OneG: A Computational Tool for Predicting Cryptic Intermediates in the Unfolding Kinetics of Proteins under Native Conditions

Understanding the relationships between conformations of proteins and their stabilities is one key to address the protein folding paradigm. The free energy change (ΔG) of unfolding reactions of proteins is measured by traditional denaturation methods and native hydrogen-deuterium (H/D) exchange methods. However, the free energy of unfolding (ΔGU) and the free energy of exchange (ΔGHX) of proteins are not in good agreement, though the experimental conditions of both methods are well matching to each other. The anomaly is due to any one or combinations of the following reasons: (i) effects of cis-trans proline isomerisation under equilibrium unfolding reactions of proteins (ii) inappropriateness in accounting the baselines of melting curves (iii) presence of cryptic intermediates, which may elude the melting curve analysis and (iv) existence of higher energy metastable states in the H/D exchange reactions of proteins. Herein, we have developed a novel computational tool, OneG, which accounts the discrepancy between ΔGU and ΔGHX of proteins by systematically accounting all the four factors mentioned above. The program is fully automated and requires four inputs: three-dimensional structures of proteins, ΔGU, ΔGU* and residue-specific ΔGHX determined under EX2-exchange conditions in the absence of denaturants. The robustness of the program has been validated using experimental data available for proteins such as cytochrome c and apocytochrome b562 and the data analyses revealed that cryptic intermediates of the proteins detected by the experimental methods and the cryptic intermediates predicted by the OneG for those proteins were in good agreement. Furthermore, using OneG, we have shown possible existence of cryptic intermediates and metastable states in the unfolding pathways of cardiotoxin III and cobrotoxin, respectively, which are homologous proteins. The unique application of the program to map the unfolding pathways of proteins under native conditions have been brought into fore and the program is publicly available at http://sblab.sastra.edu/oneg.htm

Asthma control in adolescents 10 to 11 y after exposure to the World Trade Center disaster

Background: Little is known about asthma control in adolescents who were exposed to the World Trade Center (WTC) attacks of 11 September 2001 and diagnosed with asthma after 9/11. This report examines asthma and asthma control 10–11 y after 9/11 among exposed adolescents. Methods: The WTC Health Registry adolescent Wave 3 survey (2011–2012) collected data on asthma diagnosed by a physician after 11 September 2001, extent of asthma control based on modified National Asthma Education and Prevention Program criteria, probable mental health conditions, and behavior problems. Parents reported healthcare needs and 9/11-exposures. Logistic regression was used to evaluate associations between asthma and level of asthma control and 9/11-exposure, mental health and behavioral problems, and unmet healthcare needs. Results: Poorly/very poorly controlled asthma was significantly associated with a household income of ≤$75,000 (adjusted odds ratio (AOR): 3.0; 95% confidence interval (CI): 1.1–8.8), having unmet healthcare needs (AOR: 6.2; 95% CI: 1.4–27.1), and screening positive for at least one mental health condition (AOR: 5.0; 95% CI: 1.4–17.7), but not with behavioral problems. The impact of having at least one mental health condition on the level of asthma control was substantially greater in females than in males. Conclusions: Comprehensive care of post-9/11 asthma in adolescents should include management of mental health-related comorbidities. The collapse and burning of the World Trade Center (WTC) towers on 11 September 2001 (9/11) exposed hundreds of thousands of people to a complex mixture of dust, debris, and jet fuel combustion byproducts (1). It is estimated that over 25,000 persons in lower Manhattan developed asthma symptoms after exposure to the WTC terrorist attacks and the subsequent rescue and recovery efforts (1). In the years immediately following 9/11, new-onset asthma rates were elevated among exposed adults and many of those affected continued to experience respiratory symptoms (i.e., coughing, shortness of breath) years later (1,2). An estimated 25,000 children were living or attending school in lower Manhattan near the WTC on 9/11, and potentially were in the path of the dust cloud of building debris and smoke after the collapse of the towers, as well as for several months following the attacks, and could have inhaled particulate matter and toxic substances (3,4). Associations between 9/11-related exposures and both asthma diagnosis and persistent respiratory symptoms among children and adolescents have been documented (4,5,6). A previous report found that 2 to 3 y after 9/11, over half of children under 18 y of age who were enrolled in the World Trade Center Health Registry (Registry) reported new or worsening respiratory symptoms (53%), and 5.7% reported a post-9/11 diagnosis of asthma, both of which were associated with exposure to the dust cloud that resulted from the collapse of buildings on 9/11 (4). A subsequent study of Registry enrollees under 18 y old found that respiratory symptoms persisted up to 7 y post-9/11 (5). The WTC Environmental Health Center which collected clinical data on a sample of children an average of 7.8 y after 9/11, reported new onset provider-diagnosed asthma in 21.4% of children, and found that dust cloud exposure was associated with pulmonary function abnormalities, such as isolated low forced vital capacity pattern and an obstructive pattern consistent with asthma (6). Although the association between asthma and 9/11-exposure in children and adolescents has been documented, little is known about asthma control in this population. Large population-based surveys consistently show that poor asthma control is common in many children with asthma (7,8). Asthma control is affected by many factors, including healthcare access (9,10), socioeconomic status (9,10), and comorbid mental health conditions (11,12,13). It has been observed that adolescents with symptomatic asthma are more likely than adolescents without asthma to have lower perceived well-being, more negative behaviors, and a greater number of physical and mental health comorbidities (14). Several studies found that depression has been associated with uncontrolled asthma (11,12). In adults with 9/11-related asthma, having at least one mental health condition has been associated with poorly controlled asthma (15). However, little is known about the association between mental health conditions and the level of asthma control especially among 9/11-exposed adolescents. Previous studies of adult Registry enrollees found that those with unmet healthcare needs are more likely to have severe mental health symptoms, comorbid mental and physical health problems, and have lower quality of life (1,16). Unmet healthcare needs among adolescents have been shown to be associated with poorer health status and functioning, including asthma control (17). Poorly controlled asthma has also been associated with unmet healthcare needs related to cost or access barriers (18), such as an inability to pay for asthma medications and not having access to asthma specialists (19). The goal of this study was to evaluate asthma control 10–11 y after 9/11 among Registry as children, and to determine whether poor asthma control is associated with specific factors including adolescent 9/11-exposure, adverse mental health, behavior problems, and unmet healthcare needs

Plasma and cellular fibronectin: distinct and independent functions during tissue repair

Fibronectin (FN) is a ubiquitous extracellular matrix (ECM) glycoprotein that plays vital roles during tissue repair. The plasma form of FN circulates in the blood, and upon tissue injury, is incorporated into fibrin clots to exert effects on platelet function and to mediate hemostasis. Cellular FN is then synthesized and assembled by cells as they migrate into the clot to reconstitute damaged tissue. The assembly of FN into a complex three-dimensional matrix during physiological repair plays a key role not only as a structural scaffold, but also as a regulator of cell function during this stage of tissue repair. FN fibrillogenesis is a complex, stepwise process that is strictly regulated by a multitude of factors. During fibrosis, there is excessive deposition of ECM, of which FN is one of the major components. Aberrant FN-matrix assembly is a major contributing factor to the switch from normal tissue repair to misregulated fibrosis. Understanding the mechanisms involved in FN assembly and how these interplay with cellular, fibrotic and immune responses may reveal targets for the future development of therapies to regulate aberrant tissue-repair processes

QCD and strongly coupled gauge theories : challenges and perspectives

We highlight the progress, current status, and open challenges of QCD-driven physics, in theory and in experiment. We discuss how the strong interaction is intimately connected to a broad sweep of physical problems, in settings ranging from astrophysics and cosmology to strongly coupled, complex systems in particle and condensed-matter physics, as well as to searches for physics beyond the Standard Model. We also discuss how success in describing the strong interaction impacts other fields, and, in turn, how such subjects can impact studies of the strong interaction. In the course of the work we offer a perspective on the many research streams which flow into and out of QCD, as well as a vision for future developments.Peer reviewe

Search for dark matter candidates and large extra dimensions in events with a jet and missing transverse momentum with the ATLAS detector

Open Access, Copyright CERN, for the benefit of the ATLAS collaboration. This article is distributed under the terms of the Creative Commons Attribution License which permits any use, distribution and reproduction in any medium, provided the original author(s) and source are credited