Identification of Important Nodes in Directed Biological Networks: A Network Motif Approach

Identification of important nodes in complex networks has attracted an increasing attention over the last decade. Various measures have been proposed to characterize the importance of nodes in complex networks, such as the degree, betweenness and PageRank. Different measures consider different aspects of complex networks. Although there are numerous results reported on undirected complex networks, few results have been reported on directed biological networks. Based on network motifs and principal component analysis (PCA), this paper aims at introducing a new measure to characterize node importance in directed biological networks. Investigations on five real-world biological networks indicate that the proposed method can robustly identify actually important nodes in different networks, such as finding command interneurons, global regulators and non-hub but evolutionary conserved actually important nodes in biological networks. Receiver Operating Characteristic (ROC) curves for the five networks indicate remarkable prediction accuracy of the proposed measure. The proposed index provides an alternative complex network metric. Potential implications of the related investigations include identifying network control and regulation targets, biological networks modeling and analysis, as well as networked medicine.     

Microglial activation mediates host neuronal survival induced by neural stem cells

The rational of neural stem cells (NSCs) in the therapy of neurological disease is either to replace dead neurons or to improve host neuronal survival, the latter of which has got less attention and the underlying mechanism is as yet little known. Using a transwell co‐culture system, we reported that, in organotypic brain slice cultures, NSCs significantly improved host neuronal viability. Interestingly, this beneficial effect of NSCs was abrogated by a microglial inhibitor minocycline, while it was mimicked by a microglial agonist, Toll‐like receptor 9 (TLR9) ligand CpG‐ODN, which supports the pro‐vital mediation by microglia on this NSCs‐improved neuronal survival. Moreover, we showed that NSCs significantly induced host microglial movement and higher expression of a microglial marker IBA‐1, the latter of which was positively correlated with TLR9 or extracellular‐regulated protein kinases 1/2 (ERK1/2) activation. Real‐time PCR revealed that NSCs inhibited the expression of pro‐inflammatory molecules, but significantly increased the expression of molecules associated with a neuroprotective phenotype such as CX3CR1, triggering receptor expressed on myeloid cells‐2 (TREM2) and insulin growth factor 1 (IGF‐1). Similarly, in the microglia cells, NSCs induced the same microglial response as that in the slices. Further treatment with TLR9 ligand CpG‐ODN, TLR9 inhibitor chloroquine (CQ) or ERK1/2 inhibitor U0126 demonstrated that TLR9‐ERK1/2 pathway was involved in the NSCs‐induced microglial activation. Collectively, this study indicated that NSCs improve host neuronal survival by switching microglia from a detrimental to a neuroprotective phenotype in adult mouse brain, and the microglial TLR9‐ERK1/2 pathway seems to participate in this NSCs‐mediated rescue action.     

Fermentation and metabolic characteristics of Gluconacetobacter oboediens for different carbon sources

The metabolism of Gluconacetobacter oboediens was investigated in relation to different carbon sources for the continuous cultures at the dilution rate of 0.05 h⁻¹. The ¹³C-flux result implies the formation of metabolic recycles for the case of using glucose and acetate as carbon sources. When glucose and ethanol were used as carbon sources, the specific ethanol uptake rate and the specific acetate production rate increased as the feed ethanol concentration was increased from 40 to 60 g/l, while the specific CO₂ production rate and the biomass concentration decreased, where the ¹³C-metabolic flux result indicates that the glycolysis, oxidative PP pathway, and the tricarboxylic acid (TCA) cycle were less active, resulting in less biomass concentration. The flux result also implies that oxaloacetate decarboxylase flux became negative, so that oxaloacetate is backed up by this pathway, resulting in less activity of glyoxylate pathway. When gluconate was added for the case of using glucose and ethanol as carbon sources, the acetate and cell concentrations as well as gluconate concentrations increased. The glucose and ethanol concentrations decreased concomitantly with the increased feed gluconate concentration. In accordance with these fermentation characteristics, the enzyme activity result indicates that glucose dehydrogenase and glucose-6-phosphate dehydrogenase pathways became less active, while the glycolysis and the TCA cycle was activated as the feed gluconate concentration was increased.     

O139型霍乱菌苗生产用菌株93—3稳定性研究

Ｏ１３９型霍乱菌苗生产用菌株９３－３经过３０代连续传代,与原代菌株作比较,结果表明：该菌传代前后表型生物学特征（生长特性,生化反应,特异性血清学反应,耐药性等）,及遗传学特征（Ｇ＋Ｃｍｏｌ％测定）均未发现明显差异,证明该菌株具有较好的稳定性。     

基于BIOMOD的青海湖流域高原鼠兔分布模拟

随着统计模型及空间信息数据的不断发展和完善,物种分布模型已经成为全球变化背景下研究大尺度物种分布情况的重要工具。高原鼠兔(Ochotona curzoniae)是青藏高原特有的关键物种,在青藏高原生态系统中占有重要地位。通过采集高原鼠兔的分布点数据及环境变量数据,基于R语言中BIOMOD包中的7个模型对其在青海湖流域的分布进行了模拟。结果表明,高原鼠兔主要分布于青海湖西岸和北岸、天峻县周边及布哈河流域上游,影响高原鼠兔分布的主要环境因子为距道路距离、距居民点距离、最暖月最高气温、NDVI标准差、最冷季和最干季降水量。BIOMOD组合模型中,推进式回归树模型(GBM)和最大熵模型(MAXENT)的模拟效果最好,广义线性回归模型(GLM)结果较差。而优化后的结果显示,模拟结果的集成和筛选能有效提高模型的精度和效果。     

Direct electrochemistry of hemoglobin on carbonized titania nanotubes and its application in a sensitive reagentless hydrogen peroxide biosensor

Carbonized TiO(2) nanotubes (TNT/C) prepared by carbonization with organic polymers possess advantages combined from high conductivity of carbon and nanostructure of TiO(2) nanotubes. The material was used as a supporting matrix to immobilize a redox protein, hemoglobin (Hb), to explore its direct electron transfer ability. The apparent heterogeneous electron transfer rate constant (k(ET)) of Hb on TNT/C is 108s(-1), which is much higher than that in the reported works, demonstrating excellent direct electrochemistry behavior. The TNT/C-Hb modified glassy carbon electrode (GCE) demonstrates significant electrocatalytic activity for reduction of hydrogen peroxide with a small apparent Michaelis-Menten constant (87.5 microM). The TNT/C-Hb based H(2)O(2) sensor has a low detection limit (0.92 microM), fast response time (3s) and high dynamic response range (10(-6) to 10(-4)M), a much better performance than the reported works. These results demonstrate that a direct electrochemistry behavior can be significantly enhanced through simple carbon coating on a nanostructured material for higher reaction surface area and better conductivity. This work suggests that Hb-immobilized TNT/C has potential applications in a sensitive H(2)O(2) sensor.     

Genetic evidence for functional dependency of p18Ink4c on Cdk4

The INK4 family of cyclin-dependent kinase (CDK) inhibitors negatively regulates cyclin D-dependent CDK4 and CDK6 and induces the growth-suppressive function of Rb family proteins. Mutations in the Cdk4 gene conferring INK4 resistance are associated with familial and sporadic melanoma in humans and result in a wide spectrum of tumors in mice, suggesting that INK4 is a major regulator of CDK4. Mice lacking the Cdk4 gene exhibit various defects in many organs associated with hypocellularity, whereas loss of the p18(Ink4c) gene results in widespread hyperplasia and organomegaly. To genetically test the notion that the function of INK4 is dependent on CDK4, we generated p18; Cdk4 double-mutant mice and examined the organs and tissues which developed abnormalities when either gene is deleted. We show here that, in all organs we have examined, including pituitary, testis, pancreas, kidney, and adrenal gland, hyperproliferative phenotypes associated with p18 loss were canceled. The double-mutant mice exhibited phenotypes very close to or indistinguishable from that of Cdk4 single-mutant mice. Mice lacking p27(Kip1) develop widespread hyperplasia and organomegaly similar to those developed by p18-deficient mice. The p27; Cdk4 double-mutant mice, however, displayed phenotypes intermediate between those of p27 and Cdk4 single-mutant mice. These results provide genetic evidence that in mice p18(Ink4c) and p27(Kip1) mediate the transduction of different cell growth and proliferation signals to CDK4 and that p18(Ink4c) is functionally dependent on CDK4.     

Simultaneous determination of thiamphenicol, florfenicol and florfenicol amine in eggs by reversed-phase high-performance liquid chromatography with fluorescence detection

A specific, sensitive and widely applicable reversed-phase high-performance liquid chromatography with fluorescence detection (RP-HPLC-FLD) method was developed for the simultaneous determination of thiamphenicol (TAP), florfenicol (FF) and florfenicol amine (FFA) in eggs. Samples were extracted with ethyl acetate-acetonitrile-ammonium hydroxide (49:49:2, v/v), defatted with hexane, followed by RP-HPLC-FLD determination. Liquid chromatography was performed on a 5 μm LiChrospher C(18) column using a mobile phase composed of acetonitrile (A), 0.01 M sodium dihydrogen phosphate containing 0.005 M sodium dodecyl sulfate and 0.1% triethylamine, adjusted to pH 4.8 by 85% phosphoric acid (B) (A:B, 35:65 v/v), at a flow rate of 1.0 mL/min. The fluorescence detector of HPLC was set at 224 nm for excitation wavelength and 290 nm for emission wavelength. Limits of detection (LODs) were 1.5 μg/kg for TAP and FF, 0.5 μg/kg for FFA in eggs; limits of quantitation (LOQs) were 5 μg/kg for TAP and FF, 2 μg/kg for FFA in eggs. Linear calibration curves were obtained over concentration ranges of 0.025-5.0 μg/mL for TAP with determination coefficients of 0.9997, 0.01-10.0 μg/mL for FF with determination coefficients of 0.9997 and 0.0025-2.50 μg/mL for FFA with determination coefficients of 0.9998, respectively. The recovery values ranged from 86.4% to 93.8% for TAP, 87.4% to 92.3% for FF and from 89.0% to 95.2% for FFA. The corresponding intra-day and inter-day variation (relative standard deviation, R.S.D.) found to be less than 6.7% and 10.8%, respectively.     

Quantitative determination of buagafuran in human plasma by liquid chromatography-tandem mass spectrometry

A sensitive and selective high performance liquid chromatography-tandem mass spectrometry (HPLC-MS/MS) method was developed for the determination of buagafuran in human plasma. The analyte was extracted from plasma samples with hexane after addition of isotopic internal standard and chromatographed on a RP-C(8) column. The mobile phase consisted of methanol-water (90:10, v/v) and the flow rate was 0.2 mL/min. The detection was performed on a triple quadrupole tandem mass spectrometer in multiple reactions monitoring (MRM) mode using positive electrospray ionization (ESI). The method was validated over the concentration range of 0.5-200 ng/mL. Inter- and intra-day precision (RSD%) were all within 15% and the accuracy (RE%) was equal or lower than 9.5%. The lower limit of quantitation (LLOQ) was 0.5 ng/mL. The extraction recovery was on average 38.1% and the detection was not affected by the matrix. The method was successfully applied to the pharmacokinetic study of buagafuran in healthy Chinese volunteers.     

杨树试管苗嫩茎生根过程中内源IAA的免疫金银定位

生长素类物质在木本植物生根过程中发挥重要作用。杨树生根与生长素的关系及生根过程中内源激素的变化已有大量报道,而生根过程中生长素的组织定位分析则尚未见报道。该文应用免疫化学分析方法对741杨（Populus alba×（P.davidiana×P.simonii）×P.tomentosa）嫩茎生根过程中内源IAA在组织中的分布进行了研究。结果显示,741杨的嫩茎在无外源激素的1/2MS培养基上诱导10天后可生根,14天后生根率达100%。诱导前,嫩茎基部组织中几乎没有IAA信号;诱导8天后,嫩茎基部维管组织中有大量的IAA积累,而且中部的维管组织中也有明显的IAA信号（主要分布在韧皮部和维管形成层）;10天后,形成不定根原基,此时IAA主要分布在根原基;12天后,根原基分化成不定根并突破表皮,IAA在不定根中的分布主要集中在根尖和中柱。该文对741杨的嫩茎生根过程中IAA的组织分布特点及运输途径进行了讨论。