The complete genome sequence of Thermococcus onnurineus NA1 reveals a mixed heterotrophic and carboxydotrophic metabolism

Members of the genus Thermococcus, sulfur-reducing hyperthermophilic archaea, are ubiquitously present in various deep-sea hydrothermal vent systems and are considered to play a significant role in the microbial consortia. We present the complete genome sequence and feature analysis of Thermococcus onnurineus NA1 isolated from a deep-sea hydrothermal vent area, which reveal clues to its physiology. Based on results of genomic analysis, T. onnurineus NA1 possesses the metabolic pathways for organotrophic growth on peptides, amino acids, or sugars. More interesting was the discovery that the genome encoded unique proteins that are involved in carboxydotrophy to generate energy by oxidation of CO to CO₂, thereby providing a mechanistic basis for growth with CO as a substrate. This lithotrophic feature in combination with carbon fixation via RuBisCO (ribulose 1,5-bisphosphate carboxylase/oxygenase) introduces a new strategy with a complementing energy supply for T. onnurineus NA1 potentially allowing it to cope with nutrient stress in the surrounding of hydrothermal vents, providing the first genomic evidence for the carboxydotrophy in Thermococcus.     

Statistical superiority of genome-probing microarrays as genomic DNA-DNA hybridization in revealing the bacterial phylogenetic relationship compared to conventional methods

The genomic DNA-DNA hybridization (DDH) method has been widely used as a practical method for the determination of phylogenetic relationships between closely related biological strains. Traditional DDH methods have serious limitations including low reproducibility, a high background and a time-consuming procedure. The DDH method using a genome-probing microarray (GPM) has been recently developed to complement conventional methods and could be used to overcome the limitations that are typically encountered. It is necessary to compare the GPM-based DDH method to the conventional methods before using the GPM for the estimation of genomic similarities since all of the previous scientific data have been entirely dependent on conventional DDH methods. In order to address this issue we compared the DDH values obtained using the GPM, microplate and nylon membrane methods to multi-locus sequence typing (MLST) data for 9 Salmonella genomes and an Escherichia coli type strain. The results showed that the genome similarity values and the degrees of standard deviation obtained using the GPM method were lower than those obtained with the microplate and nylon membrane methods. The dendrogram from the cluster analysis of GPM DDH values was consistent with the phylogenetic tree obtained from the multi-locus sequence typing (MLST) data but was not similar to those obtained using the microplate and nylon membrane methods. Although the signal intensity had to be maximal when the targets were hybridized to their own probe, the methods using membranes and microplates frequently produced higher signals in the heterologous hybridizations than those obtained in the homologous hybridizations. Only the GPM method produced the highest signal intensity in homologous hybridizations. These results show that the GPM method can be used to obtain results that are more accurate than those generated by the other methods tested.     

Temporal Changes of Angiopoietins and Tie2 Expression in Rat Lungs after Monocrotaline-Induced Pulmonary Hypertension

Angiogenic factors such as vascular endothelial growth factor (VEGF) are implicated in pulmonary hypertension (PH). However, the pathway of angiogenic factor-mediated pathologic angiogenesis in PH remains unclear. In this study, we evaluated the temporal expression of angiopoietin (Ang) 1, Ang2, and their receptor (Tie2) as well as VEGF, endothelial nitric oxide synthase (eNOS), inducible NOS (iNOS), and heme oxygenase 1 (HO1) in the monocrotaline-induced PH model. Histologic evaluation showed pathologic vascular remodeling in the arteries of lung sections 1 wk after monocrotaline treatment. Protein levels of Ang1, Ang2, eNOS, iNOS, HO1, and VEGF were increased 1 wk after monocrotaline treatment but Tie2 protein levels were decreased 2 wk afterward. These results suggest that Ang2 mediates vascular remodeling in PH by decreasing Tie2 expression. Therefore, the Ang–Tie2 system may play a role in the pathophysiology of PH.Abbreviations: Ang, angiopoietin; eNOS, endothelial nitric oxide synthase; HO1, heme oxygenase 1; iNOS, inducible nitric oxide synthase; PH, pulmonary hypertension; VEGF, vascular endothelial growth factorPulmonary hypertension (PH) is a disease characterized by pathologic angiogenesis caused by diffuse smooth muscle cell hyperplasia and hypertrophy of the distal pulmonary vasculature, resulting in obliteration of small pulmonary arterioles.¹³ Vascular remodeling is governed by the interaction of several angiogenic factors on endothelial and smooth muscle cells. Vascular remodeling requires complex, multistep signaling pathways and a high degree of spatial and temporal coordination among endothelial and smooth muscle cells.²⁹ However, the precise mechanisms of vascular remodeling at the cellular and molecular levels are not completely defined.The angiopoietin (Ang) family and vascular endothelial growth factor (VEGF) are 2 types of vascular regulatory molecules that have been the subject of intense investigation in both physiologic and pathologic generation of blood vessels.^2,38 Members of the Ang family have opposing effects on receptor activation, with Ang1 stimulating Tie2 and Ang2 antagonizing this stimulation.^3,8,22 In particular, Ang1 plays an important role in the assembly of newly formed vasculature and in the maintenance of vascular integrity.^7,14,36 In contrast, Ang2 antagonizes the activation of Tie2 by Ang1 and causes endothelial cell apoptosis and vascular regression.²² The functions of Ang2 appear to be more complex than those of Ang1, in that Ang2 binds to the Tie2 receptor, blocking Ang1–Tie2 signaling and acting as a vessel-destabilizing factor.²⁶ However, prolonged exposure of endothelial cells to Ang2 activates Tie2 signaling.¹⁶ Thus, the precise roles of Ang2 during the development of PH are not well understood. Tie2 is a receptor tyrosine kinase that is expressed principally on vascular endothelium and that plays a role in integrity and survival of endothelial cells.^27,30 Disrupting Tie2 function in mice results in embryonic lethality with defects in embryonic vasculature.¹¹Neither Ang1 nor Ang2 alone can trigger an angiogenic response, but both enhance angiogenesis or induce vascular remodeling, depending on the presence of VEGF or other angiogenic factors. Nitric oxide is produced by endothelial cells through the action of nitric oxide synthase (NOS). Northern blot analysis of hypoxic rat lungs showed significantly increased mRNA levels for both endothelial NOS (eNOS) and inducible NOS (iNOS).¹⁸ Increased NOS activity coincided with the beginning of the vascular remodeling process during chronic hypoxia.³⁷ Hypoxia and nitric oxide stimulate VEGF production and induce HO1 expression in vascular tissue.¹⁰ In addition, several studies have shown that VEGF works in conjunction with other angiogenic factors to produce a stable and functional microvasculature.^21,35The purpose of the present study was to demonstrate the temporal changes of several angiogenic factors during the development of PH induced by treatment of rats with monocrotaline. This research was focused on the Ang–Tie2 system and other angiogenic factors and suggested that this system plays an important role in modulating vascular remodeling during PH.     

胶东山区县域土地利用在地形梯度上的分布特征

基于RS和GIS技术,结合地形位指数和土地利用程度综合指数,探讨了1987—2003年间山东省栖霞市土地利用结构的变化,并定量分析了该区地形梯度上的土地利用程度.结果表明：研究期间,栖霞市建设用地在低地形位上的优势明显;园地优势地形位区间的下限增加了6个地形位,由聚集分布转变成均匀分布;耕地、林地、草地、水域和未利用地优势地形位基本保持稳定.根据地形梯度上土地利用程度的定量表达,将研究区地形位划分为3个区段：1～15、16～30和31～50,其面积分别占研究区面积的49.48%、43.58%和6.94%.     

干旱高温及高浓度CO2复合胁迫对冬小麦生长的影响

研究了不同CO₂浓度、不同温度和水分条件及其组合对冬小麦产量、光合及水分的影响,以阐明气候变化对冬小麦的影响.结果表明: CO₂浓度升高对冬小麦光合速率没有影响,而升温和干旱均使光合速率显著下降.升高CO₂浓度与温度对冬小麦旗叶水分条件没有影响,干旱胁迫下旗叶相对含水量显著降低,而升温与干旱同时发生可降低旗叶水势.气温、CO₂浓度升高以及干旱胁迫共同作用下,冬小麦光合速率和旗叶水分条件显著降低,产量下降41.4%.CO₂浓度升高使冬小麦增产21.2%,温度升高使产量降低12.3%,CO₂浓度和温度同时升高对产量没有影响,干旱胁迫下产量下降程度更大.未来气候变化情景下,保持较高的土壤水分含量是减少气候变暖危害的重要手段.
     

Catechin and epicatechin from Smilacis chinae rhizome protect cultured rat cortical neurons against amyloid beta protein (25-35)-induced neurotoxicity through inhibition of cytosolic calcium elevation

We previously reported that the Smilacis chinae rhizome inhibits amyloid beta protein (25-35) (Abeta (25-35))-induced neurotoxicity in cultured rat cortical neurons. Here, we isolated catechin and epicatechin from S. chinae rhizome and also studied their neuroprotective effects on Abeta (25-35)-induced neurotoxicity in cultured rat cortical neurons. Catechin and epicatechin inhibited 10 microM Abeta (25-35)-induced neuronal cell death at a concentration of 10 microM, which was measured by a 3-[4,5-dimethylthiazol-2-yl]-2,5-diphenyl-tetrazolium bromide (MTT) assay and Hoechst 33342 staining. Catechin and epicatechin inhibited 10 microM Abeta (25-35)-induced elevation of cytosolic calcium concentration ([Ca2+]c), which was measured by a fluorescent dye, Fluo-4 AM. Catechin and epicatechin also inhibited glutamate release into medium induced by 10 microM Abeta (25-35), which was measured by HPLC, generation of reactive oxygen species (ROS) and activation of caspase-3. These results suggest that catechin and epicatechin prevent Abeta (25-35)-induced neuronal cell damage by interfering with the increase of [Ca2+]c, and then by inhibiting glutamate release, generation of ROS and caspase-3 activity. Furthermore, these effects of catechin and epicatechin may be associated with the neuroprotective effect of the S. chinae rhizome.     

Structure, expression, and functional analysis of the hexokinase gene family in rice (Oryza sativa L.)

Hexokinase (HXK) is a dual-function enzyme that both phosphorylates hexose to form hexose 6−phosphate and plays an important role in sugar sensing and signaling. To investigate the roles of hexokinases in rice growth and development, we analyzed rice sequence databases and isolated ten rice hexokinase cDNAs, OsHXK1 (Oryza sativa Hexokinase 1) through OsHXK10. With the exception of the single-exon gene OsHXK1, the OsHXKs all have a highly conserved genomic structure consisting of nine exons and eight introns. Gene expression profiling revealed that OsHXK2 through OsHXK9 are expressed ubiquitously in various organs, whereas OsHXK10 expression is pollen-specific. Sugars induced the expression of three OsHXKs, OsHXK2, OsHXK5, and OsHXK6, in excised leaves, while suppressing OsHXK7 expression in excised leaves and immature seeds. The hexokinase activity of the OsHXKs was confirmed by functional complementation of the hexokinase-deficient yeast strain YSH7.4-3C (hxk1, hxk2, glk1). OsHXK4 was able to complement this mutant only after the chloroplast-transit peptide was removed. The subcellular localization of OsHXK4 and OsHXK7, observed with green fluorescent protein (GFP) fusion constructs, indicated that OsHXK4 is a plastid-stroma-targeted hexokinase while OsHXK7 localizes to the cytosol.Electronic Supplementary Material Supplementary material is available for this article at and is accessible for authorized users.     

Synthetic statistical approach reveals a high degree of richness of microbial eukaryotes in an anoxic water column

Molecular surveys suggest that communities of microbial eukaryotes are remarkably rich, because even large clone libraries seem to capture only a minority of species. This provides a qualitative picture of protistan richness but does not measure its real extent either locally or globally. Statistical analysis can estimate a community's richness, but the specific methods used to date are not always well grounded in statistical theory. Here we study a large protistan molecular survey from an anoxic water column in the Cariaco Basin (Caribbean Sea). We group individual 18S rRNA gene sequences into operational taxonomic units (OTUs) using different cutoff values for sequence similarity (99 to 50%) and systematically apply parametric models and nonparametric estimators to the OTU frequency data to estimate the total protistan diversity. The parametric models provided statistically sound estimates of protistan richness, with biologically meaningful standard errors, maximal data usage, and extensive model diagnostics and were preferable to the available nonparametric tools. Our clone library exceeded 700 clones but still covered only a minority of species and less than half of the larger protistan clades. Our estimates of total protistan richness portray the target community as very rich at all OTU levels, with hundreds of different populations apparently co-occurring in the small (3-liter) volume of our sample, as well as dozens of clades of the highest taxonomic order. These estimates are among the first for microbial eukaryotes that are obtained using state-of-the-art statistical methods and can serve as benchmark numbers for the local diversity of protists.     

干旱区多枝柽柳的生长特性

多枝柽柳是分布最为广泛的柽柳属植物之一。也是维持干旱区荒漠生态系统的关键植物种。本研究运用树轮年代学和树干解析方法。对额济纳地区不同生境条件下多枝柽柳的年轮生长、高生长和地径生长等方面的特征进行初步探讨。多枝柽柳每年形成1个年轮。树盘偏心生长极为普遍．完整树轮大多在10龄以内区域,10龄以外都呈单个或多个不完整年轮生长区。多枝柽柳单枝在1～4年高生长缓慢．4～8龄之间属于快速生长期,10年以上生长速率急剧下降。不同地下水位条件下三组样本径生长年增长速率达到极大值的年龄分别为21、56和74年,水环境条件是影响多枝柽柳径向生长的主要因素。同一年年轮宽度随枝高呈减小趋势。多枝柽柳边材的树轮数一般在3～5轮之间,进入老龄阶段有增加趋势。边材宽度随年龄增长逐渐减小。     

牛血清白蛋白对小鼠原核期胚胎玻璃化冷冻的影响

以小鼠原核期胚胎为对象,以胚胎的存活率、卵裂率、囊胚率以及囊胚细胞数作为检测指标,在M2液的基础上添加8种浓度(0,2,4,8,16,32,64,96mg/mL)牛血清白蛋白(BSA)配置防冻液,探讨防冻液和玻璃化冷冻后对胚胎发育的影响。BSA防冻液对胚胎发育影响的实验结果表明,8个浓度组间以及与对照组间胚胎的卵裂率、囊胚率以及囊胚细胞数无显著差异(P>0.05),说明在防冻液中加入一定浓度的BSA对小鼠胚胎无毒性作用。防冻液经玻璃化冷冻后对胚胎发育影响的实验表明,8个浓度组间冷冻胚胎复苏后的存活率、卵裂率、囊胚率及囊胚细胞数无显著差异(P>0.05)。表明BSA在这种防冻液中没有明显的保护作用。从经济、实用、生物安全角度考虑,不支持在玻璃化防冻液中添加BSA。