Prospects of a thousand-ion Sn2+ Coulomb-crystal clock with sub-10-19 inaccuracy.

Optical atomic clocks are the most accurate and precise measurement devices of any kind, enabling advances in international timekeeping, Earth science, fundamental physics, and more. However, there is a fundamental tradeoff between accuracy and precision, where higher precision is achieved by using more atoms, but this comes at the cost of larger interactions between the atoms that limit the accuracy. Here, we propose a many-ion optical atomic clock based on three-dimensional Coulomb crystals of order one thousand Sn2+ ions confined in a linear RF Paul trap with the potential to overcome this limitation. Sn2+ has a unique combination of features that is not available in previously considered ions: a 1S0 ↔ 3P0 clock transition between two states with zero electronic and nuclear angular momentum (I = J = F = 0) making it immune to nonscalar perturbations, a negative differential polarizability making it possible to operate the trap in a manner such that the two dominant shifts for three-dimensional ion crystals cancel each other, and a laser-accessible transition suitable for direct laser cooling and state readout. We present calculations of the differential polarizability, other relevant atomic properties, and the motion of ions in large Coulomb crystals, in order to estimate the achievable accuracy and precision of Sn2+ Coulomb-crystal clocks.

New Measurement Resolves Key Astrophysical Fe XVII Oscillator Strength Problem.

One of the most enduring and intensively studied problems of x-ray astronomy is the disagreement of state-of-the art theory and observations for the intensity ratio of two Fe XVII transitions of crucial value for plasma diagnostics, dubbed 3C and 3D. We unravel this conundrum at the PETRA III synchrotron facility by increasing the resolving power 2.5 times and the signal-to-noise ratio thousandfold compared with our previous work. The Lorentzian wings had hitherto been indistinguishable from the background and were thus not modeled, resulting in a biased line-strength estimation. The present experimental oscillator-strength ratio R_{exp}=f_{3C}/f_{3D}=3.51(2)_{stat}(7)_{sys} agrees with our state-of-the-art calculation of R_{th}=3.55(2), as well as with some previous theoretical predictions. To further rule out any uncertainties associated with the measured ratio, we also determined the individual natural linewidths and oscillator strengths of 3C and 3D transitions, which also agree well with the theory. This finally resolves the decades-old mystery of Fe XVII oscillator strengths.

Detection of the Lowest-Lying Odd-Parity Atomic Levels in Actinium.

Two lowest-energy odd-parity atomic levels of actinium, 7s^{2}7p^{2}P_{1/2}^{o}, 7s^{2}7p^{2}P_{3/2}^{o}, were observed via two-step resonant laser-ionization spectroscopy and their respective energies were measured to be 7477.36(4) and 12 276.59(2) cm^{-1}. The lifetimes of these states were determined as 668(11) and 255(7) ns, respectively. In addition, we observed the effect of the hyperfine structure on the line for the transition to ^{2}P_{3/2}^{o}. These properties were calculated using a hybrid approach that combines configuration interaction and coupled-cluster methods, in good agreement with the experiment. The data are of relevance for understanding the complex atomic spectra of actinides and for developing efficient laser cooling and ionization schemes for actinium, with possible applications for high-purity medical-isotope production and future fundamental physics experiments.

High Resolution Photoexcitation Measurements Exacerbate the Long-Standing Fe XVII Oscillator Strength Problem.

For more than 40 years, most astrophysical observations and laboratory studies of two key soft x-ray diagnostic 2p-3d transitions, 3C and 3D, in Fe XVII ions found oscillator strength ratios f(3C)/f(3D) disagreeing with theory, but uncertainties had precluded definitive statements on this much studied conundrum. Here, we resonantly excite these lines using synchrotron radiation at PETRA III, and reach, at a millionfold lower photon intensities, a 10 times higher spectral resolution, and 3 times smaller uncertainty than earlier work. Our final result of f(3C)/f(3D)=3.09(8)(6) supports many of the earlier clean astrophysical and laboratory observations, while departing by five sigmas from our own newest large-scale ab initio calculations, and excluding all proposed explanations, including those invoking nonlinear effects and population transfers.

Development of an animal model of progressive vaccinia in nu/nu mice and the use of bioluminescence imaging for assessment of the efficacy of monoclonal antibodies against vaccinial B5 and L1 proteins.

Bioluminescence imaging (BLI) was used to follow dissemination of recombinant vaccinia virus (VACV) expressing luciferase (IHD-J-Luc) in BALB/c nu/nu mice treated post-challenge with monoclonal antibodies (MAbs) against L1 and B5 VACV proteins in a model of Progressive Vaccinia (PV). Areas Under the flux Curve (AUC) were calculated for viral loads in multiple organs in individual mice. Following scarification with 105 pfu, IHD-J-Luc VACV undergoes fast replication at the injection site and disseminates rapidly to the inguinal lymph nodes followed by spleen, liver, and axillary lymph nodes within 2-3 days and before primary lesions are visible at the site of scarification. Extension of survival in nude mice treated with a combination of anti-B5 and anti-L1 MAbs 24 h post challenge correlated with a significant reduction in viral load at the site of scarification and delayed systemic dissemination. Nude mice reconstituted with 104 T cells prior to challenge with IHD-J-Luc, and treated with MAbs post-challenge, survived infection, cleared the virus from all organs and scarification site, and developed anti-VACV IgG and VACV-specific polyfunctional CD8+ T cells that co-expressed the degranulation marker CD107a, and IFNγ and TNFα cytokines. All T cell reconstituted mice survived intranasal re-challenge with IHD-J-Luc (104 pfu) two months after the primary infection. Thus, using BLI to monitor VACV replication in a PV model, we showed that anti-VACV MAbs administered post challenge extended survival of nude mice and protected T cell reconstituted nude mice from lethality by reducing replication at the site of scarification and systemic dissemination of VACV.

Estimating and adjusting for ancestry admixture in statistical methods for relatedness inference, heritability estimation, and association testing.

It is well known that genetic association studies are not robust to population stratification. Two widely used approaches for the detection and correction of population structure are principal component analysis and model-based estimation of ancestry. These methods have been shown to give reliable inference on population structure in unrelated samples. We evaluated these two approaches in Mexican American pedigrees provided by the Genetic Analysis Workshop 18. We also estimated identity-by-descent sharing probabilities and kinship coefficients, with adjustment for ancestry admixture, to confirm documented pedigree relationships as well as to identify cryptic relatedness in the sample. We also estimated the heritability of the first simulated replicate of diastolic blood pressure (DBP). Finally, we performed an association analysis with simulated DBP, comparing the performance of an association method that corrects for population structure but does not account for relatedness to a method that adjusts for both population and pedigree structure. Analyses with simulated DBP were performed with knowledge of the underlying trait model.

Identity-by-descent graphs offer a flexible framework for imputation and both linkage and association analyses.

We demonstrate the flexibility of identity-by-descent (IBD) graphs for genotype imputation and testing relationships between genotype and phenotype. We analyzed chromosome 3 and the first replicate of simulated diastolic blood pressure. IBD graphs were obtained from complete pedigrees and full multipoint marker analysis, facilitating subsequent linkage and other analyses. For rare alleles, pedigree-based imputation using these IBD graphs had a higher call rate than did population-based imputation. Combining the two approaches improved call rates for common alleles. We found it advantageous to incorporate known, rather than estimated, pedigree relationships when testing for association. Replacing missing data with imputed alleles improved association signals as well. Analyses were performed with knowledge of the underlying model.

HIV latency. Proliferation of cells with HIV integrated into cancer genes contributes to persistent infection.

Antiretroviral treatment (ART) of HIV infection suppresses viral replication. Yet if ART is stopped, virus reemerges because of the persistence of infected cells. We evaluated the contribution of infected-cell proliferation and sites of proviral integration to HIV persistence. A total of 534 HIV integration sites (IS) and 63 adjacent HIV env sequences were derived from three study participants over 11.3 to 12.7 years of ART. Each participant had identical viral sequences integrated at the same position in multiple cells, demonstrating infected-cell proliferation. Integrations were overrepresented in genes associated with cancer and favored in 12 genes across multiple participants. Over time on ART, a greater proportion of persisting proviruses were in proliferating cells. HIV integration into specific genes may promote proliferation of HIV-infected cells, slowing viral decay during ART.

Detection of Mendelian consistent genotyping errors in pedigrees.

Detection of genotyping errors is a necessary step to minimize false results in genetic analysis. This is especially important when the rate of genotyping errors is high, as has been reported for high-throughput sequence data. To detect genotyping errors in pedigrees, Mendelian inconsistent (MI) error checks exist, as do multi-point methods that flag Mendelian consistent (MC) errors for sparse multi-allelic markers. However, few methods exist for detecting MC genotyping errors, particularly for dense variants on large pedigrees. Here, we introduce an efficient method to detect MC errors even for very dense variants (e.g., SNPs and sequencing data) on pedigrees that may be large. Our method first samples inheritance vectors (IVs) using a moderately sparse but informative set of markers using a Markov chain Monte Carlo-based sampler. Using sampled IVs, we considered two test statistics to detect MC genotyping errors: the percentage of IVs inconsistent with observed genotypes (A1) or the posterior probability of error configurations (A2). Using simulations, we show that this method, even with the simpler A1 statistic, is effective for detecting MC genotyping errors in dense variants, with sensitivity almost as high as the theoretical best sensitivity possible. We also evaluate the effectiveness of this method as a function of parameters, when including the observed pattern for genotype, density of framework markers, error rate, allele frequencies, and number of sampled inheritance vectors. Our approach provides a line of defense against false findings based on the use of dense variants in pedigrees.

A statistical framework to guide sequencing choices in pedigrees.

The use of large pedigrees is an effective design for identifying rare functional variants affecting heritable traits. Cost-effective studies using sequence data can be achieved via pedigree-based genotype imputation in which some subjects are sequenced and missing genotypes are inferred on the remaining subjects. Because of high cost, it is important to carefully prioritize subjects for sequencing. Here, we introduce a statistical framework that enables systematic comparison among subject-selection choices for sequencing. We introduce a metric "local coverage," which allows the use of inferred inheritance vectors to measure genotype-imputation ability specifically in a region of interest, such as one with prior evidence of linkage. In the absence of linkage information, we can instead use a "genome-wide coverage" metric computed with the pedigree structure. These metrics enable the development of a method that identifies efficient selection choices for sequencing. As implemented in GIGI-Pick, this method also flexibly allows initial manual selection of subjects and optimizes selections within the constraint that only some subjects might be available for sequencing. In the present study, we used simulations to compare GIGI-Pick with PRIMUS, ExomePicks, and common ad hoc methods of selecting subjects. In genotype imputation of both common and rare alleles, GIGI-Pick substantially outperformed all other methods considered and had the added advantage of incorporating prior linkage information. We also used a real pedigree to demonstrate the utility of our approach in identifying causal mutations. Our work enables prioritization of subjects for sequencing to facilitate dissection of the genetic basis of heritable traits.

GIGI: an approach to effective imputation of dense genotypes on large pedigrees.

Recent emergence of the common-disease-rare-variant hypothesis has renewed interest in the use of large pedigrees for identifying rare causal variants. Genotyping with modern sequencing platforms is increasingly common in the search for such variants but remains expensive and often is limited to only a few subjects per pedigree. In population-based samples, genotype imputation is widely used so that additional genotyping is not needed. We now introduce an analogous approach that enables computationally efficient imputation in large pedigrees. Our approach samples inheritance vectors (IVs) from a Markov Chain Monte Carlo sampler by conditioning on genotypes from a sparse set of framework markers. Missing genotypes are probabilistically inferred from these IVs along with observed dense genotypes that are available on a subset of subjects. We implemented our approach in the Genotype Imputation Given Inheritance (GIGI) program and evaluated the approach on both simulated and real large pedigrees. With a real pedigree, we also compared imputed results obtained from this approach with those from the population-based imputation program BEAGLE. We demonstrated that our pedigree-based approach imputes many alleles with high accuracy. It is much more accurate for calling rare alleles than is population-based imputation and does not require an outside reference sample. We also evaluated the effect of varying other parameters, including the marker type and density of the framework panel, threshold for calling genotypes, and population allele frequencies. By leveraging information from existing genotypes already assayed on large pedigrees, our approach can facilitate cost-effective use of sequence data in the pursuit of rare causal variants.

Genome scan in familial late-onset Alzheimer's disease: a locus on chromosome 6 contributes to age-at-onset.

Alzheimer's disease (AD) is a common, genetically complex, fatal neurodegenerative disorder of late life. Although several genes are known to play a role in early-onset AD, identification of the genetic basis of late onset AD (LOAD) has been challenging, with only the APOE gene known to have a high contribution to both AD risk and age-at-onset. Here, we present the first genome-scan analysis of the complete, well-characterized University of Washington LOAD sample of 119 pedigrees, using age-at-onset as the trait of interest. The analysis approach used allows for a multilocus trait model while at the same time accommodating age censoring, effects of APOE as a known genetic covariate, and full pedigree and marker information. The results provide strong evidence for linkage of loci contributing to age-at-onset to genomic regions on chromosome 6q16.3, and to 19q13.42 in the region of the APOE locus. There was evidence for interaction between APOE and the locus on chromosome 6q and suggestive evidence for linkage to chromosomes 11p13, 15q12-14, and 19p13.12. These results provide the first independent confirmation of an AD age-at-onset locus on chromosome 6 and suggest that further efforts towards identifying the underlying causal locus or loci are warranted.

rMAT--an R/Bioconductor package for analyzing ChIP-chip experiments.

SUMMARY: Chromatin immunoprecipitation combined with DNA microarrays (ChIP-chip) has evolved as a popular technique to study DNA-protein binding or post-translational chromatin/histone modifications at the genomic level. However, the raw microarray intensities generate a massive amount of data, creating a need for efficient analysis algorithms and statistical methods to identify enriched regions. RESULTS: We present a fast, free and powerful, open source R package, rMAT, that allows the identification of regions enriched for transcription factor binding sites in ChIP-chip experiments on Affymetrix tiling arrays. AVAILABILITY: The R-package rMAT is available from the Bioconductor web site at http://bioconductor.org and runs on Linux, MAC OS and MS-Windows. rMAT is distributed under the terms of the Artistic Licence 2.0.

G-protein-coupled receptor independent, immunomodulatory properties of chemokine CXCL9.

Certain chemokines possess anti-angiogenic and antibacterial activity, in addition to their ability to recruit leukocytes. Herein, we demonstrate that CXCL9/MIG induces the expression, by a monocytic cell line and peripheral blood mononuclear cells, of a variety of chemokines including CXCL8/IL-8, CCL3/MIP-1alpha, CCL4/MIP-1beta, CCL2/MCP-1 in a pertussis toxin insensitive manner. Similarly, another cationic chemokine CCL20/MIP-3alpha, but not the non-cationic chemokines CCL2 or CCL3, stimulated monocytic cells to produce substantial amounts of CXCL8 and CCL3. Microarray experiments demonstrated that CXCL9, but not CCL2, induced the expression of hundreds of genes, many of which have known or proposed immunomodulatory functions. Induction of CXCL8 required the p38 and ERK1/2 mitogen-activated protein kinases but not NFkappaB, JAK-STAT or JNK signaling pathways. These results collectively demonstrate that CXCL9 has immunomodulatory functions that are not mediated through a G-protein coupled receptor and may possess additional roles in host defenses against infection.

Contrasting identity-by-descent estimators, association studies, and linkage analyses using the Framingham Heart Study data.

We explored the utility of population- and pedigree-based analyses using the Framingham Heart Study genome-wide 50 k single-nucleotide polymorphism marker data provided for Genetic Analysis Workshop 16. Our aims were: 1) to compare identity-by-descent sharing estimates from variable amounts of data; 2) to apply each of these estimates to a case-control association study designed to control for relatedness among samples; and 3) to contrast these results to those obtained using model-based and model-free linkage analysis methods.

Multifunctional pancreatic islet encapsulation barriers achieved via multilayer PEG hydrogels.

The diverse requirements for a successful islet encapsulation barrier suggest the benefit of a barrier system that presents differing functionalities to encapsulated cells and host cells. Initially, multifunctional hydrogels were synthesized via the sequential photopolymerization of PEG hydrogel layers, each with different isolated functionalities. The ability to achieve localized biological functionalities was confirmed by immunostaining of different entrapped antibodies within each hydrogel layer. Survival of murine islets macroencapsulated within the interior gel of two-layer hydrogel constructs was then assessed. Maintenance of encapsulated islet survival and function was observed within multilayer hydrogels over 28 days in culture. Additionally, the functionalization of the islet-containing interior PEG gel layer with cell-matrix moieties, with either 100 microg/ml laminin or 5 mM of the adhesive peptide IKVAV found in laminin, resulted in increased insulin secretion from encapsulated islets similar to that in gels without an exterior hydrogel layer. Finally, through cell seeding experiments, the ability of an unmodified, exterior PEG layer to prevent interactions, and thus attachment, between nonencapsulated fibroblasts and entrapped ECM components within the interior PEG layer was demonstrated. Together the presented results support the potential of multilayer hydrogels for use as multifunctional islet encapsulation barriers that provide a localized biologically active islet microenvironment, while presenting an inert, immunoprotective exterior surface to the host environment, to minimize graft-host interactions.

Cellular delivery of TGFbeta1 promotes osteoinductive signalling for bone regeneration.

Administration of osteoinductive growth factors to wound sites, alone or in conjunction with a delivery vehicle, is an appealing treatment option for critical bone defects. The delivery of cells transfected with genes encoding for osteoinductive growth factors, such as TGFbeta(1), represents an attractive option to locally deliver constant levels of these growth factors to stimulate new bone formation at the defect site. Using non-viral transfection methods, we showed that osteoblasts can be genetically modified in vitro to secrete sustained therapeutic levels of TGFbeta(1) in its active form through control of the transfected cell environment. In addition, delivery of TGFbeta(1) produced by genetically modified cells that contained the proper post-translational modifications provided a more robust cellular response compared to administration of bacterially-derived recombinant TGFbeta(1). Migration and subsequent proliferation of osteoblasts are critical aspects of the initial steps in the cascade of new bone tissue formation. Exposure to mammalian-derived TGFbeta(1) induced a more pronounced chemotactic response upon administration of 10 pg/ml TGFbeta(1), whereas osteoblasts showed enhanced levels of metabolic activity at 100 pg/ml, which is indicative of greater levels of cellular proliferation when compared to addition of the same levels of recombinant TGFbeta(1). This increased efficacy of cell-derived TGFbeta(1) over recombinant forms of TGFbeta(1), combined with provision of a continual source of TGFbeta(1), highlights the advantages of delivering genetically modified cells over exogenous protein delivery for bone tissue engineering.

Modifying the proliferative state of target cells to control DNA expression and identifying cell types transfected in vivo.

Although the majority of current gene transfer techniques have focused on increasing the ability of the DNA to enter the cell, it is possible that changing the proliferative and migratory state of cells will influence the cells ability to take up and express plasmid DNA. This study was designed to test the hypothesis that growth factors (basic fibroblast growth factor (bFGF) and hepatocyte growth factor/scatter factor (HGF/SF)) used to alter the proliferative and migratory state of cells can alter plasmid DNA uptake and expression. In vitro studies indicate that enhancing cell proliferation with growth factor exposure enhances plasmid DNA uptake and expression. Furthermore, dual localized delivery of bFGF and plasmid DNA in vivo increases the expression, 3-6 times over control, as compared to plasmid delivery alone. Dual delivery of a factor promoting cell proliferation and a plasmid led to a further increase in the expression of the plasmid encoding bone morphogenetic protein-2 in a rat cranial defect by specific cell populations. The results of these studies suggest that increasing the proliferative state of target cell populations can enhance non-viral gene transfer.

Multifunctional Pancreatic Islet Encapsulation Barriers Achieved via Multilayer PEG Hydrogels.

The diverse requirements for a successful islet encapsulation barrier suggest the benefit of a barrier system that presents differing functionalities to encapsulated cells and host cells. Initially, multifunctional hydrogels were synthesized via the sequential photopolymerization of PEG hydrogel layers, each with different isolated functionalities. The ability to achieve localized biological functionalities was confirmed by immunostaining of different entrapped antibodies within each hydrogel layer. Survival of murine islets macroencapsulated within the interior gel of two-layer hydrogel constructs was then assessed. Maintenance of encapsulated islet survival and function was observed within multilayer hydrogels over 28 days in culture. Additionally, the functionalization of the islet-containing interior PEG gel layer with cell-matrix moieties, with either 100 µg/ml laminin or 5 mM of the adhesive peptide IKVAV found in laminin, resulted in increased insulin secretion from encapsulated islets similar to that in gels without an exterior hydrogel layer. Finally, through cell seeding experiments, the ability of an unmodified, exterior PEG layer to prevent interactions, and thus attachment, between nonencapsulated fibroblasts and entrapped ECM components within the interior PEG layer was demonstrated. Together the presented results support the potential of multilayer hydrogels for use as multifunctional islet encapsulation barriers that provide a localized biologically active islet microenvironment, while presenting an inert, immunoprotective exterior surface to the host environment, to minimize graft-host interactions.

Synthesis of immunoisolation barriers that provide localized immunosuppression for encapsulated pancreatic islets.

Pancreatic islet encapsulation into synthetic, passive material matrixes can provide protection for transplanted islets from destruction via cell-contacted mediated interactions with autoreactive immune cells for treatment of Type I diabetes mellitus. However, one of the fundamental deficiencies with current encapsulation technology is that passive material barriers cannot protect islets from exposure to cytokines and other small, diffusible cytotoxic molecules produced by activated immune cells, subsequently leading to beta-cell destruction. Preparation of material matrixes that can actively provide localized immunosuppression of autoreactive immune cells may prolong the viability, and hence function, of encapsulated islet grafts. We have demonstrated the ability to conjugate apoptosis-inducing anti-Fas monoclonal antibodies (MAbs) to the surfaces of poly(ethylene glycol)-modified hydrogels, providing a surface that actively attempts to locally down-regulate the autoimmune response by destroying autoreactive T cells against pancreatic islet cells. We have conjugated anti-Fas MAbs to a high degree to the surface of these hydrogels, with retention of anti-Fas recognition of the Fas antigen as shown by ELISA testing. Apoptosis induction of Fas-sensitive Jurkat T cells was enhanced in the presence of anti-Fas conjugated hydrogels. In addition, this apoptosis induction was specific to anti-Fas MAbs, with no apoptosis induction with control antibodies or with Fas-insensitive T cells. These experiments promote the concept that surface-conjugated hydrogel constructs can provide localized immunosuppression for encapsulated grafted tissue.