Single nucleotide polymorphisms in uracil-processing genes, intake of one-carbon nutrients and breast cancer risk

BACKGROUND/OBJECTIVES

The misincorporation of uracil into DNA leads to genomic instability. In a previous study, some of us identified four common single nucleotide polymorphisms (SNPs) in uracil-processing genes (rs2029166 and rs7296239 in SMUG1, rs34259 in UNG and rs4775748 in DUT) that were associated with significantly altered levels of uracil in human DNA. We investigated whether any of these SNPs are associated with an altered risk of developing breast cancer and if one-carbon nutrients intake can modify their effects.

SUBJECTS/METHODS

We genotyped the four SNPs in 1077 cases of incident breast cancer and 1910 age and race-matched controls in the Western New York Exposures and Breast Cancer (WEB) Study and examined associations with breast cancer risk and interactions with intake of folate, vitamins B6 and B12.

RESULTS

After adjustment for known risk factors for breast cancer, there was increased risk of breast cancer among postmenopausal women who were heterozygous for either of the two SMUG1 SNPs (odds ratio (OR) 1.29, 95% confidence interval (CI) 1.07-1.56) and OR 1.29, 95% CI 1.07-1.55, respectively). Among premenopausal women, increased risk associated with the SMUG1 rs2029166 genotype was limited to those with low folate intake. There were no other interactions with vitamins B(6) or B(12) intake.

CONCLUSIONS

Our study suggests that the four selected SNPs are not robust determinants of breast cancer risk, but that the two SNPs in SMUG1 might modestly alter the risk of breast cancer. However, the increase in risk among heterozygotes in the two SNPs in SMUG1, which is thought to be the most active glycosylase in vivo, raises the possibility that subtle 'heterosis' effects on cancer risk might be produced by these SNPs.

Association of androgen receptor CAG repeat polymorphism with VO₂max response to hypoxic training in North China Han men

The purposes of this study were to investigate the distribution characteristics of CAG repeat polymorphism in exon 1 of androgen receptor gene and the association of CAG polymorphism with VO₂max response to hypoxic training in North China Han men. Sixty-five healthy young men completed a 30-day HiHiLo training (living high, exercise high and training low) in a simulated normobaric hypoxic environment. All subjects slept in 14.3-14.8% O₂ concentration, and participated in hypoxic training three times a week in 15.4% O₂ concentration. VO₂max (peak oxygen consumption) and body weight were measured before and after hypoxic training. A total of 15 repeat alleles were observed by CAG genotype analyze, in which (CAG)22 was most common. When using 21 and 22 alleles, respectively, as cut-off points, we found that the baseline body weight of two shorter genotype groups was significantly lower than that of longer ones, and that the ΔVO₂max and ΔrVO₂max (Δrelative value of VO₂max) of two shorter genotype groups were significantly higher than those of longer ones after hypoxic training. These findings indicated that AR CAG repeat polymorphism was associated with the exercise performance after simulated normobaric hypoxic HiHiLo training in North China Han men, and that the shorter genotypes had a better individual response to hypoxic training.

800 facets of retinal degeneration

In today's world of genomics and large computational analyses, rapid progress has been made in identifying genes associated with human retinal diseases. Nevertheless, before significant advances toward effective therapeutic intervention is made, a clearer understanding of the molecular and cellular role of these gene products in normal and diseased photoreceptor cell biology is required. Given the complexity of the vertebrate retina, these advancements are unlikely to be revealed in isolated human cell lines, but instead, will require the use of numerous model systems. Here, we describe several parallels between vertebrate and invertebrate photoreceptor cell biology that are beginning to emerge and advocate the use of Drosophila melanogaster as a powerful genetic model system for uncovering molecular mechanisms of human retinal pathologies, in particular photoreceptor neurodegeneration.

Phosphatidic acid mediates salt stress response by regulation of MPK6 in Arabidopsis thaliana

• Phospholipase D (PLD) hydrolyzes phospholipids to produce phosphatidic acid (PA) and a head group, and is involved in the response to various environmental stresses, including salinity. Here, we determined the roles of PLDα and PA in the mediation of salt (NaCl)-stress signaling through the regulation of mitogen-activated protein kinase (MAPK or MPK) in Arabidopsis thaliana. • NaCl-induced changes in the content and composition of PA were quantitatively profiled by electrospray ionization-tandem mass spectrometry (ESI-MS/MS). A specific PA species (a MAPK 16:0-18:2 PA), which was increased in abundance by exposure to NaCl, bound to a MPK6, according to filter binding and ELISA. The effect of PA on MPK6 activity was tested using in-gel analysis. • 16:0-18:2 PA stimulated the activity of MPK6 immunoprecipitated from Arabidopsis leaf extracts. Treatment with NaCl induced a transient activation of MPK6 in wild-type plant, but the activation was abolished in the pldα1 plant mutant. A plasma membrane Na(+)/H(+) antiporter (SOS1) was identified as a downstream target of MPK6. MPK6 phosphorylated the C-terminal fragment of SOS1. The MPK6 phosphorylation of SOS1 was stimulated by treatment with NaCl, as well as directly by PA. • These results suggest that PA plays a critical role in coupling MAPK cascades in response to salt stress.

Comparative genomics-guided loop-mediated isothermal amplification for characterization of Pseudomonas syringae pv. phaseolicola

AIMS

To design and evaluate a loop-mediated isothermal amplification (LAMP) protocol by combining comparative genomics and bioinformatics for characterization of Pseudomonas syringae pv. phaseolicola (PSP), the causal agent of halo blight disease of bean (Phaseolus vulgaris L.).

METHODS AND RESULTS

Genomic sequences of Pseudomonas syringae pathovars, P. fluorescens and P. aeruginosa were analysed using multiple sequence alignment. A pathovar-specific region encoding pathogenicity-related secondary metabolites in the PSP genome was targeted for developing a LAMP assay. The final assay targeted a polyketide synthase gene, and readily differentiated PSP strains from other Pseudomonas syringae pathovars and other Pseudomonas species, as well as other plant pathogenic bacteria, e.g. species of Pectobacterium, Erwinia and Pantoea.

CONCLUSION

A LAMP assay has been developed for rapid and specific characterization and identification of PSP from other pathovars of P. syringae and other plant-associated bacteria.

SIGNIFICANCE AND IMPACT OF THE STUDY

This paper describes an approach combining a bioinformatic data mining strategy and comparative genomics with the LAMP technology for characterization and identification of a plant pathogenic bacterium. The LAMP assay could serve as a rapid protocol for microbial identification and detection with significant applications in agriculture and environmental sciences.

Activation of liver X receptors inhibits pancreatic islet beta cell proliferation through cell cycle arrest

AIMS/HYPOTHESIS

Liver X receptors (LXRs) are important transcriptional regulators of lipid homeostasis and proliferation in several cell types. However, the roles of LXRs in pancreatic beta cells have not been fully established. The aim of this study was to investigate the effects of LXRs on pancreatic beta cell proliferation.

METHODS

Gene expression was analysed using real-time RT-PCR. Transient transfection and reporter gene assays were used to determine the transcriptional activity of LXRs in pancreatic beta cells. Cell viability and proliferation were analysed using 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT), DNA fluorometric, BrdU labelling and [(3)H]thymidine incorporation assays. Cell cycle distribution was investigated by flow cytometry analysis. Adenovirus-based RNA interference was used to knockdown LXRalpha, LXRbeta and p27 in MIN6 cells and mouse islets.

RESULTS

We found that both Lxralpha (also known as Nr1h3) and Lxrbeta (also known as Nr1h2) were expressed and transactivated the LXR response element in HIT-T15 and MIN6 cells. Activation of LXRs dose-dependently inhibited pancreatic beta cell viability and proliferation. This was accompanied by beta cell cycle arrest at the G1 phase. Furthermore, LXR activation increased levels of the p27 protein by inhibiting its degradation. Knockdown of p27 reversed these effects of LXR activation on growth inhibition and cell cycle arrest.

CONCLUSIONS/INTERPRETATION

Our observations indicate that LXR activation inhibits pancreatic beta cell proliferation through cell cycle arrest. A well-known regulator of pancreatic beta cell cycle progression, p27, is upregulated and mediates the effects of LXRs on growth inhibition in beta cells. These observations suggest the involvement of aberrant activation of LXR in beta cell mass inadequacy, which is an important step in the development of type 2 diabetes.

Anomalous line shape of the cross section for e{+}e{-}--> hadrons in the center-of-mass energy region between 3.650 and 3.872 GeV

We observe an obvious anomalous line shape of the e;{+}e;{-}--> hadrons total cross sections in the energy region between 3.700 and 3.872 GeV. It is inconsistent with the explanation for only one simple psi(3770) resonance with a statistical significance of 7sigma. The anomalous line shape may be explained by two possible enhancements of the inclusive hadron production near the center-of-mass energies of 3.764 and 3.779 GeV, indicating that either there is likely a new structure in addition to the psi(3770) resonance around 3.773 GeV, or there are some physics effects reflecting the DD[over ] production dynamics.

Segmentation of touching cell nuclei using gradient flow tracking

Reliable cell nuclei segmentation is an important yet unresolved problem in biological imaging studies. This paper presents a novel computerized method for robust cell nuclei segmentation based on gradient flow tracking. This method is composed of three key steps: (1) generate a diffused gradient vector flow field; (2) perform a gradient flow tracking procedure to attract points to the basin of a sink; and (3) separate the image into small regions, each containing one nucleus and nearby peripheral background, and perform local adaptive thresholding in each small region to extract the cell nucleus from the background. To show the generality of the proposed method, we report the validation and experimental results using microscopic image data sets from three research labs, with both over-segmentation and under-segmentation rates below 3%. In particular, this method is able to segment closely juxtaposed or clustered cell nuclei, with high sensitivity and specificity in different situations.

Search for the invisible decay of J/psi in psi(2S) --> pi(+)pi(-) J/psi

Using psi(2S) --> pi(+)pi(-) J/psi events in a sample of 14.0 x 10(6) psi(2S) decays collected with the BES-II detector, a search for the decay of the J/psi to invisible final states is performed. No signal is found, and an upper limit at the 90% confidence level is determined to be 1.2 x 10(-2) for the ratio B(J/psi --> invisible)/B(J/psi-->mu(+)mu(-)). This is the first search for J/psi decays to invisible final states.

Observation of Y(2175) in J/psi --> etaphif0 (980)

The decays of J/psi --> etaphif(0)(980)[eta --> gammagamma, phi --> K(+) K(-), f(0)(980) --> pi(+)pi(-)] are analyzed using a sample of 5.8 x 10(7) J/psi events collected with the BESII detector at the Beijing Electron-Positron Collider. A structure at around 2.18 GeV/c(2) with about 5 sigma significance is observed in the phif(0)(980) invariant mass spectrum. A fit with a Breit-Wigner function gives the peak mass and width of m = 2.186+/-0.010(stat)+/-0.006(syst) GeV/c(2) and Gamma = 0.065+/-0.023(stat)+/-0.017(syst) GeV/c(2), respectively, which are consistent with those of Y(2175), observed by the BABAR Collaboration in the initial-state radiation process e(+)e(-) --> gamma(ISR) phif(0)(980). The production branching ratio is determined to be Br(J/psi --> etaY(2175))Br(Y(2175)- -> phif(0)(980))Br(f(0)(980) --> pi(+)pi(-)) = [3.23+/-0.75(stat)+/-0.73(syst)] x 10(-4), assuming that the Y(2175) is a 1(--) state.

A dynamic channel assignment policy through Q-learning

One of the fundamental issues in the operation of a mobile communication system is the assignment of channels to cells and to calls. Since the number of channels allocated to a mobile communication system is limited, efficient utilization of these communication channels by using efficient channel assignment strategies is not only desirable but also imperative. This paper presents a novel approach to solving the dynamic channel assignment (DCA) problem by using a form of realtime reinforcement learning known as Q-learning in conjunction with neural network representation. Instead of relying on a known teacher, the system is designed to learn an optimal channel assignment policy by directly interacting with the mobile communication environment. The performance of the Q-learning-based DCA was examined by extensive simulation studies on a 49-cell mobile communication system under various conditions. Comparative studies with the fixed channel assignment (FCA) scheme and one of the best dynamic channel assignment strategies, MAXAVAIL, have revealed that the proposed approach is able to perform better than the FCA in various situations and capable of achieving a performance similar to that achieved by the MAXIAVIAL, but with a significantly reduced computational complexity.