Dissecting the biochemical architecture and morphological release pathways of the human platelet extracellular vesiculome

Platelet extracellular vesicles (PEVs) have emerged as potential mediators in intercellular communication. PEVs exhibit several activities with pathophysiological importance and may serve as diagnostic biomarkers. Here, imaging and analytical techniques were employed to unveil morphological pathways of the release, structure, composition, and surface properties of PEVs derived from human platelets (PLTs) activated with the thrombin receptor activating peptide (TRAP). Based on extensive electron microscopy analysis, we propose four morphological pathways for PEVs release from TRAP-activated PLTs: (1) plasma membrane budding, (2) extrusion of multivesicular α-granules and cytoplasmic vacuoles, (3) plasma membrane blistering and (4) “pearling” of PLT pseudopodia. The PLT extracellular vesiculome encompasses ectosomes, exosomes, free mitochondria, mitochondria-containing vesicles, “podiasomes” and PLT “ghosts”. Interestingly, a flow cytometry showed a population of TOM20⁺LC3⁺ PEVs, likely products of platelet mitophagy. We found that lipidomic and proteomic profiles were different between the small PEV (S-PEVs; mean diameter 103 nm) and the large vesicle (L-PEVs; mean diameter 350 nm) fractions separated by differential centrifugation. In addition, the majority of PEVs released by activated PLTs was composed of S-PEVs which have markedly higher thrombin generation activity per unit of PEV surface area compared to L-PEVs, and contribute approximately 60% of the PLT vesiculome procoagulant potency.     

A stepwise model of polyreactivity of the T cell antigen-receptor (TCR): its impact on the self–nonself discrimination and on related observations (receptor editing,anergy, dual receptor cells)

The existence of antigen-receptors, BCR, and T cell antigen-receptors, that are “polyreactive”, necessitates a rethinking of its effect on two problems faced by the “adaptive” immune system: the self (S)–nonself (NS) discrimination and the determination of effector class. Here, we will concentrate on the impact of polyreactivity on the S–NS discrimination. The anti-S cells interacting with S (i.e., responding to Signal 1) are on the pathway to inactivation. Before irreversibility sets in, these cells can be activated by a second signal (Signal 2) from an effector T-helper (eTh). As these polyreactive anti-S cells express anti-NS specificities, they can be activated by recognition of NS-epitopes in the host’s normal immunogenic load with the potential to result in autoimmunity. This problem is delineated using a discrete structural model, the corollaries of which are: (1) a two-step pathway for the purging of anti-S cells (i.e., the S–NS discrimination), and (2) defensible contexts within which to view the phenomena of receptor editing, anergy, and dual receptor cells.     

Generating new neurons to circumvent your fears: the role of IGF signaling

Extinction of fear memory is a particular form of cognitive function that is of special interest because of its involvement in the treatment of anxiety and mood disorders. Based on recent literature and our previous findings (EMBO J 30(19):4071–4083, 2011), we propose a new hypothesis that implies a tight relationship among IGF signaling, adult hippocampal neurogenesis and fear extinction. Our proposed model suggests that fear extinction-induced IGF2/IGFBP7 signaling promotes the survival of neurons at 2–4 weeks old that would participate in the discrimination between the original fear memory trace and the new safety memory generated during fear extinction. This is also called “pattern separation”, or the ability to distinguish similar but different cues (e.g., context). To understand the molecular mechanisms underlying fear extinction is therefore of great clinical importance.     

Induction of recombination between diverged sequences in a mammalian genome by a double-strand break

To investigate whether mammalian cells can carry out recombinational double-strand break (DSB) repair between highly diverged sequences, mouse fibroblasts were transfected with DNA substrates that contained a “recipient” thymidine kinase (tk) gene disrupted by the recognition site for endonuclease I-SceI. Substrates also contained a linked “donor” tk gene sequence. Following DSB induction by I-SceI, selection for tk-expressing clones allowed recovery of repair events occurring by nonhomologous end-joining or recombination with the donor sequence. Although recombinational repair was most efficient when donor and recipient shared near-perfect homology, we recovered recombination events between recipient and donor sequences displaying 20 % nucleotide mismatch. Recombination between such imperfectly matched (“homeologous”) sequences occurred at a frequency of 1.7 × 10^?7 events per cell and constituted 3 % of the DSB repair events recovered with the pair of homeologous sequences. Additional experiments were done with a substrate containing a donor sequence comprised of a region sharing high homology with the recipient and an adjacent region homeologous to the recipient. Recombinational DSB repair tracts initiating within high homology propagated into homeology in 11 of 112 repair events. These collective results contrasted with our earlier work in which spontaneous recombination (not intentionally induced by a DSB) between homeologous sequences occurred at an undetectable frequency of less than 10^?9 events per cell, and in which events initiating within high homology propagated into adjoining homeology in one of 81 events examined. Our current work suggests that homology requirements for recombination are effectively relaxed in proximity to a DSB in a mammalian genome.     

Modular localization and the holistic structure of causal quantum theory,a historical perspective

Recent insights into the conceptual structure of localization in QFT (modular localization) led to clarifications of old unsolved problems. The oldest one is the Einstein–Jordan conundrum which led Jordan in 1925 to the discovery of quantum field theory. This comparison of fluctuations in subsystems of heat bath systems (Einstein) with those resulting from the restriction of the QFT vacuum state to an open subvolume (Jordan) leads to a perfect analogy; the globally pure vacuum state becomes upon local restriction a strongly impure KMS state. This phenomenon of localization-caused thermal behavior as well as the vacuum-polarization clouds at the causal boundary of the localization region places localization in QFT into a sharp contrast with quantum mechanics and justifies the attribute “holstic”. In fact it positions the E–J Gedankenexperiment into the same conceptual category as the cosmological constant problem and the Unruh Gedankenexperiment. The holistic structure of QFT resulting from “modular localization” also leads to a revision of the conceptual origin of the crucial crossing property which entered particle theory at the time of the bootstrap S-matrix approach but suffered from incorrect use in the S-matrix settings of the dual model and string theory.The new holistic point of view, which strengthens the autonomous aspect of QFT, also comes with new messages for gauge theory by exposing the clash between Hilbert space structure and localization and presenting alternative solutions based on the use of stringlocal fields in Hilbert space. Among other things this leads to a reformulation of the Englert–Higgs symmetry breaking mechanism.     

Patient participation in the clinical encounter and clinical practice guidelines: The case of patients’ participation in a GRADEd world

It is widely acknowledged that the patient's perspective should be considered when making decisions about how her care will be managed. Patient participation in the decision making process may play an important role in bringing to light and incorporating her perspective. The GRADE framework is touted as an evidence-based process for determining recommendations for clinical practice; i.e. determining how care ought to be managed. GRADE recommendations are categorized as “strong” or “weak” based on several factors, including the “values and preferences” of a “typical” patient. The strength of the recommendation also provides instruction to the clinician about when and how patients should participate in the clinical encounter, and thus whether an individual patient's values and preferences will be heard in her clinical encounter. That is, a “strong” recommendation encourages “paternalism” and a “weak” recommendation encourages shared decision making. We argue that adoption of the GRADE framework is problematic to patient participation and may result in care that is not respectful of the individual patient's values and preferences. We argue that the root of the problem is the conception of “values and preferences” in GRADE – the framework favours population thinking (e.g. “typical” patient “values and preferences”), despite the fact that “values and preferences” are individual in the sense that they are deeply personal. We also show that tying the strength of a recommendation to a model of decision making (paternalism or shared decision making) constrains patient participation and is not justified (theoretically and/or empirically) in the GRADE literature.     

Neural map formation in the mouse olfactory system

In the mouse olfactory system, odorants are detected by ~1,000 different odorant receptors (ORs) produced by olfactory sensory neurons (OSNs). Each OSN expresses only one functional OR species, which is referred to as the “one neuron–one receptor” rule. Furthermore, OSN axons bearing the same OR converge to a specific projection site in the olfactory bulb (OB) forming a glomerular structure, i.e., the “one glomerulus–one receptor” rule. Based on these basic rules, binding signals of odorants detected by OSNs are converted to topographic information of activated glomeruli in the OB. During development, the glomerular map is formed by the combination of two genetically programmed processes: one is OR-independent projection along the dorsal–ventral axis, and the other is OR-dependent projection along the anterior-posterior axis. The map is further refined in an activity-dependent manner during the neonatal period. Here, we summarize recent progress of neural map formation in the mouse olfactory system.     

Chromogranin A binds to αvβ6-integrin and promotes wound healing in mice

Chromogranin A (CgA), a secretory protein expressed by many neuroendocrine cells, neurons, cardiomyocytes, and keratinocytes, is the precursor of various peptides that regulate the carbohydrate/lipid metabolism and the cardiovascular system. We have found that CgA, locally administered to injured mice, can accelerate keratinocyte proliferation and wound healing. This biological activity was abolished by the Asp(45)Glu mutation. CgA and its N-terminal fragments, but not the corresponding Asp(45)Glu mutants, could selectively recognize the αvβ6-integrin on keratinocytes (a cell-adhesion receptor that is up-regulated during wound healing) and regulate keratinocyte adhesion, proliferation, and migration. No binding was observed to other integrins such as αvβ3, αvβ5, αvβ8, α5β1, α1β1, α3β1, α6β4, α6β7 and α9β1. Structure-activity studies showed that the entire CgA(39-63) region is crucial for αvβ6 recognition (K(i) = 7 nM). This region contains an RGD site (residues CgA(43-45)) followed by an amphipathic α-helix (residues CgA(47-63)), both crucial for binding affinity and selectivity. These results suggest that the interaction of the RGD/α-helix motif of CgA with αvβ6 regulates keratinocyte physiology in wound healing.     

Nucleolar localization and circadian regulation of Per2S,a novel splicing variant of the Period 2 gene

In this work, we show for the first time that a second splicing variant of the core clock gene Period 2 (Per2), Per2S, is expressed at both the mRNA and protein levels in human keratinocytes and that it localizes in the nucleoli. Moreover, we show that a reversible perturbation of the nucleolar structure acts as a resetting stimulus for the cellular clock. Per2S expression and periodic oscillation upon dexamethasone treatment were assessed by qRT-PCR using specific primers. Western blot (WB) analysis using an antibody against the recombinant human PER2 (abRc) displayed an intense band at a molecular weight of ~55 kDa, close to the predicted size of Per2S, and a weaker band at the expected size of Per2 (~140 kDa). The antibody raised against PER2 pS662 (abS662), an epitope absent in PER2S, detected only the higher band. Immunolocalization studies with abRc revealed a peculiar nucleolar signal colocalizing with the nucleolar marker nucleophosmin, whereas with abS662 the signal was predominantly diffuse all over the nucleus and partially colocalized with abRc in the nucleolus. The analysis of cell fractions by WB confirmed the enrichment of PER2S and the presence of PER2 in the nucleolar compartment. Finally, a pulse (1 h) of actinomycin D (0.01 μg/ml) induced reversible nucleolar disruption, PER2S de-localization and circadian synchronization of clock and Per2S genes. Our work represents the first evidence that the Per2S splicing isoform is a clock component expressed in human cells localizing in the nucleolus. These results suggest a critical role for the nucleolus in the process of circadian synchronization in human keratinocytes.     

Complex modulation of Cav3.1 T-type calcium channel by nickel

Nickel is considered to be a selective blocker of low-voltage-activated T-type calcium channel. Recently, the Ni²⁺-binding site with critical histidine-191 (H191) within the extracellular IS3–IS4 domain of the most Ni²⁺-sensitive Ca_v3.2 T-channel isoform has been identified. All calcium channels are postulated to also have intrapore-binding site limiting maximal current carried by permeating divalent cations (PDC) and determining the blockade by non-permeating ones. However, the contribution of the two sites to the overall Ni²⁺ effect and its dependence on PDC remain uncertain. Here we compared Ni²⁺ action on the wild-type “Ni²⁺-insensitive” Ca_v3.1_w/t channel and Ca_v3.1_Q172H mutant having glutamine (Q) equivalent to H191 of Ca_v3.2 replaced by histidine. Each channel was expressed in Xenopus oocytes, and Ni²⁺ blockade of Ca²⁺, Sr²⁺, or Ba²⁺ currents was assessed by electrophysiology. Inhibition of Ca_v3.1_w/t by Ni²⁺ conformed to two sites binding. Ni²⁺ binding with high-affinity site (IC₅₀ = 0.03–3 μM depending on PDC) produced maximal inhibition of 20–30 % and was voltage-dependent, consistent with its location within the channel’s pore. Most of the inhibition (70–80 %) was produced by Ni²⁺ binding with low-affinity site (IC₅₀ = 240–700 μM). Q172H-mutation mainly affected low-affinity binding (IC₅₀ = 120–160 μM). The IC₅₀ of Ni²⁺ binding with both sites in the Ca_v3.1_w/t and Ca_v3.1_Q172H was differentially modulated by PDC, suggesting a varying degree of competition of Ca²⁺, Sr²⁺, or Ba²⁺ with Ni²⁺. We conclude that differential Ni²⁺-sensitivity of T-channel subtypes is determined only by H-containing external binding sites, which, in the absence of Ni²⁺, may be occupied by PDC, influencing in turn the channel’s permeation.     

Theories of Newtonian gravity and empirical indistinguishability

In this essay, I examine the curved spacetime formulation of Newtonian gravity known as Newton–Cartan gravity and compare it with flat spacetime formulations. Two versions of Newton–Cartan gravity can be identified in the physics literature—a “weak” version and a “strong” version. The strong version has a constrained Hamiltonian formulation and consequently a well-defined gauge structure, whereas the weak version does not (with some qualifications). Moreover, the strong version is best compared with the structure of what Earman (World enough and spacetime. Cambridge: MIT Press) has dubbed Maxwellian spacetime. This suggests that there are also two versions of Newtonian gravity in flat spacetime—a “weak” version in Maxwellian spacetime, and a “strong” version in Neo-Newtonian spacetime. I conclude by indicating how these alternative formulations of Newtonian gravity impact the notion of empirical indistinguishability and the debate over scientific realism.     

Methods for backcasting,nowcasting and forecasting using factor‐MIDAS: With an application to Korean GDP

We utilize mixed‐frequency factor‐MIDAS models for the purpose of carrying out backcasting, nowcasting, and forecasting experiments using real‐time data. We also introduce a new real‐time Korean GDP dataset, which is the focus of our experiments. The methodology that we utilize involves first estimating common latent factors (i.e., diffusion indices) from 190 monthly macroeconomic and financial series using various estimation strategies. These factors are then included, along with standard variables measured at multiple different frequencies, in various factor‐MIDAS prediction models. Our key empirical findings as follows. (i) When using real‐time data, factor‐MIDAS prediction models outperform various linear benchmark models. Interestingly, the “MSFE‐best” MIDAS models contain no autoregressive (AR) lag terms when backcasting and nowcasting. AR terms only begin to play a role in “true” forecasting contexts. (ii) Models that utilize only one or two factors are “MSFE‐best” at all forecasting horizons, but not at any backcasting and nowcasting horizons. In these latter contexts, much more heavily parametrized models with many factors are preferred. (iii) Real‐time data are crucial for forecasting Korean gross domestic product, and the use of “first available” versus “most recent” data “strongly” affects model selection and performance. (iv) Recursively estimated models are almost always “MSFE‐best,” and models estimated using autoregressive interpolation dominate those estimated using other interpolation methods. (v) Factors estimated using recursive principal component estimation methods have more predictive content than those estimated using a variety of other (more sophisticated) approaches. This result is particularly prevalent for our “MSFE‐best” factor‐MIDAS models, across virtually all forecast horizons, estimation schemes, and data vintages that are analyzed.     

Space–time philosophy reconstructed via massive Nordström scalar gravities? Laws vs. geometry,conventionality, and underdetermination

What if gravity satisfied the Klein–Gordon equation? Both particle physics from the 1920–30s and the 1890s Neumann–Seeliger modification of Newtonian gravity with exponential decay suggest considering a “graviton mass term” for gravity, which is algebraic in the potential. Unlike Nordström׳s “massless” theory, massive scalar gravity is strictly special relativistic in the sense of being invariant under the Poincaré group but not the 15-parameter Bateman–Cunningham conformal group. It therefore exhibits the whole of Minkowski space–time structure, albeit only indirectly concerning volumes. Massive scalar gravity is plausible in terms of relativistic field theory, while violating most interesting versions of Einstein׳s principles of general covariance, general relativity, equivalence, and Mach. Geometry is a poor guide to understanding massive scalar gravity(s): matter sees a conformally flat metric due to universal coupling, but gravity also sees the rest of the flat metric (barely or on long distances) in the mass term. What is the ‘true’ geometry, one might wonder, in line with Poincaré׳s modal conventionality argument? Infinitely many theories exhibit this bimetric ‘geometry,’ all with the total stress–energy׳s trace as source; thus geometry does not explain the field equations. The irrelevance of the Ehlers–Pirani–Schild construction to a critique of conventionalism becomes evident when multi-geometry theories are contemplated. Much as Seeliger envisaged, the smooth massless limit indicates underdetermination of theories by data between massless and massive scalar gravities—indeed an unconceived alternative. At least one version easily could have been developed before General Relativity; it then would have motivated thinking of Einstein׳s equations along the lines of Einstein׳s newly re-appreciated “physical strategy” and particle physics and would have suggested a rivalry from massive spin 2 variants of General Relativity (massless spin 2, Pauli and Fierz found in 1939). The Putnam–Grünbaum debate on conventionality is revisited with an emphasis on the broad modal scope of conventionalist views. Massive scalar gravity thus contributes to a historically plausible rational reconstruction of much of 20th–21st century space–time philosophy in the light of particle physics. An appendix reconsiders the Malament–Weatherall–Manchak conformal restriction of conventionality and constructs the ‘universal force’ influencing the causal structure.Subsequent works will discuss how massive gravity could have provided a template for a more Kant-friendly space–time theory that would have blocked Moritz Schlick׳s supposed refutation of synthetic a priori knowledge, and how Einstein׳s false analogy between the Neumann–Seeliger–Einstein modification of Newtonian gravity and the cosmological constant Λ generated lasting confusion that obscured massive gravity as a conceptual possibility.     

Tryptophan synthase: a mine for enzymologists

Tryptophan synthase is a pyridoxal 5′-phosphate-dependent α₂β₂ complex catalyzing the last two steps of tryptophan biosynthesis in bacteria, plants and fungi. Structural, dynamic and functional studies, carried out over more than 40 years, have unveiled that: (1) α- and β-active sites are separated by about 20 Å and communicate via the selective stabilization of distinct conformational states, triggered by the chemical nature of individual catalytic intermediates and by allosteric ligands; (2) indole, formed at α-active site, is intramolecularly channeled to the β-active site; and (3) naturally occurring as well as genetically generated mutants have allowed to pinpoint functional and regulatory roles for several individual amino acids. These key features have made tryptophan synthase a text-book case for the understanding of the interplay between chemistry and conformational energy landscapes.     

Loss of Siglec-14 reduces the risk of chronic obstructive pulmonary disease exacerbation

Chronic obstructive pulmonary disease (COPD) is a leading cause of mortality worldwide. COPD exacerbation, or episodic worsening of symptoms, often results in hospitalization and increased mortality rates. Airway infections by new bacterial strains, such as nontypeable Haemophilus influenzae (NTHi), are a major cause of COPD exacerbation. NTHi express lipooligosaccharides that contain sialic acids, and may interact with Siglec-14, a sialic acid recognition protein on myeloid cells that serves as an activating signal transduction receptor. A null allele polymorphism in SIGLEC14 may attenuate the inflammatory responses to NTHi by eliminating Siglec-14 expression. We asked if the loss of Siglec-14 attenuates the inflammatory response by myeloid cells against NTHi, and if the SIGLEC14-null polymorphism has any effect on COPD exacerbation. We found that NTHi interacts with Siglec-14 to enhance proinflammatory cytokine production in a tissue culture model. Inhibitors of the Syk tyrosine kinase suppress this response. Loss of Siglec-14, due to SIGLEC14-null allele homozygosity, is associated with a reduced risk of COPD exacerbation in a Japanese patient population. Taken together, Siglec-14 and its downstream signaling pathway facilitate the “infection–inflammation–exacerbation” axis of COPD disease progression, and may represent promising targets for therapeutic intervention.     

For the Glory of Athens: Xenophon’s Hipparchikos <Logos>, a technical treatise and instruction manual on ideal leadership

Xenophon’s Peri hippikes <technees>, “On Horsemanship,” and the Hipparchikos <logos>, “the Cavalry Commander”, writings which can be regarded as technical works with a didactic purpose, are almost unknown. Xenophon was interested in problems of leadership and the exercise of power (For the titles of the both writings and the analogous supplementary terms “technees” and “logos” compare Breitenbach, 1966, 1761. Angled brackets are used by modern editors of ancient texts as text-critical signs and are inserted here because “peri hippikes” and “hipparchikos” are adjectives and cannot stand alone; “technees” and “logos” are supplied as absent, but implied, substantives. The conventional signs “<>” clarify this supplementary act for the modern reader.). The “Cavalry Commander” (ca. 365 B.C.) intended for the instruction of potential hipparchs (calvary commanders) is simultaneously political and didactic and technical; in this text, categories of leadership that had been developed in earlier works are combined in a powerful manner. Xenophon constructed “leaders” as exempla (“examples”) of correct behaviour; military and political theory are synthesised. The Hipparchikos logos, as a didactic work, aims to produce specialists who master their techné (“art” or “skill”), to develop their ideal qualities. Both texts are directed at an Athenian society, in which the cavalry had lost their significance and pride as a result of recent political turbulence. Xenophon hoped to reform the cavalry for the benefit of Athens. The basic question of the didactic work is: how can I become the best hipparch, how can I go beyond simply filling the office, and instead develop it for the well-being of the polis and thus serve the city? The art of leadership consists in dealing with subordinates in such a manner that they obey and follow voluntarily—still an innovative and modern approach today.     

Fooling around with tenses

What, exactly, is the relation between statements about future contingents and statements concerning the spacelike? This question may be answered by transferring Thomasonian supervaluations for future tense statements to statements about the spacelike past, present and future, endorsing present contingents and past contingents. For this task, a language is described semantically which contains (frame-relative versions of) the usual quantifier-like tense operators, operators for (frame-relative) “somewhere”/“everywhere”, the operators “for every reference frame”/“for some reference frame” and three different “necessity” operators with their “possibility” counterparts. Technically, special attention is paid to interaction laws between the different kinds of operators. The “necessity” operators differ in the area on which alternatives must coincide in order to count as accessible. Supervaluations are discussed for past light-cone coincidence. Metaphysically, this approach points towards a distinction between two kinds of determinateness which were undistinguishable pre-relativistically: deictic determinateness (past light-cone) and narrative determinateness (frame-relative present-plus-past). An indeterministic solution to the problem of the “wings” is proposed which, without accepting a frame-independent spatially extended present, solves the problem of “massive coincidence” by carefully analysing the famous tunnel example as a story of decisions and by distinguishing between “whether” and “that”-clauses.