1,721,070 research outputs found
An Optimized Protocol for the Mapping of Cell Type-Specific Ribosome-Associated Transcript Isoforms from Small Mouse Brain Regions
No full textOver the past years, technological advances in transcriptomics provided deep insights into gene expression programs and their role in tissue organization and cellular functions. The isolation of ribosome-associated transcripts is a powerful approach for deep profiling of cell type-specific transcripts, and particularly well-suited for quantitative analysis of transcript isoforms. This method employs conditional ribosome epitope-tagging in genetically defined cell types, followed by affinity-isolation of ribosome-associated mRNAs. Advantages of this approach are twofold: first, the method enables rapid retrieval of mRNAs without tissue dissociation and cell sorting steps. Second, capturing of ribosome-associated mRNAs, enriches for transcripts recruited for active translation, therefore providing an approximation to the cellular translatome. Here, we describe one application of this method for the identification of the transcriptome of excitatory neuronal cells (mitral and tufted cells) of the mouse olfactory bulb, through RiboTag isolation from the vGlut2-IRES-cre mouse line as genetic driver of endogenously tagged ribosome expression
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
Examination of alternative splice code of neurexins for synaptic specification
Full text linkThe brain is composed of a large number of cells types that assemble together into highly specific circuits. Precise connectivity is crucial to ensure proper brain functions and requires mechanisms that generate molecular diversity to encode certain aspects of neuronal wiring. One possible mechanism to generate molecular diversity is alternative splicing. For example through alternative splicing Neurexin (Nrxn1-2-3) genes have the potential to give rise to more than 12’000 protein isoforms (Tabuchi and Sudhof, 2002). Neurexin has been demonstrated to be involved in synapse formation and functions (Reissner et al., 2013). Importantly, studies have reported that alternative splicing plays a pivotal role in the function of Neurexin as it regulates their interaction with a large variety of ligands (Reissner et al., 2013). This in turn can promote the differentiation of distinct postsynaptic structures (Chih et al., 2006). Therefore, Neurexins constitute ideal candidates to encode certain parameters of synaptic connectivity. However, a central question has remained unraveled. Indeed, the spatial logic of Neurexin isoforms expression in the brain is not well understood.
Here, I report that by using bichromatic reporters, alternative splicing is differentially regulated between neuronal and non-neuronal cell populations and that the alternative splicing activity within a cell population can exhibit different levels of cell-to-cell variations. By profiling Nrxn mRNA repertoires in genetically-defined neuronal cell populations, I have identified highly divergent splice insert incorporation choices in two fundamentally different neurons populations in the hippocampus. Indeed, exon 21 which encodes for splice insert at alternative splice segment 4 (AS4) in Nrxn is predominantly incorporated in mRNA in Parvalbumin interneurons compared to excitatory Camk2 pyramidal neurons. Finally I investigated the function of Neurexin isoforms containing the exon 21 in vivo by conditionally deleting them in Parvalbumin interneurons population. Anatomical analyses indicated that synaptic density and vesicle docking were unaltered. However, mice in which isoforms containing splice insert at AS4 in Nrxn 1 and 3 were deleted, displayed an impaired short-term memory formation.
Thus, my study has provided evidences that alternative splicing regulation of Nrxn genes is genetically encoded and that deletion of cell-type specific isoforms impairs neuronal functions. This highlights the relevance of cell-type specific regulation of alternative splicing
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
Physiological functions of GABAB receptor-associated proteins
Full text linkGABAB receptors (GBRs) play a crucial role in synaptic transmission (Gassmann and Bettler, 2012), and alterations of GBR levels and functions are associated with various neurological diseases (Evenseth et al., 2020; Heaney and Kinney, 2016; Kumar et al., 2013). The GBR is an obligate heterodimer composed of GB1 and GB2 subunits, comprising the core subunits of GBRs (Kaupmann et al., 1998; Schwenk et al., 2010). The GB1 subunit exists in two isoforms, GB1a and GB1b, localizing at pre-or postsynaptic sites, respectively (Vigot et al., 2006). The sole difference between the two isoforms is two sushi domains (SDs) located exclusively at the N-terminus of GB1a (Hawrot et al., 1998; Kaupmann et al., 1997). SDs are required for axonal localization and stabilization at the cell surface of GB1a/2 receptors (Biermann et al., 2010; Hannan et al., 2012). At the presynapse, GB1a/2 receptors inhibit neurotransmitter release by blocking voltage-gated Ca2+ (Cav) channels, and at the postsynapse, GB1b/2 receptors induce hyperpolarization of neurons through activating inward-rectifier K+ (Kir3) channels (Gassmann and Bettler, 2012). Native GBRs form macromolecular complexes with auxiliary subunits and various constituents, which impart distinct functional properties to GBRs (Schwenk et al., 2010; Schwenk et al., 2016).
Cytosolic potassium channel tetramerization domain (KCTD)-containing protein 8, 12, 12b, and 16 (hereafter collectively designated KCTDs) are auxiliary GBR subunits, influencing the GBR response (Schwenk et al., 2010). KCTDs comprise a T1 and an H1 domain with KCTD8 and -16 containing an additional C-terminal H2 domain (Schwenk et al., 2010). Homopentameric KCTDs interact through their T1 domain with the C-terminus of GB2 and accelerate GBR-mediated Kir3 channel responses (Schwenk et al., 2010). However, solely KCTD12 and 12b induce pronounced desensitization of GBR-mediated Kir3 currents and Cav channel inhibition by uncoupling Gβγ from the effector channel, suggesting that GBR/KCTD complexes can generate distinct functional properties (Schwenk et al., 2010; Turecek et al., 2014). Because of their overlapping expression patterns (Metz et al., 2011), it is conceivable that KCTDs also form hetero-oligomers interacting with GBRs and G proteins. In co-immunoprecipitation experiments, my colleagues identified KCTD12/KCTD16 hetero-oligomers in brain tissue that form a complex with GBRs. They further demonstrated that KCTD12 and KCTD16 retained their distinct regulatory properties in KCTD12/KCTD16 hetero-oligomers, resulting in intermediate GBR-mediated Kir3 current desensitization. They also revealed that KCTD12/KCTD16 hetero-oligomers produce slow deactivation kinetics of Kir3 currents that lead to an increase in the duration of GBR-mediated slow inhibitory postsynaptic currents (sIPSCs). However, it was yet unknown whether KCTD hetero-oligomers can interact with G proteins. My data showed that KCTD homo-and hetero-oligomers bind to the G protein in living cells, which contributed to the understanding of distinct functional properties of KCTD12/KCTD16 hetero-oligomers. Thus, my data complemented the findings of my colleagues and resulted in a co-authorship publication (Fritzius et al., 2017). Together our data show that KCTD12/KCTD16 hetero-oligomers regulate the fine-tuning of GBR-mediated Kir3 currents and enrich the molecular and functional repertoire of native GBRs.
β-amyloid precursor protein (APP), adherens junction-associated protein 1 (AJAP1), and PILRα-associated neural protein (PIANP) are single-spanning membrane proteins that interact with the N-terminal SD1 of GB1a (Dinamarca et al., 2019; Schwenk et al., 2016). Axonal GB1a/2 receptor trafficking is dependent on kinesin-1 (Valdes et al., 2012), but the SD1 required for axonal transport reside within the lumen of transport vesicles (Biermann et al., 2010; Vigot et al., 2006). Due to the interaction with the SD1, APP, AJAP1, and PIANP represent promising candidates for linking GB1a/2 receptors in transport vesicles to the kinesin motor. While APP, AJAP1, and PIANP share the ability to bind SD1 of presynaptic GB1a/2 receptors, only APP linked GB1a/2 receptors to the kinesin motor and mediated axonal trafficking of GB1a/2 receptors, as demonstrated by my colleagues. They further showed that the interaction of APP with GB1a/2 receptors resulted in mutual stabilization at the cell surface, which prevented GB1a/2 receptor internalization and reduced the proteolytic processing of APP in endosomes. However, whether the APP/GB1a/2 receptor complex formation is altered upon GB1a/2 receptor activation and whether APP modulates GB1a/2 receptor signaling remained unclear. I showed that the GB1a/2 receptor activation did not regulate the association or dissociation between APP and GB1a/2 receptors. My data further demonstrated that the co-expression of APP did not modulate GB1a/2 receptor signaling in heterologous cells. Thus, my data contributed to the characterization of the interaction of APP and GB1a/2 receptors and were integrated into a publication with me as a co-author (Dinamarca et al., 2019). Since proteolytic APP processing in the amyloidogenic pathway yields Aβ fragments, a hallmark of Alzheimer’s disease (AD) (Huang and Mucke, 2012; Muller et al., 2017; Selkoe and Hardy, 2016), and alterations in GB1 surface levels are observed in AD patients (Chu et al., 1987a, b; Iwakiri et al., 2005) and a mouse model of AD (Martin-Belmonte et al., 2020), our data reveal that APP/GB1a/2 receptor complex formation links presynaptic GB1a/2 trafficking to Aβ generation.
Proteolytic APP processing in the non-amyloidogenic pathway generates soluble APPα (sAPPα) fragments (Muller et al., 2017). sAPPα binds to SD1 of presynaptic GB1a/2 receptors (Dinamarca et al., 2019; Rice et al., 2019) and signals through G proteins (Fogel et al., 2014; Pasciuto et al., 2015). A recent publication reported that sAPPα induced presynaptic GB1a/2 receptor-mediated inhibition of neurotransmitter release in vivo (Rice et al., 2019). Likewise, a 17 residue long peptide composed of the APP sequence containing the SD1 binding motif, termed APP17, suppressed neurotransmitter release and neuronal transmission by activating endogenous GB1a/2 receptors at presynaptic sites (Rice et al., 2019). In contrast, my colleagues showed that sAPPα does not modulate GB1a/2 receptor-mediated G protein activation in heterologous cells (Dinamarca et al., 2019). Due to the controversial findings and the lack of data explaining the mechanism of GB1a/2 receptor modulation by sAPPα, I studied whether APP17 modulates recombinant GB1a/2 receptors. I confirmed binding of APP17 to GB1a/2 receptors expressed in HEK293T cells by displacing fluorescent APP17 peptides from receptors. However, my data demonstrated that APP17 does not modulate GB1a/2 receptor-mediated G protein activation or Gα signaling in heterologous cells. Using a very sensitive GB1a/2 receptor-induced firefly luciferase (FLuc) accumulation assay, my data further evidenced that APP17 does not exert subtle modulatory properties at recombinant GB1a/2 receptors. I further confirmed the absence of allosteric modulatory properties of co-expressed full-length APP at recombinant GB1a/2 receptors in G protein activation, Ga signaling and sensitive FLuc accumulation assays, confirming earlier data published in Dinamarca et al. (2019). My data further showed that the displacement of full-length APP by APP17 did not induce modulatory effects at recombinant GB1a/2 receptors. In addition, my colleagues observed that APP17 neither influenced GB1a/2 receptor-mediated Gβγ signaling in vitro nor changed GB1a/2 receptor-mediated inhibition of neurotransmitter release or neuronal transmission in vivo, using electrophysiological recordings. Hence, neither sAPPα nor APP17 modulates recombinant or native GB1a/2 receptor signaling. A manuscript reporting these findings with me as the first author is in preparation.
AJAP1 and PIANP form distinct complexes with GB1a/2 receptors and are not involved in axonal trafficking of GB1a/2 receptors (Dinamarca et al., 2019). I demonstrated that the formation of AJAP1/GB1a/2 receptor and PIANP/GB1a/2 receptor complexes in cis neither stabilized GB1a/2 receptors at the cell surface nor modulated GB1a/2 receptor-mediated G protein activation in heterologous cells. The observation of my colleagues that AJAP1 and PIANP are located in the somatodendritic compartment, together with their observation that mice genetically lacking AJAP1 or PIANP showed a deficit in presynaptic GB1a/2 receptor-mediated inhibition of neurotransmitter release (S. Früh and T. Lalanne, personal communications) (Winkler et al., 2019), suggested a trans-synaptic interaction between GB1a/2 receptors and AJAP1 or PIANP. Indeed, I demonstrated that AJAP1 and PIANP recruit and cluster transcellular GB1a/2 receptors. I further showed that the formation of AJAP1/GB1a/2 receptor and PIANP/GB1a/2 receptor complexes in trans resulted in a stabilization and negative allosteric modulation of GB1a/2 receptors. However, the maximum efficacy of transcellular GB1a/2 receptor signaling was not affected by the interaction with AJAP1 or PIANP, resulting in an increased dynamic range of receptor activity. My data further demonstrated that the negative allosteric properties exerted by AJAP1 and PIANP at transcellular GB1a/2 receptors required anchorage into the cell membrane because soluble AJAP1 (sAJAP1), which is composed exclusively of the extracellular domain of AJAP1, did not allosterically modulate GB1a/2 receptors. Earlier my colleagues identified different affinities for SD1 binding in the rank order AJAP1>PIANP>>APP (Dinamarca et al., 2019). Thus, my data support a model in which APP traffics GB1a/2 receptors to axon terminals, where they are transferred to postsynaptic AJAP1 or PIANP that precisely localize the receptor and increase its dynamic range. My data will be part of a future publication from the lab with me as a co-author.
Elucidating the physiological functions of PIANP necessitates the analysis of mice genetically lacking PIANP and compare them to WT littermates. Since no PIANP-KO mice were available at the beginning of my Ph.D., I generated PIANP-KO mice using the clustered regularly interspaced short palindromic repeats (CRISPR) / CRISPR-associated (Cas) 9 system in collaboration with the Centre for Transgenic Models (CTM) of the University of Basel. Generating PIANP-KO mice using the CRISPR/Cas9 system requires the electroporation of one-cell embryos with ribonucleoprotein (RNP) that consist of the specific guide ribonucleic acid (RNA), the trans-activating RNA, and the CRISPR/Cas9. In the first step, I identified two guide RNAs. The CTM team pre-validated the two guide RNAs, electroporated CL57B/6 one-cell embryos with the RNP, transferred the surviving embryos into pseudopregnant females, and sampled biopsies of the offspring. The biopsies were transferred to me, and I validated the genomic alterations induced by the CRISPR/Cas9 system and used the PIANP-KO offspring to establish the PIANP-KO mouse line in the lab. I further confirmed the loss of endogenous PIANP protein in the PIANP-KO mouse line that my colleagues used for electrophysiological recordings published in Dinamarca et al. (2019) and Winkler et al. (2019), publications on which I am a co-author. In the Winkler et al. (2019) publication, the electrophysiological recordings of my colleagues showed that PIANP-KO mice exerted deficits in presynaptic GB1a/2 receptor-mediated inhibition of glutamate release. Thus, these data support that PIANP deficiency results in incorrect localization and function of presynaptic GB1a/2 receptors (Winkler et al., 2019)
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
Large-scale death of retinal astrocytes during normal development is non-apoptotic and implemented by microglia
Full text linkNaturally occurring cell death is a fundamental developmental mechanism for regulating cell numbers and sculpting developing organs. This is particularly true in the nervous system, where large numbers of neurons and oligodendrocytes are eliminated via apoptosis during normal development. Given the profound impact of death upon these two major cell populations, it is surprising that developmental death of another major cell type—the astrocyte—has rarely been studied. It is presently unclear whether astrocytes are subject to significant developmental death, and if so, how it occurs. Here, we address these questions using mouse retinal astrocytes as our model system. We show that the total number of retinal astrocytes declines by over 3-fold during a death period spanning postnatal days 5–14. Surprisingly, these astrocytes do not die by apoptosis, the canonical mechanism underlying the vast majority of developmental cell death. Instead, we find that microglia engulf astrocytes during the death period to promote their developmental removal. Genetic ablation of microglia inhibits astrocyte death, leading to a larger astrocyte population size at the end of the death period. However, astrocyte death is not completely blocked in the absence of microglia, apparently due to the ability of astrocytes to engulf each other. Nevertheless, mice lacking microglia showed significant anatomical changes to the retinal astrocyte network, with functional consequences for the astrocyte-associated vasculature leading to retinal hemorrhage. These results establish a novel modality for naturally occurring cell death and demonstrate its importance for the formation and integrity of the retinal gliovascular network.</div
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