Stochastic Transition States: Reaction Geometry amidst Noise

Classical transition state theory (TST) is the cornerstone of reaction rate theory. It postulates a partition of phase space into reactant and product regions, which are separated by a dividing surface that reactive trajectories must cross. In order not to overestimate the reaction rate, the dynamics must be free of recrossings of the dividing surface. This no-recrossing rule is difficult (and sometimes impossible) to enforce, however, when a chemical reaction takes place in a fluctuating environment such as a liquid. High-accuracy approximations to the rate are well known when the solvent forces are treated using stochastic representations, though again, exact no-recrossing surfaces have not been available. To generalize the exact limit of TST to reactive systems driven by noise, we introduce a time-dependent dividing surface that is stochastically moving in phase space such that it is crossed once and only once by each transition path

Mutations in hepatitis C virus E2 located outside the CD81 binding sites lead to escape from broadly neutralizing antibodies but compromise virus infectivity.

Broadly neutralizing antibodies are commonly present in the sera of patients with chronic hepatitis C virus (HCV) infection. To elucidate possible mechanisms of virus escape from these antibodies, retrovirus particles pseudotyped with HCV glycoproteins (HCVpp) isolated from sequential samples collected over a 26-year period from a chronically infected patient, H, were used to characterize the neutralization potential and binding affinity of a panel of anti-HCV E2 human monoclonal antibodies (HMAbs). Moreover, AP33, a neutralizing murine monoclonal antibody (MAb) to a linear epitope in E2, was also tested against selected variants. The HMAbs used were previously shown to broadly neutralize HCV and to recognize a cluster of highly immunogenic overlapping epitopes, designated domain B, containing residues that are also critical for binding of viral E2 glycoprotein to CD81, a receptor essential for virus entry. Escape variants were observed at different time points with some of the HMAbs. Other HMAbs neutralized all variants except for the isolate 02.E10, obtained in 2002, which was also resistant to MAb AP33. The 02.E10 HCVpp that have reduced binding affinities for all antibodies and for CD81 also showed reduced infectivity. Comparison of the 02.E10 nucleotide sequence with that of the strain H-derived consensus variant, H77c, revealed the former to have two mutations in E2, S501N and V506A, located outside the known CD81 binding sites. Substitution A506V in 02.E10 HCVpp restored binding to CD81, but its antibody neutralization sensitivity was only partially restored. Double substitutions comprising N501S and A506V synergistically restored 02.E10 HCVpp infectivity. Other mutations that are not part of the antibody binding epitope in the context of N501S and A506V were able to completely restore neutralization sensitivity. These findings showed that some nonlinear overlapping epitopes are more essential than others for viral fitness and consequently are more invariant during earlier years of chronic infection. Further, the ability of the 02.E10 consensus variant to escape neutralization by the tested antibodies could be a new mechanism of virus escape from immune containment. Mutations that are outside receptor binding sites resulted in structural changes leading to complete escape from domain B neutralizing antibodies, while simultaneously compromising viral fitness by reducing binding to CD81

Human Monoclonal Antibodies to a Novel Cluster of Conformational Epitopes on HCV E2 with Resistance to Neutralization Escape in a Genotype 2a Isolate

The majority of broadly neutralizing antibodies to hepatitis C virus (HCV) are against conformational epitopes on the E2 glycoprotein. Many of them recognize overlapping epitopes in a cluster, designated as antigenic domain B, that contains residues G530 and D535. To gain information on other regions that will be relevant for vaccine design, we employed yeast surface display of antibodies that bound to genotype 1a H77C E2 mutant proteins containing a substitution either at Y632A (to avoid selecting non-neutralizing antibodies) or D535A. A panel of nine human monoclonal antibodies (HMAbs) was isolated and designated as HC-84-related antibodies. Each HMAb neutralized cell culture infectious HCV (HCVcc) with genotypes 1–6 envelope proteins with varying profiles, and each inhibited E2 binding to the viral receptor CD81. Five of these antibodies neutralized representative genotypes 1–6 HCVcc. Epitope mapping identified a cluster of overlapping epitopes that included nine contact residues in two E2 regions encompassing aa418–446 and aa611–616. Effect on virus entry was measured using H77C HCV retroviral pseudoparticles, HCVpp, bearing an alanine substitution at each of the contact residues. Seven of ten mutant HCVpp showed over 90% reduction compared to wild-type HCVpp and two others showed approximately 80% reduction. Interestingly, four of these antibodies bound to a linear E2 synthetic peptide encompassing aa434–446. This region on E2 has been proposed to elicit non-neutralizing antibodies in humans that interfere with neutralizing antibodies directed at an adjacent E2 region from aa410–425. The isolation of four HC-84 HMAbs binding to the peptide, aa434–446, proves that some antibodies to this region are to highly conserved epitopes mediating broad virus neutralization. Indeed, when HCVcc were passaged in the presence of each of these antibodies, virus escape was not observed. Thus, the cluster of HC-84 epitopes, designated as antigenic domain D, is relevant for vaccine design for this highly diverse virus

Security governance and networks: New theoretical perspectives in transatlantic security

The end of the Cold War has not only witnessed the rise of new transnational threats such as terrorism, crime, proliferation and civil war; it has also seen the growing role of non-state actors in the provision of security in Europe and North America. Two concepts in particular have been used to describe these transformations: security governance and networks. However, the differences and potential theoretical utility of these two concepts for the study of contemporary security have so far been under-examined. This article seeks to address this gap. It proposes that security governance can help to explain the transformation of Cold War security structures, whereas network analysis is particularly useful for understanding the relations and interactions between public and private actors in the making and implementation of national and international security policies

Global public policy, transnational policy communities, and their networks

Public policy has been a prisoner of the word "state." Yet, the state is reconfigured by globalization. Through "global public–private partnerships" and "transnational executive networks," new forms of authority are emerging through global and regional policy processes that coexist alongside nation-state policy processes. Accordingly, this article asks what is "global public policy"? The first part of the article identifies new public spaces where global policies occur. These spaces are multiple in character and variety and will be collectively referred to as the "global agora." The second section adapts the conventional policy cycle heuristic by conceptually stretching it to the global and regional levels to reveal the higher degree of pluralization of actors and multiple-authority structures than is the case at national levels. The third section asks: who is involved in the delivery of global public policy? The focus is on transnational policy communities. The global agora is a public space of policymaking and administration, although it is one where authority is more diffuse, decision making is dispersed and sovereignty muddled. Trapped by methodological nationalism and an intellectual agoraphobia of globalization, public policy scholars have yet to examine fully global policy processes and new managerial modes of transnational public administration

The Two Faces of Anomaly Mediation

Anomaly mediation is a ubiquitous source of supersymmetry (SUSY) breaking which appears in almost every theory of supergravity. In this paper, we show that anomaly mediation really consists of two physically distinct phenomena, which we dub "gravitino mediation" and "Kahler mediation". Gravitino mediation arises from minimally uplifting SUSY anti-de Sitter (AdS) space to Minkowski space, generating soft masses proportional to the gravitino mass. Kahler mediation arises when visible sector fields have linear couplings to SUSY breaking in the Kahler potential, generating soft masses proportional to beta function coefficients. In the literature, these two phenomena are lumped together under the name "anomaly mediation", but here we demonstrate that they can be physically disentangled by measuring associated couplings to the goldstino. In particular, we use the example of gaugino soft masses to show that gravitino mediation generates soft masses without corresponding goldstino couplings. This result naively violates the goldstino equivalence theorem but is in fact necessary for supercurrent conservation in AdS space. Since gravitino mediation persists even when the visible sector is sequestered from SUSY breaking, we can use the absence of goldstino couplings as an unambiguous definition of sequestering.Comment: 21 pages, 1 table; v2, references added, extended discussion in introduction and appendix; v3, JHEP versio

"Women's rights, the European Court and Supranational Constitutionalism"

This analysis examines supranational constitutionalism in the European Union. In particular, the study focuses on the role of the European Court of Justice in the creation of women’s rights. I examine the interaction between the Court and member state governments in legal integration, and also the integral role that women’s advocates – both individual activists and groups – have played in the development of EU social provisions. The findings suggest that this litigation dynamic can have the effect of fueling the integration process by creating new rights that may empower social actors and EU organizations, with the ultimate effect of diminishing member state government control over the scope and direction of EU law. This study focuses specifically on gender equality law, yet provides a general framework for examining the case law in subsequent legal domains, with the purpose of providing a more nuanced understanding of supranational governance and constitutionalism

Induction of Cell Stress in Neurons from Transgenic Mice Expressing Yellow Fluorescent Protein: Implications for Neurodegeneration Research

Peer reviewedPublisher PD

Transepithelial migration of neutrophils into the lung requires TREM-1

Acute respiratory infections are responsible for more than 4 million deaths each year. Neutrophils play an essential role in the innate immune response to lung infection. These cells have an armamentarium of pattern recognition molecules and antimicrobial agents that identify and eliminate pathogens. In the setting of infection, neutrophil triggering receptor expressed on myeloid cells 1 (TREM-1) amplifies inflammatory signaling. Here we demonstrate for the first time that TREM-1 also plays an important role in transepithelial migration of neutrophils into the airspace. We developed a TREM-1/3–deficient mouse model of pneumonia and found that absence of TREM-1/3 markedly increased mortality following Pseudomonas aeruginosa challenge. Unexpectedly, TREM-1/3 deficiency resulted in increased local and systemic cytokine production. TREM-1/3–deficient neutrophils demonstrated intact bacterial killing, phagocytosis, and chemotaxis; however, histologic examination of TREM-1/3–deficient lungs revealed decreased neutrophil infiltration of the airways. TREM-1/3–deficient neutrophils effectively migrated across primary endothelial cell monolayers but failed to migrate across primary airway epithelia grown at the air-liquid interface. These data define a new function for TREM-1 in neutrophil migration across airway epithelial cells and suggest that it amplifies inflammation through targeted neutrophil migration into the lung