Substitutions near the hemagglutinin receptor-binding site determine the antigenic evolution of influenza A H3N2 viruses in U.S. swine

Swine influenza A virus is an endemic and economically important pathogen in pigs, with the potential to infect other host species. The hemagglutinin (HA) protein is the primary target of protective immune responses and the major component in swine influenza A vaccines. However, as a result of antigenic drift, vaccine strains must be regularly updated to reflect currently circulating strains. Characterizing the cross-reactivity between strains in pigs and seasonal influenza virus strains in humans is also important in assessing the relative risk of interspecies transmission of viruses from one host population to the other. Hemagglutination inhibition (HI) assay data for swine and human H3N2 viruses were used with antigenic cartography to quantify the antigenic differences among H3N2 viruses isolated from pigs in the United States from 1998 to 2013 and the relative cross-reactivity between these viruses and current human seasonal influenza A virus strains. Two primary antigenic clusters were found circulating in the pig population, but with enough diversity within and between the clusters to suggest updates in vaccine strains are needed. We identified single amino acid substitutions that are likely responsible for antigenic differences between the two primary antigenic clusters and between each antigenic cluster and outliers. The antigenic distance between current seasonal influenza virus H3 strains in humans and those endemic in swine suggests that population immunity may not prevent the introduction of human viruses into pigs, and possibly vice versa, reinforcing the need to monitor and prepare for potential incursions

Imbalances in serum angiopoietin concentrations are early predictors of septic shock development in patients with post chemotherapy febrile neutropenia

Background: Febrile neutropenia carries a high risk of sepsis complications, and the identification of biomarkers capable to identify high risk patients is a great challenge. Angiopoietins (Ang -) are cytokines involved in the control microvascular permeability. It is accepted that Ang-1 expression maintains endothelial barrier integrity, and that Ang-2 acts as an antagonizing cytokine with barrier-disrupting functions in inflammatory situations. Ang-2 levels have been recently correlated with sepsis mortality in intensive care units. Methods: We prospectively evaluated concentrations of Ang-1 and Ang-2 at different time-points during febrile neutropenia, and explored the diagnostic accuracy of these mediators as potential predictors of poor outcome in this clinical setting before the development of sepsis complications. Results: Patients that evolved with septic shock (n = 10) presented higher levels of Ang-2 measured 48 hours after fever onset, and of the Ang-2/Ang-1 ratio at the time of fever onset compared to patients with non-complicated sepsis (n = 31). These levels correlated with sepsis severity scores. Conclusions: Our data suggest that imbalances in the concentrations of Ang-1 and Ang-2 are independent and early markers of the risk of developing septic shock and of sepsis mortality in febrile neutropenia, and larger studies are warranted to validate their clinical usefulness. Therapeutic strategies that manipulate this Ang-2/Ang-1 imbalance can potentially offer new and promising treatments for sepsis in febrile neutropenia

Determination of Conformational Equilibria in Proteins Using Residual Dipolar Couplings

In order to carry out their functions, proteins often undergo significant conformational fluctuations that enable them to interact with their partners. The accurate characterization of these motions is key in order to understand the mechanisms by which macromolecular recognition events take place. Nuclear magnetic resonance spectroscopy offers a variety of powerful methods to achieve this result. We discuss a method of using residual dipolar couplings as replica-averaged restraints in molecular dynamics simulations to determine large amplitude motions of proteins, including those involved in the conformational equilibria that are established through interconversions between different states. By applying this method to ribonuclease A, we show that it enables one to characterize the ample fluctuations in interdomain orientations expected to play an important functional role

Trends in template/fragment-free protein structure prediction

Predicting the structure of a protein from its amino acid sequence is a long-standing unsolved problem in computational biology. Its solution would be of both fundamental and practical importance as the gap between the number of known sequences and the number of experimentally solved structures widens rapidly. Currently, the most successful approaches are based on fragment/template reassembly. Lacking progress in template-free structure prediction calls for novel ideas and approaches. This article reviews trends in the development of physical and specific knowledge-based energy functions as well as sampling techniques for fragment-free structure prediction. Recent physical- and knowledge-based studies demonstrated that it is possible to sample and predict highly accurate protein structures without borrowing native fragments from known protein structures. These emerging approaches with fully flexible sampling have the potential to move the field forward

Estimation of the rotational terms of the dynamic response matrix

The dynamic response of a structure can be described by both its translational and rotational receptances. The latter ones are frequently not considered because of the difficulties in applying a pure moment excitation or in measuring rotations. However, in general, this implies a reduction up to 75% of the complete model. On the other hand, if a modification includes a rotational inertia, the rotational receptances of the unmodified system are needed. In one method, more commonly found in the literature, a so called T-block is attached to the structure. Then, a force, applied to an arm of the T-block, generates a moment together with a force at the connection point. The T-block also allows for angular displacement measurements. Nevertheless, the results are often not quite satisfactory. In this work, an alternative method based upon coupling techniques is developed, in which rotational receptances are estimated without the need of applying a moment excitation. This is accomplished by introducing a rotational inertia modification when rotating the T-block. The force is then applied in its centroid. Several numerical and experimental examples are discussed so that the methodology can be clearly described. The advantages and limitations are identified within the practical application of the methodPeer reviewedSubmitted Versio

On the estimation of rotational frequency response functions

Rotational receptances can perform an important role when predicting the dynamic behaviour both in theoretical and experimental models, especially when a modification includes a rotational inertia or a rotational stiffness. Estimation of rotational frequency response functions (FRFs) from experimental data often leads to poor results, most of the times exhibiting spurious resonance peaks. In this paper, one tries to evaluate whether or not such spurious peaks are related to torsion modes which were not considered in the model. The method used herein to determine the rotational receptances is based on FRF coupling and on a structural modification, which can be accomplished by performing several measurements using rigid fixtures of appropriate geometry. Here, one discusses the influence that these fixtures might have on the results. To avoid one of the major sources of experimental error, the excitation force is applied only at the translation co-ordinate, without application of a moment excitation. Several experimental examples are presented and discussed so that the advantages and limitations of this methodology are identified within the practical application of the method