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41.
Bernhard Y Renard Marc Kirchner Hanno Steen Judith AJ Steen Fred A Hamprecht 《BMC bioinformatics》2008,9(1):355
Background
The reliable extraction of features from mass spectra is a fundamental step in the automated analysis of proteomic mass spectrometry (MS) experiments. 相似文献42.
Christa Testerink Paul B Larsen Fionn McLoughlin Dieuwertje van der Does John AJ van Himbergen Teun Munnik 《Plant signaling & behavior》2008,3(9):681-683
Constitutive triple response 1 (CTR1) is a protein kinase that represses plant responses to ethylene. Recently, we have shown that CTR1 function is negatively regulated by the lipid second messenger phosphatidic acid (PA) in vitro.1 PA was shown to inhibit (1) CTR1''s protein kinase activity, (2) the intramolecular interaction between N-terminus and kinase domain, and (3) the interaction of CTR1 with the ethylene receptor ETR1. PA typically accumulates within minutes in response to biotic or abiotic stresses, which are known to induce ethylene formation. Although long-term treatment with ethephon does stimulate PA accumulation, our results show no fast increase in PA in response to ethylene. A speculative model is presented which explains how stress-induced PA formation could switch on downstream ethylene responses via interaction of the lipid with CTR1.Key words: lipid signaling, phosphatidic acid, ethylene, constitutive triple response 1, plant stress signaling, protein kinase, phospholipase D 相似文献
43.
The utility of the morphological variation of pollen for resolving the evolutionary history of Billia (subfam. Hippocastanoideae,Sapindaceae)
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In this study, we examined the utility of pollen morphology for resolving questions about the evolutionary history of Billia, which is a poorly known genus of Neotropical trees. Billia has been traditionally circumscribed with two species and treated as sister to Aesculus L. However, the number of species in Billia is uncertain, because the genus exhibits abundant morphological diversity but little discontinuous variation. Therefore, Billia may be monotypic and highly polymorphic, or it may have two species with blurred boundaries due to incipient speciation and/or hybridization. Moreover, one recent molecular phylogenetic study shows Billia nested withinAesculus. Our work sought to address the following questions: (i) Are there discontinuities in the pollen of Billia that may suggest species boundaries? (ii) Does the pollen of Billia show evidence for inter-specific hybridization? (iii) Do the exine morphology and size of pollen in Billia differ from those in Aesculus? Our results from scanning electron microscopy showed that pollen exine morphology is not taxonomically informative in Billia but that there are significant differences in pollen size between red- and white-flowered individuals. Thus, our pollen data support the utility of flower color in Billia for species delimitation. Our assessments of pollen viability do not support hybridization in the genus, but cannot be used to rule it out. Finally, pollen exine morphology may lend some support to an evolutionary origin ofBillia within eastern North American Aesculus. In contrast, data on pollen size suggest that Billia may belong in a topological position outside of Aesculus. 相似文献
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45.
Louis Grandjean Tomotada Iwamoto Anna Lithgow Robert H Gilman Kentaro Arikawa Noriko Nakanishi Laura Martin Edith Castillo Valentina Alarcon Jorge Coronel Walter Solano Minoo Aminian Claudia Guezala Nalin Rastogi David Couvin Patricia Sheen Mirko Zimic David AJ Moore 《PloS one》2015,10(5)
BackgroundThe comparison of Mycobacterium tuberculosis bacterial genotypes with phenotypic, demographic, geospatial and clinical data improves our understanding of how strain lineage influences the development of drug-resistance and the spread of tuberculosis.MethodsTo investigate the association of Mycobacterium tuberculosis bacterial genotype with drug-resistance. Drug susceptibility testing together with genotyping using both 15-loci MIRU-typing and spoligotyping, was performed on 2,139 culture positive isolates, each from a different patient in Lima, Peru. Demographic, geospatial and socio-economic data were collected using questionnaires, global positioning equipment and the latest national census.ResultsThe Latin American Mediterranean (LAM) clade (OR 2.4, p<0.001) was significantly associated with drug-resistance and alone accounted for more than half of all drug resistance in the region. Previously treated patients, prisoners and genetically clustered cases were also significantly associated with drug-resistance (OR''s 2.5, 2.4 and 1.8, p<0.001, p<0.05, p<0.001 respectively).ConclusionsTuberculosis disease caused by the LAM clade was more likely to be drug resistant independent of important clinical, genetic and socio-economic confounding factors. Explanations for this include; the preferential co-evolution of LAM strains in a Latin American population, a LAM strain bacterial genetic background that favors drug-resistance or the "founder effect" from pre-existing LAM strains disproportionately exposed to drugs. 相似文献
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47.
This report describes a convenient method for the rapid and efficient
release of N-linked oligosaccharides from low microgram amounts of
glycoproteins. A 96-well MultiScreen assay system containing a
polyvinylidene difluoride (PVDF) membrane is employed to immobilize
glycoproteins for subsequent enzymatic deglycosylation. Recombinant
tissue-type plasminogen activator (rt-PA) is used to demonstrate the
deglycosylation of 0.1-50 micrograms of a glycoprotein. This method enabled
the recovery of a sufficient amount of N-linked oligosaccharides released
enzymatically with peptide N-glycosidase F (PNGaseF) from as little as 0.5
microgram rt-PA for subsequent analysis by matrix-assisted laser
desorption/ionization time-of-flight (MALDI- TOF) mass spectrometry. The
immobilization of rt-PA to the PVDF membrane did not sterically inhibit the
PNGaseF-mediated release of oligosaccharides from rt-PA as determined by
tryptic mapping experiments. Comparison of the oligosaccharides released
from 50 micrograms of rt-PA by either the 96-well plate method or by a
standard solution digestion procedure showed no significant differences in
the profiles obtained by high-pH anion-exchange chromatography with pulsed
amperometric detection (HPAEC-PAD). Both neutral and sialylated
oligosaccharide standards spiked into wells were recovered equally as
determined by HPAEC-PAD. One advantage of this approach is that reduction
and alkylation can be performed on submicrogram amounts of glycoproteins
with easy removal of reagents prior to PNGaseF digestion. In addition, this
method allows 60 glycoprotein samples to be deglycosylated in 1 day with
MALDI-TOF or HPAEC-PAD analysis being performed on the following day.
相似文献
48.
Strasser-Wozak EM Hartmann BL Geley S Sgonc R Böck G AJ Santos Hattmannstorfer R Wolf H Pavelka M Kofler R 《Cell death and differentiation》1998,5(8):687-693
The tumor suppressor p53 has been implicated in gamma irradiation-induced apoptosis. To investigate possible consequences of wild-type p53 loss in leukemia, we studied the effect of a single dose of gamma irradiation upon p53-deficient human T-ALL (acute lymphoblastic leukemia) CCRF - CEM cells. Exposure to 3 - 96 Gy caused p53-independent cell death in a dose and time-dependent fashion. By electron microscopic and other criteria, this cell death was classified as apoptosis. At low to intermediate levels of irradiation, apoptosis was preceded by accumulation of cells in the G2/M phase of the cell division cycle. Expression of Bcl-2 and Bax were not detectably altered after irradiation. Expression of the temperature sensitive mouse p53 V135 mutant induced apoptosis on its own but only slightly increased the sensitivity of CCRF - CEM cells to gamma irradiation. Thus, in these, and perhaps other leukemia cells, a p53- and Bcl-2/Bax-independent mechanism is operative that efficiently senses irradiation effects and translates this signal into arrest in the G2/M phase of the cell cycle and subsequent apoptosis. 相似文献
49.
50.
Phylogenetic relationships within the Alcidae (Charadriiformes: Aves) inferred from total molecular evidence 总被引:4,自引:1,他引:3
The Alcidae is a unique assemblage of Northern Hemisphere seabirds that
forage by "flying" underwater. Despite obvious affinities among the
species, their evolutionary relationships are unclear. We analyzed
nucleotide sequences of 1,045 base pairs of the mitochondrial cytochrome b
gene and allelic profiles for 37 allozyme loci in all 22 extant species.
Trees were constructed on independent and combined data sets using maximum
parsimony and distance methods that correct for superimposed changes.
Alternative methods of analysis produced only minor differences in
relationships that were supported strongly by bootstrapping or standard
error tests. Combining sequence and allozyme data into a single analysis
provided the greatest number of relationships receiving strong support.
Addition of published morphological and ecological data did not improve
support for any additional relationship. All analyses grouped species into
six distinct lineages: (1) the dovekie (Alle alle) and auks, (2)
guillemots, (3) brachyramphine murrelets, (4) synthliboramphine murrelets,
(5) true auklets, and (6) the rhinoceros auklet (Cerorhinca monocerata) and
puffins. The two murres (genus Uria) were sister taxa, and the black
guillemot (Cepphus grylle) was basal to the other guillemots. The Asian
subspecies of the marbled murrelet (Brachyramphus marmoratus perdix) was
the most divergent brachyramphine murrelet, and two distinct lineages
occurred within the synthliboramphine murrelets. Cassin's auklet
(Ptychoramphus aleuticus) and the rhinoceros auklet were basal to the other
auklets and puffins, respectively, and the Atlantic (Fratercula arctica)
and horned (Fratercula corniculata) puffins were sister taxa. Several
relationships among tribes, among the dovekie and auks, and among the
auklets could not be resolved but resembled "star" phylogenies indicative
of adaptive radiations at different depths within the trees.
相似文献