An efficient genetic algorithm for structural RNA pairwise alignment and its application to non-coding RNA discovery in yeast

<p>Abstract</p> <p>Background</p> <p>Aligning RNA sequences with low sequence identity has been a challenging problem since such a computation essentially needs an algorithm with high complexities for taking structural conservation into account. Although many sophisticated algorithms for the purpose have been proposed to date, further improvement in efficiency is necessary to accelerate its large-scale applications including non-coding RNA (ncRNA) discovery.</p> <p>Results</p> <p>We developed a new genetic algorithm, Cofolga2, for simultaneously computing pairwise RNA sequence alignment and consensus folding, and benchmarked it using BRAliBase 2.1. The benchmark results showed that our new algorithm is accurate and efficient in both time and memory usage. Then, combining with the originally trained SVM, we applied the new algorithm to novel ncRNA discovery where we compared <it>S. cerevisiae </it>genome with six related genomes in a pairwise manner. By focusing our search to the relatively short regions (50 bp to 2,000 bp) sandwiched by conserved sequences, we successfully predict 714 intergenic and 1,311 sense or antisense ncRNA candidates, which were found in the pairwise alignments with stable consensus secondary structure and low sequence identity (≤ 50%). By comparing with the previous predictions, we found that > 92% of the candidates is novel candidates. The estimated rate of false positives in the predicted candidates is 51%. Twenty-five percent of the intergenic candidates has supports for expression in cell, i.e. their genomic positions overlap those of the experimentally determined transcripts in literature. By manual inspection of the results, moreover, we obtained four multiple alignments with low sequence identity which reveal consensus structures shared by three species/sequences.</p> <p>Conclusion</p> <p>The present method gives an efficient tool complementary to sequence-alignment-based ncRNA finders.</p

WASp-deficient B cells play a critical, cell-intrinsic role in triggering autoimmunity

In a manner dependent on CD4 T cell help and Toll-like receptor signals, B cells lacking WASp induce autoantibody production and autoimmune disease in mice

Heavy and light roles: myosin in the morphogenesis of the heart

Myosin is an essential component of cardiac muscle, from the onset of cardiogenesis through to the adult heart. Although traditionally known for its role in energy transduction and force development, recent studies suggest that both myosin heavy-chain and myosin lightchain proteins are required for a correctly formed heart. Myosins are structural proteins that are not only expressed from early stages of heart development, but when mutated in humans they may give rise to congenital heart defects. This review will discuss the roles of myosin, specifically with regards to the developing heart. The expression of each myosin protein will be described, and the effects that altering expression has on the heart in embryogenesis in different animal models will be discussed. The human molecular genetics of the myosins will also be reviewed

Vulnerability curves by centrifugation: is there an open vessel artefact, and are 'r' shaped curves necessarily invalid?

Vulnerability curves using the 'Cavitron' centrifuge rotor yield anomalous results when vessels extend from the end of the stem segment to the centre ('open-to-centre' vessels). Curves showing a decline in conductivity at modest xylem pressures ('r' shaped) have been attributed to this artefact. We determined whether the original centrifugal method with its different rotor is influenced by open-to-centre vessels. Increasing the proportion of open-to-centre vessels by shortening stems had no substantial effect in four species. Nor was there more embolism at the segment end versus centre as seen in the Cavitron. The dehydration method yielded an 'r' shaped curve in Quercus gambelii that was similar to centrifuged stems with 86% open-to-centre vessels. Both 'r' and 's' (sigmoidal) curves from Cercocarpus intricatus were consistent with each other, differing only in whether native embolism had been removed. An 'r' shaped centrifuge curve in Olea europaea was indistinguishable from the loss of conductivity caused by forcing air directly across vessel end-walls. We conclude that centrifuge curves on long-vesselled material are not always prone to the open vessel artefact when the original rotor design is used, and 'r' shaped curves are not necessarily artefacts. Nevertheless, confirming curves with native embolism and dehydration data is recommended. An 'r' shaped vulnerability curve shows an initially steep decline in the hydraulic conductivity of xylem, indicative of a population of xylem vessels that are extremely vulnerable to cavitation. Is this type of curve an artifact of the widely used centrifugal method, and is the 'r' shape related to the number of 'open' vessels that are exposed at the ends of the sample? Not according to our results because: a) curves were relatively insensitive to the number of open vessels, b) there was no anomalous embolism at segment ends, and c) 'r' shaped centrifuge curves were consistent with 'r' shaped curves from branch dehydration and single-ended air injection. Nevertheless, 'r' shaped curves invite deserved skepticism and should be checked against native conductivity measurements or dehydration curves.J.S.S. acknowledges financial support from NSF-IBN-0743148. H.T. was supported by the Japan Society for Promotion of Science to work at the University of Utah. J.M.T-R. was supported by Spanish Ministry of Science and Innovation to visit the University of Utah.Peer Reviewe

Control of embryonic meristem initiation in Arabidopsis by PHD-finger protein complexes.

Plant growth is directed by the activity of stem cells within meristems. The first meristems are established during early embryogenesis, and this process involves the specification of both stem cells and their organizer cells. One of the earliest events in root meristem initiation is marked by re-specification of the uppermost suspensor cell as hypophysis, the precursor of the organizer. The transcription factor MONOPTEROS (MP) is a key regulator of hypophysis specification, and does so in part by promoting the transport of the plant hormone auxin and by activating the expression of TARGET OF MP (TMO) transcription factors, both of which are required for hypophysis specification. The mechanisms leading to the activation of these genes by MP in a chromatin context are not understood. Here, we show that the PHD-finger proteins OBERON (OBE) and TITANIA (TTA) are essential for MP-dependent embryonic root meristem initiation. TTA1 and TTA2 are functionally redundant and function in the same pathway as OBE1 and OBE2. These PHD-finger proteins interact with each other, and genetic analysis shows that OBE-TTA heterotypic protein complexes promote embryonic root meristem initiation. Furthermore, while MP expression is unaffected by mutations in OBE/TTA genes, expression of MP targets TMO5 and TMO7 is locally lost in obe1 obe2 embryos. PHD-finger proteins have been shown to act in initiation of transcription by interacting with nucleosomes. Indeed, we found that OBE1 binds to chromatin at the TMO7 locus, suggesting a role in its MP-dependent activation. Our data indicate that PHD-finger protein complexes are crucial for the activation of MP-dependent gene expression during embryonic root meristem initiation, and provide a starting point for studying the mechanisms of developmental gene activation within a chromatin context in plants