mounting capability for boards of many types and sizes. The paper describes methods for decapsulation, thinning and backside polishing of a part ‘in situ’ on the polishing machine and allows the system to operate as a probe station for monitoring electrical characteristics while thinning. Considerations for designing board-level workholders are described – for boards that that are populated with components on one or even both sides. Using the techniques described, the quality of sample preparation and control is on a par with the processing of single package-level devices.

A New Method of Wafer Level Plan View TEM Sample Preparation by DualBeam

2008 ◽  
Author(s):  
Hyoung H. Kang ◽  
Michael A. Gribelyuk ◽  
Oliver D. Patterson ◽  
Steven B. Herschbein ◽  
Corey Senowitz
Keyword(s):  
Sample Preparation ◽  
Ex Situ ◽  
Wafer Level ◽  
Cross Sectional ◽  
Plan View ◽  
Manufacturing Line ◽  
Transmission Electron ◽  
Thin Lamella ◽  
Preparation Techniques

Abstract Cross-sectional style transmission electron microscopy (TEM) sample preparation techniques by DualBeam (SEM/FIB) systems are widely used in both laboratory and manufacturing lines with either in-situ or ex-situ lift out methods. By contrast, however, the plan view TEM sample has only been prepared in the laboratory environment, and only after breaking the wafer. This paper introduces a novel methodology for in-line, plan view TEM sample preparation at the 300mm wafer level that does not require breaking the wafer. It also presents the benefit of the technique on electrically short defects. The methodology of thin lamella TEM sample preparation for plan view work in two different tool configurations is also presented. The detailed procedure of thin lamella sample preparation is also described. In-line, full wafer plan view (S)TEM provides a quick turn around solution for defect analysis in the manufacturing line.

Scaffolds for Drug Delivery in Tissue Engineering

2008 ◽  
Vol 1 (2) ◽  
pp. 113-123 ◽  
Author(s):  
Vikas V. Gaikwad ◽  
Abasaheb B. Patil ◽  
Madhuri V. Gaikwad
Keyword(s):  
Drug Delivery ◽  
Tissue Engineering ◽  
Heart Diseases ◽  
Cartilage Regeneration ◽  
Tissue Growth ◽  
The Body ◽  
Patient Specific ◽  
In Situ Gel ◽  
Heart Muscle Cells

Scaffolds are used for drug delivery in tissue engineering as this system is a highly porous structure to allow tissue growth.  Although several tissues in the body can regenerate, other tissue such as heart muscles and nerves lack regeneration in adults. However, these can be regenerated by supplying the cells generated using tissue engineering from outside. For instance, in many heart diseases, there is need for heart valve transplantation and unfortunately, within 10 years of initial valve replacement, 50–60% of patients will experience prosthesis associated problems requiring reoperation. This could be avoided by transplantation of heart muscle cells that can regenerate. Delivery of these cells to the respective tissues is not an easy task and this could be done with the help of scaffolds. In situ gel forming scaffolds can also be used for the bone and cartilage regeneration. They can be injected anywhere and can take the shape of a tissue defect, avoiding the need for patient specific scaffold prefabrication and they also have other advantages. Scaffolds are prepared by biodegradable material that result in minimal immune and inflammatory response. Some of the very important issues regarding scaffolds as drug delivery systems is reviewed in this article.

scholarly journals Ferromagnetic soft catheter robots for minimally invasive bioprinting

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Cheng Zhou ◽  
Youzhou Yang ◽  
Jiaxin Wang ◽  
Qingyang Wu ◽  
Zhuozhi Gu ◽  
...  
Keyword(s):  
Minimally Invasive ◽  
The Body ◽  
Magnetic Actuation ◽  
Internal Organs ◽  
Planar Surfaces ◽  
Reinforced Polymer ◽  
Direct Fabrication ◽  
Digitally Controlled

AbstractIn vivo bioprinting has recently emerged as a direct fabrication technique to create artificial tissues and medical devices on target sites within the body, enabling advanced clinical strategies. However, existing in vivo bioprinting methods are often limited to applications near the skin or require open surgery for printing on internal organs. Here, we report a ferromagnetic soft catheter robot (FSCR) system capable of in situ computer-controlled bioprinting in a minimally invasive manner based on magnetic actuation. The FSCR is designed by dispersing ferromagnetic particles in a fiber-reinforced polymer matrix. This design results in stable ink extrusion and allows for printing various materials with different rheological properties and functionalities. A superimposed magnetic field drives the FSCR to achieve digitally controlled printing with high accuracy. We demonstrate printing multiple patterns on planar surfaces, and considering the non-planar surface of natural organs, we then develop an in situ printing strategy for curved surfaces and demonstrate minimally invasive in vivo bioprinting of hydrogels in a rat model. Our catheter robot will permit intelligent and minimally invasive bio-fabrication.

Sign in / Sign up

Export Citation Format

Share Document