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Aims: Ischemic cardiomyopathy (ICM) resulting from myocardial infarction is a major cause of heart failure (HF). Recently, thousands of long non-coding RNAs (lncRNAs) have been discovered and implicated in a variety of biological processes. However, the role of most lncRNAs in HF remains largely unknown. The aim of this study is to test the hypothesis that the expression and function of lncRNAs are differentially regulated in diseased hearts. Methods and results: In this study, we performed RNA deep sequencing of protein-coding and non-coding RNAs from cardiac samples of patients with ICM (n?15) and controls (n=15). Genome-wide transcriptome analysis confirmed that many protein-coding genes previously known to be involved in HF were altered in ICM hearts. Among the 145 differentially expressed lncRNAs identified in ICM hearts, we found a set of 35 lncRNAs that display strong positive expression correlation. Expression correlation coefficient analyses of differentially expressed lncRNAs and proteincoding genes revealed a strong association between lncRNAs and extracellular matrix (ECM) protein-coding genes. We overexpressed or knocked down selected lncRNAs in cardiac fibroblasts and our results suggest that lncRNAs are important regulators of fibrosis and the expression of ECM synthesis genes. Moreover, we show that lncRNAs participate in the TGF-α pathway to modulate the expression of ECM genes and myofibroblast differentiation. Conclusion: Our studies demonstrate that the expression of many lncRNAs is dynamically regulated in ICM. lncRNAs regulate the expression and function of ECM and cardiac fibrosis during the development of ICM. Our results further indicate that lncRNAs may represent novel regulators of heart function and cardiac disorders, including ICM. [ABSTRACT FROM AUTHOR]

Laodelphax striatellus Fallen (Homoptera: Delphacidae), is a serious pest in rice, Oryza sativa L., production. A mapping population consisting of 81 recombinant inbred lines (RILs), derived from a cross between japonica 'Kinmaze' and indica 'DV85' rice, was used to detect quantitative trait loci (QTLs) for the resistance to L. striatellus. Seedbox screening test (SST), antixenosis test, and antibiosis test were used to evaluate the resistance response of the two parents and 81 RILs to L. striatellus at the seedling stage, and composite interval mapping was used for QTL analysis. When the resistance was measured by SST method, two QTLs conferring resistance to L. striatellus were mapped on chromosome 11, namely, Qsbph11a and Qsbph11b, with log of odds scores 2.51 and 4.38, respectively. The two QTLs explained 16.62 and 27.78% of the phenotypic variance in this population, respectively. In total, three QTLs controlling antixenosis against L. striatellus were detected on chromosomes 3, 4, and 11, respectively, accounting for 37.5% of the total phenotypic variance. Two QTLs expressing antibiosis to L. striatellus were mapped on chromosomes 3 and 11, respectively, explaining 25.9% of the total phenotypic variance. The identified QTL located between markers XNpb202 and C1172 on chromosome 11 was detected repeatedly by three different screening methods; therefore, it may be important to confer the resistance to L. striatellus. Once confirmed in other mapping populations, these QTLs should be useful in breeding for resistance to L. striatellus by marker-assisted selection of different resistance genes in rice varieties. [ABSTRACT FROM AUTHOR]

1-Aminocyclopropane-1-carboxylate (ACC) synthase is a key enzyme in the regulation of ethylene biosynthesis in higher plants. To investigate the catalytic significances of two conserved tyrosine residues, Tyr151 and Tyr152, of a tomato ACC synthase isozyme (LeACS2), five ACC synthase mutants (Y151F, Y151G, Y152F, Y152G, and Y151F/Y152F) were constructed and over-expressed in Escherichia coli. Subsequent kinetic analysis indicated that these point mutations in mutants Y152F, Y152G, and Y151F/Y152F, either reduced the catalytic efficiency more than 98% or fully inactivated ACC synthase, while Y151F and Y151G mutants reduced the enzymatic activities by 27% and 83%, respectively. It is therefore concluded that Tyr152, especially its hydroxyl group, plays an essential role in the catalysis of ACC synthase. Thus, a revised catalytic model is hereby proposed for functional ACC synthase. [ABSTRACT FROM PUBLISHER]

Establishing the relationships among modern amphibians (lissamphibians) and their ancient relatives is necessary for our understanding of early tetrapod evolution. However, the phylogeny is still intractable because of the highly specialized anatomy and poor fossil record of lissamphibians. Paleobiologists are still not sure whether lissamphibians are monophyletic or polyphyletic, and which ancient group (temnospondyls or lepospondyls) is most closely related to them. In an attempt to address these problems, eight mitochondrial genomes of living amphibians were determined and compared with previously published amphibian sequences. A comprehensive molecular phylogenetic analysis of nucleotide sequences yields a highly resolved tree congruent with the traditional hypotheses (Batrachia). By using a molecular clock–independent approach for inferring dating information from molecular phylogenies, we present here the first molecular timescale for lissamphibian evolution, which suggests that lissamphibians first emerged about 330 million years ago. By observing the fit between molecular and fossil times, we suggest that the temnospondyl-origin hypothesis for lissamphibians is more credible than other hypotheses. Moreover, under this timescale, the potential geographic origins of the main living amphibian groups are discussed: (i) advanced frogs (neobatrachians) may possess an Africa-India origin; (ii) salamanders may have originated in east Asia; (iii) the tropic forest of the Triassic Pangaea may be the place of origin for the ancient caecilians. An accurate phylogeny with divergence times can be also helpful to direct the search for “missing” fossils, and can benefit comparative studies of amphibian evolution. [Amphibian; mitochondrial genome; molecular dating; phylogeny; timescale.] [ABSTRACT FROM AUTHOR]

Chlamydomonas reinhardtii is a unicellular green alga, the lineage of which diverged from that of land plants >1 billion years ago. Using the powerful small nucleolar RNA (snoRNA) mining platform to screen the C. reinhardtii genome, we identified 322 snoRNA genes grouped into 118 families. The 74 box C/D families can potentially guide methylation at 96 sites of ribosomal RNAs (rRNAs) and snRNAs, and the 44 box H/ACA families can potentially guide pseudouridylation at 62 sites. Remarkably, 242 of the snoRNA genes are arranged into 76 clusters, of which 77% consist of homologous genes produced by small local tandem duplications. At least 70 snoRNA gene clusters are found within introns of protein-coding genes. Although not exhaustive, this analysis reveals that C. reinhardtii has the highest number of intronic snoRNA gene clusters among eukaryotes. The prevalence of intronic snoRNA gene clusters in C. reinhardtiiis similar to that of rice but in contrast with the one-snoRNA-per-intron organization of vertebrates and fungi and with that of Arabidopsis thaliana in which only a few intronic snoRNA gene clusters were identified. This analysis of C. reinhardtii snoRNA gene organization shows the functional importance of introns in a single-celled organism and provides evolutionary insight into the origin of intron-encoded RNAs in the plant lineage. [ABSTRACT FROM AUTHOR]