A parallel approach to miRNA target prediction

Master'sMASTER OF SCIENC

Predicting the impact of scientific concepts using full‐text features

Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/134425/1/asi23612.pd

MicroTar: predicting microRNA targets from RNA duplexes

BACKGROUND: The accurate prediction of a comprehensive set of messenger RNAs (targets) regulated by animal microRNAs (miRNAs) remains an open problem. In particular, the prediction of targets that do not possess evolutionarily conserved complementarity to their miRNA regulators is not adequately addressed by current tools. RESULTS: We have developed MicroTar, an animal miRNA target prediction tool based on miRNA-target complementarity and thermodynamic data. The algorithm uses predicted free energies of unbound mRNA and putative mRNA-miRNA heterodimers, implicitly addressing the accessibility of the mRNA 3' untranslated region. MicroTar does not rely on evolutionary conservation to discern functional targets, and is able to predict both conserved and non-conserved targets. MicroTar source code and predictions are accessible at , where both serial and parallel versions of the program can be downloaded under an open-source licence. CONCLUSION: MicroTar achieves better sensitivity than previously reported predictions when tested on three distinct datasets of experimentally-verified miRNA-target interactions in C. elegans, Drosophila, and mouse

The Fission Yeast TACC Protein Mia1p Stabilizes Microtubule Arrays by Length-Independent Crosslinking

SummaryMicrotubule (MT) arrays are mechanistic effectors of polarity specification and cell division. Linear bundles in which MTs are bridged laterally [1, 2] are dynamically assembled in systems ranging from differentiated metazoan cells to fungi in a process that remains poorly understood. Often, bundled MTs slide with respect to each other via molecular motors [3, 4]. In interphase cells of the fission yeast Schizosaccharomyces pombe, MT nucleation frequently occurs at preexisting arrays [5, 6]. As the nascent MT lengthens, stable antiparallel MT overlaps are thought to form through competition between motion of the minus-end-directed kinesin Klp2p [4] and braking force exerted by the accumulating lateral crosslinker Ase1p [7–9]. Here we show that Mia1p/Alp7p, a transforming acidic coiled-coil (TACC) protein [10, 11], functions as a length-independent MT crosslinker. In cells lacking Mia1p MT-bundling activity, linear arrays frequently disassemble, accompanied by a marked increase in Ase1p off rate and erratic motion of sliding MTs. We propose that the combined action of lateral length-dependent (Ase1p) and terminal length-independent (Mia1p) crosslinkers is crucial for robust assembly and stability of linear MT arrays. Such use of qualitatively distinct crosslinking mechanisms in tandem may point to a general design principle in the engineering of stable cytoskeletal assemblies

Cell-Cycle Regulation of Dynamic Chromosome Association of the Condensin Complex

Summary: Eukaryotic cells inherit their genomes in the form of chromosomes, which are formed from the compaction of interphase chromatin by the condensin complex. Condensin is a member of the structural maintenance of chromosomes (SMC) family of ATPases, large ring-shaped protein assemblies that entrap DNA to establish chromosomal interactions. Here, we use the budding yeast Saccharomyces cerevisiae to dissect the role of the condensin ATPase and its relationship with cell-cycle-regulated chromosome binding dynamics. ATP hydrolysis-deficient condensin binds to chromosomes but is defective in chromosome condensation and segregation. By modulating the ATPase, we demonstrate that it controls condensin’s dynamic turnover on chromosomes. Mitosis-specific phosphorylation of condensin’s Smc4 subunit reduces the turnover rate. However, reducing turnover by itself is insufficient to compact chromosomes. We propose that condensation requires fine-tuned dynamic condensin interactions with more than one DNA. These results enhance our molecular understanding of condensin function during chromosome condensation. : The condensin complex is a key determinant of mitotic chromosome formation. Thadani et al. study the dynamic binding of condensin to chromosomes. They reveal how condensin turnover is regulated by its ATPase and by cell-cycle phosphorylation. Chromosome condensation in mitosis requires fine-tuning of this dynamic behavior. Keywords: chromosome condensation, mitosis, cell cycle, phosphorylation, condensin, ABC ATPase, Saccharomyces cerevisia

Primers for quantitative PCR.

<p>Primers for quantitative PCR.</p

GC-MS profile of 2^nd band.

<p>GC-MS profile of 2^nd band.</p

GC-MS profile of 1^st band.

<p>GC-MS profile of 1^st band.</p

Effect of ARCE on cytotoxicity in H9c2 cells.

<p>H9c2 cells were treated with H₂O₂ (100 μM) for 12h with or without pretreatment of ARCE (100–750 μg/ml) for 24 h. Untreated cells were used as control. % Cytotoxicity was determined by MTT Assay. The data were represented asmean ± SEM, for three independent experiments. ***P<0.001 vs. control group and ### P<0.001 vs. H₂O₂ group.</p

Anthocyanin rich extract of <i>Brassica oleracea</i> L. alleviates experimentally induced myocardial infarction

<div><p>Cardioprotective potential of anthocyanin rich red cabbage extract (ARCE) was assessed in H₂O₂ treated rat neonatal cardiomyoblasts (H9c2 cells) and isoproterenol (ISO) induced rodent model of myocardial infarction. H₂O₂ treated H9c2 cells recorded cytotoxicity (48–50%) and apoptosis (57.3%), the same were reduced in presence of ARCE (7–10% & 12.3% respectively). Rats pretreated with ARCE for 30 days followed by ISO treatment recorded favourable heart: body weight ratio as compared to ISO treated group. Also, the mRNA levels of enzymatic antioxidants (<i>sod</i> and <i>catalase</i>) and apoptotic genes (<i>bax</i> and <i>bcl-2</i>) in ARCE+ISO treated group were similar to the control group suggesting that ARCE pretreatment prevents ISO induced depletion of enzymatic antioxidants and apoptosis. Histoarchitecture of ventricular tissue of ISO treated group was marked by infracted areas (10%) and derangement of myocardium whereas, ARCE+ISO treated group (4.5%) recorded results comparable to control (0%). ARCE+ISO treated group accounted for upregulation of <i>caveolin-3</i> and <i>SERCA2a</i> expression as compared to the ISO treated group implying towards ARCE mediated reduction in membrane damage and calcium imbalance. Molecular docking scores and LigPlot analysis of cyanidin-3-glucoside (-8.7 Kcal/mol) and delphinidin-3-glucoside (-8.5 Kcal/mol) showed stable hydrophobic and electrostatic interactions with β₁ adrenergic receptor. Overall this study elucidates the mechanism of ARCE mediated prevention of experimentally induced myocardial damage.</p></div