Genetic Variants of PTPN2 are Associated with Lung Cancer Risk: a Re-Analysis of Eight GWASs in the TRICL-ILCCO Consortium

The T-cell protein tyrosine phosphatase (TCPTP) pathway consists of signaling events mediated by TCPTP. Mutations and genetic variants of some genes in the TCPTP pathway are associated with lung cancer risk and survival. In the present study, we first investigated associations of 5,162 single nucleotide polymorphisms (SNPs) in 43 genes of this TCPTP pathway with lung cancer risk by using summary data of six published genome-wide association studies (GWAS) of 12,160 cases and 16,838 controls. We identified 11 independent SNPs in eight genes after correction for multiple comparisons by a false discovery rate \u3c 0.20. Then, we performed in silico functional analyses for these 11 SNPs by eQTL analysis, two of which, PTPN2 SNPs rs2847297 and rs2847282, were chosen as tagSNPs. We further included two additional GWAS datasets of Harvard University (984 cases and 970 controls) and deCODE (1,319 cases and 26,380 controls), and the overall effects of these two SNPs among all eight GWAS studies remained significant (OR = 0.95, 95% CI = 0.92–0.98, and P = 0.004 for rs2847297; OR = 0.95, 95% CI = 0.92–0.99, and P = 0.009 for rs2847282). In conclusion, the PTPN2 rs2847297 and rs2847282 may be potential susceptible loci for lung cancer risk

Discovery and identification of potential biomarkers of pediatric Acute Lymphoblastic Leukemia

<p>Abstract</p> <p>Background</p> <p>Acute lymphoblastic leukemia (ALL) is a common form of cancer in children. Currently, bone marrow biopsy is used for diagnosis. Noninvasive biomarkers for the early diagnosis of pediatric ALL are urgently needed. The aim of this study was to discover potential protein biomarkers for pediatric ALL.</p> <p>Methods</p> <p>Ninety-four pediatric ALL patients and 84 controls were randomly divided into a "training" set (45 ALL patients, 34 healthy controls) and a test set (49 ALL patients, 30 healthy controls and 30 pediatric acute myeloid leukemia (AML) patients). Serum proteomic profiles were measured using surface-enhanced laser desorption/ionization-time-of-flight mass spectroscopy (SELDI-TOF-MS). A classification model was established by Biomarker Pattern Software (BPS). Candidate protein biomarkers were purified by HPLC, identified by LC-MS/MS and validated using ProteinChip immunoassays.</p> <p>Results</p> <p>A total of 7 protein peaks (9290 m/z, 7769 m/z, 15110 m/z, 7564 m/z, 4469 m/z, 8937 m/z, 8137 m/z) were found with differential expression levels in the sera of pediatric ALL patients and controls using SELDI-TOF-MS and then analyzed by BPS to construct a classification model in the "training" set. The sensitivity and specificity of the model were found to be 91.8%, and 90.0%, respectively, in the test set. Two candidate protein peaks (7769 and 9290 m/z) were found to be down-regulated in ALL patients, where these were identified as platelet factor 4 (PF4) and pro-platelet basic protein precursor (PBP). Two other candidate protein peaks (8137 and 8937 m/z) were found up-regulated in the sera of ALL patients, and these were identified as fragments of the complement component 3a (C3a).</p> <p>Conclusion</p> <p>Platelet factor (PF4), connective tissue activating peptide III (CTAP-III) and two fragments of C3a may be potential protein biomarkers of pediatric ALL and used to distinguish pediatric ALL patients from healthy controls and pediatric AML patients. Further studies with additional populations or using pre-diagnostic sera are needed to confirm the importance of these findings as diagnostic markers of pediatric ALL.</p

Genetics of Resistance to Common Root Rot (Spot Blotch), Fusarium Crown Rot, and Sharp Eyespot in Wheat

Due to soil changes, high density planting, and the use of straw-returning methods, wheat common root rot (spot blotch), Fusarium crown rot (FCR), and sharp eyespot (sheath blight) have become severe threats to global wheat production. Only a few wheat genotypes show moderate resistance to these root and crown rot fungal diseases, and the genetic determinants of wheat resistance to these devastating diseases are poorly understood. This review summarizes recent results of genetic studies of wheat resistance to common root rot, Fusarium crown rot, and sharp eyespot. Wheat germplasm with relatively higher resistance are highlighted and genetic loci controlling the resistance to each disease are summarized

Microwave Synthesis and High‐Mobility Charge Transport of Carbon‐Nanotube‐in‐Perovskite Single Crystals

Organolead trihalide perovskites have emerged as a new class of competitive solution-processed semiconductors due to their unique optoelectronic properties. However, poor ambient stability and charge transport are the Achilles’ heel of hybrid perovskites, thus limiting their applications. In this work, microwave-assisted synthesis is applied for the first time to rapidly grow perovskite single crystals embedded with single-wall carbon nanotubes. These nanotube-in-perovskite single crystals are endowed with a carrier mobility one order of magnitude higher than the pure counterpart and the related photodetectors show an ultrafast photo-response speed (5 and 80 ns for rise and decay time, respectively). The fast and uniform heating of microwave irradiation facilitates the synthesis of ambient-stable crystals with nanoscale additives, paving the way to creating a wide range of mixed-dimensional perovskite-based nanocomposites with optimal properties and device performance

Wheat TaRab7 GTPase Is Part of the Signaling Pathway in Responses to Stripe Rust and Abiotic Stimuli

Small GTP-binding proteins function as regulators of specific intercellular fundamental biological processes. In this study, a small GTP-binding protein Rab7 gene, designated as TaRab7, was identified and characterized from a cDNA library of wheat leaves infected with Puccinia striiformis f. sp. tritici (Pst) the wheat stripe rust pathogen. The gene was predicted to encode a protein of 206 amino acids, with a molecular mass of 23.13 KDa and an isoeletric point (pI) of 5.13. Further analysis revealed the presence of a conserved signature that is characteristic of Rab7, and phylogenetic analysis demonstrated that TaRab7 has the highest similarity to a small GTP binding protein gene (BdRab7-like) from Brachypodium distachyon. Quantitative real-time PCR assays revealed that the expression of TaRab7 was higher in the early stage of the incompatible interactions between wheat and Pst than in the compatible interaction, and the transcription level of TaRab7 was also highly induced by environmental stress stimuli. Furthermore, knocking down TaRab7 expression by virus induced gene silencing enhanced the susceptibility of wheat cv. Suwon 11 to an avirulent race CYR23. These results imply that TaRab7 plays an important role in the early stage of wheat-stripe rust fungus interaction and in stress tolerance

Why Can a Large City Like Qinhuangdao Not Accommodate a Small Individual Venture?

Hebei Daily >b>editor's note:>/b> Peasants going into the cities to go into business or the service professions is an inevitable trend that will bring prosperity to town and country and eventually solve the problem of feeding and clothing China's 800 million peasants. Allowing them to do so is a major policy decision of the party's Central Committee. At present, all localities, from municipalities directly administered by the central government down to counties and small towns, have opened their doors to this practice and are creating the necessary conditions for it. Qinhuangdao seems to be the only exception. As large as it is, it cannot even tolerate a peasant who sells meat dumplings. The city may truly be described as an iron-walled city with an impenetrable defense.

Partially linear single-index beta regression model and score test

An important model in handling the multivariate data is the partially linear single-index regression model with a very flexible distribution--beta distribution, which is commonly used to model data restricted to some open intervals on the line. In this paper, the score test is extended to the partially linear single-index beta regression model. The penalized likelihood estimation based on P-spline is proposed. Based on the estimation, the score test statistics about varying dispersion parameter is given. Its asymptotical property is investigated. Both simulated examples are used to illustrate our proposed methods.Partially linear single-index model Beta regression P-spline Penalized likelihood estimation Score test

Mineralogy and Geochemistry of the Upper Ordovician and Lower Silurian Wufeng-Longmaxi Shale on the Yangtze Platform, South China: Implications for Provenance Analysis and Shale Gas Sweet-Spot Interval

The sediment provenance influences the formation of the shale gas sweet-spot interval of the Upper Ordovician&ndash;Lower Silurian Wufeng&ndash;Longmaxi shale from the Yangtze Platform, South China. To identify the provenance, the mineralogy and geochemistry of the shale were investigated. The methods included optical microscopy analysis, X-ray diffraction testing, field-emission scanning electron imaging, and major and trace element analysis. The Wufeng&ndash;Longmaxi shale is mainly composed of quartz (avg. 39.94%), calcite (avg. 12.29%), dolomite (avg. 11.75%), and clay minerals (avg. 28.31%). The LM1 interval is the shale gas sweet-spot and has the highest contents of total quartz (avg. 62.1%, among which microcrystalline quartz accounts for 52.8% on average) and total organic carbon (avg. 4.6%). The relatively narrow range of TiO2&ndash;Zr variation and the close correlation between Th/Sc and Zr/Sc signify no obvious sorting and recycling of the sediment source rocks. Sedimentary sorting has a limited impact on the geochemical features of the shale. The relatively high value of ICV (index of compositional variability) (1.03&ndash;3.86) and the low value of CIA (chemical index of alteration values) (50.62&ndash;74.48) indicate immature sediment source rocks, probably undergoing weak to moderate chemical weathering. All samples have patterns of moderately enriched light rare-earth elements and flat heavy rare-earth elements with negative Eu anomalies (Eu/Eu* = 0.35&ndash;0.92) in chondrite-normalized diagrams. According to Th/Sc, Zr/Sc, La/Th, Zr/Al2O3, TiO2/Zr, Co/Th, SiO2/Al2O3, K2O/Na2O, and La/Sc, it can be inferred that the major sediment source rocks were acidic igneous rocks derived from the active continental margin and continental island arc. A limited terrigenous supply caused by the inactive tectonic setting is an alternative interpretation of the formation of the sweet-spot interval