Construction of an E. Coli genome-scale atom mapping model for MFA calculations

Metabolic flux analysis (MFA) has so far been restricted to lumped networks lacking many important pathways, partly due to the difficulty in automatically generating isotope mapping matrices for genome-scale metabolic networks. Here we introduce a procedure that uses a compound matching algorithm based on the graph theoretical concept of pattern recognition along with relevant reaction information to automatically generate genome-scale atom mappings which trace the path of atoms from reactants to products for every reaction. The procedure is applied to the iAF1260 metabolic reconstruction of Escherichia coli yielding the genome-scale isotope mapping model imPR90068. This model maps 90,068 non-hydrogen atoms that span all 2,077 reactions present in iAF1260 (previous largest mapping model included 238 reactions). The expanded scope of the isotope mapping model allows the complete tracking of labeled atoms through pathways such as cofactor and prosthetic group biosynthesis and histidine metabolism. An EMU representation of imPR90068 is also constructed and made available.     

湖北竹溪植被的基本特征

竹溪县现有种子植物１２７科４８３属８６３种。地理成分复杂,联系广泛,以温带成分占主导地位,占非世界分布属的６４．８３％,热带分布属则占２９．３９％,木本植物占种子植物总数的４２．５９％,主要植补类型计７个植补型组,１０个植被型,４９个联系。地处竹溪中南部的云雾溪是目前亚热带区域保存较为完整,具有多方面保护价值的综合区,建议辟为自然保护区。     

Detecting complex relations among vegetation,soil and geomorphology. An in-depth method applied to a case study in the Apennines (Italy)

Physical environment is the ruling factor of vegetation patterns in mountain areas, where vegetation mosaics are determined by a complex interplay among topography, geomorphology and soil. A deep analysis of such interplay is pivotal in order to build vegetation anamnesis and make sound projections. Instead, even recent cartographic models are still linked to standard statistical methods which are not on top of an efficient uncovering of knotty associations among these kinds of data. To this aim, in this study we propose a novel approach for: (a) assessing the associations among vegetation, soil, topography and geomorphology; (b) measuring the frequency and strength of these associations; (c) define in a rigorous way land units based on vegetation–soil–geomorphology associations; (d) advance hypotheses on the causes and prospects of the existing spatial pattern. In order to test the strength of the proposed methodology we applied it to a case study in the above-tree-line glacial cirque of Mount Prado (Northern Apennines, N Italy). In this area, the vegetation mosaic is still strongly conditioned by physical features but in a lower measure with respect to the higher alpine sites. We have been able to detect and weight 168 kinds of associations among vegetation, soil and geomorphological types, 1092 kinds of associations among vegetation and topographic variables and 12 land units with inner dominance of a particular association. The analysis of associations between vegetation types, soils, topography and landforms produced considerable insights into the ecology of the occurring plant communities. This proposed analytic methodology can be extended to other regions (e.g. mountain and alpine areas) and can also be considered a tool for interpreting present landscape heterogeneity also in a historical perspective.     

Analysis of the genome of an alkaliphilic Bacillus strain from an industrial point of view

Bacillus species and other microbes with pH optima for growth higher than pH 9 are defined as alkaliphiles. A large number of alkaliphilic Bacillus strains producing useful enzymes, have been isolated from various environments. Some of these enzymes, such as proteases and cellulases from alkaliphilic Bacillus strains, have been commercialized and have brought great advantages to industry and domestic life. To support further development of the enzyme industry, we initiated analysis of the genome of Bacillus halodurans C-125, which is 4.25 Mb in size, and constructed a physical and genetic map for comparison with the Bacillus subtilis chromosome. Systematic sequencing of the whole genome of Bacillus halodurans C-125 has been automated since the beginning of May 1998, and sequencing of 98% of the whole genome has been done so far. Through genome analysis, it became apparent that the genome organization of alkaliphilic Bacillus halodurans C-125 is totally different from that of B. subtilis orthologues. Received: July 11, 1999 / Accepted: December 27, 1999     

Physical mapping of plastid DNA variation among eleven Nicotiana species

Summary Plastid DNA of seven American and four Australian species of the genus Nicotiana was examined by restriction endonuclease analysis using the enzymes Sal I, Bgl I, Pst I, Kpn I, Xho I, Pvu II and Eco RI. These endonucleases collectively distinguish more than 120 sites on N. tabacum plastid DNA. The DNAs of all ten species exhibited restriction patterns distinguishable from those of N. tabacum for at least one of the enzymes used. All distinctive sites were physically mapped taking advantage of the restriction cleavage site map available for plastid DNA from Nicotiana tabacum (Seyer et al. 1981). This map was extended for the restriction endonucleases Pst I and Kpn I. In spite of variation in detail, the overall fragment order was found to be the same for plastid DNA from the eleven Nicotiana species. Most of the DNA changes resulted from small insertions/deletions and, possibly, inversions. They are located within seven regions scattered along the plastid chromosome. The divergence pattern of the Nicotiana plastid chromosomes was strikingly similar to that found in the genus Oenothera subsection Euoenothera (Gordon et al. 1982). The possible role of replication as a factor in the evolution of divergence patterns is discussed. The restriction patterns of plastid DNA from species within a continent resembled each other with one exception in each instance. The American species N. repanda showed patterns similar to those of most Australian species, and those of the Australian species N. debneyi resembled those of most American species.Abbreviations ims isonuclear male sterile - ptDNA plastid chloroplast DNA - Rubisco ribulosebisphosphate carboxylase/oxygenase - kbp kilobase pairs - LSU large subunit of Rubisco     

Actin surface structure revealed by antibody imprints: evaluation of phage-display analysis of anti-actin antibodies

Phage-display peptide library analysis of an anti-F actin polyclonal antibody identified 12 amino acid residues of actin that appear, in its X-ray crystal structure, to be grouped together in a surface accessible conformational epitope. Phage epitope mapping was carried out by isolating immune complexes containing members of the J404 nonapeptide phage-display library formed in diluted antiserum and isolated on a protein A affinity matrix. Immunoreactive clones were grown as plaques, replica plated onto nitrocellulose, and labeled with anti-actin immune serum. One hundred and forty-four positively staining clones identified in this way were sequenced. Of these, 54 displayed peptides with sequence similarities. When the most abundantly selected sequence, KQTWQQLWD, was produced as a synthetic peptide and derivatized to ovalbumin, the complex was strongly recognized by the antiserum on Western blots and inhibited the binding of the antibody to immobilized F-actin by 60%. A scrambled version of this sequence WQDK WLQTQ, when coupled to ovalbumin, was not recognized by the antiserum and minimally inhibited binding of antiserum to immobilized F-actin by 10%. KQTWQQLWD contained four residues that corresponded, in frame, to a highly conserved six residue region of the chicken beta-actin sequence 351TFQQMW356 (identical residues are shown in bold). Examination of the rabbit skeletal muscle X-ray crystal structure suggested that within a 15 A radius of W356, nine additional residues were arranged on the actin surface in such a way that they could be mimicked by several of the selected phage sequences with root-mean-square deviation fits of 2.1-2.5 A. We conclude that phage-display analysis can provide information about the relative location of amino acids on the surfaces of proteins using antibody imprints of the protein surface structure.     

Assessing the effect of EWDP on vegetation restoration by remote sensing in the lower reaches of Tarim River

In this study, effect of ecological water diversion on vegetation restoration in the lower reaches of Tarim River is assessed by coupling remote sensing techniques and a field-based survey. Land use/cover and fractional vegetation coverage (Fvc) maps derived from remote sensing images, ground validation data, and hydrological observation data are adopted to analyze the responses of Ecological Water Diversion Project (EWDP). The results indicate that, the EWDP has showed a positive effect on vegetation restoration in the lower part of Tarim Basin. During 2001 to 2013, transformation from unused land to nature vegetation (i.e. forest land, grassland and scrubland) was the major process of land use/cover change; the area of natural vegetation showed a 4.7% increase, and the area of unused land reduced by 6.8%. Landscape patch size was decreased, the degree of fragmentation and diversity of landscape was increased, and landscape structure in the study area became more complex. Moreover, vegetation coverage promoted from 2001 to 2013; average Fvc in 2013 was 1.5 times greater than that in 2001. The results can provide not only an accurate assessment for the EWDP, but also a visual insight for the water resources management practices in the study area, such that the sustainability for local ecosystem can be facilitated.     

Cotton genome mapping with new microsatellites from Acala ‘Maxxa’ BAC-ends

Fine mapping and positional cloning will eventually improve with the anchoring of additional markers derived from genomic clones such as BACs. From 2,603 new BAC-end genomic sequences from Gossypium hirsutum Acala ‘Maxxa’, 1,316 PCR primer pairs (designated as MUSB) were designed to flank microsatellite or simple sequence repeat motif sequences. Most (1164 or 88%) MUSB primer pairs successfully amplified DNA from three species of cotton with an average of three amplicons per marker and 365 markers (21%) were polymorphic between G. hirsutum and G. barbadense. An interspecific RIL population developed from the above two entries was used to map 433 marker loci and 46 linkage groups with a genetic distance of 2,126.3 cM covering approximately 45% of the cotton genome and an average distance between two loci of 4.9 cM. Based on genome-specific chromosomes identified in G. hirsutum tetraploid (A and D), 56.9% of the coverage was located on the A subgenome while 39.7% was assigned to the D subgenome in the genetic map, suggesting that the A subgenome may be more polymorphic and recombinationally active than originally thought. The linkage groups were assigned to 23 of the 26 chromosomes. This is the first genetic map in which the linkage groups A01 and A02/D03 have been assigned to specific chromosomes. In addition the MUSB-derived markers from BAC-end sequences markers allows fine genetic and QTL mapping of important traits and for the first time provides reconciliation of the genetic and physical maps. Limited QTL analyses suggested that loci on chromosomes 2, 3, 12, 15 and 18 may affect variation in fiber quality traits. The original BAC clones containing the newly mapped MUSB that tag the QTLs provide critical DNA regions for the discovery of gene sequences involved in biological processes such as fiber development and pest resistance in cotton. Electronic Supplementary Material Supplementary material is available for this article at and is accessible for authorized users.     

Limits to convergence of vegetation during early primary succession

Questions: Primary succession, measured by changes in species composition, is slow, usually forcing a chronose‐quence approach. A unique data set is used to explore spatial and temporal changes in vegetation structure after a 1980 volcanic eruption. On the basis of data from a transect of 20 permanent plots with an altitudinal range of 250 m sampled through 2005, two questions are asked: Do changes along the transect recapitulate succession? Do plots converge to similar composition over time? Location: A ridge between 1218 and 1468 m on Mount St. Helens, Washington, USA. Methods: Repeat sampling of plots for species cover along a 1‐km transect. Floristic changes were characterized by techniques including DCA, clustering and similarity. Results: Species richness and cover increased with time at rates that decreased with increasing elevation. The establishment of Lupinus lepidus accelerated the rate of succession and may control its trajectory. Diversity (H) at first increased with richness, then declined as dominance hierarchies developed. Primary succession was characterized by overlapping phases of species assembly (richness), vegetation maturation (diversity peaks, cover expands) and inhibition (diversity declines). Each plot passed through several community classes, but by 2005, only four classes persisted. Succession trajectories (measured by DCA) became shorter with elevation. Similarity between groups of plots defined by their classification in 2005 did not increase with time. Similarity within plot groups converged slightly at the lower elevations. Despite similarities between temporal and spatial trends in composition, trajectories of higher plots do not recapitulate those of lower plots, apparently because Lupinus was not an early colonist. Any vegetation convergence has been limited to plots that are in close proximity.