The bZIP mutant CEBPB (V285A) has sequence specific DNA binding propensities similar to CREB1

The bZIP homodimers CEBPB and CREB1 bind DNA containing methylated cytosines differently. CREB1 binds stronger to the C/EBP half-site GCAA when the cytosine is methylated. For CEBPB, methylation of the same cytosine does not affect DNA binding. The X-ray structure of CREB1 binding the half site GTCA identifies an alanine in the DNA binding region interacting with the methyl group of T, structurally analogous to the methyl group of methylated C. This alanine is replaced with a valine in CEBPB. To explore the contribution of this amino acid to binding with methylated cytosine of the GCAA half-site, we made the reciprocal mutants CEBPB(V285A) and CREB1(A297V) and used protein binding microarrays (PBM) to examine binding to four types of double-stranded DNA (dsDNA): 1) DNA with cytosine in both strands (DNA(C|C)), 2) DNA with 5-methylcytosine (M) in one strand and cytosine in the second strand (DNA(M|C)), 3) DNA with 5-hydroxymethylcytosine (H) in one strand and cytosine in the second strand (DNA(H|C)), and 4) DNA with both cytosines in all CG dinucleotides containing 5-methylcytosine (DNA(5mCG)). When binding to DNA(C|C), CEBPB (V285A) preferentially binds the CRE consensus motif (TGACGTCA), similar to CREB1. The reciprocal mutant, CREB1(A297V) binds DNA with some similarity to CEBPB, with strongest binding to the methylated PAR site 8-mer TTACGTAA. These data demonstrate that V285 residue inhibits CEBPB binding to methylated cytosine of the GCAA half-site.     

A novel adjuvant, a mixture of alum and the general opioid antagonist naloxone, elicits both humoral and cellular immune responses for heat-killed Salmonella typhimurium vaccine

In the current study, we tested the efficacy of the mixture of naloxone, an opioid receptor antagonist, and alum, as a new adjuvant, in the induction of humoral and cellular immunity in response to heat-killed Salmonella typhimurium (HKST) as a model vaccine. BALB/c mice were divided into five groups. Mice in the experimental groups received either the HKST vaccine alone or in combination with the adjuvant alum, naloxone or the alum-naloxone mixture. Mice in the negative control group received phosphate-buffered saline. All mice were immunized two times on days 0 and 14. Two weeks after the last immunization, immune responses to S. typhimurium were assessed. Our results indicated that the administration of the alum-naloxone mixture as an adjuvant increased the ability of the HKST vaccine to enhance lymphocyte proliferation, shifted the immune response towards a T-helper 1 (Th1) pattern and increased S. typhimurium-specific immunoglobulin G (IgG), IgG2a, IgG1 and the ratio of IgG2a to IgG1. This resulted in improved protective immunity against S. typhimurium. In conclusion, the administration of the alum-naloxone mixture as an adjuvant, in combination with the HKST vaccine, can enhance both humoral and cellular immunity and shift the immune responses to a Th1 pattern.     

万顺铅锌矿区蜈蚣草内生细菌砷氧化基因(aoxB)的多样性分析

【背景】近年来,由于金属矿的开采和冶炼、砷产品的加工与使用、煤的燃烧等各种因素,导致土壤环境中的砷污染越来越严重,导致许多人暴露于极度危险的砷毒毒害之下。【目的】研究四川的万顺铅锌矿区蜈蚣草根组织内生细菌aoxB基因的多样性,为提高土壤重金属污染生态修复效率提供理论依据。【方法】利用实时荧光定量PCR (Real-time quantitative PCR,qPCR)和限制性片段长度多态性(Restriction fragment length polymorphism,RFLP)技术,对四川省汉源县万顺铅锌矿区蜈蚣草根组织内生细菌aoxB基因表达量及多样性进行研究。【结果】qPCR结果表明,不同采样点间的蜈蚣草根组织内生细菌aoxB基因表达量存在明显差异,表现为选矿区进山口弃渣场尾矿区矿口。酶切图谱结果表明,不同采样点蜈蚣草根组织内生细菌aoxB基因多样性存在明显差异,多样性指数表现为尾矿矿口弃渣场进山口选矿区。Pearson相关分析显示,aoxB基因的表达量与重金属As之间呈显著负相关(P0.05),多样性指数则与重金属Pb和As之间呈极显著正相关(P0.01)。系统发育分析显示,aoxB基因的优势菌群为α-变形菌门(Alphaproteobacteria)。【结论】蜈蚣草根组织中存在丰富的含aoxB基因内生细菌种群,这些内生细菌表现出潜在的应用价值。     

Incorporation of transition to transversion ratio and nonsense mutations,improves the estimation of the number of synonymous and non-synonymous sites in codons

A common approach to estimate the strength and direction of selection acting on protein coding sequences is to calculate the dN/dS ratio. The method to calculate dN/dS has been widely used by many researchers and many critical reviews have been made on its application after the proposition by Nei and Gojobori in 1986. However, the method is still evolving considering the non-uniform substitution rates and pretermination codons. In our study of SNPs in 586 genes across 156 Escherichia coli strains, synonymous polymorphism in 2-fold degenerate codons were higher in comparison to that in 4-fold degenerate codons, which could be attributed to the difference between transition (Ti) and transversion (Tv) substitution rates where the average rate of a transition is four times more than that of a transversion in general. We considered both the Ti/Tv ratio, and nonsense mutation in pretermination codons, to improve estimates of synonymous (S) and non-synonymous (NS) sites. The accuracy of estimating dN/dS has been improved by considering the Ti/Tv ratio and nonsense substitutions in pretermination codons. We showed that applying the modified approach based on Ti/Tv ratio and pretermination codons results in higher values of dN/dS in 29 common genes of equal reading-frames between E. coli and Salmonella enterica. This study emphasizes the robustness of amino acid composition with varying codon degeneracy, as well as the pretermination codons when calculating dN/dS values.     

Synergistic Effect of Bimetallic MOF Modified Separator for Long Cycle Life Lithium-Sulfur Batteries

Severe polysulfide dissolution and shuttling are the main challenges that plague the long cycle life and capacity retention of lithium-sulfur (Li-S) batteries. To address these challenges, efficient separators are designed and modified with a dual functional bimetallic metal-organic framework (MOF). Flower-shaped bimetallic MOFs (i.e., Fe-ZIF-8) with nanostructured pores are synthesized at 35 °C in water by introducing dopant metal sites (Fe), which are then coated on a polypropylene (PP) separator to provide selective channels, thereby effectively inhibiting the migration of lithium polysulfides while allowing homogeneous transport of Li-ions. The active sites of the Fe-ZIF-8 enable electrocatalytic conversion, facilitating the conversion of lithium polysulfides. Moreover, the developed separator can prevent dendrite formation due to the uniform pore size and hence the even Li-ion transport and deposition. A coin cell using a Fe-ZIF-8/PP separator with S-loaded carbon cathode displayed a high cycle life of 1000 cycles with a high initial discharge capacity of 863 mAh g⁻¹ at 0.5 C and a discharge capacity of 746 mAh g⁻¹ at a high rate of 3 C. Promising specific capacity has been documented even under high sulfur loading of 5.0 mg cm⁻² and electrolyte to the sulfur ratio (E/S) of 5 µL mg⁻¹.     

Renal Cell Carcinoma Metastatic to the Liver: Early Response Assessment after Intraarterial Therapy Using 3D Quantitative Tumor Enhancement Analysis

PURPOSELiver metastases from renal cell carcinoma (RCC) are not uncommon in the course of disease. However, data about tumor response to intraarterial therapy (IAT) are scarce. This study assessed whether changes of enhancing tumor volume using quantitative European Association for the Study of the Liver (qEASL) on magnetic resonance imaging (MRI) and computed tomography (CT) can evaluate tumor response and predict overall survival (OS) early after therapy.RESULTSMean qEASL (cm³) decreased from 93.5 to 67.2 cm³ (P= .004) and mean qEASL (%) from 63.1% to 35.6% (P= .001). No significant changes were observed using other response criteria. qEASL was the only significant predictor of OS when used to stratify patients into responders and nonresponders with median OS of 31.9 versus 11.1 months (hazard ratio [HR], 0.43; 95% confidence interval [CI], 0.19-0.97; P= .042) for qEASL (cm³) and 29.9 versus 10.2 months (HR, 0.09; 95% CI, 0.01-0.74; P= .025) for qEASL (%).CONCLUSIONThree-dimensional (3D) quantitative tumor analysis is a reliable predictor of OS when assessing treatment response after IAT in patients with RCC metastatic to the liver. qEASL outperforms conventional non-3D methods and can be used as a surrogate marker for OS early after therapy.     

Effects of Plasma Membrane Cholesterol Level and Cytoskeleton F-Actin on Cell Protrusion Mechanics

Protrusions are deformations that form at the surface of living cells during biological activities such as cell migration. Using combined optical tweezers and fluorescent microscopy, we quantified the mechanical properties of protrusions in adherent human embryonic kidney cells in response to application of an external force at the cell surface. The mechanical properties of protrusions were analyzed by obtaining the associated force-length plots during protrusion formation, and force relaxation at constant length. Protrusion mechanics were interpretable by a standard linear solid (Kelvin) model, consisting of two stiffness parameters, k ₀ and k ₁ (with k ₀>k ₁), and a viscous coefficient. While both stiffness parameters contribute to the time-dependant mechanical behavior of the protrusions, k ₀ and k ₁ in particular dominated the early and late stages of the protrusion formation and elongation process, respectively. Lowering the membrane cholesterol content by 25% increased the k ₀ stiffness by 74%, and shortened the protrusion length by almost half. Enhancement of membrane cholesterol content by nearly two-fold increased the protrusion length by 30%, and decreased the k ₀ stiffness by nearly two-and-half-fold as compared with control cells. Cytoskeleton integrity was found to make a major contribution to protrusion mechanics as evidenced by the effects of F-actin disruption on the resulting mechanical parameters. Viscoelastic behavior of protrusions was further characterized by hysteresis and force relaxation after formation. The results of this study elucidate the coordination of plasma membrane composition and cytoskeleton during protrusion formation.     

Roles of glutamate receptors and the mammalian target of rapamycin (mTOR) signaling pathway in activity-dependent dendritic protein synthesis in hippocampal neurons

Local protein synthesis in neuronal dendrites is critical for synaptic plasticity. However, the signaling cascades that couple synaptic activation to dendritic protein synthesis remain elusive. The purpose of this study is to determine the role of glutamate receptors and the mammalian target of rapamycin (mTOR) signaling in regulating dendritic protein synthesis in live neurons. We first characterized the involvement of various subtypes of glutamate receptors and the mTOR kinase in regulating dendritic synthesis of a green fluorescent protein (GFP) reporter controlled by alphaCaMKII 5' and 3' untranslated regions in cultured hippocampal neurons. Specific antagonists of N-methyl-d-aspartic acid (NMDA), alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid (AMPA), and metabotropic glutamate receptors abolished glutamate-induced dendritic GFP synthesis, whereas agonists of NMDA and metabotropic but not AMPA glutamate receptors activated GFP synthesis in dendrites. Inhibitions of the mTOR signaling, as well as its upstream activators, phosphatidylinositol 3-kinase and AKT, blocked NMDA receptor-dependent dendritic GFP synthesis. Conversely, activation of mTOR signaling stimulated dendritic GFP synthesis. In addition, we also found that inhibition of the mTOR kinase blocked dendritic synthesis of the endogenous alphaCaMKII and MAP2 proteins induced by tetanic stimulations in hippocampal slices. These results identify critical roles of NMDA receptors and the mTOR signaling pathway for control of synaptic activity-induced dendritic protein synthesis in hippocampal neurons.     

Gawky is a component of cytoplasmic mRNA processing bodies required for early Drosophila development

In mammalian cells, the GW182 protein localizes to cytoplasmic bodies implicated in the regulation of messenger RNA (mRNA) stability, translation, and the RNA interference pathway. Many of these functions have also been assigned to analogous yeast cytoplasmic mRNA processing bodies. We have characterized the single Drosophila melanogaster homologue of the human GW182 protein family, which we have named Gawky (GW). Drosophila GW localizes to punctate, cytoplasmic foci in an RNA-dependent manner. Drosophila GW bodies (GWBs) appear to function analogously to human GWBs, as human GW182 colocalizes with GW when expressed in Drosophila cells. The RNA-induced silencing complex component Argonaute2 and orthologues of LSm4 and Xrn1 (Pacman) associated with 5'-3' mRNA degradation localize to some GWBs. Reducing GW activity by mutation or antibody injection during syncytial embryo development leads to abnormal nuclear divisions, demonstrating an early requirement for GWB-mediated cytoplasmic mRNA regulation. This suggests that gw represents a previously unknown member of a small group of genes that need to be expressed zygotically during early embryo development.