AID in antibody perfection

Expressed immunoglobulin (Ig) genes undergo alterations in sequence and genomic structure in order to optimize antibody function. A single B cell-specific factor, activation-induced deaminase (AID), initiates these changes by deamination of cytosine to uracil. Uracil in DNA is encountered commonly, and conserved pathways are responsible for its faithful repair. However, at the Ig loci of B cells, AID-initiated damage is processed to produce three distinct outcomes: somatic hypermutation, class switch recombination and gene conversion. This review focuses on the role of AID in Ig gene diversification, emphasizing how AID functions within the mechanism of the Ig gene diversification pathway; and highlights open questions for future research, particularly the most provocative current question: what makes a gene a target for AID-initiated mutagenesis?     

The current structural and functional understanding of APOBEC deaminases

The apolipoprotein B mRNA-editing enzyme catalytic polypeptide (APOBEC) family of cytidine deaminases has emerged as an intensively studied field as a result of their important biological functions. These enzymes are involved in lipid metabolism, antibody diversification, and the inhibition of retrotransposons, retroviruses, and some DNA viruses. The APOBEC proteins function in these roles by deaminating single-stranded (ss) DNA or RNA. There are two high-resolution crystal structures available for the APOBEC family, Apo2 and the C-terminal catalytic domain (CD2) of Apo3G or Apo3G-CD2 [Holden et al. (Nature 456:121–124, 2008); Prochnow et al. (Nature 445:447–451, 2007)]. Additionally, the structure of Apo3G-CD2 has also been determined using NMR [Chen et al. (Nature 452:116–119, 2008); Furukawa et al. (EMBO J 28:440–451, 2009); Harjes et al. (J Mol Biol, 2009)]. A detailed structural analysis of the APOBEC proteins and a comparison to other zinc-coordinating deaminases can facilitate our understanding of how APOBEC proteins bind nucleic acids, recognize substrates, and form oligomers. Here, we review the recent development of structural and functional studies that apply to Apo3G as well as the APOBEC deaminase family.     

Targeting epigenetics using synthetic lethality in precision medicine

Technological breakthroughs in genomics have had a significant impact on clinical therapy for human diseases, allowing us to use patient genetic differences to guide medical care. The “synthetic lethal approach” leverages on cancer-specific genetic rewiring to deliver a therapeutic regimen that preferentially targets malignant cells while sparing normal cells. The utility of this system is evident in several recent studies, particularly in poor prognosis cancers with loss-of-function mutations that become “treatable” when two otherwise discrete and unrelated genes are targeted simultaneously. This review focuses on the chemotherapeutic targeting of epigenetic alterations in cancer cells and consolidates a network that outlines the interplay between epigenetic and genetic regulators in DNA damage repair. This network consists of numerous synergistically acting relationships that are druggable, even in recalcitrant triple-negative breast cancer. This collective knowledge points to the dawn of a new era of personalized medicine.     

Conserved amino acids participate in the structure networks deputed to intramolecular communication in the lutropin receptor

The luteinizing hormone receptor (LHR) is a G protein-coupled receptor (GPCR) particularly susceptible to spontaneous pathogenic gain-of-function mutations. Protein structure network (PSN) analysis on wild-type LHR and two constitutively active mutants, combined with in vitro mutational analysis, served to identify key amino acids that are part of the regulatory network responsible for propagating communication between the extracellular and intracellular poles of the receptor. Highly conserved amino acids in the rhodopsin family GPCRs participate in the protein structural stability as network hubs in both the inactive and active states. Moreover, they behave as the most recurrent nodes in the communication paths between the extracellular and intracellular sides in both functional states with emphasis on the active one. In this respect, non-conservative loss-of-function mutations of these amino acids is expected to impair the most relevant way of communication between activating mutation sites or hormone-binding domain and G protein recognition regions.     

Computationally driven deletion of broadly distributed T cell epitopes in a biotherapeutic candidate

Biotherapeutics are subject to immune surveillance within the body, and anti-biotherapeutic immune responses can compromise drug efficacy and patient safety. Initial development of targeted antidrug immune memory is coordinated by T cell recognition of immunogenic subsequences, termed “T cell epitopes.” Biotherapeutics may therefore be deimmunized by mutating key residues within cognate epitopes, but there exist complex trade-offs between immunogenicity, mutational load, and protein structure–function. Here, a protein deimmunization algorithm has been applied to P99 beta-lactamase, a component of antibody-directed enzyme prodrug therapies. The algorithm, integer programming for immunogenic proteins, seamlessly integrates computational prediction of T cell epitopes with both 1- and 2-body sequence potentials that assess protein tolerance to epitope-deleting mutations. Compared to previously deimmunized P99 variants, which bore only one or two mutations, the enzymes designed here contain 4–5 widely distributed substitutions. As a result, they exhibit broad reductions in major histocompatibility complex recognition. Despite their high mutational loads and markedly reduced immunoreactivity, all eight engineered variants possessed wild-type or better catalytic activity. Thus, the protein design algorithm is able to disrupt broadly distributed epitopes while maintaining protein function. As a result, this computational tool may prove useful in expanding the repertoire of next-generation biotherapeutics.     

Optic atrophy 3 as a protein of the mitochondrial outer membrane induces mitochondrial fragmentation

The optic atrophy 3 (OPA3) gene, which has no known homolog or biological function, is mutated in patients with hereditary optic neuropathies. Here, we identified OPA3 as an integral protein of the mitochondrial outer membrane (MOM), with a C-terminus exposed to the cytosol and an N-terminal mitochondrial targeting domain. By quantitative analysis, we demonstrated that overexpression of OPA3 significantly induced mitochondrial fragmentation, whereas OPA3 knockdown resulted in highly elongated mitochondria. Cells with mitochondria fragmented by OPA3 did not undergo spontaneous apoptotic cell death, but were significantly sensitized to staurosporine- and TRAIL-induced apoptosis. In contrast, overexpression of a familial OPA3 mutant (G93S) induced mitochondrial fragmentation and spontaneous apoptosis, suggesting that OPA3 mutations may cause optic atrophy via a gain-of-function mechanism. Together, these results indicate that OPA3, as an integral MOM protein, has a crucial role in mitochondrial fission, and provides a direct link between mitochondrial morphology and optic atrophy.     

Forecasting price delay and future stock returns: The role of corporate social responsibility

This paper investigates the role of corporate social responsibility (CSR) performance in forecasting companys' stock prices and future returns. The forecasting analysis identifies a negative association between CSR performance and proxies of price delay. The negative CSR–delay association is weak for state‐owned enterprises (SOEs) because of their politically oriented motivation of CSR activities, but significantly strong for non‐SOEs. Furthermore, we find that forecasting delayed firms is expected to have higher future returns. In particular, the returns premium is most attributable to the CSR component of delay, compared with the non‐CSR component. Taken together, these results suggest that CSR performance plays a positive role in enhancing stock price efficiency, and a potential explanation is that CSR performance can be considered as additional information for equity predictions.     

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.     

Analysis of the relationship between age of larvae at mutagen treatment and frequency and size of spots in the wing somatic mutation and recombination test inDrosophila melanogaster

The relationship between the induction of mutant clones and the time of mutagen treatment was studied in the somatic mutation and recombination test (SMART) in wing cells ofDrosophila melanogaster. Larvae trans-heterozygous for the recessive marker mutations multiple wing hairs (mwh) and flare (flr) were produced. Batches of these larvae were then treated with mutagen at different ages spanning all three larval instars. Methyl methanesulfonate was fed acutely for 2 h by immersing the larvae in a solution of the mutagen mixed with powdered cellulose. Wings of the surviving adult flies were mounted and scored for the presence of spots. The frequency and size of single and twin spots were recorded separately. Twin spots are produced exclusively by mitotic recombination, whereas single spots can results from various types of mutational and exchange events. There exists a clear correlation between time of induction and frequency as well as size of the single spots. In young larvae only few but very large spots are induced, whereas in older larvae the frequencies are considerably increased but the sizes are smaller. The twin spots show a different relationship. Practically no twin spots are found in very young and in very old larvae. The results demonstrate that in the wing spot test the optimal age of the larvae for mutagen treatment is 72 h.     

The physics and metaphysics of Tychistic Bohmian Mechanics

The paper takes up Bell's (1987) “Everett (?) theory” and develops it further. The resulting theory is about the system of all particles in the universe, each located in ordinary, 3-dimensional space. This many-particle system as a whole performs random jumps through 3N-dimensional configuration space – hence “Tychistic Bohmian Mechanics” (TBM). The distribution of its spontaneous localisations in configuration space is given by the Born Rule probability measure for the universal wavefunction. Contra Bell, the theory is argued to satisfy the minimal desiderata for a Bohmian theory within the Primitive Ontology framework (for which we offer a metaphysically more perspicuous formulation than is customary). TBM's formalism is that of ordinary Bohmian Mechanics (BM), without the postulate of continuous particle trajectories and their deterministic dynamics. This “rump formalism” receives, however, a different interpretation. We defend TBM as an empirically adequate and coherent quantum theory. Objections voiced by Bell and Maudlin are rebutted. The “for all practical purposes”-classical, Everettian worlds (i.e. quasi-classical histories) exist sequentially in TBM (rather than simultaneously, as in the Everett interpretation). In a temporally coarse-grained sense, they quasi-persist. By contrast, the individual particles themselves cease to persist.     

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.     

The relative facts interpretation and Everett's note added in proof

In the published version of Hugh Everett III's doctoral dissertation, he inserted what has become a famous footnote, the “note added in proof”. This footnote is often the strongest evidence given for any of various interpretations of Everett (the many worlds, many minds, many histories and many threads interpretations). In this paper I will propose a new interpretation of the footnote. One that is supported by evidence found in letters written to and by Everett; one that is suggested by a new interpretation of Everett, an interpretation that takes seriously the central position of relative states in Everett's pure wave mechanics: the relative facts interpretation. Of central interest in this paper is how to make sense of Everett's claim in the “note added in proof” that “all elements of a superposition (all “branches”) are “actual,” none any more “real” than the rest.”     

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.     

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.     

The Ehrenfest Classification of Phase Transitions: Introduction and Evolution

The first classification of general types of transition between phases of matter, introduced by Paul Ehrenfest in 1933, lies at a crossroads in the thermodynamical study of critical phenomena. It arose following the discovery in 1932 of a suprising new phase transition in liquid helium, the “lambda transition,” when W. H. Keesom and coworkers in Leiden, Holland observed a λhaped “jump” discontinuity in the curve giving the temperature dependence of the specific heat of helium at a critical value. This apparent jump led Ehrenfest to introduce a classification of phase transitions on the basis of jumps in derivatives of the free energy function. This classification was immediately applied by A.J. Rutgers to the study of the transition from the normal to superconducting state in metals. Eduard Justi and Max von Laue soon questioned the possibility of its class of “second-order phase transitions” -- of which the “lambda transition was believed to be the arche type -- but C.J. Gorter and H.B.G. Casimir used an “order parameter to demonstrate their existence in superconductors. As a crossroads of study, the Ehrenfest classification was forced to undergo a slow, adaptive evolution during subsequent decades. During the 1940s the classification was increasingly used in discussions of liquid-gas, order-disorder, paramagnetic-ferromagnetic and normal-super-conducting phase transitions. Already in 1944 however, Lars Onsagers solution of the Ising model for two-dimensional magnets was seen to possess a derivative with a logarithmic divergence rather than a jump as the critical point was approached. In the 1950s, experiments further revealed the lambda transition in helium to exhibit similar behavior. Rather than being a prime example of an Ehrenfest phase transition, the lambda transition was seen to lie outside the Ehrenfest classification. The Ehrenfest scheme was then extended to include such singularities, most notably by A. Brain Pippard in 1957, with widespread acceptance. During the 1960s these logarithmic infinities were the focus of the investigation of “scaling” by Leo Kadanoff, B. Widom and others. By the 1970s, a radically simplified binary classification of phase transitions into “first-order” and “continuous” transitions was increasingly adopted.     

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.