scholarly journals Isolation of Extracellular Vesicles: General Methodologies and Latest Trends

2018 ◽  
Vol 2018 ◽  
pp. 1-27 ◽  
Author(s):  
Maria Yu. Konoshenko ◽  
Evgeniy A. Lekchnov ◽  
Alexander V. Vlassov ◽  
Pavel P. Laktionov
Keyword(s):  
Extracellular Vesicles ◽  
State Of The Art ◽  
Data Interpretation ◽  
Biochemical Properties ◽  
Mixed Population ◽  
Isolation Method ◽  
Modern Biology ◽  
Advantages And Disadvantages ◽  
Isolation Methods ◽  
Labor Consumption

Background. Extracellular vesicles (EVs) play an essential role in the communication between cells and transport of diagnostically significant molecules. A wide diversity of approaches utilizing different biochemical properties of EVs and a lack of accepted protocols make data interpretation very challenging. Scope of Review. This review consolidates the data on the classical and state-of-the-art methods for isolation of EVs, including exosomes, highlighting the advantages and disadvantages of each method. Various characteristics of individual methods, including isolation efficiency, EV yield, properties of isolated EVs, and labor consumption are compared. Major Conclusions. A mixed population of vesicles is obtained in most studies of EVs for all used isolation methods. The properties of an analyzed sample should be taken into account when planning an experiment aimed at studying and using these vesicles. The problem of adequate EVs isolation methods still remains; it might not be possible to develop a universal EV isolation method but the available protocols can be used towards solving particular types of problems. General Significance. With the wide use of EVs for diagnosis and therapy of various diseases the evaluation of existing methods for EV isolation is one of the key problems in modern biology and medicine.

scholarly journals Current methods for the isolation of extracellular vesicles

2013 ◽  
Vol 394 (10) ◽  
pp. 1253-1262 ◽  
Author(s):  
Fatemeh Momen-Heravi ◽  
Leonora Balaj ◽  
Sara Alian ◽  
Pierre-Yves Mantel ◽  
Allison E. Halleck ◽  
...  
Keyword(s):  
Extracellular Vesicles ◽  
Molecular Mechanisms ◽  
Magnetic Beads ◽  
Cell Types ◽  
Target Cells ◽  
Cell Of Origin ◽  
Novel Technologies ◽  
Advantages And Disadvantages ◽  
Isolation Methods ◽  
Technical Advances

Abstract Extracellular vesicles (EVs), including microvesicles and exosomes, are nano- to micron-sized vesicles, which may deliver bioactive cargos that include lipids, growth factors and their receptors, proteases, signaling molecules, as well as mRNA and non-coding RNA, released from the cell of origin, to target cells. EVs are released by all cell types and likely induced by mechanisms involved in oncogenic transformation, environmental stimulation, cellular activation, oxidative stress, or death. Ongoing studies investigate the molecular mechanisms and mediators of EVs-based intercellular communication at physiological and oncogenic conditions with the hope of using this information as a possible source for explaining physiological processes in addition to using them as therapeutic targets and disease biomarkers in a variety of diseases. A major limitation in this evolving discipline is the hardship and the lack of standardization for already challenging techniques to isolate EVs. Technical advances have been accomplished in the field of isolation with improving knowledge and emerging novel technologies, including ultracentrifugation, microfluidics, magnetic beads and filtration-based isolation methods. In this review, we will discuss the latest advances in methods of isolation methods and production of clinical grade EVs as well as their advantages and disadvantages, and the justification for their support and the challenges that they encounter.

Platelet monitoring for PCI

2009 ◽  
Vol 29 (04) ◽  
pp. 376-380 ◽  
Author(s):  
D. Capodanno ◽  
D. J. Angiolillo
Keyword(s):  
Interindividual Variability ◽  
State Of The Art ◽  
Coronary Intervention ◽  
Functional Tests ◽  
Treatment Regimens ◽  
Advantages And Disadvantages ◽  
Coronary Syndrome ◽  
Combined Use ◽  
Increased Risk ◽  
Percutaneous Coronary

SummaryDespite the clinical benefit associated with the combined use of aspirin and clopidogrel in patients with acute coronary syndrome or those undergoing percutaneous coronary intervention, a considerable interindividual variability in response to these drugs have been consistently reported. There is a growing interest on applying platelet functional tests with the goal of identifying patients at increased risk of recurrent ischaemic events and potentially tailoring antiplatelet treatment regimens.This manuscript will review the state of the art on the most commonly available platelet functional tests, describing their advantages and disadvantages and exploring their applicability in clinical practice.

Multi-Resolution Autoregressive Graph-to-Graph Translation for Molecules

2019 ◽  
Author(s):  
Wengong Jin ◽  
Regina Barzilay ◽  
Tommi S Jaakkola
Keyword(s):  
Drug Discovery ◽  
State Of The Art ◽  
Molecular Graph ◽  
Biochemical Properties ◽  
Large Margin ◽  
Previous State ◽  
Translation Methods ◽  
Atom Level ◽  
Precursor Molecules ◽  
Prior State

The problem of accelerating drug discovery relies heavily on automatic tools to optimize precursor molecules to afford them with better biochemical properties. Our work in this paper substantially extends prior state-of-the-art on graph-to-graph translation methods for molecular optimization. In particular, we realize coherent multi-resolution representations by interweaving trees over substructures with the atom-level encoding of the original molecular graph. Moreover, our graph decoder is fully autoregressive, and interleaves each step of adding a new substructure with the process of resolving its connectivity to the emerging molecule. We evaluate our model on multiple molecular optimization tasks and show that our model outperforms previous state-of-the-art baselines by a large margin.

scholarly journals A Systematic Review of Recommender Systems and Their Applications in Cybersecurity

Sensors ◽  
2021 ◽  
Vol 21 (15) ◽  
pp. 5248
Author(s):  
Aleksandra Pawlicka ◽  
Marek Pawlicki ◽  
Rafał Kozik ◽  
Ryszard S. Choraś
Keyword(s):  
Systematic Review ◽  
Recommender Systems ◽  
Recommender System ◽  
State Of The Art ◽  
The State ◽  
Advantages And Disadvantages ◽  
Comprehensive Survey ◽  
Security Concerns ◽  
Valuable Role

This paper discusses the valuable role recommender systems may play in cybersecurity. First, a comprehensive presentation of recommender system types is presented, as well as their advantages and disadvantages, possible applications and security concerns. Then, the paper collects and presents the state of the art concerning the use of recommender systems in cybersecurity; both the existing solutions and future ideas are presented. The contribution of this paper is two-fold: to date, to the best of our knowledge, there has been no work collecting the applications of recommenders for cybersecurity. Moreover, this paper attempts to complete a comprehensive survey of recommender types, after noticing that other works usually mention two–three types at once and neglect the others.

scholarly journals Bacterial Membrane Vesicles in Pneumonia: From Mediators of Virulence to Innovative Vaccine Candidates

2021 ◽  
Vol 22 (8) ◽  
pp. 3858
Author(s):  
Felix Behrens ◽  
Teresa C. Funk-Hilsdorf ◽  
Wolfgang M. Kuebler ◽  
Szandor Simmons
Keyword(s):  
Extracellular Vesicles ◽  
Inflammatory Responses ◽  
Significant Proportion ◽  
Treatment Strategies ◽  
Membrane Vesicles ◽  
Multidrug Resistant ◽  
Biochemical Properties ◽  
Outer Membrane Vesicles ◽  
Vaccine Candidates ◽  
Treatment Regimens

Pneumonia due to respiratory infection with most prominently bacteria, but also viruses, fungi, or parasites is the leading cause of death worldwide among all infectious disease in both adults and infants. The introduction of modern antibiotic treatment regimens and vaccine strategies has helped to lower the burden of bacterial pneumonia, yet due to the unavailability or refusal of vaccines and antimicrobials in parts of the global population, the rise of multidrug resistant pathogens, and high fatality rates even in patients treated with appropriate antibiotics pneumonia remains a global threat. As such, a better understanding of pathogen virulence on the one, and the development of innovative vaccine strategies on the other hand are once again in dire need in the perennial fight of men against microbes. Recent data show that the secretome of bacteria consists not only of soluble mediators of virulence but also to a significant proportion of extracellular vesicles—lipid bilayer-delimited particles that form integral mediators of intercellular communication. Extracellular vesicles are released from cells of all kinds of organisms, including both Gram-negative and Gram-positive bacteria in which case they are commonly termed outer membrane vesicles (OMVs) and membrane vesicles (MVs), respectively. (O)MVs can trigger inflammatory responses to specific pathogens including S. pneumonia, P. aeruginosa, and L. pneumophila and as such, mediate bacterial virulence in pneumonia by challenging the host respiratory epithelium and cellular and humoral immunity. In parallel, however, (O)MVs have recently emerged as auspicious vaccine candidates due to their natural antigenicity and favorable biochemical properties. First studies highlight the efficacy of such vaccines in animal models exposed to (O)MVs from B. pertussis, S. pneumoniae, A. baumannii, and K. pneumoniae. An advanced and balanced recognition of both the detrimental effects of (O)MVs and their immunogenic potential could pave the way to novel treatment strategies in pneumonia and effective preventive approaches.

scholarly journals A multiparametric extraction method for Vn96-isolated plasma extracellular vesicles and cell-free DNA that enables multi-omic profiling

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Jeremy W. Roy ◽  
Catherine A. Taylor ◽  
Annie P. Beauregard ◽  
Surendar R. Dhadi ◽  
D. Craig Ayre ◽  
...  
Keyword(s):  
Extracellular Vesicles ◽  
Liquid Biopsy ◽  
Small Rna Sequencing ◽  
Isolation Method ◽  
Protein Biomarkers ◽  
Cell Free Dna ◽  
Extraction Protocol ◽  
Free Dna ◽  
Rich Material ◽  
Short Timeframe

AbstractExtracellular vesicles (EVs) have been recognized as a rich material for the analysis of DNA, RNA, and protein biomarkers. A remaining challenge for the deployment of EV-based diagnostic and prognostic assays in liquid biopsy testing is the development of an EV isolation method that is amenable to a clinical diagnostic lab setting and is compatible with multiple types of biomarker analyses. We have previously designed a synthetic peptide, known as Vn96 (ME kit), which efficiently isolates EVs from multiple biofluids in a short timeframe without the use of specialized lab equipment. Moreover, it has recently been shown that Vn96 also facilitates the co-isolation of cell-free DNA (cfDNA) along with EVs. Herein we describe an optimized method for Vn96 affinity-based EV and cfDNA isolation from plasma samples and have developed a multiparametric extraction protocol for the sequential isolation of DNA, RNA, and protein from the same plasma EV and cfDNA sample. We are able to isolate sufficient material by the multiparametric extraction protocol for use in downstream analyses, including ddPCR (DNA) and ‘omic profiling by both small RNA sequencing (RNA) and mass spectrometry (protein), from a minimum volume (4 mL) of plasma. This multiparametric extraction protocol should improve the ability to analyse multiple biomarker materials (DNA, RNA and protein) from the same limited starting material, which may improve the sensitivity and specificity of liquid biopsy tests that exploit EV-based and cfDNA biomarkers for disease detection and monitoring.

scholarly journals Summer Research Placements – State-of-the-Art Science by pre-University Students

MRS Advances ◽  
2016 ◽  
Vol 1 (56) ◽  
pp. 3715-3720 ◽  
Author(s):  
R. A. Sporea ◽  
S. Lygo-Baker
Keyword(s):  
University Students ◽  
State Of The Art ◽  
Group Learning ◽  
Student Interaction ◽  
Research Tool ◽  
Skills Acquisition ◽  
Advantages And Disadvantages ◽  
Effective Training ◽  
Training And Research ◽  
Student Training

ABSTRACTSummer research placements are an effective training and research tool. Over three years, our group has hosted nine pre-university students over periods of four to six weeks. Apart from student training and skills acquisition, the placements have produced several peer-reviewed technical publications. Our approach relies on careful pre-planning of activities, frequent student interaction, coupled with independent and group learning. We explore the advantages and disadvantages of this manner of running summer placements.

New Trends in Asymptotic Approaches: Summation and Interpolation Methods

2001 ◽  
Vol 54 (1) ◽  
pp. 69-92 ◽  
Author(s):  
Igor V. Andrianov ◽  
Jan Awrejcewicz
Keyword(s):  
Applied Sciences ◽  
Solid Mechanics ◽  
State Of The Art ◽  
Asymptotic Methods ◽  
Perturbation Series ◽  
Review Article ◽  
Point Of View ◽  
Advantages And Disadvantages ◽  
New Methods ◽  
Local Character

In this review article, we present in some detail new trends in application of asymptotic techniques to mechanical problems. First we consider the various methods which allows for the possibility of extending the perturbation series application space and hence omiting their local character. While applying the asymptotic methods very often the following situation appears: an existence of the asymptotics ε → 0 implies an existence of the asymptotics ε → ∞ (or, in a more general sense, ε → a and ε → b). Therefore, an idea of constructing a single solution valid for a whole interval of parameter ε changes is very attractive. In other words, we discuss a problem of asymptotically equivalent function constructions possessing for ε → a and ε → b a known asymptotic behavior. The defined problems are very important from the point of view of both theoretical and applied sciences. In this work, we review the state-of-the-art, by presenting the existing methods and by pointing out their advantages and disadvantages, as well as the fields of their applications. In addition, some new methods are also proposed. The methods are demonstrated on a wide variety of static and dynamic solid mechanics problems and some others involving fluid mechanics. This review article contains 340 references.

scholarly journals Biased nicking of mitochondrial DNA during extraction can be avoided by choice of isolation method

2021 ◽  
Author(s):  
Bruno Marçal Repolês ◽  
Choco Michael Gorospe ◽  
Phong Tran ◽  
Anna Karin Nilsson ◽  
Paulina H. Wanrooij
Keyword(s):  
Skeletal Muscle ◽  
Mitochondrial Dna ◽  
Dna Isolation ◽  
Isolation Procedure ◽  
Isolation Method ◽  
Strand Breaks ◽  
Careful Choice ◽  
Isolation Methods ◽  
Solid Tissues ◽  
Long Range Pcr

AbstractThe integrity of mitochondrial DNA (mtDNA) isolated from solid tissues is critical for analyses such as long-range PCR. We show that a commonly-used DNA isolation procedure preferentially introduces strand breaks into the mtDNA extracted from the skeletal muscle of aged mice, while mtDNA from adult animals is less affected. We present a comparison of mtDNA isolation methods and identify one that avoids this biased loss of muscle mtDNA integrity. Our results highlight the importance of a careful choice of mtDNA isolation method and serve as a resource to researchers planning analysis of mtDNA isolated from solid tissues.

scholarly journals Tetraspanin immunocapture phenotypes extracellular vesicles according to biofluid source but may limit identification of multiplexed cancer biomarkers

2021 ◽  
Author(s):  
Rachel R. Mizenko ◽  
Terza Brostoff ◽  
Tatu Rojalin ◽  
Hanna J. Koster ◽  
Hila S. Swindell ◽  
...  
Keyword(s):  
Flow Cytometry ◽  
Extracellular Vesicles ◽  
Fluorescence Detection ◽  
Single Particle ◽  
Cancer Biomarkers ◽  
Surface Markers ◽  
Isolation Method ◽  
Standard Methods

AbstractTetraspanin expression of extracellular vesicles (EVs) is often used as a surrogate for their general detection and classification from background contaminants. This common practice typically assumes a consistent expression of tetraspanins across EV sources, thus obscuring subpopulations of variable or limited tetraspanin expression. While some recent studies indicate differential expression of tetraspanins across bulk isolated EVs, here we present analysis of single EVs isolated using various field-standard methods from a variety of in vitro and in vivo sources to identify distinct patterns in colocalization of tetraspanin expression. We report an optimized method for the use of antibodycapture single particle interferometric reflectance imaging sensing (SP-IRIS) and fluorescence detection to identify subpopulations according to tetraspanin expression and compare our findings with nanoscale flow cytometry. Using SP-IRIS and immunofluorescence, we report that tetraspanin profile is consistent from a given EV source regardless of isolation method, but that tetraspanin profiles are distinct across various sources. Tetraspanin profiles as measured by flow cytometry do not share similar trends, suggesting that limitations in subpopulation detection significantly impact apparent protein expression. We further analyzed tetraspanin expression of single EVs captured non-specifically, revealing that tetraspanin capture can bias the apparent multiplexed tetraspanin profile. Finally, we demonstrate that this bias can have significant impact on diagnostic sensitivity for tumor-associated EV surface markers. Our findings may reveal key insights into the complexities of the EV biogenesis and signaling pathways and better inform EV capture and detection platforms for diagnostic or other downstream use.

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