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MOTIVATION: Recently, we described a Maximum Weighted Matching (MWM) method
for RNA structure prediction. The MWM method is capable of detecting
pseudoknots and other tertiary base-pairing interactions in a
computationally efficient manner (Cary and Stormo, Proceedings of the Third
International Conference on Intelligent Systems for Molecular Biology, pp.
75-80, 1995). Here we report on the results of our efforts to improve the
MWM method's predictive accuracy, and show how the method can be extended
to detect base interactions formerly inaccessible to automated RNA modeling
techniques. RESULTS: Improved performance in MWM structure prediction was
achieved in two ways. First, new ways of calculating base pair likelihoods
have been developed. These allow experimental data and combined statistical
and thermodynamic information to be used by the program. Second, accuracy
was improved by developing techniques for filtering out spurious base pairs
predicted by the MWM program. We also demonstrate here a means by which the
MWM folding method may be used to detect the presence of base triples in
RNAs. AVAILABILITY: http://www.cshl.org/mzhanglab/tabaska/j axpage. html
CONTACT: tabaska@cshl.org
相似文献
26.
van Hoek AH; van Alen TA; Sprakel VS; Hackstein JH; Vogels GD 《Molecular biology and evolution》1998,15(9):1195-1206
The 18S and 5.8S rDNA genes and the internal transcribed spacers ITS-1 and
ITS-2 of ciliates living in the hindgut of frogs, millipedes, and
cockroaches were analyzed in order to study the evolution of intestinal
protists. All ciliates studied here belong to the genus Nycrotherus.
Phylogenetic analysis revealed that these ciliates from a monophyletic
group that includes the distantly related anaerobic free-living
heterotrichous ciliates Metopus palaeformis and Metopus contortus. The
intestinal ciliates from the different vertebrate and invertebrate hosts
are clearly divergent at the level of their rDNA repeats. This argues for
the antiquity of the associations and a predominantly vertical
transmission. This mode of transmission seems to be controlled primarily by
the behavior of the host. The different degrees of divergence between
ciliates living in different strains of one and the same cockroach species
most likely reflect the different geographical origins of the hosts. In
addition, host switches must have occurred during the evolution of
cockroaches, since identical ciliates were found only in distantly related
hosts. These phenomena prevent the reconstruction of potential cospeciation
events.
相似文献
27.
GD Robson E Prebble A Rickers S Hosking DW Denning APJ Trinci W Robertson 《Fungal genetics and biology : FG & B》1996,20(4):289-298
Robson, G. D., Prebble, E., Rickers, A., Hosking, S., Denning, D. W., Trinci, A. P. J., and Robertson, W. 1996. Polarized growth of fungal hyphae is defined by an alkaline pH gradient. Fungal Genetics and Biology 20, 289-298. Polarized cell growth is exhibited by a diverse range of eukaryotic and prokaryotic cells. The events which are responsible for this growth are poorly understood. However, the existence of ion gradients may play an important role in establishing and driving cell polarity. Using a pH-sensitive, ratiometric fluorescent dye to monitor intracellular pH in growing fungal hyphae, we report a gradient at the extending hyphal tip that is up to 1.4 pH units more alkaline than more distal regions. Both the magnitude and the length of the pH gradient were strongly correlated with the rate of hyphal extension and eradication of the gradient-arrested growth. These results suggest that alkaline pH gradients may be integral to hyphal extension in fungi. 相似文献
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Matteo Audano Silvia Pedretti Gaia Cermenati Elisabetta Brioschi Giuseppe Riccardo Diaferia Serena Ghisletti Alessandro Cuomo Tiziana Bonaldi Franco Salerno Marina Mora Liliana Grigore Katia Garlaschelli Andrea Baragetti Fabrizia Bonacina Alberico Luigi Catapano Giuseppe Danilo Norata Maurizio Crestani Donatella Caruso Enrique Saez Emma De Fabiani Nico Mitro 《EMBO reports》2018,19(4)
Mitochondria are the energy‐generating hubs of the cell. In spite of considerable advances, our understanding of the factors that regulate the molecular circuits that govern mitochondrial function remains incomplete. Using a genome‐wide functional screen, we identify the poorly characterized protein Zinc finger CCCH‐type containing 10 (Zc3h10) as regulator of mitochondrial physiology. We show that Zc3h10 is upregulated during physiological mitochondriogenesis as it occurs during the differentiation of myoblasts into myotubes. Zc3h10 overexpression boosts mitochondrial function and promotes myoblast differentiation, while the depletion of Zc3h10 results in impaired myoblast differentiation, mitochondrial dysfunction, reduced expression of electron transport chain (ETC) subunits, and blunted TCA cycle flux. Notably, we have identified a loss‐of‐function mutation of Zc3h10 in humans (Tyr105 to Cys105) that is associated with increased body mass index, fat mass, fasting glucose, and triglycerides. Isolated peripheral blood mononuclear cells from individuals homozygotic for Cys105 display reduced oxygen consumption rate, diminished expression of some ETC subunits, and decreased levels of some TCA cycle metabolites, which all together derive in mitochondrial dysfunction. Taken together, our study identifies Zc3h10 as a novel mitochondrial regulator. 相似文献
29.
Hyphae of Saprolegnia ferax growing under normal or low-turgor conditions were exposed to 0.1-10 &mgr;g/ml latrunculin B, an actin inhibitor. In the first 10 s of addition, hyphae with normal turgor levels accelerated while those with low turgor decelerated, consistent with the suggestion that actin restrains or protrudes tips under these respective turgor conditions. Both sets of hyphae then decelerated and eventually ceased extension within 60 s. These changes were reflected in rhodamine-phalloidin staining patterns, which showed that actin caps were disrupted progressively under both conditions in a time-dependent manner. After 60 s, normal-turgored hyphae started to swell rapidly while low-turgored hyphae showed little or no swelling. Swelling was characteristically subapical, which is best explained by tip growth models which incorporate actin-mediated exocytosis. 相似文献
30.
Ashish Dhyani Gianpaolo Tibolla Andrea Baragetti Katia Garlaschelli Fabio Pellegatta Liliana Grigore Giuseppe Danilo Norata Alberico Luigi Catapano 《PloS one》2015,10(4)
Inducible degrader of the low density lipoprotein receptor (IDOL), is an E3 ubiquitin ligase that negatively modulates low density lipoprotein receptor (LDL-R) expression. Genome-wide association studies (GWAS) indicated that genetic variants in IDOL gene contributes to variation in LDL-C plasma levels and the detailed analysis of a specific locus resulted in the identification of the functional common single nucleotide polymorphism (SNP) rs9370867 (c.G1025A, p.N342S) associates with increased LDL-R degradation and increased LDL-C levels. These findings, however, were not confirmed in two other independent cohorts and no data about the impact of this variant on atherosclerosis progression and cardiovascular risk are available. Aim of this study was to investigate the association between a functional variant in IDOL and atherosclerosis progression in an Italian general population. 1384 subjects enrolled in the PLIC study (Progression of Lesions in the Intima of Carotid) were genotyped by Q-PCR allelic discrimination and the association with anthropometric parameters, plasma lipids and the carotid intima media thickness (cIMT) and the impact on cardiovascular disease (CVD) incidence were investigated. The N342S variant was not associated with changes of the plasma lipid profile among GG, AG or AA carriers, including total cholesterol (249±21, 249±19 and 248±21 mg/dl respectively), LDL-C (158±25, 161±22 and 160±23 mg/dL), cIMT (0.74±0.14, 0.75±0.17 and 0.77±0.15 mm) and CVD incidence. In agreement, the expression of LDLR and the uptake of LDL was similar in macrophages derived from GG and AA carriers. Taken together our findings indicate that the N342S variant does not impact plasma lipid profile and is not associated with atherosclerosis progression and CVD in the general population, suggesting that other variants in the IDOL gene might be functionally linked with cholesterol metabolism. 相似文献