Mouse obesity network reconstruction with a variational Bayes algorithm to employ aggressive false positive control

<p>Abstract</p> <p>Background</p> <p>We propose a novel variational Bayes network reconstruction algorithm to extract the most relevant disease factors from high-throughput genomic data-sets. Our algorithm is the only scalable method for regularized network recovery that employs Bayesian model averaging and that can internally estimate an appropriate level of sparsity to ensure few false positives enter the model without the need for cross-validation or a model selection criterion. We use our algorithm to characterize the effect of genetic markers and liver gene expression traits on mouse obesity related phenotypes, including weight, cholesterol, glucose, and free fatty acid levels, in an experiment previously used for discovery and validation of network connections: an F2 intercross between the C57BL/6 J and C3H/HeJ mouse strains, where apolipoprotein E is null on the background.</p> <p>Results</p> <p>We identified eleven genes, Gch1, Zfp69, Dlgap1, Gna14, Yy1, Gabarapl1, Folr2, Fdft1, Cnr2, Slc24a3, and Ccl19, and a quantitative trait locus directly connected to weight, glucose, cholesterol, or free fatty acid levels in our network. None of these genes were identified by other network analyses of this mouse intercross data-set, but all have been previously associated with obesity or related pathologies in independent studies. In addition, through both simulations and data analysis we demonstrate that our algorithm achieves superior performance in terms of power and type I error control than other network recovery algorithms that use the lasso and have bounds on type I error control.</p> <p>Conclusions</p> <p>Our final network contains 118 previously associated and novel genes affecting weight, cholesterol, glucose, and free fatty acid levels that are excellent obesity risk candidates.</p

A variational Bayes algorithm for fast and accurate multiple locus genome-wide association analysis

<p>Abstract</p> <p>Background</p> <p>The success achieved by genome-wide association (GWA) studies in the identification of candidate loci for complex diseases has been accompanied by an inability to explain the bulk of heritability. Here, we describe the algorithm V-Bay, a variational Bayes algorithm for multiple locus GWA analysis, which is designed to identify weaker associations that may contribute to this missing heritability.</p> <p>Results</p> <p>V-Bay provides a novel solution to the computational scaling constraints of most multiple locus methods and can complete a simultaneous analysis of a million genetic markers in a few hours, when using a desktop. Using a range of simulated genetic and GWA experimental scenarios, we demonstrate that V-Bay is highly accurate, and reliably identifies associations that are too weak to be discovered by single-marker testing approaches. V-Bay can also outperform a multiple locus analysis method based on the lasso, which has similar scaling properties for large numbers of genetic markers. For demonstration purposes, we also use V-Bay to confirm associations with gene expression in cell lines derived from the Phase II individuals of HapMap.</p> <p>Conclusions</p> <p>V-Bay is a versatile, fast, and accurate multiple locus GWA analysis tool for the practitioner interested in identifying weaker associations without high false positive rates.</p

Phosphorylation of CENP-A on serine 7 does not control centromere function

CENP-A is the histone H3 variant necessary to specify the location of all eukaryotic centromeres via its CENP-A targeting domain and either one of its terminal regions. In humans, several post-translational modifications occur on CENP-A, but their role in centromere function remains controversial. One of these modifications of CENP-A, phosphorylation on serine 7, has been proposed to control centromere assembly and function. Here, using gene targeting at both endogenous CENP-A alleles and gene replacement in human cells, we demonstrate that a CENP-A variant that cannot be phosphorylated at serine 7 maintains correct CENP-C recruitment, faithful chromosome segregation and long-term cell viability. Thus, we conclude that phosphorylation of CENP-A on serine 7 is dispensable to maintain correct centromere dynamics and function

Disruption of the Hippocampal and Hypothalamic Blood-Brain Barrier in a Diet-Induced Obese Model of Type II Diabetes: Prevention and Treatment by the Mitochondrial Carbonic Anhydrase Inhibitor, Topiramate

Background: Type II diabetes is a vascular risk factor for cognitive impairment and increased risk of dementia. Disruption of the blood–retinal barrier (BRB) and blood–brain barrier (BBB) are hallmarks of subsequent retinal edema and central nervous system dysfunction. However, the mechanisms by which diet or metabolic syndrome induces dysfunction are not understood. A proposed mechanism is an increase in reactive oxygen species (ROS) and oxidative stress. Inhibition of mitochondrial carbonic anhydrase (mCA) decreases ROS and oxidative stress. In this study, topiramate, a mCA inhibitor, was examined for its ability to protect the BRB and BBB in diet-induced obese type II diabetic mice. Methods: BBB and BRB permeability were assessed using 14C-sucrose and 99mTc-albumin in CD-1 mice fed a low-fat (control) or a high-fat diet. Topiramate administration was compared to saline controls in both preventative and efficacy arms examining BRB and BBB disruption. Body weight and blood glucose were measured weekly and body composition was assessed using EchoMRI. Metabolic activity was measured using a comprehensive laboratory animal monitoring system. Brain tissues collected from the mice were assessed for changes in oxidative stress and tight junction proteins. Results: High-fat feeding caused increased entry of 14C-sucrose and 99mTc-albumin into the brains of diet-induced obese type II diabetic mice. Increased permeability to 14C-sucrose was observed in the hypothalamus and hippocampus, and attenuated by topiramate treatment, while increased permeability to 99mTc-albumin occurred in the whole brain and was also attenuated by topiramate. Treatment with topiramate decreased measures of oxidative stress and increased expression of the tight junction proteins ZO-1 and claudin-12. In the retina, we observed increased entry of 99mTc-albumin simultaneously with increased entry into the whole brain during the preventative arm. This occurred prior to increased entry to the retina for 14C-sucrose which occurred during the efficacy arm. Treatment with topiramate had no effect on the retina. Conclusions: Blood–brain barrier and blood–retinal barrier dysfunction were examined in a mouse model of diet-induced obese type II diabetes. These studies demonstrate that there are spatial and temporal differences in 14C-sucrose and 99mTc-albumin permeability in the brain and retina of diet-induced obese type II diabetic mice. Topiramate, a mitochondrial carbonic anhydrase inhibitor, is efficacious at both preventing and treating BBB disruption in this diet-induced obese type II diabetic mouse model

Soil Moisture Sensing via Swept Frequency Based Microwave Sensors

There is a need for low-cost, high-accuracy measurement of water content in various materials. This study assesses the performance of a new microwave swept frequency domain instrument (SFI) that has promise to provide a low-cost, high-accuracy alternative to the traditional and more expensive time domain reflectometry (TDR). The technique obtains permittivity measurements of soils in the frequency domain utilizing a through transmission configuration, transmissometry, which provides a frequency domain transmissometry measurement (FDT). The measurement is comparable to time domain transmissometry (TDT) with the added advantage of also being able to separately quantify the real and imaginary portions of the complex permittivity so that the measured bulk permittivity is more accurate that the measurement TDR provides where the apparent permittivity is impacted by the signal loss, which can be significant in heavier soils. The experimental SFI was compared with a high-end 12 GHz TDR/TDT system across a range of soils at varying soil water contents and densities. As propagation delay is the fundamental measurement of interest to the well-established TDR or TDT technique; the first set of tests utilized precision propagation delay lines to test the accuracy of the SFI instrument’s ability to resolve propagation delays across the expected range of delays that a soil probe would present when subjected to the expected range of soil types and soil moisture typical to an agronomic cropping system. The results of the precision-delay line testing suggests the instrument is capable of predicting propagation delays with a RMSE of +/−105 ps across the range of delays ranging from 0 to 12,000 ps with a coefficient of determination of r2 = 0.998. The second phase of tests noted the rich history of TDR for prediction of soil moisture and leveraged this history by utilizing TDT measured with a high-end Hewlett Packard TDR/TDT instrument to directly benchmark the SFI instrument over a range of soil types, at varying levels of moisture. This testing protocol was developed to provide the best possible comparison between SFI to TDT than would otherwise be possible by using soil moisture as the bench mark, due to variations in soil density between soil water content levels which are known to impact the calibration between TDR’s estimate of soil water content from the measured propagation delay which is converted to an apparent permittivity measurement. This experimental decision, to compare propagation delay of TDT to FDT, effectively removes the errors due to variations in packing density from the evaluation and provides a direct comparison between the SFI instrument and the time domain technique of TDT. The tests utilized three soils (a sand, an Acuff loam and an Olton clay-loam) that were packed to varying bulk densities and prepared to provide a range of water contents and electrical conductivities by which to compare the performance of the SFI technology to TDT measurements of propagation delay. For each sample tested, the SFI instrument and the TDT both performed the measurements on the exact same probe, thereby both instruments were measuring the exact same soil/soil-probe response to ensure the most accurate means to compare the SFI instrument to a high-end TDT instrument. Test results provided an estimated instrumental accuracy for the SFI of +/−0.98% of full scale, RMSE basis, for the precision delay lines and +/−1.32% when the SFI was evaluated on loam and clay loam soils, in comparison to TDT as the bench-mark. Results from both experiments provide evidence that the low-cost SFI approach is a viable alternative to conventional TDR/TDT for high accuracy applications

Chromosomes. CENP-C reshapes and stabilizes CENP-A nucleosomes at the centromere

Inheritance of each chromosome depends upon its centromere. A histone H3 variant, centromere protein A (CENP-A), is essential for epigenetically marking centromere location. We find that CENP-A is quantitatively retained at the centromere upon which it is initially assembled. CENP-C binds to CENP-A nucleosomes and is a prime candidate to stabilize centromeric chromatin. Using purified components, we find that CENP-C reshapes the octameric histone core of CENP-A nucleosomes, rigidifies both surface and internal nucleosome structure, and modulates terminal DNA to match the loose wrap that is found on native CENP-A nucleosomes at functional human centromeres. Thus, CENP-C affects nucleosome shape and dynamics in a manner analogous to allosteric regulation of enzymes. CENP-C depletion leads to rapid removal of CENP-A from centromeres, indicating their collaboration in maintaining centromere identity.NIH grants: (GM082989, CA186430, GM008275, GM008216, GM007229); American Heart Association predoctoral fellowship; American Cancer Society postdoctoral fellowship; NSF grant: (agreement DMR-0944772)

A genomic survey of the fish parasite Spironucleus salmonicida indicates genomic plasticity among diplomonads and significant lateral gene transfer in eukaryote genome evolution

BACKGROUND: Comparative genomic studies of the mitochondrion-lacking protist group Diplomonadida (diplomonads) has been lacking, although Giardia lamblia has been intensively studied. We have performed a sequence survey project resulting in 2341 expressed sequence tags (EST) corresponding to 853 unique clones, 5275 genome survey sequences (GSS), and eleven finished contigs from the diplomonad fish parasite Spironucleus salmonicida (previously described as S. barkhanus). RESULTS: The analyses revealed a compact genome with few, if any, introns and very short 3' untranslated regions. Strikingly different patterns of codon usage were observed in genes corresponding to frequently sampled ESTs versus genes poorly sampled, indicating that translational selection is influencing the codon usage of highly expressed genes. Rigorous phylogenomic analyses identified 84 genes – mostly encoding metabolic proteins – that have been acquired by diplomonads or their relatively close ancestors via lateral gene transfer (LGT). Although most acquisitions were from prokaryotes, more than a dozen represent likely transfers of genes between eukaryotic lineages. Many genes that provide novel insights into the genetic basis of the biology and pathogenicity of this parasitic protist were identified including 149 that putatively encode variant-surface cysteine-rich proteins which are candidate virulence factors. A number of genomic properties that distinguish S. salmonicida from its human parasitic relative G. lamblia were identified such as nineteen putative lineage-specific gene acquisitions, distinct mutational biases and codon usage and distinct polyadenylation signals. CONCLUSION: Our results highlight the power of comparative genomic studies to yield insights into the biology of parasitic protists and the evolution of their genomes, and suggest that genetic exchange between distantly-related protist lineages may be occurring at an appreciable rate in eukaryote genome evolution

Cognitive stimulation therapy for dementia: provision in National Health Service settings in England, Scotland and Wales

Objectives: Cognitive stimulation therapy (CST) is a brief, non-pharmacological intervention for people with dementia, with an established evidence base for improving cognition and quality of life. It is widely implemented in National Health Service (NHS) settings, but little is known about its naturalistic use. The aim of this survey was to identify and explore inclusion criteria, dose and quality of CST across services in Great Britain (England, Scotland and Wales). Methods: All NHS memory clinics and services for people with dementia were contacted and asked to complete a mixed methods online survey on CST delivery in their service. Questions were centred on who provided CST, who received CST, the dose of CST and any outcomes that were routinely measured. Results: A total of 57/186 services responded, giving a response rate of 30.7%. While the majority reported offering CST (87.7%), there was variability in how this was delivered. Differing inclusion criteria included the use of varying cognitive and behavioural outcome measures, and CST was reported as being offered once and twice weekly. Services also differed in how they evaluated the quality of CST and how this evidence was incorporated for future sessions. Conclusion: While there was a low response rate, this survey indicates that there is significant variability in how CST is used in clinical practice, with many trusts not adhering to the evidence base. To ensure that people with dementia are consistently offered evidence-based, high-quality CST across NHS settings, further standardisation of inclusion criteria, dose and outcomes is needed

Y Dwarf Trigonometric Parallaxes from the Spitzer Space Telescope

Y dwarfs provide a unique opportunity to study free-floating objects with masses <30 M_(Jup) and atmospheric temperatures approaching those of known Jupiter-like exoplanets. Obtaining distances to these objects is an essential step toward characterizing their absolute physical properties. Using Spitzer's Infrared Array Camera (IRAC) [4.5] images taken over baselines of ~2–7 years, we measure astrometric distances for 22 late-T and early Y dwarfs, including updated parallaxes for 18 objects and new parallax measurements for 4 objects. These parallaxes will make it possible to explore the physical parameter space occupied by the coldest brown dwarfs. We also present the discovery of six new late-T dwarfs, updated spectra of two T dwarfs, and the reclassification of a new Y dwarf, WISE J033605.04−014351.0, based on Keck/NIRSPEC J-band spectroscopy. Assuming that effective temperatures are inversely proportional to absolute magnitude, we examine trends in the evolution of the spectral energy distributions of brown dwarfs with decreasing effective temperature. Surprisingly, the Y dwarf class encompasses a large range in absolute magnitude in the near- to mid-infrared photometric bandpasses, demonstrating a larger range of effective temperatures than previously assumed. This sample will be ideal for obtaining mid-infrared spectra with the James Webb Space Telescope because their known distances will make it easier to measure absolute physical properties