scholarly journals Velocity Gradient Separation Reveals a New Extracellular Vesicle Population Enriched in miR-155 and Mitochondrial DNA

Pathogens ◽  
2021 ◽  
Vol 10 (5) ◽  
pp. 526
Author(s):  
Myriam Vaillancourt ◽  
Audrey Hubert ◽  
Caroline Subra ◽  
Julien Boucher ◽  
Wilfried Wenceslas Bazié ◽  
...  
Keyword(s):  
Mitochondrial Dna ◽  
Velocity Gradient ◽  
Messenger Rna ◽  
Sucrose Density Gradient ◽  
Extracellular Vesicle ◽  
Therapeutic Interventions ◽  
Optimal Separation ◽  
Velocity Gradients ◽  
Commercial Kits ◽  
Hiv 1

Extracellular vesicles (EVs) and their contents (proteins, lipids, messenger RNA, microRNA, and DNA) are viewed as intercellular signals, cell-transforming agents, and shelters for viruses that allow both diagnostic and therapeutic interventions. EVs circulating in the blood of individuals infected with human immunodeficiency virus (HIV-1) may provide insights into pathogenesis, inflammation, and disease progression. However, distinguishing plasma membrane EVs from exosomes, exomeres, apoptotic bodies, virions, and contaminating proteins remains challenging. We aimed at comparing sucrose and iodixanol density and velocity gradients along with commercial kits as a means of separating EVs from HIV particles and contaminating protein like calprotectin; and thereby evaluating the suitability of current plasma EVs analysis techniques for identifying new biomarkers of HIV-1 immune activation. Multiple analysis have been performed on HIV-1 infected cell lines, plasma from HIV-1 patients, or plasma from HIV-negative individuals spiked with HIV-1. Commercial kits, the differential centrifugation and density or velocity gradients to precipitate and separate HIV, EVs, and proteins such as calprotectin, have been used. EVs, virions, and contaminating proteins were characterized using Western blot, ELISA, RT-PCR, hydrodynamic size measurement, and enzymatic assay. Conversely to iodixanol density or velocity gradient, protein and virions co-sedimented in the same fractions of the sucrose density gradient than AChE-positive EVs. Iodixanol velocity gradient provided the optimal separation of EVs from viruses and free proteins in culture supernatants and plasma samples from a person living with HIV (PLWH) or a control and revealed a new population of large EVs enriched in microRNA miR-155 and mitochondrial DNA. Although EVs and their contents provide helpful information about several key events in HIV-1 pathogenesis, their purification and extensive characterization by velocity gradient must be investigated thoroughly before further use as biomarkers. By revealing a new population of EVs enriched in miR-155 and mitochondrial DNA, this study paves a way to increase our understanding of HIV-1 pathogenesis.

scholarly journals Integrated whole transcriptome and small RNA analysis revealed multiple regulatory networks in colorectal cancer

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Hibah Shaath ◽  
Salman M. Toor ◽  
Mohamed Abu Nada ◽  
Eyad Elkord ◽  
Nehad M. Alajez
Keyword(s):  
Colorectal Cancer ◽  
Messenger Rna ◽  
Regulatory Networks ◽  
Potential Interaction ◽  
Therapeutic Interventions ◽  
Signaling Networks ◽  
Protein Coding ◽  
Paired Samples ◽  
And Migration ◽  
Whole Transcriptome

AbstractColorectal cancer (CRC) remains a global disease burden and a leading cause of cancer related deaths worldwide. The identification of aberrantly expressed messenger RNA (mRNA), long non-coding RNA (lncRNA), and microRNA (miRNA), and the resulting molecular interactions and signaling networks is essential for better understanding of CRC, identification of novel diagnostic biomarkers and potential development of therapeutic interventions. Herein, we performed microRNA (miRNA) sequencing on fifteen CRC and their non-tumor adjacent tissues and whole transcriptome RNA-Seq on six paired samples from the same cohort and identified alterations in miRNA, mRNA, and lncRNA expression. Computational analyses using Ingenuity Pathway Analysis (IPA) identified multiple activated signaling networks in CRC, including ERBB2, RABL6, FOXM1, and NFKB networks, while functional annotation highlighted activation of cell proliferation and migration as the hallmark of CRC. IPA in combination with in silico prediction algorithms and experimentally validated databases gave insight into the complex associations and interactions between downregulated miRNAs and upregulated mRNAs in CRC and vice versa. Additionally, potential interaction between differentially expressed lncRNAs such as H19, SNHG5, and GATA2-AS1 with multiple miRNAs has been revealed. Taken together, our data provides thorough analysis of dysregulated protein-coding and non-coding RNAs in CRC highlighting numerous associations and regulatory networks thus providing better understanding of CRC.

scholarly journals Broadly neutralizing antibodies and vaccine design against HIV-1 infection

2019 ◽  
Vol 14 (1) ◽  
pp. 30-42 ◽  
Author(s):  
Qian Wang ◽  
Linqi Zhang
Keyword(s):  
Neutralizing Antibodies ◽  
Vaccine Development ◽  
Vaccine Design ◽  
Therapeutic Interventions ◽  
Type I ◽  
Broadly Neutralizing Antibodies ◽  
Dynamic Studies ◽  
Immunodeficiency Virus ◽  
Hiv 1 ◽  
Remarkable Progress

AbstractRemarkable progress has been achieved for prophylactic and therapeutic interventions against human immunodeficiency virus type I (HIV-1) through antiretroviral therapy. However, vaccine development has remained challenging. Recent discoveries in broadly neutralizing monoclonal antibodies (bNAbs) has led to the development of multiple novel vaccine approaches for inducing bNAbs-like antibody response. Structural and dynamic studies revealed several vulnerable sites and states of the HIV-1 envelop glycoprotein (Env) during infection. Our review aims to highlight these discoveries and rejuvenate our endeavor in HIV-1 vaccine design and development.

The influence of agitation on aggregates formed during treatment of water with a content of humic substances

2006 ◽  
Vol 6 (1) ◽  
pp. 211-218 ◽  
Author(s):  
L. Pivokonska ◽  
M. Pivokonsky
Keyword(s):  
Humic Substances ◽  
Velocity Gradient ◽  
Laboratory Tests ◽  
Treatment Plant ◽  
Water Treatment Plant ◽  
Aluminium Chloride ◽  
Velocity Gradients ◽  
Perforated Baffle ◽  
Wide Size Distribution

This study aims to evaluate the influence of agitation conditions on the efficiency of the aggregation process when treating surface water containing humic substances. Laboratory tests were conducted by the jar tests using a variable speed paddle gang stirrer. Optimization of agitation intensity was determined by a Couette flocculator. Suspension was prepared using aluminium chloride as a destabilising reagent. Aggregation efficiency was evaluated by the determination of the degree of aggregation and by the test of aggregation. For all surface waters treated, the optimum treatability was demonstrated by applying higher velocity gradients (G=200–250 s−1). In addition to the laboratory tests, the plant measurements with water containing increased amounts of humic substances were taken to evaluate the aggregation efficiency. The results obtained by the aggregation efficiency measurements show that the intensity of agitation, with the assistance of perforated baffle-type flocculation chamber, attains a low level of velocity gradient (G=22–113 s−1), in contrast to the optimized velocity gradient level (G=200–250 s−1). The aggregates formed in the water treatment plant have an unsuitably wide size-distribution.

scholarly journals Self-gravitating filament formation from shocked flows: velocity gradients across filaments

2020 ◽  
Vol 494 (3) ◽  
pp. 3675-3685 ◽  
Author(s):  
Che-Yu Chen ◽  
Lee G Mundy ◽  
Eve C Ostriker ◽  
Shaye Storm ◽  
Arnab Dhabal
Keyword(s):  
Velocity Gradient ◽  
Unit Length ◽  
Selection Effect ◽  
Major Axis ◽  
Large Area ◽  
North West ◽  
Preferred Direction ◽  
The North ◽  
Velocity Gradients ◽  
Field Lines

ABSTRACT In typical environments of star-forming clouds, converging supersonic turbulence generates shock-compressed regions, and can create strongly magnetized sheet-like layers. Numerical magnetohydrodynamic simulations show that within these post-shock layers, dense filaments and embedded self-gravitating cores form via gathering material along the magnetic field lines. As a result of the preferred-direction mass collection, a velocity gradient perpendicular to the filament major axis is a common feature seen in simulations. We show that this prediction is in good agreement with recent observations from the CARMA Large Area Star Formation Survey (CLASSy), from which we identified several filaments with prominent velocity gradients perpendicular to their major axes. Highlighting a filament from the north-west part of Serpens South, we provide both qualitative and quantitative comparisons between simulation results and observational data. In particular, we show that the dimensionless ratio Cv ≡ Δvh2/(GM/L), where Δvh is half of the observed perpendicular velocity difference across a filament, and M/L is the filament’s mass per unit length, can distinguish between filaments formed purely due to turbulent compression and those formed due to gravity-induced accretion. We conclude that the perpendicular velocity gradient observed in the Serpens South north-west filament can be caused by gravity-induced anisotropic accretion of material from a flattened layer. Using synthetic observations of our simulated filaments, we also propose that a density-selection effect may explain observed subfilaments (one filament breaking into two components in velocity space) as reported in recent observations.

Investigate the role of GPR15/BOB in the SLE patients

2018 ◽  
Vol 6 (1) ◽  
pp. 19-32
Author(s):  
Caroline G. Jackson ◽  
Donald R. Kwan
Keyword(s):  
Peripheral Blood ◽  
Messenger Rna ◽  
Viral Envelope ◽  
Orphan Receptor ◽  
Blood Monocytes ◽  
Rt Pcr ◽  
Peripheral Blood Monocytes ◽  
Healthy Donors ◽  
Hiv 1

GPR15 functions as a cellular co-receptor for some isolates of HIV-1, HIV-2, and SIV through interactions with several viral envelope proteins. The objective of this study was to investigate the expression of orphan receptor GPR15/BOB in the serum of SLE patients and non-SLE healthy people. GPR15/BOB expression was analysed by flow cytometry while, GPR15/BOB messenger RNA was examined in peripheral blood monocytes by RT-PCR. GPR15/BOB mRNA was detected in all periphral blood of SLE patients examined. Further, a significant increase in GPR15/BOB expression as measured by mean fluorescence intensity was observed on SLE PB neutrophils compared to these cell populations from healthy donors. We concluded that GPR15/BOB is expressed in monocytes and neutrophils in peripheral blood, and expression is up-regulated in SLE patients compared to controls. GPR15/BOB may play a role in SLE pathogenesis.

Reply to Peter Hubral by the Author

Geophysics ◽  
1978 ◽  
Vol 43 (5) ◽  
pp. 1024-1025
Author(s):  
Paul Michaels
Keyword(s):  
Velocity Gradient ◽  
Horizontal Velocity ◽  
Lateral Velocity ◽  
Velocity Gradients ◽  
Coordinate Rotation

Peter Hubral’s extension of the raypath migration calculator program to include a lateral velocity gradient is quite ingenious. In such cases where the vertical and horizontal velocity gradients are constant, the net effect is a simple coordinate rotation. The theoretical raypath remains circular, but is only rotated about its intersection with the datum plane.

scholarly journals Identification of storage-protein messenger RNA of the fleshfly Sarcophaga peregrina

1982 ◽  
Vol 203 (3) ◽  
pp. 571-575 ◽  
Author(s):  
T Tahara ◽  
Y Maeda ◽  
A Kuroiwa ◽  
K Ueno ◽  
M Obinata ◽  
...  
Keyword(s):  
Density Gradient ◽  
Storage Protein ◽  
Messenger Rna ◽  
Fat Body ◽  
Density Gradient Centrifugation ◽  
Signal Sequence ◽  
Gradient Centrifugation ◽  
Sucrose Density Gradient ◽  
Sucrose Density Gradient Centrifugation

Storage-protein mRNA was found to be abundant in poly(A)-containing RNA extracted from the fat-body of third-instar larvae of Sarcophaga peregrina (fleshfly). This RNA sedimented at the position of 19S on sucrose-density-gradient centrifugation and the product of its translation in vitro was 75K protein (protein of mol.wt. 75 000), which was precipitated specifically with antibody against storage protein. This product was suggested to contain a signal sequence that is missing in mature storage protein. The poly(A)-containing RNA was also found to contain much of another mRNA coding for 25K protein (protein of mol.wt. 25 000), but the function of this protein is unknown.

scholarly journals CONTROLLED PROTEOLYSIS OF NASCENT POLYPEPTIDES IN RAT LIVER CELL FRACTIONS

1970 ◽  
Vol 45 (1) ◽  
pp. 146-157 ◽  
Author(s):  
D. D. Sabatini ◽  
G. Blobel
Keyword(s):  
Amino Acid ◽  
Messenger Rna ◽  
Close Association ◽  
Membrane Integrity ◽  
Sucrose Density Gradient ◽  
Electron Microscopic ◽  
Microsomal Membranes ◽  
Membrane Bound ◽  
Cell Fractions

Rough microsomes were incubated in an in vitro amino acid-incorporating system for labeling the nascent polypeptide chains on the membrane-bound ribosomes. Sucrose density gradient analysis showed that ribosomes did not detach from the membranes during incorporation in vitro. Trypsin and chymotrypsin treatment of microsomes at 0° led to the detachment of ribosomes from the membranes; furthermore, trypsin produced the dissociation of released, messenger RNA-free ribosomes into subunits. Electron microscopic observations indicated that the membranes remained as closed vesicles. In contrast to the situation with free polysomes, nascent chains contained in rough microsomes were extensively protected from proteolytic attach. By separating the microsomal membranes from the released subunits after proteolysis, it was found that nascent chains are split into two size classes of fragments when the ribosomes are detached. These were shown by column chromatography on Sephadex G-50 to be: (a) small (39 amino acid residues) ribosome-associated fragments and (b) a mixture of larger membrane-associated fragments excluded from the column. The small fragments correspond to the carboxy-terminal segments which are protected by the large subunits of free polysomes. The larger fragments associated with the microsomal membranes depend for their protection on membrane integrity. These fragments are completely digested if the microsomes are subjected to proteolysis in the presence of detergents. These results indicate that when the nascent polypeptides growing in the large subunits of membrane-bound ribosomes emerge from the ribosomes they enter directly into a close association with the microsomal membrane.

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