Indicators of replicative damage in equine tendon fibroblast monolayers

<p>Background: Superficial digital flexor tendon (SDFT) injuries of horses usually follow cumulative matrix microdamage; it is not known why the reparative abilities of tendon fibroblasts are overwhelmed or subverted. Relevant in vitro studies of this process require fibroblasts not already responding to stresses caused by the cell culture protocols. We investigated indicators of replicative damage in SDFT fibroblast monolayers, effects of this on their reparative ability, and measures that can be taken to reduce it.</p> <p>Results: We found significant evidence of replicative stress, initially observing consistently large numbers of binucleate (BN) cells. A more variable but prominent feature was the presence of numerous gammaH2AX (γH2AX) puncta in nuclei, this being a histone protein that is phosphorylated in response to DNA double-stranded breaks (DSBs). Enrichment for injury detection and cell cycle arrest factors (p53 (ser15) and p21) occurred most frequently in BN cells; however, their numbers did not correlate with DNA damage levels and it is likely that the two processes have different causative mechanisms. Such remarkable levels of injury and binucleation are usually associated with irradiation, or treatment with cytoskeletal-disrupting agents.</p> <p>Both DSBs and BN cells were greatest in subconfluent (replicating) monolayers. The DNA-damaged cells co-expressed the replication markers TPX2/repp86 and centromere protein F. Once damaged in the early stages of culture establishment, fibroblasts continued to express DNA breaks with each replicative cycle. However, significant levels of cell death were not measured, suggesting that DNA repair was occurring. Comet assays showed that DNA repair was delayed in proportion to levels of genotoxic stress.</p> <p>Conclusions: Researchers using tendon fibroblast monolayers should assess their “health” using γH2AX labelling. Continued use of early passage cultures expressing initially high levels of γH2AX puncta should be avoided for mechanistic studies and ex-vivo therapeutic applications, as this will not be resolved with further replicative cycling. Low density cell culture should be avoided as it enriches for both DNA damage and mitotic defects (polyploidy). As monolayers differing only slightly in baseline DNA damage levels showed markedly variable responses to a further injury, studies of effects of various stressors on tendon cells must be very carefully controlled.</p&gt

A high-resolution 6.0-megabase transcript map of the type 2 diabetes susceptibility region on human chromosome 20

Recent linkage studies and association analyses indicate the presence of at least one type 2 diabetes susceptibility gene in human chromosome region 20q12-q13.1. We have constructed a high-resolution 6.0-megabase (Mb) transcript map of this interval using two parallel, complementary strategies to construct the map. We assembled a series of bacterial artificial chromosome (BAC) contigs from 56 overlapping BAC clones, using STS/marker screening of 42 genes, 43 ESTs, 38 STSs, 22 polymorphic, and 3 BAC end sequence markers. We performed map assembly with GraphMap, a software program that uses a greedy path searching algorithm, supplemented with local heuristics. We anchored the resulting BAC contigs and oriented them within a yeast artificial chromosome (YAC) scaffold by observing the retention patterns of shared markers in a panel of 21 YAC clones. Concurrently, we assembled a sequence-based map from genomic sequence data released by the Human Genome Project, using a seed-and-walk approach. The map currently provides near-continuous coverage between SGC32867 and WI-17676 (∼ 6.0 Mb). EST database searches and genomic sequence alignments of ESTs, mRNAs, and UniGene clusters enabled the annotation of the sequence interval with experimentally confirmed and putative transcripts. We have begun to systematically evaluate candidate genes and novel ESTs within the transcript map framework. So far, however, we have found no statistically significant evidence of functional allelic variants associated with type 2 diabetes. The combination of the BAC transcript map, YAC-to-BAC scaffold, and reference Human Genome Project sequence provides a powerful integrated resource for future genomic analysis of this region

Second-order corrections to neutrino two-flavor oscillation parameters in the wave packet approach

We report about an analytic study involving the {\em intermediate} wave packet formalism for quantifying the physically relevant information which appear in the neutrino two-flavor conversion formula and help us to obtain more precise limits and ranges for neutrino flavor oscillation. By following the sequence of analytic approximations where we assume a strictly peaked momentum distribution and consider the second-order corrections in a power series expansion of the energy, we point out a {\em residual} time-dependent phase which, coupled with the {\em spreading/slippage} effects, can subtly modify the neutrino oscillation parameters and limits. Such second-order effects are usually ignored in the relativistic wave packet treatment, but they present an evident dependence on the propagation regime so that some small modifications to the oscillation pattern, even in the ultra-relativistic limit, can be quantified. These modifications are implemented in the confront with the neutrino oscillation parameter range (mass-squared difference \Delta m^{\2} and the mixing-angle $\theta$) where we assume the same wave packet parameters previously noticed in the literature in a kind of {\em toy model} for some reactor experiments. Generically speaking, our analysis parallels the recent experimental purposes which concern with higher precision parameter measurements. To summarize, we show that the effectiveness of a more accurate determination of \Delta m^{\2} and $\theta$ depends on the wave packet width $a$ and on the averaged propagating energy flux $\bar{E}$ which still correspond to open variables for some classes of experiments. \Comment: 25 pages, 5 figure

Spatial Periodicity of Galaxy Number Counts, CMB Anisotropy, and SNIa Hubble Diagram Based on the Universe Accompanied by a Non-Minimally Coupled Scalar Field

We have succeeded in establishing a cosmological model with a non-minimally coupled scalar field $\phi$ that can account not only for the spatial periodicity or the {\it picket-fence structure} exhibited by the galaxy $N$-$z$ relation of the 2dF survey but also for the spatial power spectrum of the cosmic microwave background radiation (CMB) temperature anisotropy observed by the WMAP satellite. The Hubble diagram of our model also compares well with the observation of Type Ia supernovae. The scalar field of our model universe starts from an extremely small value at around the nucleosynthesis epoch, remains in that state for sufficiently long periods, allowing sufficient time for the CMB temperature anisotropy to form, and then starts to grow in magnitude at the redshift $z$ of $\sim 1$, followed by a damping oscillation which is required to reproduce the observed picket-fence structure of the $N$-$z$ relation. To realize such behavior of the scalar field, we have found it necessary to introduce a new form of potential $V(\phi)\propto \phi^2\exp(-q\phi^2)$, with $q$ being a constant. Through this parameter $q$, we can control the epoch at which the scalar field starts growing.Comment: 19 pages, 18 figures, Accepted for publication in Astrophysics & Space Scienc

Big bounce from spin and torsion

The Einstein-Cartan-Sciama-Kibble theory of gravity naturally extends general relativity to account for the intrinsic spin of matter. Spacetime torsion, generated by spin of Dirac fields, induces gravitational repulsion in fermionic matter at extremely high densities and prevents the formation of singularities. Accordingly, the big bang is replaced by a bounce that occurred when the energy density $\epsilon\propto gT^4$ was on the order of $n^2/m_\textrm{Pl}^2$ (in natural units), where $n\propto gT^3$ is the fermion number density and $g$ is the number of thermal degrees of freedom. If the early Universe contained only the known standard-model particles ($g\approx 100$), then the energy density at the big bounce was about 15 times larger than the Planck energy. The minimum scale factor of the Universe (at the bounce) was about $10^{32}$ times smaller than its present value, giving \approx 50 \mum. If more fermions existed in the early Universe, then the spin-torsion coupling causes a bounce at a lower energy and larger scale factor. Recent observations of high-energy photons from gamma-ray bursts indicate that spacetime may behave classically even at scales below the Planck length, supporting the classical spin-torsion mechanism of the big bounce. Such a classical bounce prevents the matter in the contracting Universe from reaching the conditions at which a quantum bounce could possibly occur.Comment: 6 pages; published versio

Photon mixing in universes with large extra-dimensions

In presence of a magnetic field, photons can mix with any particle having a two-photon vertex. In theories with large compact extra-dimensions, there exists a hierachy of massive Kaluza-Klein gravitons that couple to any photon entering a magnetic field. We study this mixing and show that, in comparison with the four dimensional situation where the photon couples only to the massless graviton, the oscillation effect may be enhanced due to the existence of a large number of Kaluza-Klein modes. We give the conditions for such an enhancement and then investigate the cosmological and astrophysical consequences of this phenomenon; we also discuss some laboratory experiments. Axions also couple to photons in the same way; we discuss the effect of the existence of bulk axions in universes with large extra-dimensions. The results can also be applied to neutrino physics with extra-dimensions.Comment: 41 pages, LaTex, 6 figure

Best Practices and Joint Calling of the HumanExome BeadChip: The CHARGE Consortium

Genotyping arrays are a cost effective approach when typing previously-identified genetic polymorphisms in large numbers of samples. One limitation of genotyping arrays with rare variants (e.g., minor allele frequency [MAF] <0.01) is the difficulty that automated clustering algorithms have to accurately detect and assign genotype calls. Combining intensity data from large numbers of samples may increase the ability to accurately call the genotypes of rare variants. Approximately 62,000 ethnically diverse samples from eleve

Genetic loci associated with plasma phospholipid N-3 fatty acids: A Meta-Analysis of Genome-Wide association studies from the charge consortium

Long-chain n-3 polyunsaturated fatty acids (PUFAs) can derive from diet or from α-linolenic acid (ALA) by elongation and desaturation. We investigated the association of common genetic variation with plasma phospholipid levels of the four major n-3 PUFAs by performing genome-wide association studies in five population-based cohorts comprising 8,866 subjects of European ancestry. Minor alleles of SNPs in FADS1 and FADS2 (desaturases) were associated with higher levels of ALA (p = 3×10-64) and lower levels of eicosapentaenoic acid (EPA, p = 5×10-58) and docosapentaenoic acid (DPA, p = 4×10-154). Minor alleles of SNPs in ELOVL2 (elongase) were associated with higher EPA (p = 2×10-12) and DPA (p = 1×10-43) and lower docosahexaenoic acid (DHA, p = 1×10-15). In addition to genes in the n-3 pathway, we identified a novel association of DPA with several SNPs in GCKR (glucokinase regulator, p = 1×10-8). We observed a weaker association between ALA and EPA among carriers of the minor allele of a representative SNP in FADS2 (rs1535), suggesting a lower rate of ALA-to-EPA conversion in these subjects. In samples of African, Chinese, and Hispanic ancestry, associations of n-3 PUFAs were similar with a representative SNP in FADS1 but less consistent with a representative SNP in ELOVL2. Our findings show that common variation in n-3 metabolic pathway genes and in GCKR influences plasma phospholipid levels of n-3 PUFAs in populations of European ancestry and, for FADS1, in other ancestries