1,721,075 research outputs found
Exomeres and supermeres: Monolithic or diverse?
Full text linkAbstract Extracellular vesicles (EVs), including exosomes and microvesicles, are far from being the only RNA‐containing extracellular particles (EPs). Recently, new 35‐nm‐sized EPs were discovered by asymmetric‐flow field‐flow fractionation and termed ‘exomeres’. Purification of exomeres was later performed by differential ultracentrifugation as well. More recently, the supernatant of the high‐speed ultracentrifugation used to collect exomeres was further centrifuged to collect a new class of EP, termed ‘supermeres’. Supermeres contain high quantities of extracellular RNA and are enriched in miR‐1246. They are also replete in disease biomarkers and can induce metabolic and adaptive changes in recipient cells. Here, we reanalysed proteomic and transcriptomic data obtained in this exciting study to obtain further insights into the molecular composition of exomeres and supermeres. We found that the top‐ranking RNAs in supermeres correspond to the footprints of extracellular protein complexes. These complexes protect fragments of the small nuclear RNA U2 and the 28S rRNA from extracellular ribonucleases (exRNases). We suggest that intracellular nanoparticles such as the U2 ribonucleoprotein, ribosomes and LGALS3BP ring‐like decamers are released into the extracellular space. These heterogeneous EPs might be further processed by exRNases and co‐isolate by ultracentrifugation with other components of exomeres and supermeres. We look forward to continuing progress in defining exRNA carriers, bridging process definitions with molecular composition and function
Going Beyond Counting First Authors in Author Co-citation Analysis
Full text linkThe present study examines one of the fundamental aspects of author co-citation analysis (ACA) - the way co-citation
counts are defined. Co-citation counting provides the data on which all subsequent statistical analyses and mappings
are based, and we compare ACA results based on two different types of co-citation counting - the traditional type that
only counts the first one among a cited work's authors on the one hand and a non-traditional type that takes into
account the first 5 authors of a cited work on the other hand. Results indicate that the picture produced through this non-traditional author co-citation counting contains more coherent author groups and is therefore considerably clearer. However, this picture represents fewer specialties in the research field being studied than that produced through the traditional first-author co-citation counting when the same number of top-ranked authors is selected and analyzed. Reasons for these effects are discussed
Variations on the Author
Full text link“Variations on the Author” discusses two of Eduardo Coutinho’s recent films (Um Dia na Vida, from 2010, and Últimas Conversas, posthumously released in 2015) and their contribution to the general question of documentary authorship. The director’s filmography is characterized by a consistent yet self-effacing form of authorial self-inscription: Coutinho often features as an interviewer that rather than express opinions propels discourses; an interviewer that is good at listening. This mode of self-inscription characterizes him as an author who is not expressive but who is nonetheless markedly present on the screen. In Um Dia na Vida, however, Coutinho is completely absent form the image, while Últimas Conversas, on the contrary, includes a confessional prologue that moves the director from the margins to the center of his films. This article examines the ways in which these works stand out in the filmography of a director who offers new insights into the notion of cinematic authorship
Appropriate Similarity Measures for Author Cocitation Analysis
Full text linkWe provide a number of new insights into the methodological discussion about author cocitation analysis. We first argue that the use of the Pearson correlation for measuring the similarity between authors’ cocitation profiles is not very satisfactory. We then discuss what kind of similarity measures may be used as an alternative to the Pearson correlation. We consider three similarity measures in particular. One is the well-known cosine. The other two similarity measures have not been used before in the bibliometric literature. Finally, we show by means of an example that our findings have a high practical relevance.information science;Pearson correlation;cosine;similarity measure;author cocitation analysis
High-resolution characterization of HIV and extracellular vesicles by STORM-FISHing: combining dSTORM and smFISH
Full text linkOver the last two decades, advancements in optical microscopy have led to the development of a variety of super-resolution microscopy (SRM) methods, each with the capacity to examine subcellular structures at high resolution, including the virions of exogenous viruses such as human immunodeficiency virus (HIV) and host extracellular vesicles (EVs). Accurately identifying and characterizing complete virions within complex biological samples is essential for advancing our understanding of the structural diversity of virions and virus-like particles. However, few approaches take advantage of the detailed structural insights that SRM can offer to characterize free-floating virions and multiple types of molecules associated with them. In this study, we evaluate STORM-FISH, a dual-labeling technique that combines antibody-based HIV protein labeling and smFISH-based HIV RNA labeling with dSTORM for accurate, high-resolution characterization of HIV virions. Using smFISH probes specific to BaL HIV vRNA, we observed high specificity for virion labeling in dSTORM imaging, with minimal levels of binding in control samples (DCL4 plant probes and non-BaL HIV strains). While individual labeling of viral proteins (gp120) alone resulted in considerable non-specific binding to host-derived EVs, the combined use of gp120 antibodies and BaL smFISH probes allowed clear identification of complete BaL HIV virions, as demonstrated by distinct populations of double-positive (BaL smFISH+/gp120+) and triple-positive (BaL smFISH+/gp120+/CD63+) particles. Interestingly, the smFISH probes sometimes localized externally to gp120+ particles, raising questions about the origin of this potential external vRNA. The high-resolution imaging capabilities of STORM-FISH allow for detailed analysis of virion structure, protein localization, and component orientation, facilitating deeper insights into the structural dynamics of HIV. Our results validate STORM-FISH as an effective technique for dual protein/RNA labeling of free-floating virions in dSTORM microscopy and could translate well into furthering virological research and characterization of therapeutic extracellular vesicles or virus-mediated gene delivery systems
High-resolution characterization of HIV and extracellular vesicles by STORM-FISHing: combining dSTORM and smFISH
Full text linkOver the last two decades, advancements in optical microscopy have led to the development of a variety of super-resolution microscopy (SRM) methods, each with the capacity to examine subcellular structures at high resolution, including the virions of exogenous viruses such as human immunodeficiency virus (HIV) and host extracellular vesicles (EVs). Accurately identifying and characterizing complete virions within complex biological samples is essential for advancing our understanding of the structural diversity of virions and virus-like particles. However, few approaches take advantage of the detailed structural insights that SRM can offer to characterize free-floating virions and multiple types of molecules associated with them. In this study, we evaluate STORM-FISH, a dual-labeling technique that combines antibody-based HIV protein labeling and smFISH-based HIV RNA labeling with dSTORM for accurate, high-resolution characterization of HIV virions. Using smFISH probes specific to BaL HIV vRNA, we observed high specificity for virion labeling in dSTORM imaging, with minimal levels of binding in control samples (DCL4 plant probes and non-BaL HIV strains). While individual labeling of viral proteins (gp120) alone resulted in considerable non-specific binding to host-derived EVs, the combined use of gp120 antibodies and BaL smFISH probes allowed clear identification of complete BaL HIV virions, as demonstrated by distinct populations of double-positive (BaL smFISH+/gp120+) and triple-positive (BaL smFISH+/gp120+/CD63+) particles. Interestingly, the smFISH probes sometimes localized externally to gp120+ particles, raising questions about the origin of this potential external vRNA. The high-resolution imaging capabilities of STORM-FISH allow for detailed analysis of virion structure, protein localization, and component orientation, facilitating deeper insights into the structural dynamics of HIV. Our results validate STORM-FISH as an effective technique for dual protein/RNA labeling of free-floating virions in dSTORM microscopy and could translate well into furthering virological research and characterization of therapeutic extracellular vesicles or virus-mediated gene delivery systems
Dispelling the Myths Behind First-author Citation Counts
Full text linkWe conducted a full-scale evaluative citation analysis study of scholars in the XML research field to explore just how different from each other author rankings resulting from different citation counting methods actually are, and to demonstrate the capability of emerging data and tools on the Web in supporting more realistic citation counting methods. Our results contest some common arguments for the continued
use of first-author citation counts in the evaluation of scholars, such as high correlations between author rankings by first-author citation counts and other citation
counting methods, and high costs of using more realistic citation counting methods that are not well-supported by the ISI databases. It is argued that increasingly available digital full text research papers make it possible for citation analysis studies to go beyond what the ISI databases have directly supported and to employ more
sophisticated methods
THE MECHANISM AND FUNCTION OF EXTRACELLULAR VESICLE RELEASE BY GDE2 AND GDE3
No full textGDE2 and GDE3 (Glycerophosphodiester phosphodiesterase 2/3) are members of a small family of six-transmembrane proteins. These proteins have the catalytic ability to cleave GPI-APs (Glycosylphosphatidylinositol-anchored proteins) off the cell surface, which is linked to most of their known biological functions. During my thesis, I discovered a novel role for these enzymes in releasing extracellular vesicles (EVs). EVs are small lipid particles released by cells that are important for intercellular communication. Overexpression of GDE2 or GDE3 in HEK293T cells is sufficient to release EVs. Characterization of GDE3-EVs indicates that they are a subtype of EV released from the plasma membrane called Microvesicles (MVs). These GDE3-MVs contain AnnexinA1 and GDE3 itself. In astrocytes, where GDE3 is expressed, GDE3 releases MVs by remodeling the actin cytoskeleton via the protein WAVE3 (WASF3, Wiskott-Aldrich syndrome protein family member 3). Because EVs function as intercellular signaling platforms, I hypothesized that GDE3-derived EVs regulate neuronal function. In a series of experiments with Daniel Daudelin, we found that neurons of Gde3-KO (knock-out) mice have impaired post-synaptic function and that EVs produced by WT (wild-type) astrocytes can restore this post-synaptic deficit. Importantly, EVs produced by Gde3-KO astrocytes, or astrocytes with inhibited WAVE3 function, cannot restore post-synaptic function of Gde3-KO neurons. This reinforces the specificity of the GDE3-WAVE3 biogenesis pathway for producing functionally distinct EVs. The biology of GDE2-derived EVs remains less clear. Unlike with GDE3-EVs, the molecules that define GDE2-EVs and the biogenesis pathway of these EVs are unknown. GDE2 is expressed in neurons where it appears to play a role in the production of EVs following stimulation of neurons. To advance EV work on GDE2 and GDE3, I developed external epitope-tagged versions of both proteins, which allowed immunoprecipitation of EVs containing either protein. This allows for precise capture of GDE2/3+ EVs, which will assist in the unbiased characterization of them in vitro and in vivo. In my thesis, I advanced our understanding of the GDE enzymes by defining a new role in EV release. My work has also highlighted the diversity of EV types, biogenesis pathways, and functions
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