The Application of FAST-NMR for the Identification of Novel Drug Discovery Targets

The continued success of genome sequencing projects has resulted in a wealth of information, but 40-50% of identified genes correspond to hypothetical proteins or proteins of unknown function. The Functional Annotation Screening Technology by NMR (FAST-NMR) screen was developed to assign a biological function for these unannotated proteins with a structure solved by the Protein Structure Initiative. FAST-NMR is based on the premise that a biological function can be described by a similarity in binding sites and ligand interactions with proteins of known function. The resulting co-structure and functional assignment may provide a starting point for a drug discovery effort

A Correlation between Protein Function and Ligand Binding Profiles

We report that proteins with the same function bind the same set of small molecules from a standardized chemical library. This observation led to a quantifiable and rapidly adaptable method for protein functional analysis using experimentally-derived ligand binding profiles. Ligand binding is measured using a high-throughput NMR ligand affinity screen with a structurally diverse chemical library. The method was demonstrated using a set of 19 proteins with a range of functions. A statistically significant similarity in ligand binding profiles was only observed between the two functionally identical albumins and between the five functionally similar amylases. This new approach is independent of sequence, structure or evolutionary information, and therefore, extends our ability to analyze and functionally annotate novel genes

Searching for Signatures of Cosmic Superstrings in the CMB

Because cosmic superstrings generically form junctions and gauge theoretic strings typically do not, junctions may provide a signature to distinguish between cosmic superstrings and gauge theoretic cosmic strings. In cosmic microwave background anisotropy maps, cosmic strings lead to distinctive line discontinuities. String junctions lead to junctions in these line discontinuities. In turn, edge detection algorithms such as the Canny algorithm can be used to search for signatures of strings in anisotropy maps. We apply the Canny algorithm to simulated maps which contain the effects of cosmic strings with and without string junctions. The Canny algorithm produces edge maps. To distinguish between edge maps from string simulations with and without junctions, we examine the density distribution of edges and pixels crossed by edges. We find that in string simulations without Gaussian noise (such as produced by the dominant inflationary fluctuations) our analysis of the output data from the Canny algorithm can clearly distinguish between simulations with and without string junctions. In the presence of Gaussian noise at the level expected from the current bounds on the contribution of cosmic strings to the total power spectrum of density fluctuations, the distinction between models with and without junctions is more difficult. However, by carefully analyzing the data the models can still be differentiated.Comment: 15 page

Perfluorooctanoic Acid–Induced Immunomodulation in Adult C57BL/6J or C57BL/6N Female Mice

BackgroundPerfluorooctanoic acid (PFOA), an environmentally persistent compound of regulatory concern, has been reported to reduce antibody responses in mice at a single dose.ObjectiveThe aim of this study was to evaluate PFOA effects on humoral and cellular immunity using standard assays for assessing immune function, and to derive dose–response data.MethodsC57BL/6J mice received 0 or 30 mg PFOA/kg/day for 10 days; half of the exposed groups were switched to vehicle and half continued on PFOA for five days. C57BL/6N mice received 0–30 mg/kg/day of PFOA in drinking water for 15 days. Mice were immunized with sheep red blood cells or sensitized to bovine serum albumin in Freund’s complete adjuvant on day 10 of exposure; immune responses were determined 1 day post-exposure.ResultsWe found that 30 mg PFOA/kg/day given for 10 or 15 days reduced IgM synthesis; serum collected 1 day postexposure contained 8.4 × 104 or 2.7 × 105 ng PFOA/mL, respectively. IgM synthesis was suppressed at exposures ≥ 3.75 mg PFOA/kg/day in a dose-dependent manner, and IgG titers were elevated at 3.75 and 7.5 mg PFOA/kg/day. Serum PFOA at 3.75 mg/kg/day was 7.4 × 104 ng/mL 1 day postexposure, or 150-fold greater than the levels reported in individuals living near a PFOA production site. Using a second-degree polynomial model, we calculated a benchmark dose of 3 mg/kg/day, with a lower bound (95% confidence limit) of 1.75 mg/kg/day. Cell-mediated function was not affected.ConclusionsIgM antibodies were suppressed after PFOA exposure. The margin of exposure for reduced IgM antibody synthesis was approximately 150 for highly exposed human populations

A lateral nanoflow assay reveals nanoplastic fluorescence heterogeneity

Colloidal nanoplastics present technological opportunities, environmental concerns, and measurement challenges. To meet these challenges, we develop a lateral nanoflow assay from sample-in to answer-out. Our measurement system integrates complex nanofluidic replicas, super-resolution optical microscopy, and comprehensive statistical analyses to measure polystyrene nanoparticles that sorb and carry hydrophobic fluorophores. An elegant scaling of surface forces within our silicone devices hydrodynamically automates the advection and dominates the diffusion of the nanoparticles. Through steric interaction with the replica structure, the particle size distribution reciprocally probes the unknown limits of replica function. Multiple innovations in the integration and calibration of device and microscope improve the accuracy of identifying single nanoparticles and quantifying their diameters and fluorescence intensities. A statistical model of the measurement approaches the information limit of the system, discriminates size exclusion from surface adsorption, and reduces nonideal data to return the particle size distribution with nanometer resolution. A Bayesian statistical analysis of the dimensional and optical properties of single nanoparticles reveals their fundamental structure-property relationship. Fluorescence intensity shows a super-volumetric dependence, scaling with nanoparticle diameter to nearly the fourth power and confounding basic concepts of chemical sorption. Distributions of fluorescivity - the product of the number density, absorption cross section, and quantum yield of an ensemble of fluorophores - are ultrabroad and asymmetric, limiting ensemble analysis and dimensional or chemical inference from fluorescence intensity. These results reset expectations for optimizing nanoplastic products, understanding nanoplastic byproducts, and applying nanoplastic standards

POLG2 deficiency causes adult-onset syndromic sensory neuropathy, ataxia and parkinsonism

Objective: Mitochondrial dysfunction plays a key role in the pathophysiology of neurodegenerative disorders such as ataxia and Parkinson's disease. We describe an extended Belgian pedigree where seven individuals presented with adult-onset cerebellar ataxia, axonal peripheral ataxic neuropathy, and tremor, in variable combination with parkinsonism, seizures, cognitive decline, and ophthalmoplegia. We sought to identify the underlying molecular etiology and characterize the mitochondrial pathophysiology of this neurological syndrome. Methods: Clinical, neurophysiological, and neuroradiological evaluations were conducted. Patient muscle and cultured fibroblasts underwent extensive analyses to assess mitochondrial function. Genetic studies including genome-wide sequencing were conducted. Results: Hallmarks of mitochondrial dysfunction were present in patients' tissues including ultrastructural anomalies of mitochondria, mosaic cytochrome c oxidase deficiency, and multiple mtDNA deletions. We identified a splice acceptor variant in POLG2, c.970-1G>C, segregating with disease in this family and associated with a concomitant decrease in levels of POLG2 protein in patient cells. Interpretation: This work extends the clinical spectrum of POLG2 deficiency to include an overwhelming, adult-onset neurological syndrome that includes cerebellar syndrome, peripheral neuropathy, tremor, and parkinsonism. We therefore suggest to include POLG2 sequencing in the evaluation of ataxia and sensory neuropathy in adults, especially when it is accompanied by tremor or parkinsonism with white matter disease. The demonstration that deletions of mtDNA resulting from autosomal-dominant POLG2 variant lead to a monogenic neurodegenerative multicomponent syndrome provides further evidence for a major role of mitochondrial dysfunction in the pathomechanism of nonsyndromic forms of the component neurodegenerative disorders

Virtual Screening of acyclovir derivatives as potential antiviral agents: design, synthesis, and biological evaluation of new acyclic nucleoside ProTides

Following our findings on the anti-human immunodeficiency virus (HIV) activity of acyclovir (ACV) phosphate prodrugs, we herein report the ProTide approach applied to a series of acyclic nucleosides aimed at the identification of novel and selective antiviral, in particular anti-HIV agents. Acyclic nucleoside analogues used in this study were identified through a virtual screening using HIV-reverse transcriptase (RT), adenylate/guanylate kinase, and human DNA polymerase γ. A total of 39 new phosphate prodrugs were synthesized and evaluated against HIV-1 (in vitro and ex vivo human tonsillar tissue system) and human herpes viruses. Several ProTide compounds showed substantial potency against HIV-1 at low micromolar range while the parent nucleosides were not effective. Also, pronounced inhibition of herpesvirus replication was observed. A carboxypeptidase-mediated hydrolysis study was performed for a selection of compounds to assess the formation of putative metabolites and support the biological activity observed

On the Generation of a Scale-Invariant Spectrum of Adiabatic Fluctuations in Cosmological Models with a Contracting Phase

In Pre-Big-Bang and in Ekpyrotic Cosmology, perturbations on cosmological scales today are generated from quantum vacuum fluctuations during a phase when the Universe is contracting (viewed in the Einstein frame). The backgrounds studied to date do not yield a scale invariant spectrum of adiabatic fluctuations. Here, we present a new contracting background model (neither of Pre-Big-Bang nor of the Ekpyrotic form) involving a single scalar field coupled to gravity in which a scale-invariant spectrum of curvature fluctuations and gravitational waves results. The equation of state of this scalar field corresponds to cold matter. We demonstrate that if this contracting phase can be matched via a nonsingular bounce to an expanding Friedmann cosmology, the scale-invariance of the curvature fluctuations is maintained. We also find new background solutions for Pre-Big-Bang and for Ekpyrotic cosmology, which involve two scalar fields with exponential potentials with background values which are evolving in time. We comment on the difficulty of obtaining a scale-invariant spectrum of adiabatic fluctuations with background solutions which have been studied in the past.Comment: 8 pages, revised version without the section on perturbations, matching the version published on Phys. Rev. D. For cosmological perturbations in the two field model see astro-ph/021127

Reducing the impact of physical inactivity: evidence to support the case for targeting people with chronic mental and physical conditions

Background : Recent evidence suggests that small increases in the physical activity of those considered least active can have a bigger health impact than raising levels of those already achieving or close to achieving recommendations. Profiling the characteristics of those who are least active allows for appropriate targeting of interventions. This study therefore examined the characteristics of people in the lowest physical activity bracket. Methods : Data were taken from the Collaboration for Leadership in Applied Health Research and Care (CLAHRC) funded ‘South Yorkshire Cohort’, a longitudinal observational dataset of residents of South Yorkshire, England. Five separate outcomes based on a shortened version of the GPPAQ were used to represent the lowest levels of physical activity. Potential predictors examined were age, sex, body mass index, ethnicity, chronic conditions, current employment and deprivation. Descriptive statistics and logistic regression were conducted. Results : Individuals with chronic mental and physical conditions (fatigue, insomnia, anxiety, depression, diabetes, breathing problems, high blood pressure, heart disease, stroke and cancer) were more likely to report the lowest levels of physical activity across all five outcomes. Demographic variations were also observed. Conclusions : Targeting people with chronic mental and physical conditions has the potential to reduce the impact of physical inactivity.</p