Cold nuclear matter effects on J/ψ yields as a function of rapidity and nuclear geometry in d+A collisions at sqrt[s(NN)]=200 GeV

We present measurements of J/ψ yields in d+Au collisions at sqrt[s(NN)]=200  GeV recorded by the PHENIX experiment and compare them with yields in p+p collisions at the same energy per nucleon-nucleon collision. The measurements cover a large kinematic range in J/ψ rapidity (-2.2<y<2.4) with high statistical precision and are compared with two theoretical models: one with nuclear shadowing combined with final state breakup and one with coherent gluon saturation effects. In order to remove model dependent systematic uncertainties we also compare the data to a simple geometric model. The forward rapidity data are inconsistent with nuclear modifications that are linear or exponential in the density weighted longitudinal thickness, such as those from the final state breakup of the bound state.

Gene expression profiling and shared promoter motif for cell wall-modifying proteins expressed in soybean cyst nematode-infected roots

We hypothesized that soybean cyst nematode (SCN; Heterodera glycines) co-opts part or all of one or more innate developmental process in soybean (Glycine max) to establish its feeding structure, syncytium, in soybean roots. The syncytium is formed within the vascular bundle by partial degradation of cell walls and membranes between adjacent parenchyma cells. A mature syncytium incorporates as many as 200 cells into one large multinucleated cell. Gene expression patterns for several cell wall-modifying proteins were compared in multiple tissues undergoing major shifts in cell wall integrity. These included SCN-colonized roots, root tips where vascular differentiation occurs, flooded roots (aerenchyma), adventitious rooting in hypocotyls, and leaf abscission zones. A search in the 5' upstream promoters of these genes identified a motif (SCNbox1: WGCATGTG) common to several genes that were up-regulated in several different tissues. The polygalacturonase 11 promoters (GmPG11a/b) include the SCNbox1 motif. The expression pattern for GmPG11a was examined further in transgenic soybean containing a PG11a promoter fused to a β-glucuronidase (GUS) reporter gene. GUS expression was highest in cells undergoing radial expansion in the stele and/or cell wall dissolution. GUS staining was not observed in cortical cells where a lateral root tip or a growing nematode emerged through the root cortex.

Abstract 869: Characterization of malignant melanoma families with CDK4 germ-line mutation

Background: CDKN2A (p16) and CDK4 are high-risk susceptibility genes for cutaneous melanoma. CDKN2A is the major identified high-risk gene and CDKN2A-mutated families have been extensively characterized. Melanoma families with CDK4 mutation are very rare. Only 10 such families have been published and a systematic investigation of their phenotype is lacking.

Aim of study: We evaluated all known CDK4-mutated families with regard to phenotypic features of their melanocytic disease. We also examined if common variants of the melanocortin-1 receptor (MC1R) gene had an effect on age of melanoma onset.

Methods: CDK4-melanoma families, previously ascertained by different research groups, were selected for this study either by contacting the authors of published papers or by requests via the GenoMEL Melanoma Genetics Consortium. Phenotypic data related to melanoma and pigmentation were collected via a standardized form. For all family members with available DNA, exon 2 of CDK4 and the complete coding region of the MC1R gene were sequenced.

Results: Thirteen CDK4 families (including three unpublished) were enrolled in the study. Altogether, 83 subjects with malignant melanoma, having a total of 125 melanomas, were verified in the pedigrees. The mean and median age of melanoma diagnosis was 38.5 years and 36.5 years, respectively. Of the 83 melanoma-positive subjects, 29 (34.9%) had multiple primary melanoma. Superficially spreading melanoma was the most common histological diagnosis (52.2%). DNA was available from 198 members of the pedigrees, and 81 tested positive for either the CDK4 R24H or R24C mutation; 117 subjects including 39 spouses tested negative. Subjects with the CDK4 mutation or with verified melanoma had a much higher prevalence of atypical nevi (79.5% and 77.2%, respectively) than CDK4-negative family members (26.0%; p&lt;0.001 for both groups). The pedigrees included only one verified case of pancreatic cancer, occurring in a non-tested subject with melanoma. There did not appear to be evidence for a predisposition to other non-melanoma cancers. The analysis of MC1R gene variants is ongoing.

Conclusion: CDK4-positive melanoma families are phenotypically similar to families with a CDKN2A mutation with regard to age of melanoma diagnosis, histological tumor type and the presence of atypical nevi/multiple melanomas. In a clinical setting, the CDK4 gene should therefore be examined if a melanoma family is negative for a CDKN2A mutation. Although based on only 13 CDK4 families, mutation carriers do not appear to have an increased predisposition to pancreatic cancer as noted in some pedigrees with CDKN2A mutations.

Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 102nd Annual Meeting of the American Association for Cancer Research; 2011 Apr 2-6; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2011;71(8 Suppl):Abstract nr 869. doi:10.1158/1538-7445.AM2011-869

LeERF-1, a novel AP2/ERF family gene within the B3 subcluster, is down-regulated by light signals in Lithospermum erythrorhizon

We previously showed that ethylene might be involved in the process of shikonin biosynthesis regulated by light signals. Here, we cloned a full-length cDNA of LeERF-1, a putative ethylene response factor gene, from Lithospermum erythrorhizon using the RACE (rapid amplification of cDNA ends) method. Phylogenetic analysis revealed that LeERF-1 was classified in the B3 subfamily, together with ERF1 and ORA59 of Arabidopsis. Heterologous expression of LeERF-1 in Arabidopsis showed that LeERF-1:eGFP fusion protein was precisely localised to the nucleus, implying that it might function as a transcription factor. Detailed expression analysis with real-time PCR showed that LeERF-1 was significantly down-regulated by white, blue and red light, although the inhibitory effect of red light was relatively weak compared to other light conditions. Tissue-specific expression analysis also indicated that LeERF-1 was dominantly expressed in the roots, which grow in soil in darkness. These patterns are all consistent with the effects of different light signals on regulating formation of shikonin and its derivatives, indicating that LeERF-1 might be a crucial positive regulator, like other B3 subfamily proteins (such as ORCA3 and ORA59), in regulating biosynthesis of secondary metabolites.

Thermal Oxidation of Amorphous Silicon-Boron Alloy

The thermal oxidation of amorphous silicon-boron alloy (prepared by low pressure chemical vapor deposition) with boron contents ranged from 0–40% at a temperature range of 25- 700 °C has been carried out. Crystalline silicon and polycrystalline boron have also been studied for comparison purposes. The resultant thin oxide overlayers were characterized by X-ray photoelectron spectroscopy. It was found that both the oxidation of Si and of B are enhanced by mixing of the two elements. The oxidation of boron is significantly slower than silicon. During oxidation of silicon-boron alloy, preferential oxidation of silicon occurs at the oxide/bulk interface and the silicon oxide overlayer advances into the bulk faster than the boron oxide.

Cross section and parity-violating spin asymmetries of W± boson production in polarized p + p collisions at sqrt[s] = 500 GeV

Large parity-violating longitudinal single-spin asymmetries A(L)(e+) = -0.86(-0.14) (+0.30) and A(L)(e-) = 0.88(-0.71) (+0.12) are observed for inclusive high transverse momentum electrons and positrons in polarized p+p collisions at a center-of-mass energy of sqrt[s] = 500 GeV with the PHENIX detector at RHIC. These e± come mainly from the decay of W± and Z0 bosons, and their asymmetries directly demonstrate parity violation in the couplings of the W± to the light quarks. The observed electron and positron yields were used to estimate W± boson production cross sections for the e± channels of σ(pp → W+ X) × BR(W+ → e+ ν(e)) = 144.1 ± 21.2(stat)(-10.3) (+3.4) (syst) ± 21.6(norm)  pb, and σ(pp → W- X) × BR(W- → e- ν[over ¯](e)) = 31.7 ± 12.1(stat)(-8.2) (+10.1) (syst) ± 4.8(norm)  pb.

Genotypes of NK cell KIR receptors, their ligands, and Fcγ receptors in the response of neuroblastoma patients to Hu14.18-IL2 immunotherapy

Response to immunocytokine (IC) therapy is dependent on natural killer cells in murine neuroblastoma (NBL) models. Furthermore, killer immunoglobulin-like receptor (KIR)/KIR-ligand mismatch is associated with improved outcome to autologous stem cell transplant for NBL. Additionally, clinical antitumor response to monoclonal antibodies has been associated with specific polymorphic-FcγR alleles. Relapsed/refractory NBL patients received the hu14.18-IL2 IC (humanized anti-GD2 monoclonal antibody linked to human IL2) in a Children's Oncology Group phase II trial. In this report, these patients were genotyped for KIR, HLA, and FcR alleles to determine whether KIR receptor-ligand mismatch or specific FcγR alleles were associated with antitumor response. DNA samples were available for 38 of 39 patients enrolled: 24 were found to have autologous KIR/KIR-ligand mismatch; 14 were matched. Of the 24 mismatched patients, 7 experienced either complete response or improvement of their disease after IC therapy. There was no response or comparable improvement of disease in patients who were matched. Thus KIR/KIR-ligand mismatch was associated with response/improvement to IC (P = 0.03). There was a trend toward patients with the FcγR2A 131-H/H genotype showing a higher response rate than other FcγR2A genotypes (P = 0.06). These analyses indicate that response or improvement of relapsed/refractory NBL patients after IC treatment is associated with autologous KIR/KIR-ligand mismatch, consistent with a role for natural killer cells in this clinical response.

On resonant scatterers as a factor limiting carrier mobility in graphene

We show that graphene deposited on a substrate has a non-negligible density of atomic scale defects. This is evidenced by a previously unnoticed D peak in the Raman spectra with intensity of ∼1% with respect to the G peak. We evaluated the effect of such impurities on electron transport by mimicking them with hydrogen adsorbates and measuring the induced changes in both mobility and Raman intensity. If the intervalley scatterers responsible for the D peak are monovalent, their concentration is sufficient to account for the limited mobilities currently achievable in graphene on a substrate.

Azimuthal anisotropy of π⁰ production in Au+Au collisions at sqrt((s)NN)=200 GeV: path-length dependence of jet quenching and the role of initial geometry

We have measured the azimuthal anisotropy of π⁰ production for 1<p(T)<18  GeV/c for Au+Au collisions at sqrt((s)NN)=200  GeV. The observed anisotropy shows a gradual decrease for 3≲p(T)≲7-10  GeV/c, but remains positive beyond 10  GeV/c. The magnitude of this anisotropy is underpredicted, up to at least ∼10  GeV/c, by current perturbative QCD (PQCD) energy-loss model calculations. An estimate of the increase in anisotropy expected from initial-geometry modification due to gluon saturation effects and fluctuations is insufficient to account for this discrepancy. Calculations that implement a path-length dependence steeper than what is implied by current PQCD energy-loss models show reasonable agreement with the data.

Density of states and zero Landau Level probed through capacitance of graphene

We report capacitors in which a finite electronic compressibility of graphene dominates the electrostatics, resulting in pronounced changes in capacitance as a function of magnetic field and carrier concentration. The capacitance measurements have allowed us to accurately map the density of states D, and compare it against theoretical predictions. Landau oscillations in D are robust and zero Landau level (LL) can easily be seen at room temperature in moderate fields. The broadening of LLs is strongly affected by charge inhomogeneity that leads to zero LL being broader than other levels.