535 research outputs found
Exploring universality in nuclear clusters with Halo EFT
I present results and highlight aspects of halo EFT to loosely bound systems
composed of nucleons and alpha particles, with emphasis on Coulomb
interactions.Comment: 3 pages, 2 figures, talk given at the 21th European Conference on
Few-Body Problems in Physics, Salamanca, Aug. 29th - Sep. 3rd, 201
Diet-induced gene expression of isolated pancreatic islets from a polygenic mouse model of the metabolic syndrome
AIMS/HYPOTHESIS: Numerous new genes have recently been identified in genome-wide association studies for type 2 diabetes. Most are highly expressed in beta cells and presumably play important roles in their function. However, these genes account for only a small proportion of total risk and there are likely to be additional candidate genes not detected by current methodology. We therefore investigated islets from the polygenic New Zealand mouse (NZL) model of diet-induced beta cell dysfunction to identify novel genes and pathways that may play a role in the pathogenesis of diabetes. METHODS: NZL mice were fed a diabetogenic high-fat diet (HF) or a diabetes-protective carbohydrate-free HF diet (CHF). Pancreatic islets were isolated by laser capture microdissection (LCM) and subjected to genome-wide transcriptome analyses. RESULTS: In the prediabetic state, 2,109 islet transcripts were differentially regulated (>1.5-fold) between HF and CHF diets. Of the genes identified, 39 (e.g. Cacna1d, Chd2, Clip2, Igf2bp2, Dach1, Tspan8) correlated with data from the Diabetes Genetics Initiative and Wellcome Trust Case Control Consortium genome-wide scans for type 2 diabetes, thus validating our approach. HF diet induced early changes in gene expression associated with increased cell-cycle progression, proliferation and differentiation of islet cells, and oxidative stress (e.g. Cdkn1b, Tmem27, Pax6, Cat, Prdx4 and Txnip). In addition, pathway analysis identified oxidative phosphorylation as the predominant gene-set that was significantly upregulated in response to the diabetogenic HF diet. CONCLUSIONS/INTERPRETATION: We demonstrated that LCM of pancreatic islet cells in combination with transcriptional profiling can be successfully used to identify novel candidate genes for diabetes. Our data strongly implicate glucose-induced oxidative stress in disease progression
Alternative exon splicing and differential expression in pancreatic islets reveals candidate genes and pathways implicated in early diabetes development
Type 2 diabetes (T2D) has a strong genetic component. Most of the gene variants driving the pathogenesis of T2D seem to target pancreatic β-cell function. To identify novel gene variants acting at early stage of the disease, we analyzed whole transcriptome data to identify differential expression (DE) and alternative exon splicing (AS) transcripts in pancreatic islets collected from two metabolically diverse mouse strains at 6 weeks of age after three weeks of high-fat-diet intervention. Our analysis revealed 1218 DE and 436 AS genes in islets from NZO/Hl vs C3HeB/FeJ. Whereas some of the revealed genes present well-established markers for β-cell failure, such as Cd36 or Aldh1a3, we identified numerous DE/AS genes that have not been described in context with β-cell function before. The gene Lgals2, previously associated with human T2D development, was DE as well as AS and localizes in a quantitative trait locus (QTL) for blood glucose on Chr.15 that we reported recently in our N2(NZOxC3H) population. In addition, pathway enrichment analysis of DE and AS genes showed an overlap of only half of the revealed pathways, indicating that DE and AS in large parts influence different pathways in T2D development. PPARG and adipogenesis pathways, two well-established metabolic pathways, were overrepresented for both DE and AS genes, probably as an adaptive mechanism to cope for increased cellular stress. Our results provide guidance for the identification of novel T2D candidate genes and demonstrate the presence of numerous AS transcripts possibly involved in islet function and maintenance of glucose homeostasis
alpha-alpha Scattering in Halo Effective Field Theory
We study the two-alpha-particle (alpha-alpha) system in an Effective Field
Theory (EFT) for halo-like systems. We propose a power counting that
incorporates the subtle interplay of strong and electromagnetic forces leading
to a narrow resonance at an energy of about 0.1 MeV. We investigate the EFT
expansion in detail, and compare its results with existing low-energy
alpha-alpha phase shifts and previously determined effective-range parameters.
Good description of the data is obtained with a surprising amount of
fine-tuning. This scenario can be viewed as an expansion around the limit
where, when electromagnetic interactions are turned off, the Be-8 ground state
is at threshold and exhibits conformal invariance. We also discuss possible
extensions to systems with more than two alpha particles.Comment: 19 pages, 2 figures, published versio
Galaxy and Apollo as a biologist-friendly interface for high-quality cooperative phage genome annotation
In the modern genomic era, scientists without extensive bioinformatic training need to apply
high-power computational analyses to critical tasks like phage genome annotation. At the
Center for Phage Technology (CPT), we developed a suite of phage-oriented tools housed
in open, user-friendly web-based interfaces. A Galaxy platform conducts computationally
intensive analyses and Apollo, a collaborative genome annotation editor, visualizes the
results of these analyses. The collection includes open source applications such as the
BLAST+ suite, InterProScan, and several gene callers, as well as unique tools developed at
the CPT that allow maximum user flexibility. We describe in detail programs for finding
Shine-Dalgarno sequences, resources used for confident identification of lysis genes such
as spanins, and methods used for identifying interrupted genes that contain frameshifts or
introns. At the CPT, genome annotation is separated into two robust segments that are facilitated through the automated execution of many tools chained together in an operatio
Meta-analysis of heterogeneous Down Syndrome data reveals consistent genome-wide dosage effects related to neurological processes
<p>Abstract</p> <p>Background</p> <p>Down syndrome (DS; trisomy 21) is the most common genetic cause of mental retardation in the human population and key molecular networks dysregulated in DS are still unknown. Many different experimental techniques have been applied to analyse the effects of dosage imbalance at the molecular and phenotypical level, however, currently no integrative approach exists that attempts to extract the common information.</p> <p>Results</p> <p>We have performed a statistical meta-analysis from 45 heterogeneous publicly available DS data sets in order to identify consistent dosage effects from these studies. We identified 324 genes with significant genome-wide dosage effects, including well investigated genes like <it>SOD1</it>, <it>APP</it>, <it>RUNX1 </it>and <it>DYRK1A </it>as well as a large proportion of novel genes (N = 62). Furthermore, we characterized these genes using gene ontology, molecular interactions and promoter sequence analysis. In order to judge relevance of the 324 genes for more general cerebral pathologies we used independent publicly available microarry data from brain studies not related with DS and identified a subset of 79 genes with potential impact for neurocognitive processes. All results have been made available through a web server under <url>http://ds-geneminer.molgen.mpg.de/</url>.</p> <p>Conclusions</p> <p>Our study represents a comprehensive integrative analysis of heterogeneous data including genome-wide transcript levels in the domain of trisomy 21. The detected dosage effects build a resource for further studies of DS pathology and the development of new therapies.</p
A Simple Model of an Oil Based Global Savings Glut - The 'China Factor' and the OPEC Cartel
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Biomarker discovery and redundancy reduction towards classification using a multi-factorial MALDI-TOF MS T2DM mouse model dataset
Diabetes like many diseases and biological processes is not mono-causal. On the one hand multifactorial studies with complex experimental design are required for its comprehensive analysis. On the other hand, the data from these studies often include a substantial amount of redundancy such as proteins that are typically represented by a multitude of peptides. Coping simultaneously with both complexities (experimental and technological) makes data analysis a challenge for Bioinformatics
Finite-size effect on two-particle production in continuous and discrete spectrum
The formalism allowing one to account for the effect of a finite space-time
extent of particle production region is given. Its applications to the lifetime
measurement of hadronic atoms produced by a high-energy beam in a thin target,
as well as to the femtoscopy techniques widely used to measure space-time
characteristics of the production processes, are discussed. Particularly, it is
found that the neglect of the finite-size effect on the pionium lifetime
measurement in the experiment DIRAC at CERN could lead to the lifetime
overestimation comparable with the 10% statistical error. The theoretical
systematic errors arising in the calculation of the finite-size effect due to
the neglect of non-equal emission times in the pair center-of-mass system, the
space-time coherence and the residual charge are shown to be negligible.Comment: LaTeX, 77 pages including 5 tables and 18 figures. Somewhat extended
version to be published in Phys. El. Part. At. Nuc
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