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Electrical lysis and RNA extraction from single cells fixed by dithiobis (succinimidyl propionate)

Research Abstract
We present a microfluidic method for electrical lysis and RNA extraction from single fixed cells leveraging reversible cross-linker dithiobis(succinimidyl propionate) (DSP). Our microfluidic system captures a single DSP-fixed cell at a hydrodynamic trap, reverse-cross-links the DSP molecules on a chip with dithiothreitol, lyses the plasma membrane via electrical field, and extracts cytoplasmic RNA with isotachophoresis-aided nucleic acids extraction. All of the on-chip processes complete in less than 5 min. We demonstrated the method using K562 leukemia cells and benchmarked the performance of RNA extraction with reverse transcription quantitative polymerase chain reaction. We also demonstrated the integration of our method with single-cell RNA sequencing.
Research Authors
Sangamithirai Subramanian Parimalam,
Yusuke Oguchi,
Mahmoud N. Abdelmoez,
Arata Tsuchida,
Yuka Ozaki,
Ryuji Yokokawa,
Ryuji Yokokawa,
Hidetoshi Kotera, and
Hirofumi Shintaku
Research Journal
Analytical Chemistry
Research Member
Research Pages
12512-12518
Research Publisher
American Chemical Society
Research Rank
1
Research Vol
Vol: 90. Issue:21
Research Website
https://pubs.acs.org/doi/abs/10.1021/acs.analchem.8b02338
Research Year
2018

SINC-seq: correlation of transient gene expressions between nucleus and cytoplasm reflects single-cell physiology

Research Abstract
We report a microfluidic system that physically separates nuclear RNA (nucRNA) and cytoplasmic RNA (cytRNA) from a single cell and enables single-cell integrated nucRNA and cytRNA-sequencing (SINC-seq). SINC-seq constructs two individual RNA-seq libraries, nucRNA and cytRNA, per cell, quantifies gene expression in the subcellular compartments, and combines them to create novel single-cell RNA-seq data. Leveraging SINC-seq, we discover distinct natures of correlation among cytRNA and nucRNA that reflect the transient physiological state of single cells. These data provide unique insights into the regulatory network of messenger RNA from the nucleus toward the cytoplasm at the single-cell level.
Research Authors
Mahmoud N. Abdelmoez,
Kei Iida,
Yusuke Oguchi,
Hidekazu Nishikii,
Ryuji Yokokawa,
Hidetoshi Kotera,
Sotaro Uemura,
Juan G. Santiago, and
Hirofumi Shintaku
Research Journal
Genome Biology
Research Member
Research Pages
NULL
Research Publisher
Springer Nature
Research Rank
1
Research Vol
Vol: 19. Issue:1
Research Website
https://genomebiology.biomedcentral.com/
Research Year
2018

Distinct Kinetics in Electrophoretic Extraction of Cytoplasmic RNA from Single Cells

Research Abstract
The physical fractionation of cytoplasmic versus nuclear components of cells is a key step for studying the subcellular localization of molecules. The application of an electric field is an emerging method for subcellular fractionation of proteins and nucleic acids from single cells. However, the multibiophysical process that involves electrical lysis of cytoplasmic membranes, electrophoresis, and diffusion of charged molecules remains unclear. Here we study RNA dynamics in single cells during the electrophoretic extraction via a microfluidic system that enables stringent fractionation of the subcellular components leveraging a focused electric field. We identified two distinct kinetics in the extraction of RNA molecules, which were respectively associated with soluble RNA and mitochondrial RNA. We show that the extraction kinetics of soluble RNA is dominated by electrophoresis over diffusion and has a time constant of 0.15 s. Interestingly, the extraction of mitochondrial RNA showed unexpected heterogeneity in the extraction with slower kinetics (3.8 s), while reproducibly resulting in the extraction of 98.9% ± 2% after 40 s. Together, we uncover that the microfluidic system uniquely offers length bias-free fractionation of RNA molecules for quantitative analysis of correlations among subcellular compartments by exploiting the homogeneous electrophoretic properties of RNA.
Research Authors
Mahmoud N. Abdelmoez,
Yusuke Oguchi,
Yuka Ozaki,
Ryuji Yokokawa,
Hidetoshi Kotera, and
Hirofumi Shintaku
Research Journal
Analytical Chemistry
Research Member
Research Pages
1485-1492
Research Publisher
American Chemical Society
Research Rank
1
Research Vol
Vol: 92. Issue:1
Research Website
https://pubs.acs.org/doi/abs/10.1021/acs.analchem.9b04739
Research Year
2019

Pile-soil-structure interaction effect on structural response of piled jacket-supported offshore platform through in-place analysis

Research Abstract
In-place analysis for offshore platforms is essentially required to make proper design for new structures and true assessment for existing structures, in addition to the structural integrity of platforms components under the maximum and minimum operating loads when subjected to the environmental conditions. In-place analysis have been executed to check that the structural member with all appurtenance´s robustness have the capability to support the applied loads in either storm or operating conditions. A nonlinear finite element analysis is adopted for the platform structure above the seabed and pile-soil interaction to estimate the in-place behavior of a typical fixed offshore platform. The SACS software is utilized to calculate the dynamic characteristics of the platform model and the response of platform joints then the stresses at selected members, as well as their nodal displacements. The directions of environmental loads and water depth variations have significant effects in the results of the in-place analysis behavior. The most of bending moment responses of the piles are in the first fourth of pile penetration depth from pile head level. The axial deformations of piles in all load combinations cases of all piles are inversely proportional with penetration depth. The largest values of axial soil reaction are shown at the pile tips levels (the maximum penetration level). The most of lateral soil reactions resultant are in the first third of pile penetration depth from pile head level and approximately vanished after that penetration. The influence of the soil-structure interaction on the response of the jacket foundation predicts that the flexible foundation model is necessary to estimate the force responses demands of the offshore platform with a piled jacket-support
Research Authors
Shehata E Abdel Raheem, Elsayed M. Abdel Aal, Aly G.A. AbdelShafy, Mohamed F.M. Fahmyd and Mahmoud H Mansour
Research Department
Research Journal
Earthquakes and Structures, An International Journal
Research Pages
407-421
Research Publisher
Techno-Press Publishers
Research Rank
1
Research Vol
18(4)
Research Website
http://www.techno-press.org/content/?page=article&journal=eas&volume=18&num=4&ordernum=1
Research Year
2020

Pile-soil-structure interaction effect on structural response of piled jacket-supported offshore platform through in-place analysis

Research Abstract
In-place analysis for offshore platforms is essentially required to make proper design for new structures and true assessment for existing structures, in addition to the structural integrity of platforms components under the maximum and minimum operating loads when subjected to the environmental conditions. In-place analysis have been executed to check that the structural member with all appurtenance´s robustness have the capability to support the applied loads in either storm or operating conditions. A nonlinear finite element analysis is adopted for the platform structure above the seabed and pile-soil interaction to estimate the in-place behavior of a typical fixed offshore platform. The SACS software is utilized to calculate the dynamic characteristics of the platform model and the response of platform joints then the stresses at selected members, as well as their nodal displacements. The directions of environmental loads and water depth variations have significant effects in the results of the in-place analysis behavior. The most of bending moment responses of the piles are in the first fourth of pile penetration depth from pile head level. The axial deformations of piles in all load combinations cases of all piles are inversely proportional with penetration depth. The largest values of axial soil reaction are shown at the pile tips levels (the maximum penetration level). The most of lateral soil reactions resultant are in the first third of pile penetration depth from pile head level and approximately vanished after that penetration. The influence of the soil-structure interaction on the response of the jacket foundation predicts that the flexible foundation model is necessary to estimate the force responses demands of the offshore platform with a piled jacket-support
Research Authors
Shehata E Abdel Raheem, Elsayed M. Abdel Aal, Aly G.A. AbdelShafy, Mohamed F.M. Fahmyd and Mahmoud H Mansour
Research Department
Research Journal
Earthquakes and Structures, An International Journal
Research Member
Research Pages
407-421
Research Publisher
Techno-Press Publishers
Research Rank
1
Research Vol
18(4)
Research Website
http://www.techno-press.org/content/?page=article&journal=eas&volume=18&num=4&ordernum=1
Research Year
2020

Pile-soil-structure interaction effect on structural response of piled jacket-supported offshore platform through in-place analysis

Research Abstract
In-place analysis for offshore platforms is essentially required to make proper design for new structures and true assessment for existing structures, in addition to the structural integrity of platforms components under the maximum and minimum operating loads when subjected to the environmental conditions. In-place analysis have been executed to check that the structural member with all appurtenance´s robustness have the capability to support the applied loads in either storm or operating conditions. A nonlinear finite element analysis is adopted for the platform structure above the seabed and pile-soil interaction to estimate the in-place behavior of a typical fixed offshore platform. The SACS software is utilized to calculate the dynamic characteristics of the platform model and the response of platform joints then the stresses at selected members, as well as their nodal displacements. The directions of environmental loads and water depth variations have significant effects in the results of the in-place analysis behavior. The most of bending moment responses of the piles are in the first fourth of pile penetration depth from pile head level. The axial deformations of piles in all load combinations cases of all piles are inversely proportional with penetration depth. The largest values of axial soil reaction are shown at the pile tips levels (the maximum penetration level). The most of lateral soil reactions resultant are in the first third of pile penetration depth from pile head level and approximately vanished after that penetration. The influence of the soil-structure interaction on the response of the jacket foundation predicts that the flexible foundation model is necessary to estimate the force responses demands of the offshore platform with a piled jacket-support
Research Authors
Shehata E Abdel Raheem, Elsayed M. Abdel Aal, Aly G.A. AbdelShafy, Mohamed F.M. Fahmyd and Mahmoud H Mansour
Research Department
Research Journal
Earthquakes and Structures, An International Journal
Research Member
Research Pages
407-421
Research Publisher
Techno-Press Publishers
Research Rank
1
Research Vol
18(4)
Research Website
http://www.techno-press.org/content/?page=article&journal=eas&volume=18&num=4&ordernum=1
Research Year
2020

Pile-soil-structure interaction effect on structural response of piled jacket-supported offshore platform through in-place analysis

Research Abstract
In-place analysis for offshore platforms is essentially required to make proper design for new structures and true assessment for existing structures, in addition to the structural integrity of platforms components under the maximum and minimum operating loads when subjected to the environmental conditions. In-place analysis have been executed to check that the structural member with all appurtenance´s robustness have the capability to support the applied loads in either storm or operating conditions. A nonlinear finite element analysis is adopted for the platform structure above the seabed and pile-soil interaction to estimate the in-place behavior of a typical fixed offshore platform. The SACS software is utilized to calculate the dynamic characteristics of the platform model and the response of platform joints then the stresses at selected members, as well as their nodal displacements. The directions of environmental loads and water depth variations have significant effects in the results of the in-place analysis behavior. The most of bending moment responses of the piles are in the first fourth of pile penetration depth from pile head level. The axial deformations of piles in all load combinations cases of all piles are inversely proportional with penetration depth. The largest values of axial soil reaction are shown at the pile tips levels (the maximum penetration level). The most of lateral soil reactions resultant are in the first third of pile penetration depth from pile head level and approximately vanished after that penetration. The influence of the soil-structure interaction on the response of the jacket foundation predicts that the flexible foundation model is necessary to estimate the force responses demands of the offshore platform with a piled jacket-support
Research Authors
Shehata E Abdel Raheem, Elsayed M. Abdel Aal, Aly G.A. AbdelShafy, Mohamed F.M. Fahmyd and Mahmoud H Mansour
Research Department
Research Journal
Earthquakes and Structures, An International Journal
Research Pages
407-421
Research Publisher
Techno-Press Publishers
Research Rank
1
Research Vol
18(4)
Research Website
http://www.techno-press.org/content/?page=article&journal=eas&volume=18&num=4&ordernum=1
Research Year
2020

Smart Monitoring System for Distribution Power Grid

Research Abstract
NULL
Research Authors
Wael Ahmed
Research Department
Research Journal

researchgate.net
Research Pages
NULL
Research Publisher
NULL
Research Rank
1
Research Vol
NULL
Research Website
https://www.researchgate.net/project/Smart-Monitoring-System-for-Distribution-Power-Grid-2
Research Year
2019

Prediction of Fault Location along Overhead Power Transmission Lines Discussion Committee

Research Abstract
NULL
Research Authors
Wael Ahmed
Research Department
Research Journal
Faculty of Engineering, Assiut University
Research Pages
NULL
Research Publisher
NULL
Research Rank
2
Research Vol
NULL
Research Website
https://www.researchgate.net/publication/334657119_Prediction_of_Fault_Location_along_Overhead_Power_Transmission_Lines_Discussion_Committee
Research Year
2019

Simulated Testing Algorithm for µPMU Full Observation of Balanced Radial Distribution Grid

Research Abstract
Today’s electric power distribution systems with development of distributed energy resources introduce variability, uncertainty, and opportunities to recruit diverse resources for grid services. Multiple resources on each feeder have more complex impacts on the circuit behavior that can be observed with voltage and current phase angle variations. Micro Phasor Measurement Units (μPMUs) take timesynchronized measurements of voltage, current and frequency that can tell grid operators what is happening, where, and when. This paper presents a new μPMUs power flow algorithm for complete observation of balanced radial distribution grid. This algorithm calculates all voltages in both high and low voltage buses, currents in all branches, line active and reactive power flow in all branches and total active and reactive power losses in the grid. This algorithm provides high quality data for distribution planners and operators, which will translate into better model accuracy and thus better results from distribution analysis tools. To test the validity of proposed algorithm, backward / forward sweep power flow program is developed and tested by ETAP software.
Research Authors
Wael Ahmed, Ibrahem Hassan, Ibrahem Hassan, M. Nayel, Hossam Gaber
Research Department
Research Journal
Conference: 2019 IEEE 7th International Conference on Smart Energy Grid Engineering (SEGE)
Research Pages
NULL
Research Publisher
NULL
Research Rank
3
Research Vol
NULL
Research Website
NULL
Research Year
2019
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