Composition and dynamics of microbial community in a zeolite biofilter-membrane bioreactor treating coking wastewater

In this study, a lab-scale anaerobic/anoxic/zeolite biofilter-membrane bioreactor (A₁/A₂/ZB-MBR) was designed to treat coking wastewater. The 454 pyrosequencing was used to obtain the composition and dynamics of microbial community about the treatment system. The results showed that the system yielded stable effluent chemical oxidation demand (158.5?±?21.8 mg/L) and ammonia (8.56?±?7.30 mg/L), but fluctuant total nitrogen (31.4–165.1 mg/L) concentrations. In addition, 66,256 16S rRNA gene sequences were obtained from A₂ and ZB-MBR, and the microbial diversity and richness for five samples were determined. Although community compositions in the five samples were quite different, bacteria assigned to phylum Proteobacteria and class Flavobacteria commonly existed and dominated the microbial populations. The pyrosequencing analysis revealed that the microbial community shifted in the ZB-MBR with the presence of zeolite. Some taxa began to appear in ZB-MBR and contributed to the system performance. Additionally, Nitrosomonas and Nitrobacter gradually became the dominant ammonia-oxidizing bacteria and nitrite-oxidizing bacteria during the operation, respectively, which are favorable for the stabilized ammonia removal. Our results proved that the ZB-MBR is an alternative technique for treating coking wastewater.     

Long-term effects of multi-walled carbon nanotubes on the performance and microbial community structures of an anaerobic granular sludge system

Multi-walled carbon nanotubes (MWCNTs) released into the sewage may cause negative and/or positive effects on the treatment system. The objective of this study was to explore over 110 days’ effect of MWCNTs on the performance of anaerobic granular sludge and microbial community structures in an upflow anaerobic sludge blanket (UASB) reactor. The results showed that MWCNTs had no significant effect on the removal of chemical oxidation demand (COD) and ammonia in UASB reactor, but the total phosphorus (TP) removal efficiency increased by 29.34%. The biogas production of the reactor did not change. The anaerobic granular sludge tended to excrete more EPS to resist the effects of MWCNTs during the long-term impact. Illumina MiSeq sequencing of 16S rRNA gene revealed that MWCNTs did not affect the microbial diversity, but altered the composition and structure of microbial community in the reactor. In this process, Saccharibacteria replaced Proteobacteria as the highest abundant bacterial phylum. MWCNTs promoted the differentiation of methanogen structure, resulting in increase of Methanomassiliicoccus, Methanoculleus, and the uncultured WCHA1–57. These results indicated that MWCNTs impacted the performance of UASB reactor and the structures of the microbial community in anaerobic granular sludge.

     

Novel Biomarkers for Non-functioning Invasive Pituitary Adenomas were Identified by Using Analysis of microRNAs Expression Profile

The microRNAs (miRNAs) are involved in multiple pathological processes among various types of tumors. However, the functions of miRNAs in benign brain tumors are largely unexplored. In order to explore the pathogenesis of the invasiveness in non-functional pituitary adenoma (NFPA), the miRNAs expression profile was analyzed between invasive and non-invasive non-functional pituitary adenoma by miRNAs microarray. Six most significant differentially expressed miRNAs were identified including four upregulated miRNAs hsa-miR-181b-5p, hsa-miR-181d, hsa-miR-191-3p, and hsa-miR-598 and two downregulated miRNAs hsa-miR-3676-5p and hsa-miR-383. The functions and corresponding signaling pathways of differentially expressed miRNAs were investigated by bioinformatics techniques, including Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis. The result of GO analysis indicates regulation of voltage-gated potassium channel activity, positive regulation of sodium ion transport, positive regulation of GTPase activity, negative regulation of Notch signaling pathway, etc. KEGG pathway reveals a series of biological processes, including prolactin signaling pathway, endocrine and other factor-regulated calcium reabsorption, fatty acid metabolism, neuroactive ligand-receptor interaction, etc. The miRNAs hsa-miR-181a-5p was verified by quantitative real-time PCR, and the expression level was in accordance with the microarray result. Our result can provide the evidence on featured miRNAs which play a prominent role in pituitary adenoma as effective biomarkers and therapeutic targets in the future.     

森林伐后碳减排核算方法演进与展望

森林生态系统的碳汇功能对我国完成“双碳目标”具有独特意义,其中森林伐后碳减排,包括木质林产品全生命周期内的碳储和替代减排,是增强林业中长期碳减排能力的重要路径。当前我国森林伐后碳减排研究尚落后于欧美等发达国家,不利于我国林业国家碳库模型的构建以及更好地指导固碳增汇的森林管理策略。系统回顾了近30余年国内外学术界关于森林伐后碳减排方法学的演进动态,总结了碳循环和碳减排模型的核心参数,为推进我国森林伐后碳减排研究提供理论基础。学术界近30余年涉及方法模型的主要成果如下：(1)建立并完善了立足于木材采伐国的生产法和简单分解法,以及立足于终端木质林产品消费国的储量变化法和大气流动法两类方法框架;(2)形成了体系化的碳储计算模型,并在包括发达国家和主要发展中国家取得了大量实测数据和参数积累;(3)初步完成了替代减排分析模型和基于情景设定的分析框架,并在以欧美国家为主体的部分地区进行了应用。在梳理历史文献的基础上,本研究认为当前存在的方法缺陷包括：第一,既有依靠实测调研获取数据的成本过高,限制了研究国家的深度和广度,尤其导致广大发展中国家研究较为薄弱;第二,当前方法框架在追踪木质林产品贸易流方面较...     

Cytoplasmic domain phosphorylation of heparin-binding EGF-like growth factor

Heparin-binding EGF-like growth factor (HB-EGF) is synthesized as a transmembrane precursor protein that is anchored to the plasma membrane. The extracellular EGF-like domain acts as a mitogen and motogen upon ectodomain shedding, but the functional roles of the transmembrane and cytoplasmic domains are largely unknown. We demonstrate here that cytoplasmic domain of HB-EGF is phosphorylated by external stimuli, and that the phosphorylation site is involved in HB-EGF-dependent tumorigenesis. Treatment of Vero cells overexpressing human HB-EGF with 12-O-tetradecanoylphorbol-13-acetate (TPA) caused ectodomain shedding of HB-EGF and generated two carboxyl (C)-terminal fragments with distinct electrophoretic mobilities. Mutation analysis showed that Ser207 in the cytoplasmic domain of HB-EGF is phosphorylated upon TPA stimulation, generating two C-terminal fragments with distinct phosphorylation states. Treatment of cells with lysophosphatidic acid, anisomycin, and calcium ionophore, all of which are known to induce ectodomain shedding, also caused phosphorylation of HB-EGF. Although ectodomain shedding and phosphorylation of HB-EGF occurred coordinately, Ala substitution of Ser207 had no effect on TPA-induced or constitutive ectodomain shedding. Injection of cells overexpressing HB-EGF into nude mice showed that Ala substitution of Ser207 reduced the tumorigenic activity of HB-EGF, even though the cell surface level and ectodomain shedding of HB-EGF were not affected by the mutation. Moreover, we found that the cytoplasmic domain of another EGFR ligand, transforming growth factor-alpha, is phosphorylated upon TPA stimulation. Thus, the present results suggest a novel role for the cytoplasmic domain of HB-EGF and other EGF family growth factors that is regulated by phosphorylation.     

IndexToolkit: an open source toolbox to index protein databases for high-throughput proteomics

A software package, IndexToolkit, aimed at overcoming the disadvantage of FASTA-format databases for frequent searching, is developed to utilize an indexing strategy to substantially accelerate sequence queries. IndexToolkit includes user-friendly tools and an Application Programming Interface (API) to facilitate indexing, storage and retrieval of protein sequence databases. As open source, it provides a sequence-retrieval developing framework, which is easily extensible for high-speed-request proteomic applications, such as database searching or modification discovering. We applied IndexToolkit to database searching engine pFind to demonstrate its effect. Experimental studies show that IndexToolkit is able to support significantly faster searches of protein database. AVAILABILITY: The IndexToolkit is free to use under the open source GNU GPL license. The source code and the compiled binary can be freely accessed through the website http://pfind.jdl.ac.cn/IndexToolkit. In this website, the more detailed information including screenshots and documentations for users and developers is also available.     

Atypical OmpR/PhoB Subfamily Response Regulator GlnR of Actinomycetes Functions as a Homodimer,Stabilized by the Unphosphorylated Conserved Asp-focused Charge Interactions

The OmpR/PhoB subfamily protein GlnR of actinomycetes is an orphan response regulator that globally coordinates the expression of genes related to nitrogen metabolism. Biochemical and genetic analyses reveal that the functional GlnR from Amycolatopsis mediterranei is unphosphorylated at the potential phosphorylation Asp⁵⁰ residue in the N-terminal receiver domain. The crystal structure of this receiver domain demonstrates that it forms a homodimer through the α4-β5-α5 dimer interface highly similar to the phosphorylated typical response regulator, whereas the so-called “phosphorylation pocket” is not conserved, with its space being occupied by an Arg⁵² from the β3-α3 loop. Both in vitro and in vivo experiments confirm that GlnR forms a functional homodimer via its receiver domain and suggest that the charge interactions of Asp⁵⁰ with the highly conserved Arg⁵² and Thr⁹ in the receiver domain may be crucial in maintaining the proper conformation for homodimerization, as also supported by molecular dynamics simulations of the wild type GlnR versus the deficient mutant GlnR(D50A). This model is backed by the distinct phenotypes of the total deficient GlnR(R52A/T9A) double mutant versus the single mutants of GlnR (i.e. D50N, D50E, R52A and T9A), which have only minor effects upon both dimerization and physiological function of GlnR in vivo, albeit their DNA binding ability is weakened compared with that of the wild type. By integrating the supportive data of GlnRs from the model Streptomyces coelicolor and the pathogenic Mycobacterium tuberculosis, we conclude that the actinomycete GlnR is atypical with respect to its unphosphorylated conserved Asp residue being involved in the critical Arg/Asp/Thr charge interactions, which is essential for maintaining the biologically active homodimer conformation.     

Activation of ERK signaling upon alternative protease nexin-1 internalization mediated by syndecan-1

Protease nexin-1 (PN-1), an inhibitor of serine proteases, contributes to tissue homeostasis and influences the behavior of some tumor cells. The internalization of PN-1 protease complexes is considered to be mediated by the low-density lipoprotein receptor related protein 1 (LRP1). In this study, both wild-type and LRP1-/- mouse embryonic fibroblasts (MEF) were shown to internalize PN-1. Receptor associated protein (RAP) interfered with PN-1 uptake only in wild-type MEF cells, indicating that another receptor mediates PN-1 uptake in the absence of LRP1. In LRP1-/- MEF cells, inhibitor sensitivity and kinetic values (t(1/2) at 45 min) of PN-1 uptake showed a similarity to syndecan-1-mediated endocytosis. In these cells, PN-1 uptake was increased by overexpression of full-length syndecan-1 and decreased by RNA interference targeting this proteoglycan. Most important, in contrast to PKA activation known to be triggered by LRP1-mediated internalization, our study shows that syndecan-1-mediated internalization of PN-1 stimulated the Ras-ERK signaling pathway.     

重金属铜、锌、镉复合胁迫对麻疯树幼苗生理生化的影响

该研究以Cu~(2+)、Zn~(2+)、Cd~(2+)单一胁迫为对照,探讨不同浓度的Cu~(2+)、Zn~(2+)、Cd~(2+)复合胁迫对麻疯树幼苗生理生化指标的影响。结果表明:随着Cu~(2+)、Zn~(2+)、Cd~(2+)浓度的增加,麻疯树幼苗叶片中的蛋白质(Pro)、丙二醛(MDA)含量均逐渐增加,其叶片叶绿素含量随着Zn~(2+)胁迫浓度的增加呈现出先降后升的趋势,在中等浓度(100 mg·L-1)的Zn~(2+)胁迫时含量最低、随着Cu~(2+)胁迫浓度的增加叶绿素含量先升高后降低,在Cu~(2+)浓度为200 mg·L-1时含量最高,达到1 200 mg·g-1FW; Cd~(2+)胁迫对叶绿素含量和根系活力无明显影响。根系活力在Zn~(2+)浓度为100 mg·L~(-1)时最强,随着Cu~(2+)浓度的增加而减弱。低浓度的Cu~(2+)、Zn~(2+)、Cd~(2+)对过氧化物酶活性和可溶性糖含量都具有促进作用。Cu~(2+)、Zn~(2+)、Cd~(2+)复合胁迫时对可溶性蛋白、叶绿素和丙二醛含量均无明显影响,随着复合胁迫时浓度的增加,可溶性糖含量和根系活力先增后减。这表明麻疯树对三种重金属的胁迫具有一定的抗性,过高浓度的胁迫会影响麻疯树幼苗生理生化的一些指标,但是麻疯树可以通过自身的防御系统使伤害降到最小。此外,重金属复合胁迫可以在一定程度上减轻单一胁迫对麻疯树幼苗造成的毒害作用。