Links between archaeal community structure, vegetation type and methanogenic pathway in Alaskan peatlands

Although northern peatlands contribute significantly to natural methane emissions, recent studies of the importance and type of methanogenesis in these systems have provided conflicting results. Mechanisms controlling methanogenesis in northern peatlands remain poorly understood, despite the importance of methane as a greenhouse gas. We used 16S rRNA gene retrieval and denaturing gradient gel electrophoresis (DGGE) to analyse archaeal communities in 15 high-latitude peatland sites in Alaska and three mid-latitude peatland sites in Massachusetts. Archaeal community composition was analysed in the context of environmental, vegetation and biogeochemical factors characterized in a parallel study. Phylogenetic analysis revealed that Alaskan sites were dominated by a cluster of uncultivated crenarchaeotes and members of the families Methanomicrobiaceae and Methanobacteriaceae, which are not acetoclastic. Members of the acetoclastic family Methanosarcinaceae were not detected, whereas those of the family Methanosaetaceae were either not detected or were minor. These results are consistent with biogeochemical evidence that acetoclastic methanogenesis is not a predominant terminal decomposition pathway in most of the sites analysed. Ordination analyses indicated a link between vegetation type and archaeal community composition, suggesting that plants (and/or the environmental conditions that control their distribution) influence both archaeal community activity and dynamics.     

The virus as metabolic engineer

Recent genome-wide screens of host genetic requirements for viral infection have reemphasized the critical role of host metabolism in enabling the production of viral particles. In this review, we highlight the metabolic aspects of viral infection found in these studies, and focus on the opportunities these requirements present for metabolic engineers. In particular, the objectives and approaches that metabolic engineers use are readily comparable to the behaviors exhibited by viruses during infection. As a result, metabolic engineers have a unique perspective that could lead to novel and effective methods to combat viral infection.     

Thermodynamic and electrostatic properties of ternary Oxytricha nova TEBP-DNA complex

Telomeres constitute the nucleoprotein ends of eukaryotic chromosomes which are essential for their proper function. Telomere end binding protein (TEBP) from Oxytricha nova was among the first telomeric proteins, which were well characterized biologically. TEBP consists of two protein subunits (alpha, beta) and forms a ternary complex with single stranded telomeric DNA containing tandem repeats TTTTGGGG. This work presents the characterization of the thermodynamic and electrostatic properties of this complex by computational chemistry methods (continuum Poisson-Boltzmann and solvent accessible surface calculations). Our calculations give a new insight into molecular properties of studied system. Based on the thermodynamic analysis we provide a rationale for the experimental observation that alpha and ssDNA forms a binary complex and the beta subunit joins alpha:ssDNA complex only after the latter is formed. Calculations of distribution of the molecular electrostatic potential for protein subunits alone and for all possible binary complexes revealed the important role of the "guiding funnel" potential generated by alpha:ssDNA complex. This potential may help the beta subunit to dock to the already formed alpha:DNA intermediate in highly steric and electrostatic favorable manner. Our pK(a) calculations of TEBP are able to explain the experimental mobility shifts of the complex in electrophoretic non-denaturating gels.     

HeLa细胞中Skp2的表达调控p21WAFCIP1稳定性

泛素 蛋白酶体抑制剂MG 132处理的HeLa和SaoS 2细胞中 ,低表达的p2 1WAF CIP1受泛素 蛋白酶体通路调控 .为探讨肿瘤细胞中高表达的E3连接酶底物结合亚基 Skp2和低表达的p2 1WAF CIP1之间的关系 ,在HeLa细胞中转染Skp2的反义寡核苷酸后 ,p2 1表达水平明显升高 .同时 ,相对于转染空载体和Skp2ΔF(Skp2的F box缺失突变体 )的真核表达载体 ,转染全长Skp2的HeLa细胞中 ,p2 1表达水平显著下降 ,说明肿瘤细胞中Skp2调节p2 1的稳定性 ,并且这种调控作用依赖于Skp2蛋白中的F box结构 .免疫荧光结果表明 ,Skp2和p2 1共定位于细胞核 ,这为两者间的相互作用提供了前提 ;体内相互免疫共沉淀结果表明 ,p2 1和其它SCFSkp2 的底物一样与Skp2直接结合 ,并且它们之间的结合区不在F box结构域 ,这一结果在体外的GST pulldown实验中得到验证     

Building protein interaction maps for Down's syndrome.

Now that the complete sequences for human chromosome 21 and the orthologous mouse genomic regions are known, reasonably complete, conserved, protein-coding gene catalogues are also available. The central issue now facing Down's syndrome researchers is the correlation of increased expression of specific, normal, chromosome 21 genes with the development of specific deficits in learning and memory. Because of the number of candidate genes involved, the number of alternative splice variants of individual genes and the number of pathways in which these genes function, a pathway analysis approach will be critical to success. Here, three examples, both gene specific and pathway related, that would benefit from pathway analysis are discussed: (1) the potential roles of eight chromosome 21 proteins in RNA processing pathways; (2) the chromosome 21 protein intersectin 1 and its domain composition, alternative splicing, protein interactions and functions; and (3) the interactions of ten chromosome 21 proteins with components of the mitogen-activated protein kinase and the calcineurin signalling pathways. A productive approach to developing gene-phenotype correlations in Down's syndrome will make use of known and predicted functions and interactions of chromosome 21 genes to predict pathways that may be perturbed by their increased levels of expression. Investigations may then be targeted in animal models to specific interactions, intermediate steps or end-points of such pathways and the downstream - perhaps amplified - consequences of gene dosage directly assessed. Once pathway perturbations have been identified, the potential for rational design of therapeutics becomes practical.     

p53 Represses the Mevalonate Pathway to Mediate Tumor Suppression

1. Download high-res image (125KB)
2. Download full-size image

     

Matriptase-2- and proprotein convertase-cleaved forms of hemojuvelin have different roles in the down-regulation of hepcidin expression

Hemojuvelin (HJV) is an important regulator of iron metabolism. Membrane-anchored HJV up-regulates expression of the iron regulatory hormone, hepcidin, through the bone morphogenic protein (BMP) signaling pathway by acting as a BMP co-receptor. HJV can be cleaved by the furin family of proprotein convertases, which releases a soluble form of HJV that suppresses BMP signaling and hepcidin expression by acting as a decoy that competes with membrane HJV for BMP ligands. Recent studies indicate that matriptase-2 binds and degrades HJV, leading to a decrease in cell surface HJV. In the present work, we show that matriptase-2 cleaves HJV at Arg(288), which produces one major soluble form of HJV. This shed form of HJV has decreased ability to bind BMP6 and does not suppress BMP6-induced hepcidin expression. These results suggest that the matriptase-2 and proprotein convertase-cleavage products have different roles in the regulation of hepcidin expression.     

In silico analysis of expression pattern of a Wnt/β-catenin responsive gene ANLN in gastric cancer

Actin-binding protein anillin (ANLN) is primarily involved in the cytokinesis and known to be dysregulated in many cancers including gastric cancer (GC). However, the regulation and clinical significance of ANLN in GC are far less clear. In the present study, we aimed to investigate the clinical significance and possible regulators of ANLN in GC. We have identified the Wnt/β-catenin associated regulation of ANLN by analyzing the in vitro perturbed β-catenin mRNA expression profiles. Investigating the gastric tumors from publicly available genome-wide mRNA expression profiles, we have identified the over expression of ANLN in gastric tumors. Association between ANLN expression and clinical characteristics of GC showed elevated expression in intestinal type GC. Performing a single sample prediction method across GC mRNA expression profiles, we have identified the over expression of ANLN in proliferative type gastric tumors compared to the invasive and metabolic type gastric tumors. In silico pathway prediction analysis revealed the association between Wnt/β-catenin signaling and ANLN expression in gastric tumors. Our results highlight that expression of a Wnt/β-catenin responsive gene ANLN in GC is a molecular predictor of intestinal and proliferative type gastric tumors.     

Improved abundance prediction from presence–absence data

Aim   Many ecological surveys record only the presence or absence of species in the cells of a rectangular grid. Ecologists have investigated methods for using these data to predict the total abundance of a species from the number of grid cells in which the species is present. Our aim is to improve such predictions by taking account of the spatial pattern of occupied cells, in addition to the number of occupied cells.
Innovation   We extend existing prediction models to include a spatial clustering variable. The extended models can be viewed as combining two macroecological regularities, the abundance–occupancy regularity and a spatial clustering regularity. The models are estimated using data from five tropical forest censuses, including three Panamanian censuses (4, 6 and 50 ha), one Costa Rican census (16 ha) and one Puerto Rican census (16 ha). A serpentine grassland census (8 × 8 m) from northern California is also studied.
Main conclusions   Taking account of the spatial clustering of occupied cells improves abundance prediction from presence–absence data, reducing the mean square error of log-predictions by roughly 54% relative to a benchmark Poisson predictor and by roughly 34% relative to current prediction methods. The results have high statistical significance.     

模糊线性回归模型在河流水体总氮浓度预测中的应用

以湘江熬洲断面为例,将该断面水体中总氮浓度及其有关影响因子用三角模糊数来表征.同时,结合己有的模糊线性回归模型成果,构造了带有三角模糊参数的水体中总氮浓度模糊线性回归预测模型.并应用所建模型预测该断面水体中2002-2005年总氮浓度,所得的预测值与已有的实测值之间的相对误差均小于20%,完全满足实际应用对误差的要求,预测合格率为100%,说明这种预测模型在预测河流水体总氮浓度变化中有一定的实用性,为今后开展河流水体中污染物浓度预测提供了新途径.