常氧条件下高原鼢鼠、甘肃鼢鼠及SD大鼠血液理化特征比较

为探讨不同低氧环境适应动物的血液理化特征,用美国雅培手掌血气分析仪分别测定常氧适应4周的高原鼢鼠(Myospalax baileyi)及甘肃鼢鼠(M.cansus)血液的血气、酸碱及电解质指标,并与SD大鼠(Rattus norvegicus)进行比较。结果显示,常氧适应后,甘肃鼢鼠与高原鼢鼠动脉氧分压(PaO2)、静脉氧分压(PvO2)、动静脉氧分压差(PaO2﹣PvO2)、动脉氧饱和度(SaO2)、静脉氧饱和度(SvO2)及氧利用率均无显著性差异,两种动物静脉血的氧分压和氧饱和度均极显著低于SD大鼠,氧利用率极显著高于SD大鼠;高原鼢鼠与甘肃鼢鼠动、静脉血红蛋白(Hb)及动、静脉红细胞压积(HCT)无显著性差异,血红蛋白含量与SD大鼠无显著性差异,但红细胞压积(HCT)极显著低于SD大鼠;高原鼢鼠和甘肃鼢鼠血液酸碱特征趋于一致,不同于SD大鼠,动静脉pH差(pHa﹣pHv)及动静脉CO2总含量差(TvCO2﹣TaCO2)显著高于SD大鼠,动脉二氧化碳分压(PaCO2)极显著低于SD大鼠,动静脉二氧化碳分压差(PvCO2﹣PaCO2)极显著高于SD大鼠;高原鼢鼠和甘肃鼢鼠血浆中钠离子(Na+)浓度、钾离子(K+)浓度、游离钙离子(iCa2+)浓度及动静脉钠离子浓度差(Na+v﹣Na+a)、钾离子浓度差(K+v﹣K+a)和游离钙离子浓度差(iCa2+v﹣iCa2+a)无显著性差异;高原鼢鼠动脉血钾离子浓度显著低于SD大鼠,钾离子浓度差显著高于SD大鼠;甘肃鼢鼠钾离子浓度差及动、静脉血钙离子浓度显著高于SD大鼠。这些结果说明,低氧适应动物血气、酸碱及电解质特征一致,与地面生活的SD大鼠差异很大,表现出较低的红细胞压积和较高的氧利用率,血液能耐受较宽范围的酸碱变化,维持电解质稳定,保证内环境稳态。     

The Role of Mitochondrial dNTP Levels in Cells with Reduced TK2 Activity

Both the nuclear and mitochondrial DNA (mtDNA) depend on separate balanced pools of dNTPs for correct function of DNA replication and repair of DNA damage. Import of dNTPs from the cytosolic compartment to the mitochondria has been suggested to have the potential of rectifying a mitochondrial dNTP imbalance. Reduced TK2 activity has been demonstrated to result in mitochondrial dNTP imbalance and consequently mutations of mtDNA in non-dividing cells. In this study, the consequences of a reduced thymidine kinase 2 (TK2) activity were measured in proliferating HeLa cells, on both whole-cell as well as mitochondrial dNTP levels. With the exception of increased mitochondrial dCTP level no significant difference was found in cells with reduced TK2 activity. Our results suggest that import of cytosolic dNTPs in mitochondria of proliferating cells can compensate a TK2 induced imbalance of the mitochondrial dNTP pool.     

Biochemical characterization of maize (Zea mays L.) for salt tolerance

The inherent differences for salt tolerance in two maize cultivars (Agatti-2002 and Sahiwal-2002) were evaluated in pot experiments. Plants were grown in half-strength of Hoagland nutrient solution added with 0, 80, 100, 120, 140 and 160 mM of NaCl. Salt stress markedly reduced the shoot and root lengths and fresh and dry masses. Reduction in growth attributes was more pronounced in cv. Agatti-2002 than cv. Sahiwal-2002. Both maize cultivars exhibited significant perturbations in important biochemical attributes being employed for screening the crops for salt tolerance. Cultivar Sahiwal-2002 was found salt tolerant as compared to cv. Agatti-2002 because it exhibited lower levels of H₂O₂, malondialdehyde (MDA) and higher activities of antioxidant enzymes. In addition, cultivar Sahiwal-2002 exhibited less salt-induced degradation of photosynthetic pigments, lower levels of toxic Na⁺ and Cl^?  and higher endogenous levels of K⁺ and K⁺/Na⁺ ratio. The results indicate that salt stress induced a marked increase in MDA, H₂O₂, relative membrane permeability, total soluble proteins and activities of antioxidant enzymes (superoxide dismutase, peroxidase, catalase andascorbate peroxidase). Moreover, increase in endogenous levels of Na⁺ and Cl^?  and decrease in K⁺ and K⁺/Na⁺ ratio and photosynthetic pigments were recorded in plants grown under salinity regimes.     

Pan cancer patterns of allelic imbalance from chromosomal alterations in 33 tumor types

Somatic copy number alterations (SCNAs) serve as hallmarks of tumorigenesis and often result in deviations from one-to-one allelic ratios at heterozygous loci, leading to allelic imbalance (AI). The Cancer Genome Atlas (TCGA) reports SCNAs identified using a circular binary segmentation algorithm, providing segment mean copy number estimates from single-nucleotide polymorphism DNA microarray total intensities (log R ratio), but not allele-specific intensities (“B allele” frequencies) that inform of AI. Our approach provides more sensitive identification of SCNAs by modeling the “B allele” frequencies jointly, thereby bolstering the catalog of chromosomal alterations in this widely utilized resource. Here we present AI summaries for all 33 tumor sites in TCGA, including those induced by SCNAs and copy-neutral loss-of-heterozygosity (cnLOH). We identified AI in 94% of the tumors, higher than in previous reports. Recurrent events included deletions of 17p, 9q, 3p, amplifications of 8q, 1q, 7p, as well as mixed event types on 8p and 13q. We also observed both site-specific and pan-cancer (spanning 17p) cnLOH, patterns which have not been comprehensively characterized. The identification of such cnLOH events elucidates tumor suppressors and multi-hit pathways to carcinogenesis. We also contrast the landscapes inferred from AI- and total intensity-derived SCNAs and propose an automated procedure to improve and adjust SCNAs in TCGA for cases where high levels of aneuploidy obscured baseline intensity identification. Our findings support the exploration of additional methods for robust automated inference procedures and to aid empirical discoveries across TCGA.     

肠道菌群失调与肝硬化伴SBP患者疾病发展的关系及三联活菌胶囊干预性研究

目的分析肠道菌群失调与肝硬化伴自发性细菌性腹膜炎(SBP)患者疾病发展的关系及三联活菌胶囊的应用价值。方法将我院2017年1月至2019年12月间收治的94例肝硬化伴SBP患者作为观察组研究对象,50例健康者作为本研究对照组,将观察组患者依照随机信封法分为B组及A组,B组采用三联活菌胶囊治疗,A组采用常规方案治疗。采用16S rDNA测序技术检测患者肠道菌群种类和多样性。结果观察组患者诺卡氏菌科、盐单胞菌科、肠杆菌科、链球菌科、韦荣球菌科丰度均高于对照组,拟杆菌科、普雷沃菌科、毛螺菌科均低于对照组,OTUs、Chao、Shannon指数明显低于对照组。肠道菌群种类、OTUs、Chao、Shannon指数是影响肝硬化伴SBP患者疾病发展的影响因素,以上差异均就有统计学意义(P0.05)。治疗后B组患者肠道菌群OTUs、Chao和Shannon明显高于对照组,差异均具有统计学意义(P0.05)。结论肠道菌群失调是影响肝硬化伴SBP患者疾病发展的独立影响因素,采用三联活菌胶囊干预可有效纠正患者体内肠道菌群失调。     

Yule-generated trees constrained by node imbalance

The Yule   process generates a class of binary trees which is fundamental to population genetic models and other applications in evolutionary biology. In this paper, we introduce a family of sub-classes of ranked trees, called Ω-trees, which are characterized by imbalance of internal nodes. The degree of imbalance is defined by an integer 0≤ω$0\le \omega$. For caterpillars  , the extreme case of unbalanced trees, ω=0$\omega =0$. Under models of neutral evolution, for instance the Yule model, trees with small ω are unlikely to occur by chance. Indeed, imbalance can be a signature of permanent selection pressure, such as observable in the genealogies of certain pathogens. From a mathematical point of view it is interesting to observe that the space of Ω-trees maintains several statistical invariants although it is drastically reduced in size compared to the space of unconstrained Yule trees. Using generating functions, we study here some basic combinatorial properties of Ω-trees. We focus on the distribution of the number of subtrees with two leaves. We show that expectation and variance of this distribution match those for unconstrained trees already for very small values of ω.     

Evidence of expression variation and allelic imbalance in Crohn's disease susceptibility genes NOD2 and ATG16L1 in human dendritic cells

Human dendritic cells (DCs) play an important role in induction and progression of Crohn's disease (CD). Accumulating evidence suggests that viral infection is required to trigger CD pathogenesis in genetically predisposed individuals. NOD2 and ATG16L1 are among the major CD susceptibility genes implicated in impaired immune response to bacterial infection. In this study, we investigated gene expression and allelic imbalance (AI) of NOD2 and ATG16L1 using common variants in human monocyte-derived DCs. Significant AI was observed in ~ 40% and ~ 70% of NOD2 and ATG16L1 heterozygotes, respectively (p < 0.05). AI of NOD2 was inversely associated with its expression level (p = 0.015). No correlation was detected between gene expression and AI for ATG16L1. When infected with Newcastle Disease Virus (NDV), NOD2 expression in DCs was induced about four-fold (p < 0.001), whereas ATG16L1 expression was not affected (p = 0.88). In addition, NDV infection tended to lower the variance in AI among DC populations for the NOD2 gene (p = 0.05), but not the ATG16L1 gene (p = 0.32). Findings of a simulation study, aimed to verify whether the observed variation in gene expression and AI is a result of sample-to-sample variability or experimental measurement error, suggested that NOD2 AI is likely to result from a deterministic event at a single cell level. Overall, our results present initial evidence that AI of the NOD2 and ATG16L1 genes exists in populations of human DCs. In addition, our findings suggest that viral infection may regulate NOD2 expression.     

Structure of vesicles formed from non-ionic dialkylglycerol poly(oxyethylene) ether surfactants: effect of electrolyte and cholesterol

Five non-ionic dialkylglycerol poly(oxyethylene) ether surfactants, designated 2C_mE_n (where m, the number of carbons in each alkyl chain = 16 or 18, and n, the number of oxyethylene units = 12, 16 or 17) have been examined for their ability to form vesicles when dispersed in water or in an aqueous solution of 154 mM NaCl, alone or in the presence of 50 mol% cholesterol. Freeze fracture electron microscopy and light scattering showed that regardless of the hydrating fluid, all the non-ionic surfactants, with the exception of 2C₁₆E₁₇ and 2C₁₈E₁₇, formed vesicles in the absence of cholesterol – 2C₁₆E₁₇ and 2C₁₈E₁₇ instead formed micellar aggregates. All surfactants, however, formed vesicles in the presence of 50 mol% cholesterol. Small angle neutron scattering studies of the surfactant vesicles enabled the bilayer thickness and repeat distance (d-spacing) to be determined. The bilayers formed by all the non-ionic surfactants in the absence of cholesterol were surprisingly thin (∼50 Å for the E₁₂ containing surfactants and ∼64 Å for 2C₁₈E₁₆) most likely due to the intrusion of oxyethylene groups into the hydrophobic core of the bilayers. In contrast, however, the non-ionic surfactants exhibited a relatively large d-spacing of around ∼130–150 Å. The addition of 50 mol% cholesterol had a dramatic effect on the thickness of the vesicle bilayer, increasing its size by 10–20 Å, most probably because of an extrusion of oxyethylene from the hydrophobic region of the bilayer and/or a reduction in the tilt on the surfactant alkyl chains. Additionally the presence of cholesterol in a vesicle tended to reduce slightly both the d-spacing and the thickness of the water layer separating the bilayers. The presence of NaCl, even at the low concentrations used in the study, did affect the properties of the bilayer such that it reduced the d-spacing and, in the case of cholesterol-containing systems, also reduced bilayer thickness.     

Nutrients and water availability constrain the seasonality of vegetation activity in a Mediterranean ecosystem

Anthropogenic nitrogen (N) deposition and resulting differences in ecosystem N and phosphorus (P) ratios are expected to impact photosynthetic capacity, that is, maximum gross primary productivity (GPP_max). However, the interplay between N and P availability with other critical resources on seasonal dynamics of ecosystem productivity remains largely unknown. In a Mediterranean tree–grass ecosystem, we established three landscape‐level (24 ha) nutrient addition treatments: N addition (NT), N and P addition (NPT), and a control site (CT). We analyzed the response of ecosystem to altered nutrient stoichiometry using eddy covariance fluxes measurements, satellite observations, and digital repeat photography. A set of metrics, including phenological transition dates (PTDs; timing of green‐up and dry‐down), slopes during green‐up and dry‐down period, and seasonal amplitude, were extracted from time series of GPP_max and used to represent the seasonality of vegetation activity. The seasonal amplitude of GPP_max was higher for NT and NPT than CT, which was attributed to changes in structure and physiology induced by fertilization. PTDs were mainly driven by rainfall and exhibited no significant differences among treatments during the green‐up period. Yet, both fertilized sites senesced earlier during the dry‐down period (17–19 days), which was more pronounced in the NT due to larger evapotranspiration and water usage. Fertilization also resulted in a faster increase in GPP_max during the green‐up period and a sharper decline in GPP_max during the dry‐down period, with less prominent decline response in NPT. Overall, we demonstrated seasonality of vegetation activity was altered after fertilization and the importance of nutrient–water interaction in such water‐limited ecosystems. With the projected warming‐drying trend, the positive effects of N fertilization induced by N deposition on GPP_max may be counteracted by an earlier and faster dry‐down in particular in areas where the N:P ratio increases, with potential impact on the carbon cycle of water‐limited ecosystems.