The RNA Template Channel of the RNA-Dependent RNA Polymerase as a Target for Development of Antiviral Therapy of Multiple Genera within a Virus Family

The genus Enterovirus of the family Picornaviridae contains many important human pathogens (e.g., poliovirus, coxsackievirus, rhinovirus, and enterovirus 71) for which no antiviral drugs are available. The viral RNA-dependent RNA polymerase is an attractive target for antiviral therapy. Nucleoside-based inhibitors have broad-spectrum activity but often exhibit off-target effects. Most non-nucleoside inhibitors (NNIs) target surface cavities, which are structurally more flexible than the nucleotide-binding pocket, and hence have a more narrow spectrum of activity and are more prone to resistance development. Here, we report a novel NNI, GPC-N114 (2,2''-[(4-chloro-1,2-phenylene)bis(oxy)]bis(5-nitro-benzonitrile)) with broad-spectrum activity against enteroviruses and cardioviruses (another genus in the picornavirus family). Surprisingly, coxsackievirus B3 (CVB3) and poliovirus displayed a high genetic barrier to resistance against GPC-N114. By contrast, EMCV, a cardiovirus, rapidly acquired resistance due to mutations in 3D^pol. In vitro polymerase activity assays showed that GPC-N114 i) inhibited the elongation activity of recombinant CVB3 and EMCV 3D^pol, (ii) had reduced activity against EMCV 3D^pol with the resistance mutations, and (iii) was most efficient in inhibiting 3D^pol when added before the RNA template-primer duplex. Elucidation of a crystal structure of the inhibitor bound to CVB3 3D^pol confirmed the RNA-binding channel as the target for GPC-N114. Docking studies of the compound into the crystal structures of the compound-resistant EMCV 3D^pol mutants suggested that the resistant phenotype is due to subtle changes that interfere with the binding of GPC-N114 but not of the RNA template-primer. In conclusion, this study presents the first NNI that targets the RNA template channel of the picornavirus polymerase and identifies a new pocket that can be used for the design of broad-spectrum inhibitors. Moreover, this study provides important new insight into the plasticity of picornavirus polymerases at the template binding site.     

Addressing Palliative Sedation during Expert Consultation: A Descriptive Analysis of the Practice of Dutch Palliative Care Consultation Teams

Main Objective

Since palliative sedation is considered a complex intervention, consultation teams are increasingly established to support general practice. This study aims to offer insight into the frequency and characteristics of expert consultations regarding palliative sedation.

Methods

We performed a retrospective analysis of a longitudinal database. This database contained all patient-related consultations by Dutch Palliative Care Consultation teams, that were requested between 2004 and 2011. We described the frequency and characteristics of these consultations, in particular of the subgroup of consultations in which palliative sedation was addressed (i.e. PSa consultations). We used multivariate regression analysis to explore consultation characteristics associated with a higher likelihood of PSa consultations.

Main Results and Their Significance

Of the 44,443 initial consultations, most were requested by general practitioners (73%) and most concerned patients with cancer (86%). Palliative sedation was addressed in 18.1% of all consultations. Palliative sedation was relatively more often discussed during consultations for patients with a neurologic disease (OR 1.79; 95% CI: 1.51–2.12) or COPD (OR 1.39; 95% CI: 1.15–1.69) than for patients with cancer. We observed a higher likelihood of PSa consultations if the following topics were also addressed during consultation: dyspnoea (OR 1.30; 95% CI: 1.22–1.40), agitation/delirium (OR 1.57; 95% CI: 1.47–1.68), exhaustion (OR 2.89; 95% CI: 2.61–3.20), euthanasia-related questions (OR 2.65; 95% CI: 2.37–2.96) or existential issues (OR 1.55; 95% CI: 1.31–1.83).

Conclusion

In conclusion, PSa consultations accounted for almost one-fifth of all expert consultations and were associated with several case-related characteristics. These characteristics may help clinicians in identifying patients at risk for a more complex disease trajectory at the end of life.     

Seasonal Alterations in Host Range and Fidelity in the Polyphagous Mirid Bug,Apolygus lucorum (Heteroptera: Miridae)

In herbivorous insects, host plant switching is commonly observed and plays an important role in their annual life cycle. However, much remains to be learned about seasonal host switching of various pestiferous arthropods under natural conditions. From 2006 until 2012, we assessed Apolygus lucorum (Meyer-Dür) host plant use in successive spring, summer and winter seasons at one single location (Langfang, China). Data were used to quantify changes in host plant breadth and host fidelity between seasons. Host fidelity of A. lucorum differed between seasons, with 87.9% of spring hosts also used in the summer and 36.1% of summer hosts used in winter. In contrast, as little as 25.6% host plant species were shared between winter and spring. Annual herbaceous plants are most often used for overwintering, while perennial woody plants are relatively important for initial population build-up in the spring. Our study contributes to an improved understanding of evolutionary interactions between A. lucorum and its host plants and lays the groundwork for the design of population management strategies for this important pest in myriad crops.     

Cadherins and tissue formation: integrating adhesion and signaling

Cadherins and other cell–substrate and cell–cell adhesion molecules play an essential role during development. Through their cytoplasmic interaction with the cytoskeleton, cell adhesion molecules physically link cells with the extracellular matrix and/or with each other. These interactions create architectural and structural entities that enable the tissues in the embryo to restrain the physical forces encountered during development. Regulated cell adhesion is also often the driving force of morphogenetic movements. This review goes beyond the adhesive aspect of cadherins, focusing on their roles as signaling molecules in development. We discuss how cadherins, through their effects on cell proliferation, cell death, cell polarization, and differentiation, play a role in the formation of tissues and organs in the developing embryo. BioEssays 21:211–220, 1999. © 1999 John Wiley & Sons, Inc.     

A computationally tractable birth-death model that combines phylogenetic and epidemiological data

Inferring the dynamics of pathogen transmission during an outbreak is an important problem in infectious disease epidemiology. In mathematical epidemiology, estimates are often informed by time series of confirmed cases, while in phylodynamics genetic sequences of the pathogen, sampled through time, are the primary data source. Each type of data provides different, and potentially complementary, insight. Recent studies have recognised that combining data sources can improve estimates of the transmission rate and the number of infected individuals. However, inference methods are typically highly specialised and field-specific and are either computationally prohibitive or require intensive simulation, limiting their real-time utility. We present a novel birth-death phylogenetic model and derive a tractable analytic approximation of its likelihood, the computational complexity of which is linear in the size of the dataset. This approach combines epidemiological and phylodynamic data to produce estimates of key parameters of transmission dynamics and the unobserved prevalence. Using simulated data, we show (a) that the approximation agrees well with existing methods, (b) validate the claim of linear complexity and (c) explore robustness to model misspecification. This approximation facilitates inference on large datasets, which is increasingly important as large genomic sequence datasets become commonplace.     

Micropropagation of Chokecherry and Pincherry cultivars

In vitro culture establishment, shoot proliferation and ex vitro rooting responses of chokecherry (Prunus virginiana L.), `Garrington', and pincherry (P. pensylvanica L.f), `Mary Liss' and `Jumping Pound', were examined using various combinations of growth regulators. Dormant winter buds were used as explants. MSMO medium supplemented with 0.49 μM IBA and either 4.44 or 8.87 μM BA was found to be optimal for culture initiation of both species and cultivars. GA₃ (28.89 μM) significantly reduced (p=0.0001) the number of successfully established cultures. BA concentrations 8.87–12.82 μM gave optimal shoot proliferation in chokecherry and 4.44 μM BA in both cultivars of pincherry. Auxin treatments were required for ex vitro rooting of approximately 10 mm long shoots in peat/perlite (1:1 v/v) mixture, at 25 °C, under mist. The best rooting (84%) was obtained with IBA/NAA (9.80/2.69 μM). A commercial rooting powder, Rootone F, containing IBA/NAA (0.057/0.067%) mixture, was also effective (75%). The ex vitro rooted plantlets did not require any additional acclimatization prior to transplanting to the regular greenhouse conditions. This revised version was published online in August 2006 with corrections to the Cover Date.     

Conformational restriction of Tyr and Phe side chains in opioid peptides: Information about preferred and bioactive side-chain topology

The side chain of Tyr and Phe was fixed into the gauche (−) or gauche (+) conformation by using the Tic or Htc structures, and into the trans conformation by using an aminobenzazepine-type (Aba) structure. When incorporated into dermorphin or deltorphin II, the Tic and Htc analogues all showed a large decrease in both μ and δ affinities and activities. Fixation of Phe³ in the trans rotamer resulted in a large increase in δ affinity in the dermorphin analogue, whereas in the [Aba³-Gly⁴] deltorphin II analogue, good δ affinity is maintained despite the removal of the Glu side chain. Whereas several authors propose a gauche (−) preferred conformation for the Phe³ side chain, these results suggest a trans conformation at the δ receptor. The use of these conformationally constrained residues for evaluating the preferred solution conformation in the flexible N-terminal tripeptide Tyr-D-Ala-Phe is illustrated. The ¹H-nmr parameters—chemical shift, temperature dependence, and nuclear Overhauser effects to the D-Ala² methyl protons in the different analogues—provide direct evidence to confirm the proposed sandwich conformation in the native peptides. © 1996 John Wiley & Sons, Inc.     

Detoxification requirements for bioconversion of softwood dilute acid hydrolyzates to succinic acid

In this work an Escherichia coli metabolically engineered to ferment lignocellulosic biomass sugars to succinic acid was tested for growth and fermentation of detoxified softwood dilute sulfuric acid hydrolyzates, and the minimum detoxification requirements were investigated with activated carbon and/or overliming treatments. Detoxified hydrolyzates supported fast growth and complete fermentation of all hydrolyzate sugars to succinate at yields comparable to pure sugar, while untreated hydrolyzates were unable to support either growth or fermentation. Activated carbon treatment was able to remove significantly more HMF and phenolics than overliming. However, in some cases, overliming treatment was capable of generating a fermentable hydrolyzate where activated carbon treatment was not. The implications of this are that in addition to the known organic inhibitors, the changes in the inorganic content and/or composition due to overliming are significant to the hydrolyzate toxicity. It was also found that any HMF remaining after detoxification was completely metabolized during aerobic cell growth on the hydrolyzates that were capable of supporting growth.