Genomic Mutation Profile of Primary Gastrointestinal Diffuse Large B-Cell Lymphoma.

Primary gastrointestinal diffuse large B-cell lymphoma (GI-DLBCL) is the most common gastrointestinal lymphoma, but its genetic features are poorly understood. We performed whole-exome sequencing of 25 primary tumor samples from patients with GI-DLBCL and 23 matched normal tissue samples. Oncogenic mutations were screened, and the correlations between genetic mutations and clinicopathological characteristics were analyzed. Twenty-five patients with GI-DLBCL were enrolled in the genetic mutation analysis with a median of 184 (range 79-382) protein-altering variants per patient. We identified recurrent oncogenic mutations in GI-DLBCL, including those in TP53, MUC16, B2M, CCND3, HIST1H1C, NEB, and ID3. Compared with nodal DLBCL, GI-DLBCL exhibited an increased mutation frequency of TP53 and reduced mutation frequencies of PIM1, CREBBP, BCL2, KMT2D, and EZH2. Moreover, GI-DLBCL exhibited fewer MYD88 and CD79B mutations than DLBCL in the testis and central nervous system. GI-DLBCLs with HLA-B, MEF2A, RHOA, and NAV3 mutations exhibited a tendency toward a high proliferation index. MUC16 and ETV6 mutations often occurred in tumors with early clinical staging. Our data provide a comprehensive understanding of the landscape of mutations in a small subset of GI-DLBCLs. The genetic mutation profiles of GI-DLBCL differ from those of nodal DLBCL and DLBCL in immune-privileged sites. The different mutated genes are related to the NF-κB and JAK-STAT pathways, and the different pathogenetic mechanisms leading to the development of DLBCL may be influenced by the tissue microenvironment. Differences in genetic alterations might influence the clinicopathological characteristics of GI-DLBCL

Software for the frontiers of quantum chemistry:An overview of developments in the Q-Chem 5 package

This article summarizes technical advances contained in the fifth major release of the Q-Chem quantum chemistry program package, covering developments since 2015. A comprehensive library of exchange–correlation functionals, along with a suite of correlated many-body methods, continues to be a hallmark of the Q-Chem software. The many-body methods include novel variants of both coupled-cluster and configuration-interaction approaches along with methods based on the algebraic diagrammatic construction and variational reduced density-matrix methods. Methods highlighted in Q-Chem 5 include a suite of tools for modeling core-level spectroscopy, methods for describing metastable resonances, methods for computing vibronic spectra, the nuclear–electronic orbital method, and several different energy decomposition analysis techniques. High-performance capabilities including multithreaded parallelism and support for calculations on graphics processing units are described. Q-Chem boasts a community of well over 100 active academic developers, and the continuing evolution of the software is supported by an “open teamware” model and an increasingly modular design

‘Fertile island’ effects on the soil microbial community beneath the canopy of Tetraena mongolica, an endangered and dominant shrub in the West Ordos Desert, North China

Abstract Background The fertile islands formed by shrubs are major drivers of the structure and function of desert ecosystems, affecting seedling establishment, plant–plant interactions, the diversity and productivity of plant communities, and microbial activity/diversity. Although an increasing number of studies have shown the critical importance of soil microbes in fertile island formation, how soil microbial community structure and function are affected by the different fertile island effect intensities is still unknown. As an endangered and dominant shrub species in the West Ordos Desert, Tetraena mongolica was selected for further exploration of its fertile island effect on the soil microbial community in the present study to test the following two hypotheses: (1) T. mongolica shrubs with different canopy sizes exert fertile island effects of different strengths; (2) the soil microbial community structure and function beneath the T. mongolica canopy are affected by the fertile island, and the strength of these effects varies depending on the shrub canopy size. Results The contents of soil total nitrogen (TN) and available phosphorus (AVP) were significantly greater beneath T. mongolica shrub canopy than outside the shrub canopy. With increasing shrub canopy size, the enrichment of soil TN and AVP increased, indicating a stronger fertile island effect. The structure and function of soil microbial communities, including fungal, archaeal and bacterial communities, are affected by the fertile island effect. An increase in canopy size increased the relative abundance of Ascomycota (Fungi) and Thaumarchaeota (Archaea). For the soil microbial functional groups, the relative abundance of endophytes in the fungal functional groups; steroid hormone biosynthesis, sphingolipid metabolism, and steroid biosynthesis genes in the bacterial functional groups; and nonhomologous end-joining and bisphenol degradation functional genes in the archaeal functional groups increased significantly with increasing T. mongolica canopy size. Conclusions These results revealed that T. mongolica had a fertile island effect, which affected the soil microbial community structure and functions, and that the fertile island effect might increase with increasing shrub canopy size. The fertile island effect may strengthen the interaction between T. mongolica shrubs and microbes, which may be beneficial to the growth and maintenance of T. mongolica

Effect of eNOS on Ischemic Postconditioning-Induced Autophagy against Ischemia/Reperfusion Injury in Mice

Autophagy is involved in the development of numerous illnesses, including ischemia/reperfusion (I/R). Endothelial nitric oxide synthase (eNOS) participates in the protective effects of ischemic postconditioning (IPostC). However, it remains unclear whether eNOS-mediated autophagy serves as a critical role in IPostC in the hearts of mice, in protecting against I/R injury. In the present study, the hearts of mice with left anterior descending coronary artery ligation were studied as I/R models. H9c2 cells underwent exposure to hypoxia/reoxygenation (H/R) and were examined as in vitro model. IPostC reduced mice myocardial infarct size and improved the structure of the heart. IPostC increased the formation of autophagosomes and increased the phosphorylation of eNOS and adenosine monophosphate-activated protein kinase (AMPK). Autophagy and eNOS inhibition suppressed the cardioprotective effects of IPostC. AMPK or eNOS inhibition abolished the improvement effect of IPostC on autophagy. AMPK inhibition decreased eNOS phosphorylation in the heart. Additionally, H9c2 cells suffering hypoxia were used as in vitro model. Autophagy or eNOS inhibition abolished the protective effects of hypoxic postconditioning (HPostC) against H/R injury. AMPK and eNOS inhibition/knockout decreased autophagic activity in the HPostC group. These results indicated that IPostC protects the heart against I/R injury, partially via promoting AMPK/eNOS-mediated autophagy

Interactions between Graphene and Ionic Liquid Electrolyte in Supercapacitors

The graphene material prepared by the chemical reduction method usually has oxygenic functional groups in it and such functional groups often result in interactions between the graphene electrode and the electrolyte in supercapacitors. We have examined the existential form of interactions between graphene as the electrode and three kinds of ionic liquid, 1-ethyl-3-methylimidazolium bis (trifluoromethylsulfonyl) imide (EMI-TFSI), 1-ethyl-3-methylimidazolium tetrafluoroborate (EMI-BF4), and 1-methyl-1-propylpiperidinium bis (trifluoromethyl sulfonyl) imide (MPPp-TFSI), as the electrolyte of a supercapacitor. Mass spectroscopy (MS) and Fourier transform infrared spectroscopy (FT-IR) analyses confirmed that the residual hydroxyl groups in graphene were transferred to EMI+ and TFSI lost oxygen atoms to graphene, while little reaction took place in BF4 or MPPp(+), during the process of charging. The chemical reactions are suggested to contribute to the device capacitance while it is also one of the reasons for the decreased electrochemical stability window. In this study the highest energy density achieved using the graphene electrode is 169 Wh kg (1) in MPPp-TFSI electrolyte charged to 4.4 V. (C) 2016 Elsevier Ltd. All rights reserved

Ionic liquid modified graphene for supercapacitors with high rate capability

Ionic liquids (ILs) with large electrochemical windows up to 4 V have been employed as the electrolyte to boost the energy density of graphene-based supercapacitors. However, due to the larger molecular size, lower conductivity, and higher viscosity of the IL electrolyte, graphene-based supercapacitors in IL electrolyte usually exhibit low rate capability. To make graphene-based electrodes more compatible with the IL electrolyte, we functionalized chemically reduced graphene oxide with the same IL which is also used as the electrolyte. Electrochemical test results show that the relaxation time and charge transfer resistance at electrode-electrolyte interface for IL modified electrode is one third and one fourth of that for the pristine graphene electrode, respectively, indicating the improved compatibility between the IL modified electrode and the electrolyte. Furthermore, the capacitance retention of the IL modified electrode from current density of 0.5 to 20 A g(-1) is 85%, which is much higher than that of the pristine electrode (53%). (C) 2015 Elsevier Ltd. All rights reserved

Formation of Halogenated Polyaromatic Compounds by Laccase Catalyzed Transformation of Halophenols

Laccases are a type of extracellular enzyme produced by fungi, bacteria, and plants. Laccase can catalyze one-electron oxidation of a variety of phenolic compounds using molecular oxygen as the electron acceptor. In this study, transformation of halophenols (XPs) in laccase-catalyzed oxidation processes was explored. We first examined the intrinsic reaction kinetics and found that the transformation of XPs appeared first order to the concentrations of both XPs and laccase. A numerical model was developed to describe the role of humic acid (HA) in this process. It was demonstrated that HA could reverse the oxidation of XPs by acting as the inner filtrator of XP radical intermediates formed upon reactions between the substrates and laccase. The extent of such reversion was proportional to HA concentration. MS analysis in combination with quantum chemistry computation suggested that coupling products were generated. XPs coupled to each via CC or COC pathways, generating hydroxyl polyhalogenated biphenyl ethers (OH-PCDEs) and hydroxyl polyhalogenated biphenyls, respectively. Many of these polyhalogenated products are known to be hazardous to the ecosystem and human health, but they are not synthetic chemicals. This study shed light on their genesis in the environmental media