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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
23.
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
24.
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
25.
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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James GD Prendergast Harry Campbell Nick Gilbert Malcolm G Dunlop Wendy A Bickmore Colin AM Semple 《BMC evolutionary biology》2007,7(1):72
Background
Evolutionary rates are not constant across the human genome but genes in close proximity have been shown to experience similar levels of divergence and selection. The higher-order organisation of chromosomes has often been invoked to explain such phenomena but previously there has been insufficient data on chromosome structure to investigate this rigorously. Using the results of a recent genome-wide analysis of open and closed human chromatin structures we have investigated the global association between divergence, selection and chromatin structure for the first time. 相似文献28.
Mar JC Matigian NA Mackay-Sim A Mellick GD Sue CM Silburn PA McGrath JJ Quackenbush J Wells CA 《PLoS genetics》2011,7(8):e1002207
Gene expression analysis has become a ubiquitous tool for studying a wide range of human diseases. In a typical analysis we compare distinct phenotypic groups and attempt to identify genes that are, on average, significantly different between them. Here we describe an innovative approach to the analysis of gene expression data, one that identifies differences in expression variance between groups as an informative metric of the group phenotype. We find that genes with different expression variance profiles are not randomly distributed across cell signaling networks. Genes with low-expression variance, or higher constraint, are significantly more connected to other network members and tend to function as core members of signal transduction pathways. Genes with higher expression variance have fewer network connections and also tend to sit on the periphery of the cell. Using neural stem cells derived from patients suffering from Schizophrenia (SZ), Parkinson's disease (PD), and a healthy control group, we find marked differences in expression variance in cell signaling pathways that shed new light on potential mechanisms associated with these diverse neurological disorders. In particular, we find that expression variance of core networks in the SZ patient group was considerably constrained, while in contrast the PD patient group demonstrated much greater variance than expected. One hypothesis is that diminished variance in SZ patients corresponds to an increased degree of constraint in these pathways and a corresponding reduction in robustness of the stem cell networks. These results underscore the role that variation plays in biological systems and suggest that analysis of expression variance is far more important in disease than previously recognized. Furthermore, modeling patterns of variability in gene expression could fundamentally alter the way in which we think about how cellular networks are affected by disease processes. 相似文献
29.
Characterization of a complex chemosensory signal transduction system which controls twitching motility in Pseudomonas aeruginosa 总被引:2,自引:0,他引:2
Whitchurch CB Leech AJ Young MD Kennedy D Sargent JL Bertrand JJ Semmler AB Mellick AS Martin PR Alm RA Hobbs M Beatson SA Huang B Nguyen L Commolli JC Engel JN Darzins A Mattick JS 《Molecular microbiology》2004,52(3):873-893
Virulence of the opportunistic pathogen Pseudomonas aeruginosa involves the coordinate expression of a wide range of virulence factors including type IV pili which are required for colonization of host tissues and are associated with a form of surface translocation termed twitching motility. Twitching motility in P. aeruginosa is controlled by a complex signal transduction pathway which shares many modules in common with chemosensory systems controlling flagella rotation in bacteria and which is composed, in part, of the previously described proteins PilG, PilH, PilI, PilJ and PilK. Here we describe another three components of this pathway: ChpA, ChpB and ChpC, as well as two downstream genes, ChpD and ChpE, which may also be involved. The central component of the pathway, ChpA, possesses nine potential sites of phosphorylation: six histidine-containing phosphotransfer (HPt) domains, two novel serine- and threonine-containing phosphotransfer (SPt, TPt) domains and a CheY-like receiver domain at its C-terminus, and as such represents one of the most complex signalling proteins yet described in nature. We show that the Chp chemosensory system controls twitching motility and type IV pili biogenesis through control of pili assembly and/or retraction as well as expression of the pilin subunit gene pilA. The Chp system is also required for full virulence in a mouse model of acute pneumonia. 相似文献
30.
Sequencing and analysis of an Irish human genome 总被引:1,自引:0,他引:1
Pin Tong James GD Prendergast Amanda J Lohan Susan M Farrington Simon Cronin Nial Friel Dan G Bradley Orla Hardiman Alex Evans James F Wilson Brendan Loftus 《Genome biology》2010,11(9):1-14