What´s floating on my plasma?

We report on a preanalytical issue we encountered during routine clinical chemistry analyses, potentially leading to deviated analysis results and believe that it might help other laboratories to overcome similar problems. In a heparin-gel tube we measured an implausible glucose value of 0.06 mmol/L. Re-measurement of the same sample resulted in a glucose value of 5.4 mmol/L. After excluding an analytical error, we inspected the sample closer and found a white material as well as fatty droplets floating on the surface of the plasma tube. Evaluation of these structures revealed that the white particulate matter (WPM) consisted of fibrinogen, platelets and leukocytes and the fatty droplets most probably originated from the separator gel. We concluded that these structures formed a temporary clot in the instruments pipetting needle thereby altering the sampling volume and subsequently the measured glucose value. The formation of WPM might be attributable to high speed centrifugation, high cholesterol levels, the gel formulation or a combination of several issues such as temperature, heparin concentration, pH and patient-specific factors. The gel droplets were most probably caused by an aberrant gel formulation in combination with an improper storage of the empty tubes on the wards prior to phlebotomy. After adding an additional instrument cleansing cycle and changing to another batch of heparin tubes the problems could be significantly reduced

A new measurement of the properties of the rare decay K -> pi+ e+ e-

A large low-background sample of events (10300) has been collected for the rare decay of kaons in flight K+ -> pi+ e+ e- by experiment E865 at the Brookhaven AGS. The decay products were accepted by a broad band high-resolution charged particle spectrometer with particle identification. The branching ratio (2.94 +- 0.05(stat.) +- 0.13(syst.) +- 0.05(model))*10**{-7} was determined normalizing to events from the decay chain K+ -> pi+ pi0; pi0 -> e+ e- gamma. From the analysis of the decay distributions the vector nature of this decay is firmly established now, and limits on scalar and tensor contributions are deduced. From the (e+ e-) invariant mass distribution the decay form factor f(z)=f0(1+ delta*z) (z=M(ee)**2/m(K)**2) is determined with delta=2.14 +- 0.13 +- 0.15. Chiral QCD perturbation theory predictions for the form factor are also tested, and terms beyond leading order O(p**4) are found to be important.Comment: 4 pages, 5 figure

A Quintessentially Geometric Model

We consider string inspired cosmology on a solitary $D3$-brane moving in the background of a ring of branes located on a circle of radius $R$. The motion of the $D3$-brane transverse to the plane of the ring gives rise to a radion field which can be mapped to a massive non-BPS Born-Infeld type field with a cosh potential. For certain bounds of the brane tension we find an inflationary phase is possible, with the string scale relatively close to the Planck scale. The relevant perturbations and spectral indices are all well within the expected observational bounds. The evolution of the universe eventually comes to be dominated by dark energy, which we show is a late time attractor of the model. However we also find that the equation of state is time dependent, and will lead to late time Quintessence.Comment: 11 pages, 3 figures. References and comments adde

Dark Energy from structure: a status report

The effective evolution of an inhomogeneous universe model in any theory of gravitation may be described in terms of spatially averaged variables. In Einstein's theory, restricting attention to scalar variables, this evolution can be modeled by solutions of a set of Friedmann equations for an effective volume scale factor, with matter and backreaction source terms. The latter can be represented by an effective scalar field (`morphon field') modeling Dark Energy. The present work provides an overview over the Dark Energy debate in connection with the impact of inhomogeneities, and formulates strategies for a comprehensive quantitative evaluation of backreaction effects both in theoretical and observational cosmology. We recall the basic steps of a description of backreaction effects in relativistic cosmology that lead to refurnishing the standard cosmological equations, but also lay down a number of challenges and unresolved issues in connection with their observational interpretation. The present status of this subject is intermediate: we have a good qualitative understanding of backreaction effects pointing to a global instability of the standard model of cosmology; exact solutions and perturbative results modeling this instability lie in the right sector to explain Dark Energy from inhomogeneities. It is fair to say that, even if backreaction effects turn out to be less important than anticipated by some researchers, the concordance high-precision cosmology, the architecture of current N-body simulations, as well as standard perturbative approaches may all fall short in correctly describing the Late Universe.Comment: Invited Review for a special Gen. Rel. Grav. issue on Dark Energy, 59 pages, 2 figures; matches published versio

Sequencing of BAC pools by different next generation sequencing platforms and strategies

<p>Abstract</p> <p>Background</p> <p>Next generation sequencing of BACs is a viable option for deciphering the sequence of even large and highly repetitive genomes. In order to optimize this strategy, we examined the influence of read length on the quality of Roche/454 sequence assemblies, to what extent Illumina/Solexa mate pairs (MPs) improve the assemblies by scaffolding and whether barcoding of BACs is dispensable.</p> <p>Results</p> <p>Sequencing four BACs with both FLX and Titanium technologies revealed similar sequencing accuracy, but showed that the longer Titanium reads produce considerably less misassemblies and gaps. The 454 assemblies of 96 barcoded BACs were improved by scaffolding 79% of the total contig length with MPs from a non-barcoded library.</p> <p>Assembly of the unmasked 454 sequences without separation by barcodes revealed chimeric contig formation to be a major problem, encompassing 47% of the total contig length. Masking the sequences reduced this fraction to 24%.</p> <p>Conclusion</p> <p>Optimal BAC pool sequencing should be based on the longest available reads, with barcoding essential for a comprehensive assessment of both repetitive and non-repetitive sequence information. When interest is restricted to non-repetitive regions and repeats are masked prior to assembly, barcoding is non-essential. In any case, the assemblies can be improved considerably by scaffolding with non-barcoded BAC pool MPs.</p

Symmetry Breaking Boundary States and Defect Lines

We present a large and universal class of new boundary states which break part of the chiral symmetry in the underlying bulk theory. Our formulas are based on coset constructions and they can be regarded as a non-abelian generalization of the ideas that were used by Maldacena, Moore and Seiberg to build new boundary states for SU(N). We apply our expressions to construct defect lines joining two conformal field theories with possibly different central charge. Such defects can occur e.g. in the AdS/CFT correspondence when branes extend to the boundary of the AdS-space.Comment: 36 pages, LaTeX, 1 figure, V1: typos corrected and references added, v2: we added a short remark concerning the geometry of symmetry breaking D-branes in group manifold

Expression of G protein-coupled receptors and related proteins in HEK293, AtT20, BV2, and N18 cell lines as revealed by microarray analysis

<p>Abstract</p> <p>Background</p> <p>G protein coupled receptors (GPCRs) are one of the most widely studied gene superfamilies. Thousands of GPCR research studies have utilized heterologous expression systems such as human embryonic kidney cells (HEK293). Though often treated as 'blank slates', these cell lines nevertheless endogenously express GPCRs and related signaling proteins. The outcome of a given GPCR study can be profoundly influenced by this largely unknown complement of receptors and/or signaling proteins. Little easily accessible information exists that describes the expression profiles of the GPCRs in cell lines. What is accessible is often limited in scope - of the hundreds of GPCRs and related proteins, one is unlikely to find information on expression of more than a dozen proteins in a given cell line. Microarray technology has allowed rapid analysis of mRNA levels of thousands of candidate genes, but though often publicly available, the results can be difficult to efficiently access or even to interpret.</p> <p>Results</p> <p>To bridge this gap, we have used microarrays to measure the mRNA levels of a comprehensive profile of non-chemosensory GPCRs and over a hundred GPCR signaling related gene products in four cell lines frequently used for GPCR research: HEK293, AtT20, BV2, and N18.</p> <p>Conclusions</p> <p>This study provides researchers an easily accessible mRNA profile of the endogenous signaling repertoire that these four cell lines possess. This will assist in choosing the most appropriate cell line for studying GPCRs and related signaling proteins. It also provides a better understanding of the potential interactions between GPCRs and those signaling proteins.</p

Complete Genome Sequence of Mycoplasma suis and Insights into Its Biology and Adaption to an Erythrocyte Niche

Mycoplasma suis, the causative agent of porcine infectious anemia, has never been cultured in vitro and mechanisms by which it causes disease are poorly understood. Thus, the objective herein was to use whole genome sequencing and analysis of M. suis to define pathogenicity mechanisms and biochemical pathways. M. suis was harvested from the blood of an experimentally infected pig. Following DNA extraction and construction of a paired end library, whole-genome sequencing was performed using GS-FLX (454) and Titanium chemistry. Reads on paired-end constructs were assembled using GS De Novo Assembler and gaps closed by primer walking; assembly was validated by PFGE. Glimmer and Manatee Annotation Engine were used to predict and annotate protein-coding sequences (CDS). The M. suis genome consists of a single, 742,431 bp chromosome with low G+C content of 31.1%. A total of 844 CDS, 3 single copies, unlinked rRNA genes and 32 tRNAs were identified. Gene homologies and GC skew graph show that M. suis has a typical Mollicutes oriC. The predicted metabolic pathway is concise, showing evidence of adaptation to blood environment. M. suis is a glycolytic species, obtaining energy through sugars fermentation and ATP-synthase. The pentose-phosphate pathway, metabolism of cofactors and vitamins, pyruvate dehydrogenase and NAD+ kinase are missing. Thus, ribose, NADH, NADPH and coenzyme A are possibly essential for its growth. M. suis can generate purines from hypoxanthine, which is secreted by RBCs, and cytidine nucleotides from uracil. Toxins orthologs were not identified. We suggest that M. suis may cause disease by scavenging and competing for host' nutrients, leading to decreased life-span of RBCs. In summary, genome analysis shows that M. suis is dependent on host cell metabolism and this characteristic is likely to be linked to its pathogenicity. The prediction of essential nutrients will aid the development of in vitro cultivation systems

Construction of a map-based reference genome sequence for barley, Hordeum vulgare L.

Barley (Hordeum vulgare L.) is a cereal grass mainly used as animal fodder and raw material for the malting industry. The map-based reference genome sequence of barley cv. `Morex' was constructed by the International Barley Genome Sequencing Consortium (IBSC) using hierarchical shotgun sequencing. Here, we report the experimental and computational procedures to (i) sequence and assemble more than 80,000 bacterial artificial chromosome (BAC) clones along the minimum tiling path of a genome-wide physical map, (ii) find and validate overlaps between adjacent BACs, (iii) construct 4,265 non-redundant sequence scaffolds representing clusters of overlapping BACs, and (iv) order and orient these BAC clusters along the seven barley chromosomes using positional information provided by dense genetic maps, an optical map and chromosome conformation capture sequencing (Hi-C). Integrative access to these sequence and mapping resources is provided by the barley genome explorer (BARLEX).Peer reviewe