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81.
Robert Walker Elizabeth Watkin Rui Tian Lambert Br?u Graham O’Hara Lynne Goodwin James Han Elizabeth Lobos Marcel Huntemann Amrita Pati Tanja Woyke Konstantinos Mavromatis Victor Markowitz Natalia Ivanova Nikos Kyrpides Wayne Reeve 《Standards in genomic sciences》2014,9(3):551-561
Burkholderia sp. strain WSM2230 is an aerobic, motile, Gram-negative, non-spore-forming acid-tolerant rod isolated from acidic soil collected in 2001 from Karijini National Park, Western Australia, using Kennedia coccinea (Coral Vine) as a host. WSM2230 was initially effective in nitrogen-fixation with K. coccinea, but subsequently lost symbiotic competence. Here we describe the features of Burkholderia sp. strain WSM2230, together with genome sequence information and its annotation. The 6,309,801 bp high-quality-draft genome is arranged into 33 scaffolds of 33 contigs containing 5,590 protein-coding genes and 63 RNA-only encoding genes. The genome sequence of WSM2230 failed to identify nodulation genes and provides an explanation for the observed failure of the laboratory grown strain to nodulate. The genome of this strain is one of 100 sequenced as part of the DOE Joint Genome Institute 2010 Genomic Encyclopedia for Bacteria and Archaea-Root Nodule Bacteria (GEBA-RNB) project. 相似文献
82.
Pérez-Martín J Castillo-Lluva S Sgarlata C Flor-Parra I Mielnichuk N Torreblanca J Carbó N 《Molecular genetics and genomics : MGG》2006,276(3):211-229
Activation of virulence in pathogenic fungi often involves differentiation processes that need the reset of the cell cycle and induction of a new morphogenetic program. Therefore, the fungal capability to modify its cell cycle constitutes an important determinant in carrying out a successful infection. The dimorphic fungus Ustilago maydis is the causative agent of corn smut disease and has lately become a highly attractive model in addressing fundamental questions about development in pathogenic fungi. The different morphological and genetic changes of U. maydis cells during the pathogenic process advocate an accurate control of the cell cycle in these transitions. This is why this model pathogen deserves attention as a powerful tool in analyzing the relationships between cell cycle, morphogenesis, and pathogenicity. The aim of this review is to summarize recent advances in the unveiling of cell cycle regulation in U. maydis. We also discuss the connection between cell cycle and virulence and how cell cycle control is an important downstream target in the fungus-plant interaction. 相似文献
83.
Camilla Dornfeld Alexandra J. Weisberg Ritesh K C Natalia Dudareva John G. Jelesko Hiroshi A. Maeda 《The Plant cell》2014,26(7):3101-3114
The aromatic amino acid Phe is required for protein synthesis and serves as the
precursor of abundant phenylpropanoid plant natural products. While Phe is
synthesized from prephenate exclusively via a phenylpyruvate intermediate in model
microbes, the alternative pathway via arogenate is predominant in plant Phe
biosynthesis. However, the molecular and biochemical evolution of the plant arogenate
pathway is currently unknown. Here, we conducted phylogenetically informed
biochemical characterization of prephenate aminotransferases (PPA-ATs) that belong to class-Ib aspartate aminotransferases
(AspAT Ibs) and catalyze the first
committed step of the arogenate pathway in plants. Plant PPA-ATs and succeeding arogenate dehydratases (ADTs) were found to be most closely related to
homologs from Chlorobi/Bacteroidetes bacteria. The Chlorobium
tepidum
PPA-AT and ADT homologs indeed efficiently converted prephenate and arogenate into
arogenate and Phe, respectively. A subset of AspAT
Ib enzymes exhibiting PPA-AT
activity was further identified from both Plantae and prokaryotes and, together with
site-directed mutagenesis, showed that Thr-84 and Lys-169 play key roles in specific
recognition of dicarboxylic keto (prephenate) and amino (aspartate) acid substrates.
The results suggest that, along with ADT, a gene encoding
prephenate-specific PPA-AT was transferred
from a Chlorobi/Bacteroidetes ancestor to a eukaryotic ancestor of Plantae, allowing
efficient Phe and phenylpropanoid production via arogenate in plants today. 相似文献
84.
85.
Jimenez N Canals R Lacasta A Kondakova AN Lindner B Knirel YA Merino S Regué M Tomás JM 《Journal of bacteriology》2008,190(9):3176-3184
By the isolation of three different Aeromonas hydrophila strain AH-3 (serotype O34) mutants with an altered lipopolysaccharide (LPS) migration in gels, three genomic regions encompassing LPS core biosynthesis genes were identified and characterized. When possible, mutants were constructed using each gene from the three regions, containing seven, four, and two genes (regions 1 to 3, respectively). The mutant LPS core structures were elucidated by using mass spectrometry, methylation analysis, and comparison with the full core structure of an O-antigen-lacking AH-3 mutant previously established by us. Combining the gene sequence and complementation test data with the structural data and phenotypic characterization of the mutant LPSs enabled a presumptive assignment of all LPS core biosynthesis gene functions in A. hydrophila AH-3. The three regions and the genes contained are in complete agreement with the recently sequenced genome of A. hydrophila ATCC 7966. The functions of the A. hydrophila genes waaC in region 3 and waaF in region 2 were completely established, allowing the genome annotations of the two heptosyl transferase products not previously assigned. Having the functions of all genes involved with the LPS core biosynthesis and most corresponding single-gene mutants now allows experimental work on the role of the LPS core in the virulence of A. hydrophila. 相似文献
86.
Natalia Kuczyńska-Kippen 《Hydrobiologia》2007,593(1):27-37
The distribution of rotifer communities between emergent (Typha angustifolia) and submerged (Chara tomentosa) vegetation and a comparatively open water zone were compared during the spring, summer and autumn seasons at three macrophyte-dominated
lakes. This survey identified 107 rotifera species of which 58% of the taxonomical structure was common for the three examined
lakes. Stoneworts with a more complicated spatial and morphological structure (having a much longer stem length than the narrow
leaf cattail), supported higher rotifer densities. The stem length appeared to be the best predictor of all the macrophyte
parameters and pH and chlorophyll a for the chemical variables, for explaining the variation of rotifer densities using the stepwise multiple forward regressions.
The distribution of pelagic species did not differ between particular sites, which may have reflected the behavioural requirements
of those rotifers. Some of them remained in the open water zone while others seeking an anti-predator refuge, gathered within
macrophyte stands during the daytime. Moreover, there were nine Chara-associated species recorded and only one Typha-associated species was noted. The similarity of rotifer communities was most strongly influenced by particular habitat and
season.
Guest editors: S. S. S. Sarma, R. D. Gulati, R. L. Wallace, S. Nandini, H. J. Dumont & R. Rico-Martínez
Advances in Rotifer Research 相似文献
87.
Moore CM Hubbard GB Dick E Dunn BG Raveendran M Rogers J Williams V Gomez JJ Butler SD Leland MM Schlabritz-Loutsevitch NE 《American journal of primatology》2007,69(10):1105-1118
Trisomy 13 in humans is the third most common autosomal abnormality at birth, after trisomy 21 and trisomy 18. It has a reported incidence of between 1:5,000 and 1:30,000 live births. It is associated with multiple abnormalities, many of which shorten lifespan. We describe here the first reported case of a baboon (Papio hamadryas) with trisomy of chromosome 17, which is homologous to human chromosome 13. The trisomic infant was born to a consanguineous pair of baboons and had morphological characteristics similar to those observed in human trisomy 13, including bilateral polydactyly in the upper limbs, a patent foramen ovale, and pyelectasis. Molecular DNA analysis using human chromosome 13 markers was consistent with the affected infant inheriting two copies of chromosome 17 derived from the same parental chromosome. This trisomy was, therefore, due to either an error in meiosis II or the result of postzygotic nondisjunction. The parental origin, however, could not be determined. 相似文献
88.
T. Sasaki Natalia A. Pronina M. Maeshima I. Iwasaki N. Kurano S. Miyachi 《Plant biology (Stuttgart, Germany)》1999,1(1):68-75
Abstract: The number and cross-sectional area of vacuoles in Chlorococcum littorale cells visualized with a differential interfer ence fluorescence microscope increased after their transfer from air to 40% CO2 . An immunological observation indicated that the level of subunit B of vacuolar H*ATPase also increased under 40% CO2 conditions. The activity of nitrate-sensitive ATP-ase associated with the vacuolar membrane was 2–fold higher in 40% CO2 -- grown cells than in air-grown cells. The effects of inhi bitors on the ATPase activity confirmed that these activities were derived from vacuolar-type H-ATPase. These results sug gest that vacuole development associated with that of vacuolar H+ -ATPase occurred during the acclimatization of C. littorale cells to extremely high CO2 conditions. 相似文献
89.
Complex epidemiological situation, nosocomial infections, microbial contamination, and infection risks in hospital and dental
equipment have led to an ever-growing need for prevention of microbial infection in these various areas. Macromolecular systems,
due to their properties, allow one to efficiently use them in various fields, including the creation of polymers with the
antimicrobial activity. In the past decade, the intensive development of a large class of antimicrobial macromolecular systems,
polymers, and copolymers, either quaternized or functionalized with bioactive groups, has been continued, and they have been
successfully used as biocides. Various permanent microbicidal surfaces with non-leaching polymer antimicrobial coatings have
been designed. Along with these trends, new moderately hydrophobic polymer structures have been synthesized and studied, which
contain protonated primary or secondary/tertiary amine groups that exhibited rather high antimicrobial activity, often unlike
their quaternary analogues. This mini-review briefly highlights and summarizes the results of studies during the past decade
and especially in recent years, which concern the mechanism of action of different antimicrobial polymers and non-leaching
microbicidal surfaces, and factors influencing their activity and toxicity, as well as major applications of antimicrobial
polymers. 相似文献
90.
Mavromatis K Ivanova N Barry K Shapiro H Goltsman E McHardy AC Rigoutsos I Salamov A Korzeniewski F Land M Lapidus A Grigoriev I Richardson P Hugenholtz P Kyrpides NC 《Nature methods》2007,4(6):495-500
Metagenomics is a rapidly emerging field of research for studying microbial communities. To evaluate methods presently used to process metagenomic sequences, we constructed three simulated data sets of varying complexity by combining sequencing reads randomly selected from 113 isolate genomes. These data sets were designed to model real metagenomes in terms of complexity and phylogenetic composition. We assembled sampled reads using three commonly used genome assemblers (Phrap, Arachne and JAZZ), and predicted genes using two popular gene-finding pipelines (fgenesb and CRITICA/GLIMMER). The phylogenetic origins of the assembled contigs were predicted using one sequence similarity-based (blast hit distribution) and two sequence composition-based (PhyloPythia, oligonucleotide frequencies) binning methods. We explored the effects of the simulated community structure and method combinations on the fidelity of each processing step by comparison to the corresponding isolate genomes. The simulated data sets are available online to facilitate standardized benchmarking of tools for metagenomic analysis. 相似文献