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121.
Isabel Larridon Kenneth Bauters Marc Reynders Wim Huygh A. Muthama Muasya David A. Simpson Paul Goetghebeur 《Botanical journal of the Linnean Society. Linnean Society of London》2013,172(1):106-126
Maximum likelihood and Bayesian inference analyses of nuclear ribosomal DNA (ETS1f) and plastid DNA (rpl32‐trnL, trnH‐psbA) sequence data are presented for ‘C4 Cyperus’ (Cyperaceae). The term ‘C4 Cyperus’ encompasses all species of Cyperus s.l. that use C4 photosynthesis linked with chlorocyperoid vegetative anatomy. Sampling comprises 107 specimens of 104 different taxa, including many of the subdivisions of C4 Cyperus s.s. and all C4 segregate genera (Alinula, Ascolepis, Kyllinga, Lipocarpha, Pycreus, Queenslandiella, Remirea, Sphaerocyperus and Volkiella). According to our results, C4 Cyperus is a well‐supported monophyletic clade nested in C3 Cyperus. Despite the lack of resolution along the backbone of the C4 Cyperus clade and for some internal branches, several well‐supported clades can be distinguished. The first clade in C4 Cyperus is formed by Cyperus cuspidatus and C. waterloti. Other recognizable and well‐supported clades correspond to segregate genera, i.e. Ascolepis, Lipocarpha including Volkiella, and Kyllinga. Species of C4 Cyperus s.s. form a core grade in which the C4 segregate genera are embedded. Pycreus, the largest segregate genus composed of c. 120 species, is not monophyletic as it includes several C4 species of Cyperus s.s. This study establishes a phylogenetic framework for revising the classification and character evolution in Cyperus s.l. © 2013 The Linnean Society of London 相似文献
122.
Céleste Sèle Frank Gabel Irina Gutsche Ivan Ivanov Wim P. Burmeister Frédéric Iseni Nicolas Tarbouriech 《Journal of virology》2013,87(3):1679-1689
Smallpox caused by the poxvirus variola virus is a highly lethal disease that marked human history and was eradicated in 1979 thanks to a worldwide mass vaccination campaign. This virus remains a significant threat for public health due to its potential use as a bioterrorism agent and requires further development of antiviral drugs. The viral genome replication machinery appears to be an ideal target, although very little is known about its structure. Vaccinia virus is the prototypic virus of the Orthopoxvirus genus and shares more than 97% amino acid sequence identity with variola virus. Here we studied four essential viral proteins of the replication machinery: the DNA polymerase E9, the processivity factor A20, the uracil-DNA glycosylase D4, and the helicase-primase D5. We present the recombinant expression and biochemical and biophysical characterizations of these proteins and the complexes they form. We show that the A20D4 polymerase cofactor binds to E9 with high affinity, leading to the formation of the A20D4E9 holoenzyme. Small-angle X-ray scattering yielded envelopes for E9, A20D4, and A20D4E9. They showed the elongated shape of the A20D4 cofactor, leading to a 150-Å separation between the polymerase active site of E9 and the DNA-binding site of D4. Electron microscopy showed a 6-fold rotational symmetry of the helicase-primase D5, as observed for other SF3 helicases. These results favor a rolling-circle mechanism of vaccinia virus genome replication similar to the one suggested for tailed bacteriophages. 相似文献
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124.
This study reports on kinetics of the fluorescence decay in a suspension of the alga Scenedesmus quadricauda after actinic illumination. These are monitored as the variable fluorescence signal in the dark following light pulses of variable intensity and duration. The decay reflects the restoration of chlorophyll fluorescence quenching of the photosystem II (PSII) antennas and shows a polyphasic pattern which suggests the involvement of different processes. The overall quenching curve after a fluorescence-saturating pulse (SP) of 250-ms duration, commonly used in pulse amplitude modulation applications as the tool for estimating the maximal fluorescence (F m), has been termed P–O, in which P and O have the same meaning as used in the OJIP induction curve in the light. Deconvolution of this signal shows at least three distinguishable exponential phases with reciprocal rate constants of the order of 10, 102, and 103 ms. The size of the long (>103 ms) and moderate (~102 ms) lasting components relative to the complete quenching signal after an SP increases with the duration of the actinic pulse concomitantly with an increase in the reciprocal rate constants of the fast (~10 ms) and moderate quenching phases. Fluorescence responses upon single turnover flashes of 30-μs duration (STFs) given at discrete times during the P–O quenching were used as tools for identifying the quencher involved in the P–O quenching phase preceding the STF excitation. Results are difficult to interpret in terms of a single-hit two-state trapping mechanism with distinguishable quenching properties of open and closed reaction centers only. They give support for an earlier hypothesis on a double-hit three-state trapping mechanism in which the so-called semi-closed reaction centers of PSII are considered. In these trapping-competent centers the single reduced acceptor pair [PheQ A]1?, depending on the size of photoelectrochemically induced pH effects on the Q B-binding site, functions as an efficient fluorescence quencher. 相似文献
125.
The 16S rRNA gene has been used in the last decades as a gold standard for determining the phylogenetic position of bacteria and their taxonomy. It is a well conserved gene, with some variations, present in all bacteria and allows the reconstruction of genealogies of microorganisms. Nevertheless, this gene has its limitations when inferring phylogenetic relationships between closely related isolates. To overcome this problem, DNA–DNA hybridization appeared as a solution to clarify interspecies relationships when the sequence similarity of the 16S rRNA gene is above 97 %. However, this technique is time consuming, expensive and laborious and so, researchers developed other molecular markers such as sequencing of housekeeping or functional genes for accurate determination of bacterial phylogeny. One of these genes that have been used successfully, particularly in clinical microbiology, codes for the beta subunit of the RNA polymerase (rpoB). The rpoB gene is sufficiently conserved to be used as a molecular clock, it is present in all bacteria and it is a mono-copy gene. In this study, rpoB gene sequencing was applied to the phylum Planctomycetes. Based on the genomes of 19 planctomycetes it was possible to determine the correlation between the rpoB gene sequence and the phylogenetic position of the organisms at a 95–96 % sequence similarity threshold for a novel species. A 1200-bp fragment of the rpoB gene was amplified from several new planctomycetal isolates and their intra and inter-species relationships to other members of this group were determined based on a 96.3 % species border and 98.2 % for intraspecies resolution. 相似文献
126.
γ-secretase, which assembles as a tetrameric complex, is an aspartyl protease that proteolytically cleaves substrate proteins within their membrane-spanning domain; a process also known as regulated intramembrane proteolysis (RIP). RIP regulates signaling pathways by abrogating or releasing signaling molecules. Since the discovery, already > 15 years ago, of its catalytic component, presenilin, and even much earlier with the identification of amyloid precursor protein as its first substrate, γ-secretase has been commonly associated with Alzheimer's disease. However, starting with Notch and thereafter a continuously increasing number of novel substrates, γ-secretase is becoming linked to an equally broader range of biological processes. This review presents an updated overview of the current knowledge on the diverse molecular mechanisms and signaling pathways controlled by γ-secretase, with a focus on organ development, homeostasis and dysfunction. This article is part of a Special Issue entitled: Intramembrane Proteases. 相似文献
127.
Petra Schwertman Karel Bezstarosti Charlie Laffeber Wim Vermeulen Jeroen A.A. Demmers Jurgen A. Marteijn 《Analytical biochemistry》2013,440(2):227-236
Protein ubiquitination plays an important role in the regulation of many cellular processes, including protein degradation, cell cycle regulation, apoptosis, and DNA repair. To study the ubiquitin proteome we have established an immunoaffinity purification method for the proteomic analysis of endogenously ubiquitinated protein complexes. A strong, specific enrichment of ubiquitinated factors was achieved using the FK2 antibody bound to protein G-beaded agarose, which recognizes monoubiquitinated and polyubiquitinated conjugates. Mass spectrometric analysis of two FK2 immunoprecipitations (IPs) resulted in the identification of 296 FK2-specific proteins in both experiments. The isolation of ubiquitinated and ubiquitination-related proteins was confirmed by pathway analyses (using Ingenuity Pathway Analysis and Gene Ontology-annotation enrichment). Additionally, comparing the proteins that specifically came down in the FK2 IP with databases of ubiquitinated proteins showed that a high percentage of proteins in our enriched fraction was indeed ubiquitinated. Finally, assessment of protein–protein interactions revealed that significantly more FK2-specific proteins were residing in protein complexes than in random protein sets. This method, which is capable of isolating both endogenously ubiquitinated proteins and their interacting proteins, can be widely used for unraveling ubiquitin-mediated protein regulation in various cell systems and tissues when comparing different cellular states. 相似文献
128.
Raymond van der Ham Gijs Grob Wilbert Hetterscheid Wim Star Bertie Joan van Heuven 《Grana》2013,52(4):252-265
A strict consensus tree based on chloroplast and nuclear sequences (rbcL, matK, trnL, FLint2) from 46 Amorphophallus species, two Pseudodracontium species and six outgroups is used to develop a hypothesis for the evolution of ornamentation and ectexine ultrastructure in the pollen of Amorphophallus. There are four main clades: an exclusively African, largely psilate clade (‘African clade’), an Asian, largely psilate clade (‘Asian psilate clade’) and an Asian, largely striate clade consisting of a mainly continental SE Asian clade (‘continental SE Asian striate clade’) and one centred in Malesia (‘Malesian striate clade’). Ultrastructure provides a valuable contribution towards understanding pollen ornamentation in Amorphophallus. Pollen with a thin psilate ectexine without dark granules might be plesiomorphic in Amorphophallus. Then the diverse striate type would be derived. Within both striate clades, reversals to the psilate type occur. Striate pollen with psilate caps, which is nested in the continental SE Asian striate clade, is a synapomorphy of Pseudodracontium. The fossulate type is also diverse, and its distribution in the tree indicates a polyphyletic origin. Areolate, echinate and verrucate ornamentation, occur in single species in the tree, but are found also in species not included in the molecular analysis. All three are heterogeneous and probably polyphyletic too. Reticulate, scabrate and striate/scabrate ornamentation are autapomorphies, of which the reticulate type and the striate/scabrate type may derive from psilate and striate ornamentation, respectively. Of the four main clades, the Asian psilate and African clade seem to be basal, while both striate clades might have evolved from the Asian psilate clade via a species like A. rhizomatosus. Dark granules evolved more than once, which might explain their diverse size, shape and distribution. 相似文献
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130.
Jacqueline MacDonald Gibson Jens Thomsen Frederic Launay Elizabeth Harder Nicholas DeFelice 《PloS one》2013,8(3)