Dual-acting stapled peptides target both HIV-1 entry and assembly

Background: Previously, we reported the conversion of the 12-mer linear and cell-impermeable peptide CAI to a cell-penetrating peptide NYAD-1 by using an i,i + 4 hydrocarbon stapling technique and confirmed its binding to the C-terminal domain (CTD) of the HIV-1 capsid (CA) protein with an improved affinity (Kd ~ 1 μM) compared to CAI (Kd ~ 15 μM). NYAD-1 disrupts the formation of both immature- and mature-like virus particles in in vitro and cell-based assembly assays. In addition, it displays potent anti-HIV-1 activity in cell culture against a range of laboratory-adapted and primary HIV-1 isolates.<p></p> Results: In this report, we expanded the study to i,i + 7 hydrocarbon-stapled peptides to delineate their mechanism of action and antiviral activity. We identified three potent inhibitors, NYAD-36, -66 and -67, which showed strong binding to CA in NMR and isothermal titration calorimetry (ITC) studies and disrupted the formation of mature-like particles. They showed typical α-helical structures and penetrated cells; however, the cell penetration was not as efficient as observed with the i,i + 4 peptides. Unlike NYAD-1, the i,i + 7 peptides did not have any effect on virus release; however, they impaired Gag precursor processing. HIV-1 particles produced in the presence of these peptides displayed impaired infectivity. Consistent with an effect on virus entry, selection for viral resistance led to the emergence of two mutations in the gp120 subunit of the viral envelope (Env) glycoprotein, V120Q and A327P, located in the conserved region 1 (C1) and the base of the V3 loop, respectively.<p></p> Conclusion: The i,i + 7 stapled peptides derived from CAI unexpectedly target both CA and the V3 loop of gp120. This dual-targeted activity is dependent on their ability to penetrate cells as well as their net charge. This mechanistic revelation will be useful in further modifying these peptides as potent anti-HIV-1 agents.<p></p&gt

Diversity in the structures and ligand binding sites of nematode fatty acid and retinol binding proteins revealed by Na-FAR-1 from Necator americanus

Fatty acid and retinol binding proteins (FARs) comprise a family of unusual α-helix rich lipid binding proteins found exclusively in nematodes. They are secreted into host tissues by parasites of plants, animals and humans. The structure of a FAR protein from the free-living nematode Caenorhabditis elegans is available, but this protein (Ce-FAR-7) is from a subfamily of FARs that does not appear to be important at the host-parasite interface. We have therefore examined Na-FAR-1 from the blood-feeding intestinal parasite of humans, Necator americanus . The three dimensional structure of Na-FAR-1 in its ligand-free and ligand-bound forms, determined by nuclear magnetic resonance spectroscopy (NMR) and X-ray crystallography, respectively, reveals an a-helical fold similar to Ce-FAR-7, but Na-FAR-1 possesses a larger and more complex internal ligand binding cavity and an additional C-terminal a-helix. Titration of apo -Na-FAR-1 with oleic acid, analysed by NMR chemical shift perturbation, reveals that at least four distinct protein:ligand complexes can be formed. Na-FAR-1, and possibly other FARs, may have a wider repertoire for hydrophobic ligand binding, as confirmed here by our finding that a range of neutral and polar lipids co-purify with the bacterial recombinant protein. Finally, we show by immunohistochemistry that Na-FAR-1 is present in adult worms with a tissue distribution indicative of possible roles in nutrient acquisition by the parasite and in reproduction in the male

Quark zero modes in intersecting center vortex gauge fields

The zero modes of the Dirac operator in the background of center vortex gauge field configurations in $\R^2$ and $\R^4$ are examined. If the net flux in D=2 is larger than 1 we obtain normalizable zero modes which are mainly localized at the vortices. In D=4 quasi-normalizable zero modes exist for intersecting flat vortex sheets with the Pontryagin index equal to 2. These zero modes are mainly localized at the vortex intersection points, which carry a topological charge of $\pm 1/2$. To circumvent the problem of normalizability the space-time manifold is chosen to be the (compact) torus \T^2 and \T^4, respectively. According to the index theorem there are normalizable zero modes on \T^2 if the net flux is non-zero. These zero modes are localized at the vortices. On \T^4 zero modes exist for a non-vanishing Pontryagin index. As in $\R^4$ these zero modes are localized at the vortex intersection points.Comment: 20 pages, 4 figures, LaTeX2e, references added, treatment of ideal vortices on the torus shortene

Out-of-equilibrium evolution of quantum fields in the hybrid model with quantum back reaction

The hybrid model with a scalar "inflaton" field coupled to a "Higgs" field with a broken symmetry potential is one of the promising models for inflation and (p)reheating after inflation. We consider the nonequilibrium evolution of the quantum fields of this model with quantum back reaction in the Hartree approximation, in particular the transition of the Higgs field from the metastable "false vacuum" to the broken symmetry phase. We have performed the renormalization of the equations of motion, of the gap equations and of the energy density, using dimensional regularization. We study the influence of the back reaction on the evolution of the classical fields and of the quantum fluctuations. We observe that back reaction plays an important role over a wide range of parameters. Some implications of our investigation for the preheating stage after cosmic inflation are presented.Comment: 35 pages, 16 eps figures, revtex4; v2: typos corrected and references added, accepted for publication in Physical Review

Development and validation of a computational model of the knee joint for the evaluation of surgical treatments for osteoarthritis

A three-dimensional (3D) knee joint computational model was developed and validated to predict knee joint contact forces and pressures for different degrees of malalignment. A 3D computational knee model was created from high-resolution radiological images to emulate passive sagittal rotation (full-extension to 658-flexion) and weight acceptance. A cadaveric knee mounted on a six-degree-of-freedom robot was subjected to matching boundary and loading conditions. A ligamenttuning process minimised kinematic differences between the robotically loaded cadaver specimen and the finite element (FE) model. The model was validated by measured intra-articular force and pressure measurements. Percent full scale error between FE-predicted and in vitro-measured values in the medial and lateral compartments were 6.67% and 5.94%, respectively, for normalised peak pressure values, and 7.56% and 4.48%, respectively, for normalised force values. The knee model can accurately predict normalised intra-articular pressure and forces for different loading conditions and could be further developed for subject-specific surgical planning

Aquatic carbon and GHG export from a permafrost catchment; identifying source areas and primary flow paths

The aquatic pathway is increasingly being recognized as an important component of landscape scale greenhouse gas (GHG) budgets. Due to low temperatures and short residence times limiting in-stream production in northern headwater catchments, much of the exported carbon is likely to be allochthonous, transported via throughflow to the surface drainage system. Identifying sources and primary flow pathways is therefore essential in understanding and predicting changes in the aquatic flux magnitude. Arctic landscapes are now widely recognised as being particularly vulnerable to climate driven changes. The HYDRA project (“Permafrost catchments in transition: hydrological controls on carbon cycling and greenhouse gas budgets”) aims to understand the fundamental role that hydrological processes play in regulating landscape-scale carbon fluxes, and predict how changes in vegetation and active layer depth in permafrost environments influence the delivery and export of aquatic carbon. In this study we present aquatic concentrations and fluxes of carbon and GHG species collected across two field seasons (2013, 2014) from an arctic headwater catchment in northern Canada. Measured species include dissolved organic (DOC) and inorganic carbon (DIC), CO2, CH4 and N2O. Measurements were made across a range of freshwater types within the tundra landscape, including lakes, ice-wedge polygons, and the ‘Siksik’ stream which drains the (c.a. 1 km2) primary study catchment. A nested sub-catchment approach was used along the ‘Siksik’ stream; ‘snapshot’ sampling of eight points along the stream length allowed specific vegetation communities to be targeted to assess individually their contribution to aquatic export. A combination of stable isotopes and major ion concentrations measured at each sampling point provide additional information to trace source areas and flow paths within the main study catchment. Catchment scale evasion and downstream export were calculated and an initial comparison between the relative importance of different water body types presented

Astroparticle Physics with a Customized Low-Background Broad Energy Germanium Detector

The MAJORANA Collaboration is building the MAJORANA DEMONSTRATOR, a 60 kg array of high purity germanium detectors housed in an ultra-low background shield at the Sanford Underground Laboratory in Lead, SD. The MAJORANA DEMONSTRATOR will search for neutrinoless double-beta decay of 76Ge while demonstrating the feasibility of a tonne-scale experiment. It may also carry out a dark matter search in the 1-10 GeV/c^2 mass range. We have found that customized Broad Energy Germanium (BEGe) detectors produced by Canberra have several desirable features for a neutrinoless double-beta decay experiment, including low electronic noise, excellent pulse shape analysis capabilities, and simple fabrication. We have deployed a customized BEGe, the MAJORANA Low-Background BEGe at Kimballton (MALBEK), in a low-background cryostat and shield at the Kimballton Underground Research Facility in Virginia. This paper will focus on the detector characteristics and measurements that can be performed with such a radiation detector in a low-background environment.Comment: Submitted to NIMA Proceedings, SORMA XII. 9 pages, 4 figure

Materiality, health informatics and the limits of knowledge production

© IFIP International Federation for Information Processing 2014 Contemporary societies increasingly rely on complex and sophisticated information systems for a wide variety of tasks and, ultimately, knowledge about the world in which we live. Those systems are central to the kinds of problems our systems and sub-systems face such as health and medical diagnosis, treatment and care. While health information systems represent a continuously expanding field of knowledge production, we suggest that they carry forward significant limitations, particularly in their claims to represent human beings as living creatures and in their capacity to critically reflect on the social, cultural and political origins of many forms of data ‘representation’. In this paper we take these ideas and explore them in relation to the way we see healthcare information systems currently functioning. We offer some examples from our own experience in healthcare settings to illustrate how unexamined ideas about individuals, groups and social categories of people continue to influence health information systems and practices as well as their resulting knowledge production. We suggest some ideas for better understanding how and why this still happens and look to a future where the reflexivity of healthcare administration, the healthcare professions and the information sciences might better engage with these issues. There is no denying the role of health informatics in contemporary healthcare systems but their capacity to represent people in those datascapes has a long way to go if the categories they use to describe and analyse human beings are to produce meaningful knowledge about the social world and not simply to replicate past ideologies of those same categories

Special and inclusive education in the Republic of Ireland: reviewing the literature from 2000 to 2009

Provision for pupils with special educational needs in Ireland has undergone considerable change and review in the first decade of the twenty first century. In response to international demands for a more equitable education system which recognises diversity and considers how schools might address the needs of pupils who have been previously marginalised, Irish legislation has focused upon the development of inclusive schooling. Researchers during this period have endeavoured to understand how responses to the demand for greater inclusion have impacted upon the perceived need for change. This paper reviews the research literature for this period and identifies four key themes under which research has been conducted. The literature pertaining to these themes is explored and a possible agenda for future researchers identifie