Scale specific determinants of tree diversity in an old growth temperate forest in China

The major processes generating pattern in plant community composition depend upon the spatial scale and resolution of observation, therefore understanding the role played by spatial scale on species patterns is of major concern. In this study, we investigate how well environmental (topography and soil variables) and spatial variables explain variation in species composition in a 25-ha temperate forest in northeastern China. We used new variation partitioning approaches to discover the spatial scale (using multi-scale spatial PCNM variables) at which environmental heterogeneity and other spatially structured processes influence tree community composition. We also test the effect of changing grain of the study (i.e. quadrat size) on the variation partitioning results. Our results indicate that (1) species composition in the Changbai mixed broadleaf-conifer forest was controlled mainly by spatially structured soil variation at broad scales, while at finer scales most of the explained variation was of a spatial nature, pointing to the importance of biotic processes. (2) These results held at all sampling grains. However, reducing quadrat size progressively reduced both spatially and environmentally explained variance. This probably partly reflects increasing stochasticity in species abundances, and the smaller proportion of quadrats occupied by each species, when quadrat size is reduced. The results suggest that environmental heterogeneity (i.e. niche processes) and other biotic processes such as dispersal work together, but at different spatial scales, to build up diversity patterns.     

Microtubules induce self-organization of polarized PAR domains in Caenorhabditis elegans zygotes

A hallmark of polarized cells is the segregation of the PAR polarity regulators into asymmetric domains at the cell cortex. Antagonistic interactions involving two conserved kinases, atypical protein kinase C (aPKC) and PAR-1, have been implicated in polarity maintenance, but the mechanisms that initiate the formation of asymmetric PAR domains are not understood. Here, we describe one pathway used by the sperm-donated centrosome to polarize the PAR proteins in Caenorhabditis elegans zygotes. Before polarization, cortical aPKC excludes PAR-1 kinase and its binding partner PAR-2 by phosphorylation. During symmetry breaking, microtubules nucleated by the centrosome locally protect PAR-2 from phosphorylation by aPKC, allowing PAR-2 and PAR-1 to access the cortex nearest the centrosome. Cortical PAR-1 phosphorylates PAR-3, causing the PAR-3-aPKC complex to leave the cortex. Our findings illustrate how microtubules, independently of actin dynamics, stimulate the self-organization of PAR proteins by providing local protection against a global barrier imposed by aPKC.     

Intraflagellar transport delivers tubulin isotypes to sensory cilium middle and distal segments

Sensory cilia are assembled and maintained by kinesin-2-dependent intraflagellar transport (IFT). We investigated whether two Caenorhabditis elegans α- and β-tubulin isotypes, identified through mutants that lack their cilium distal segments, are delivered to their assembly sites by IFT. Mutations in conserved residues in both tubulins destabilize distal singlet microtubules. One isotype, TBB-4, assembles into microtubules at the tips of the axoneme core and distal segments, where the microtubule tip tracker EB1 is found, and localizes all along the cilium, whereas the other, TBA-5, concentrates in distal singlets. IFT assays, fluorescence recovery after photobleaching analysis and modelling indicate that the continual transport of sub-stoichiometric numbers of these tubulin subunits by the IFT machinery can maintain sensory cilia at their steady-state length.     

Clustering 16S rRNA for OTU prediction: a method of unsupervised Bayesian clustering

MOTIVATION: With the advancements of next-generation sequencing technology, it is now possible to study samples directly obtained from the environment. Particularly, 16S rRNA gene sequences have been frequently used to profile the diversity of organisms in a sample. However, such studies are still taxed to determine both the number of operational taxonomic units (OTUs) and their relative abundance in a sample. RESULTS: To address these challenges, we propose an unsupervised Bayesian clustering method termed Clustering 16S rRNA for OTU Prediction (CROP). CROP can find clusters based on the natural organization of data without setting a hard cut-off threshold (3%/5%) as required by hierarchical clustering methods. By applying our method to several datasets, we demonstrate that CROP is robust against sequencing errors and that it produces more accurate results than conventional hierarchical clustering methods. Availability and Implementation: Source code freely available at the following URL: http://code.google.com/p/crop-tingchenlab/, implemented in C++ and supported on Linux and MS Windows.     

The first insight into the <Emphasis Type="Italic">Taxus</Emphasis> genome via fosmid library construction and end sequencing

Taxus mairei is a critically endangered and commercially important cultured medicinal gymnosperm in China and forms an important medicinal resource, but the research of its genome is absent. In this study, we constructed a T. mairei fosmid library and analyzed the fosmid end sequences to provide a preliminary assessment of the genome. The library consists of one million clones with an average insert size of about 39 kb, amounting to 3.9 genome equivalents. Fosmid stability assays indicate that T. mairei DNA was stable during propagation in the fosmid system. End sequencing of both 5′ and 3′ ends of 968 individual clones generated 1,923 sequences after trimming, with an average sequence length of 839 bp. BLASTN searches of the nr and EST databases of GenBank and BLASTX searches of the nr database resulted in 560 (29.1%) significant hits (E < e⁻⁵). Repetitive sequences analysis revealed that 20.8% of end sequences are repetitive elements, which were composed of retroelements, DNA transposons, satellites, simple repeats, and low complexity sequences. The distribution pattern of various repeat types was found to be more similar to the gymnosperm Pinus and Picea than to the monocot and dicot. The satellites of T. mairei were significantly longer than those of P. taeda and P. glauca. The tetra-nucleotide repeats of T. mairei were much longer than those of P. glauca and P. taeda. The fosmid library and the fosmid end sequences, for the first time, will serve as a useful resource for large-scale genome sequencing, physical mapping, SSR marker development and positional cloning, and provide a better understanding of the Taxus genome.     

Enhanced welan gum production using a two-stage agitation speed control strategy in Alcaligenes sp. CGMCC2428

Batch fermentative production of welan gum by Alcaligenes sp. CGMCC2428 was investigated under various oxygen supply conditions using regulating agitation speed. Based on a three kinetic parameters analysis that includes specific cell growth rate (μ), specific glucose consumption rate (q _s), and specific welan formation rate (q _p), a two-stage agitation speed control strategy was proposed to achieve high concentration, high yield, and high viscosity of welan. During the first 22 h, the agitation speed in 7.5 L fermenter was controlled at 800 rpm to maintain high μ for cell growth. The agitation was then reduced step-wise to 600 rpm to maintain a changing profile with stable dissolved oxygen levels and obtain high qp for high welan accumulation. Finally, the maximum concentration of welan was reached at 26.3 ± 0.89 g L⁻¹ with a yield of 0.53 ± 0.003 g g⁻¹ and the welan gum viscosity of 3.05 ± 0.10 Pa s, which increased by an average of 15.4, 15.2, and 20.1% over the best results controlled by constant agitation speeds.     

Electrochemical analysis of Clostridium propionicum and its acrylic acid production in microbial fuel cells

Currently, acrylic acid is produced at a low yield by the resting cells of Clostridium propionicum with the supplement of extra electron acceptors. As an alternative way, acrylic acid production coupled with electricity generation was achieved by C. propionicum‐based microbial fuel cells (MFCs). Electricity was generated in the salt‐bridge MFCs with cysteine and resazurin in the anode chamber as mediators, and K₃Fe(CN)₆ as the cathode electron acceptor. Power generation was 21.78 mW/m² with an internal resistance of 9809 Ω. Cyclic voltammograms indicated the main mechanism of power production was the electron transfer facilitated by mediators in the system. In the salt‐bridge MFC system, 0.694 mM acrylic acid was produced together with electricity generation.     

乌司他丁联合连续性血液净化治疗重症脓毒症临床研究

目的：研究连续性血液净化联合乌司他丁对重症脓毒症患者炎症反应的影响及其临床疗效。方法：70例重症脓毒症患者随机分为对照组（n=22例）、CBP组（n=23例）和CBP＋乌司他丁组（n=25例）,其中对照组采用经典治疗方案,CBP组在此基础上加用连续性血液净化,CBP＋乌司他丁组在CBP组基础上加用乌司他丁治疗。观察比较患者病情发展,分别于治疗前后进行血液生化指标、凝血功能检测和动脉血气分析,ELISA法检测血清CRP水平。结果：①与对照组和CBP组相比,CBP＋鸟司他丁纽患者病死率、ICU住院时间、MODS发生率均明显下降（P〈0．05）。②经过治疗,CBP＋乌司他丁组患者APACHEⅡ评分降至15．46±3．96,与对照组（18．06±4．25）和CBP组（17．14±5．55）比较差异有统计学意义（P〈0．05）。③治疗后,患者BUN、HR降低程度依次为CBP＋乌司他丁组〉CBP组〉对照组,组问比较差异有显著性（P〈0．05）,而治疗前后PH值、HCO3-、MAP比较差并不明显（P〉0．05）。④CBP＋乌司他丁纽血清CRP含量下降,WBC数量减少,其变化程度明显大于CBP组和对照组（P〈0．05）。⑤对照组、CBP组和CBP＋乌司他丁组患者PT、TT和APTT时间延长,血小板数量下降,其中CBP＋鸟司他丁组PT、APTT时间短于CBP组和对照组（P〈0．05）。结论：连续性血液净化联合乌司他丁可有效抑制脓毒症患者炎症反应,缓解病情,改善患者预后。     

Bacillus amyloliquefaciens ES-2发酵产抗菌脂肽消泡剂的筛选及脂肽的提取和纯化

将大豆油、有机硅消泡剂和聚醚类消泡剂3种消泡剂分别用于Bacillus amyloliquefaciens ES-2抗菌脂肽发酵,研究表明大豆油既可以实现消泡,又有利于抗菌脂肽的发酵,使其产量达到了2497.67mg/L。经过提取得到纯度为55.68%的产品,提取率达到88.72%。此外还比较了不同大孔树脂对抗菌脂肽吸附和解吸附效果,发现大孔树脂X-5最适合抗菌脂肽的纯化。纯化的工艺参数为:上样浓度14.4mg/ml、上样速率1ml/min,洗脱速率2ml/min、洗脱剂用量2.5BV,产品的回收率达90.01%,纯度达74.4%。