Identification of miRNAs from French bean (Phaseolus vulgaris) under low nitrate stress

Objective: In this study, we report the role of miRNAs involved under nitrogen starvation from widely grown vegetable crop, French bean. In recent years, a great deal of attention has been paid to the elucidation of miRNAs involved in low nitrate stress. Methods: To identify miRNAs expressed under stress, cDNA libraries were analyzed. Results: We reported the nine potential miRNAs with 67 targets involved in nutrient transporters and other stress specific genes. Among the miRNA sequences obtained 6 sequences belong to miR172 family, one with miR169. RT-PCR analysis of expression of miR172 family was induced upon low nitrate stress while miR169 family was repressed. In addition, Pvu-SN7b and Pvu-miR16 may be new members of miRNA172 and miR169 families, respectively. Conclusion: The targets of Pvu-SN7b were major protein kinases, one among which is the Protein Kinase CK2. CK2 Kinase is found to involve in transcription-directed signaling, gene control and cell-cycle regulation. Other targets of Pvu-SN7b were involved in DNA-dependent transcription regulation, photo-periodism, calcium-mediated signaling. Pvu-miR16 targets Thymidine kinase, the key enzyme of deoxy-nucleotide synthesis. The cleavage of these targets affects cell proliferation there by affecting nodule formation. Pvu-miR8 inhibits translation of its target protein Pre-protein translocase, a membrane-bound protein transporter involved in trans-membrane protein transportation. Together these results denote the response and role of miRNAs to nitrate-limiting conditions in French bean.

Translation Induction on Indian Language Corpora Using Translingual Themes from Other Languages

Identifying translations from comparable corpora is a well-known problem with several applications, e.g. dictionary creation in resource-scarce languages. Scarcity of high quality corpora, especially in Indian languages, makes this problem hard, e.g. state-of-the-art techniques achieve a mean reciprocal rank (MRR) of 0.66 for English-Italian, and a mere 0.187 for Telugu-Kannada. There exist comparable corpora in many Indian languages with other ``auxiliary'' languages. We observe that translations have many topically related words in common in the auxiliary language. To model this, we define the notion of a translingual theme, a set of topically related words from auxiliary language corpora, and present a probabilistic framework for translation induction. Extensive experiments on 35 comparable corpora using English and French as auxiliary languages show that this approach can yield dramatic improvements in performance (e.g. MRR improves by 124% to 0.419 for Telugu-Kannada). A user study on WikiTSu, a system for cross-lingual Wikipedia title suggestion that uses our approach, shows a 20% improvement in the quality of titles suggested.

A Single Mammalian Mitochondrial Translation Initiation Factor Functionally Replaces Two Bacterial Factors

The mechanism of translation in eubacteria and organelles is thought to be similar. In eubacteria, the three initiation factors IF1, IF2, and IF3 are vital. Although the homologs of IF2 and IF3 are found in mammalian mitochondria, an IF1 homolog has never been detected. Here, we show that bovine mitochondrial IF2 (IF2mt) complements E. coli containing a deletion of the IF2 gene (E. coli ΔinfB). We find that IF1 is no longer essential in an IF2mt-supported E. coli ΔinfB strain. Furthermore, biochemical and molecular modeling data show that a conserved insertion of 37 amino acids in the IF2mt substitutes for the function of IF1. Deletion of this insertion from IF2mt supports E. coli for the essential function of IF2. However, in this background, IF1 remains essential. These observations provide strong evidence that a single factor (IF2mt) in mammalian mitochondria performs the functions of two eubacterial factors, IF1 and IF2.

Role of 16S ribosomal RNA methylations in translation initiation in Escherichia coli

Translation initiation from the ribosomal P-site is the specialty of the initiator tRNAs (tRNA(fMet)). Presence of the three consecutive G-C base pairs (G29-C41, G30-C40 and G31-C39) in their anticodon stems, a highly conserved feature of the initiator tRNAs across the three kingdoms of life, has been implicated in their preferential binding to the P-site. How this feature is exploited by ribosomes has remained unclear. Using a genetic screen, we have isolated an Escherichia coli strain, carrying a G122D mutation in folD, which allows initiation with the tRNA(fMet) containing mutations in one, two or all the three G-C base pairs. The strain shows a severe deficiency of methionine and S-adenosylmethionine, and lacks nucleoside methylations in rRNA. Targeted mutations in the methyltransferase genes have revealed a connection between the rRNA modifications and the fundamental process of the initiator tRNA selection by the ribosome.

Effect of some organic acids on leaf phosphatase from French beans

1. The common organic acids inhibited leaf phosphatase activity, This effect is mostly due to the hydroxyl groups in them. 2. The less common organic acids, which have only carboxyl groups, did not show any marked inhibitory action on phosphatase activity. 3. The less common organic acids eluted the leaf phosphatase after adsorption on aluminacγ gel to a greater extent than the more common organic acids. 4. The second elution of the purified enzyme from the aluminacγ gel was not possible with the organic acids as it was adsorbed on the gel.

Polypyrimidine tract-binding protein interacts with coxsackievirus B3 RNA and influences its translation

We have investigated the possible role of trans-acting factors interacting with the untranslated regions (UTRs) of coxsackievirus B3 (CVB3) RNA. We show here that polypyrimidine tract-binding protein (PTB) binds specifically to both 5' and 3' UTRs, but with different affinity. We have demonstrated that PTB is a bona fide internal ribosome entry site (IRES) trans-acting factor (ITAF) for CVB3 RNA by characterizing the effect of partial silencing of FIB ex vivo in He La cells. Furthermore, IRES activity in BSC-1 cells, which are reported to have a very low level of endogenous FIB, was found to be significantly lower than that in He La cells. Additionally, we have mapped the putative contact points of PTB on the 5' and 3' UTRs by an RNA toe-printing assay. We have shown that the 3' UTR is able to stimulate CVB3 IRES-mediated translation. Interestingly, a deletion of 15 nt at the 5' end or 14 rut at the 3' end of the CVB3 3' UTR reduced the 3' UTR-mediated enhancement of IRES activity ex vivo significantly, and a reduced interaction was shown with PTB. It appears that the FIB protein might help in circularization of the CVB3 RNA by bridging the ends necessary for efficient translation of the viral RNA.

Inhibition of in Vitro Aminoacylation and Translation by RNA Reactive Antibodies

Antibodies were raised against guanosine-BSA, GMP-BSA and tRNA-mBSA conjugates separately in rabbits. Binding characteristics of these antibodies to various RNAs were studied using a sensitive avidin-biotin micro ELISA. These antibodies inhibited in vitro aminoacylation of tRNA in a dose dependent manner. This inhibition was reversed by the addition of the respective homologous haptens thereby showing the specificity of these antibodies. In vitro translation of endogenous mRNAs in rabbit reticulocyte lysate was also inhibited by these antibodies in a dose dependent manner.

Optimal polygon placement by translation

Let M be an m-sided simple polygon and N be an n-sided polygon with holes. In this paper we consider the problem of computing the feasible region, i.e., the set of all placements by translation of M so that M lies inside N without intersecting any hole. First we propose an O (mn(2)) time algorithm for computing the feasible region for the case when M is a monotone polygon. Then we consider the general case when M is a simple polygon and propose an O(m(2)n(2)) time algorithm for computing the feasible region. Both algorithms are optimal upto a constant factor.

Unsteady compressible flow due to relative rotation and translation of a viscous fluid on a disk

The modification of the axisymmetric viscous flow due to relative rotation of the disk or fluid by a translation of the boundary is studied. The fluid is taken to be compressible, and the relative rotation and translation velocity of the disk or fluid are time-dependent. The nonlinear partial differential equations governing the motion are solved numerically using an implicit finite difference scheme and Newton's linearisation technique. Numerical solutions are obtained at various non-dimensional times and disk temperatures. The non-symmetric part of the flow (secondary flow) describing the translation effect generates a velocity field at each plane parallel to the disk. The cartesian components of velocity due to secondary flow exhibit oscillations when the motion is due to rotation of the fluid on a translating disk. Increase in translation velocity produces an increment in the radial skin friction but reduces the tangential skin friction.