189 research outputs found
Turnip crinkle virus coat protein mediates suppression of RNA silencing in nicotiana benthamiana
AbstractAll of the protein products of Turnip crinkle virus (TCV; Tombusviridae, Carmovirus) were tested for their ability to suppress RNA silencing of a reporter gene after transient expression in Agrobacterium-infiltrated Nicotiana benthamiana leaves. Only the capsid protein, P38, showed suppression activity, although this was not obvious when P38 was expressed as part of a TCV infection of the same tissues. When P38 was expressed from a PVX vector, symptoms with enhanced severity that correlated with increased PVX RNA accumulation were observed. This contradiction between ectopic expression of P38 and TCV infection could be accounted for if the active determinant of suppressor activity within P38 was sequestered within the capsid protein structure. The N-terminal 25 amino acids were shown to be important for this activity. This region forms part of the unexposed R-domain that interacts with the RNA within the virus particle. This observation throws light on some of the complex biology exhibited by TCV
Genome-wide computational prediction of tandem gene arrays: application in yeasts
<p>Abstract</p> <p>Background</p> <p>This paper describes an efficient <it>in silico </it>method for detecting tandem gene arrays (TGAs) in fully sequenced and compact genomes such as those of prokaryotes or unicellular eukaryotes. The originality of this method lies in the search of protein sequence similarities in the vicinity of each coding sequence, which allows the prediction of tandem duplicated gene copies independently of their functionality.</p> <p>Results</p> <p>Applied to nine hemiascomycete yeast genomes, this method predicts that 2% of the genes are involved in TGAs and gene relics are present in 11% of TGAs. The frequency of TGAs with degenerated gene copies means that a significant fraction of tandem duplicated genes follows the birth-and-death model of evolution. A comparison of sequence identity distributions between sets of homologous gene pairs shows that the different copies of tandem arrayed paralogs are less divergent than copies of dispersed paralogs in yeast genomes. It suggests that paralogs included in tandem structures are more recent or more subject to the gene conversion mechanism than other paralogs.</p> <p>Conclusion</p> <p>The method reported here is a useful computational tool to provide a database of TGAs composed of functional or nonfunctional gene copies. Such a database has obvious applications in the fields of structural and comparative genomics. Notably, a detailed study of the TGA catalog will make it possible to tackle the fundamental questions of the origin and evolution of tandem gene clusters.</p
Spin chirality induced by the Dzyaloshinskii-Moriya interaction and the polarized neutron scattering
We discuss the influence of the Dzyaloshinskii-Moriya (DM) interaction in the
Heizenberg spin chain model for the observables in the polarized neutron
scattering experiments. We show that different choices of the parameters of DM
interaction may leave the spectrum of the problem unchanged, while the
observable spin-spin correlation functions may differ qualitatively.
Particularly, for the uniform DM interaction one has the incommensurate
fluctuations and polarization-dependent neutron scattering in the paramagnetic
phase. We sketch the possible generalization of our treatment to higher
dimensions.Comment: 4 pages, REVTEX, no figures, references added, to appear in PR
Ultrafast optical generation of coherent phonons in CdTe1-xSex quantum dots
We report on the impulsive generation of coherent optical phonons in
CdTe0.68Se0.32 nanocrystallites embedded in a glass matrix. Pump probe
experiments using femtosecond laser pulses were performed by tuning the laser
central energy to resonate with the absorption edge of the nanocrystals. We
identify two longitudinal optical phonons, one longitudinal acoustic phonon and
a fourth mode of a mixed longitudinal-transverse nature. The amplitude of the
optical phonons as a function of the laser central energy exhibits a resonance
that is well described by a model based on impulsive stimulated Raman
scattering. The phases of the coherent phonons reveal coupling between
different modes. At low power density excitations, the frequency of the optical
coherent phonons deviates from values obtained from spontaneous Raman
scattering. This behavior is ascribed to the presence of electronic impurity
states which modify the nanocrystal dielectric function and, thereby, the
frequency of the infrared-active phonons
Structural Insights into Viral Determinants of Nematode Mediated Grapevine fanleaf virus Transmission
Many animal and plant viruses rely on vectors for their transmission from host to
host. Grapevine fanleaf virus (GFLV), a picorna-like virus from
plants, is transmitted specifically by the ectoparasitic nematode
Xiphinema index. The icosahedral capsid of GFLV, which
consists of 60 identical coat protein subunits (CP), carries the determinants of
this specificity. Here, we provide novel insight into GFLV transmission by
nematodes through a comparative structural and functional analysis of two GFLV
variants. We isolated a mutant GFLV strain (GFLV-TD) poorly transmissible by
nematodes, and showed that the transmission defect is due to a glycine to
aspartate mutation at position 297 (Gly297Asp) in the CP. We next determined the
crystal structures of the wild-type GFLV strain F13 at 3.0 Å and of
GFLV-TD at 2.7 Å resolution. The Gly297Asp mutation mapped to an exposed
loop at the outer surface of the capsid and did not affect the conformation of
the assembled capsid, nor of individual CP molecules. The loop is part of a
positively charged pocket that includes a previously identified determinant of
transmission. We propose that this pocket is a ligand-binding site with
essential function in GFLV transmission by X. index. Our data
suggest that perturbation of the electrostatic landscape of this pocket affects
the interaction of the virion with specific receptors of the nematode's
feeding apparatus, and thereby severely diminishes its transmission efficiency.
These data provide a first structural insight into the interactions between a
plant virus and a nematode vector
In vitro initial attachment of HIV-1 integrase to viral ends: control of the DNA specific interaction by the oligomerization state
HIV-1 integrase (IN) oligomerization and DNA recognition are crucial steps for the subsequent events of the integration reaction. Recent advances described the involvement of stable intermediary complexes including dimers and tetramers in the in vitro integration processes, but the initial attachment events and IN positioning on viral ends are not clearly understood. In order to determine the role of the different IN oligomeric complexes in these early steps, we performed in vitro functional analysis comparing IN preparations having different oligomerization properties. We demonstrate that in vitro IN concerted integration activity on a long DNA substrate containing both specific viral and nonspecific DNA sequences is highly dependent on binding of preformed dimers to viral ends. In addition, we show that IN monomers bound to nonspecific DNA can also fold into functionally different oligomeric complexes displaying nonspecific double-strand DNA break activity in contrast to the well known single strand cut catalyzed by associated IN. Our results imply that the efficient formation of the active integration complex highly requires the early correct positioning of monomeric integrase or the direct binding of preformed dimers on the viral ends. Taken together the data indicates that IN oligomerization controls both the enzyme specificity and activity
Predictors of diagnostic yield in bronchoscopy: a retrospective cohort study comparing different combinations of sampling techniques
<p>Abstract</p> <p>Background</p> <p>The reported diagnostic yield from bronchoscopies in patients with lung cancer varies greatly. The optimal combination of sampling techniques has not been finally established.</p> <p>The objectives of this study were to find the predictors of diagnostic yield in bronchoscopy and to evaluate different combinations of sampling techniques.</p> <p>Methods</p> <p>All bronchoscopies performed on suspicion of lung malignancy in 2003 and 2004 were reviewed, and 363 patients with proven malignant lung disease were included in the study. Sampling techniques performed were biopsy, transbronchial needle aspiration (TBNA), brushing, small volume lavage (SVL), and aspiration of fluid from the entire procedure. Logistic regression analyses were adjusted for sex, age, endobronchial visibility, localization (lobe), distance from carina, and tumor size.</p> <p>Results</p> <p>The adjusted odds ratios (OR) with 95% confidence intervals (CI) for a positive diagnostic yield through all procedures were 17.0 (8.5–34.0) for endobronchial lesions, and 2.6 (1.3–5.2) for constriction/compression, compared to non-visible lesions; 3.8 (1.3–10.7) for lesions > 4 cm, 6.7 (2.1–21.8) for lesions 3–4 cm, and 2.5 (0.8–7.9) for lesions 2–3 cm compared with lesions <= 2 cm. The combined diagnostic yield of biopsy and TBNA was 83.7% for endobronchial lesions and 54.2% for the combined group without visible lesions. This was superior to either technique alone, whereas additional brushing, SVL, and aspiration did not significantly increase the diagnostic yield.</p> <p>Conclusion</p> <p>In patients with malignant lung disease, visible lesions and larger tumor size were significant predictors of higher diagnostic yield, after adjustment for sex, age, distance from carina, side and lobe. The combined diagnostic yield of biopsy and TBNA was significant higher than with either technique alone.</p
Toksikokinetika prometrina u mozgu miševa
Prometryne is a methylthio-s-triazine herbicide. Signifi cant trace amounts are found in the environment,
mainly in water, soil, and food plants. The aim of this study was to establish brain and blood prometryne levels after single oral dose (1 g kg-1) in adult male and female mice. Prometryne was measured using the GC/MS assay at 1, 2, 4, 8, and 24 h after prometryne administration. Peak brain and blood prometryne values were observed 1 h after administration and they decreased in a time-dependent manner. Male mice had consistently higher brain and blood prometryne levels than female mice. The observed prometryne
kinetics was similar to that reported for the structurally related herbicide atrazine.Prometrin je metiltio-s-triazinski herbicid. Značajne količine prometrina zaostaju u tragovima u okolišu, poglavito u vodi, tlu i biljkama koje rabimo za prehranu. Cilj je rada izmjeriti količinu prometrina koja se apsorbira u mozgu i krvi nakon primijenjene akutne oralne doze (1 g kg-1 tjelesne mase) u odraslih miševa
obaju spolova. Razine prometrina u mozgu i krvi izmjerene su GC/MS-om tijekom 1., 2., 4., 8. i 24. sata nakon izlaganja. Utvrđeno je da je udio prometrina koji se zadržava u živčanom tkivu relativno nizak ali detektabilan u odnosu na koncentraciju u krvi i koncentraciju primijenjene doze. Najviše koncentracije u krvi i maseni udjeli u mozgu zabilježeni su tijekom 1. sata nakon izlaganja, a s vremenom izmjerene vrijednosti značajno opadaju. Uočena je značajna razlika između mužjaka i ženki pri čemu mužjaci imaju
značajno više razine prometrina u mozgu i krvi nego ženke. Opisana toksikokinetika prometrina pokazuje sličnosti s otprije opisanom i poznatom toksikokinetikom strukturalno sličnog herbicida atrazina
Cortical dynamics and subcortical signatures of motor-language coupling in Parkinson’s disease
ABSTRACT: Impairments of action language have been documented in early stage Parkinson’s disease (EPD). The action-sentence compatibility effect (ACE) paradigm has revealed that EPD involves deficits to integrate action-verb processing and ongoing motor actions. Recent studies suggest that an abolished ACE in EPD reflects a cortico-subcortical disruption, and recent neurocognitive models highlight the role of the basal ganglia (BG) in motor-language coupling. Building on such breakthroughs, we report the first exploration of convergent cortical and subcortical signatures of ACE in EPD patients and matched controls. Specifically, we combined cortical recordings of the motor potential, functional connectivity measures, and structural analysis of the BG through voxelbased morphometry. Relative to controls, EPD patients exhibited an impaired ACE, a reduced motor potential, and aberrant frontotemporal connectivity. Furthermore, motor potential abnormalities during the ACE task were predicted by overall BG volume and atrophy. These results corroborate that motor-language coupling is mainly subserved by a cortico-subcortical network including the BG as a key hub. They also evince that action-verb processing may constitute a neurocognitive marker of
EPD. Our findings suggest that research on the relationship between language and motor domains is crucial to develop models of motor cognition as well as diagnostic and intervention strategies
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