Selective peroxisome proliferator-activated receptor δ isosteric selenium agonists as potent anti-atherogenic agents in vivo

We report the synthesis and in vivo activity of a novel anti-atherogenic agent, isosteric selenium PPARδ-selective ligand. This ligand did not cause significant body or liver weight changes and did not have obvious adverse effects on intestinal polyp formation. Our overall results clearly demonstrate that PPARδ is a viable drug candidate for targeting and treating atherosclerosis.     

Fine mapping and candidate gene analysis of the floury endosperm gene, FLO(a), in rice

In addition to its role as an energy source for plants, animals and humans, starch is also an environmentally friendly alternative to fossil fuels. In rice, the eating and cooking quality of the grain is determined by its starch properties. The floury endosperm of rice has been explored as an agronomical trait in breeding and genetics studies. In the present study, we characterized a floury endosperm mutant, flo(a), derived from treatment of Oryza sativa ssp. japonica cultivar Hwacheong with MNU. The innermost endosperm of the flo(a) mutant exhibited floury characteristics while the outer layer of the endosperm appeared normal. Starch granules in the flo(a) mutant formed a loosely-packed crystalline structure and X-ray diffraction revealed that the overall crystallinity of the starch was decreased compared to wild-type. The FLO(a) gene was isolated via a map-based cloning approach and predicted to encode the tetratricopeptide repeat domaincontaining protein, OsTPR. Three mutant alleles contain a nucleotide substitution that generated one stop codon or one splice site, respectively, which presumably disrupts the interaction of the functionally conserved TPR motifs. Taken together, our map-based cloning approach pinpointed an OsTPR as a strong candidate of FLO(a), and the proteins that contain TPR motifs might play a significant role in rice starch biosynthetic pathways.     

Relative Codon Adaptation: A Generic Codon Bias Index for Prediction of Gene Expression

The development of codon bias indices (CBIs) remains an active field of research due to their myriad applications in computational biology. Recently, the relative codon usage bias (RCBS) was introduced as a novel CBI able to estimate codon bias without using a reference set. The results of this new index when applied to Escherichia coli and Saccharomyces cerevisiae led the authors of the original publications to conclude that natural selection favours higher expression and enhanced codon usage optimization in short genes. Here, we show that this conclusion was flawed and based on the systematic oversight of an intrinsic bias for short sequences in the RCBS index and of biases in the small data sets used for validation in E. coli. Furthermore, we reveal that how the RCBS can be corrected to produce useful results and how its underlying principle, which we here term relative codon adaptation (RCA), can be made into a powerful reference-set-based index that directly takes into account the genomic base composition. Finally, we show that RCA outperforms the codon adaptation index (CAI) as a predictor of gene expression when operating on the CAI reference set and that this improvement is significantly larger when analysing genomes with high mutational bias.     

Ontogenetic changes of habitat selection and thyroid hormone levels in black rockfish (Sebastes schlegelii) reared in captivity

This study examined the ontogenetic change in vertical distribution associated with algae and the thyroid hormone profiles of black rockfish (Sebastes schlegelii) under rearing conditions. Experimental observations on distribution were carried on black rockfish from the newly born larval stage to juveniles 75 days after birth (DAB). Position was categorized by vertical location [upper layer, mid layer and lower layer (LL)] and by association with artificial algae (floating algae, bottom algae and no association). Position of fish was observed four times a day, at 0400 (dawn), 1200 (noon), 1800 (dusk) and 2400 (midnight) hours. The majority of fish (>80%) reached transforming larval stage [17.8 ± 0.7 mm total length (TL)] at 25 DAB and juvenile stage (24.3 ± 0.6 mm TL) at 35 DAB. Newly born larvae were mainly distributed at surface and middle layers, the shift of vertical distribution to the LL occurred between 10 and 25 DAB, and over 98% of the individuals were distributed near the bottom after 35 DAB. Association behavior with algae was first observed from 20 to 30 DAB depending on the time of day. Percentage of fish associated with bottom algae increased from 25 to 40 DAB and reached 50–70% thereafter. Thyroid hormone (T₄) showed two surges at 30 and 50 DAB. The first surge corresponded to the transforming larval stage and the occurrence of association behavior with algae. The results indicate that pelagic larvae settle to the bottom layer before metamorphosis, and association behavior with algae appears at the transforming larval stage. A high T₄ concentration at 30 DAB indicates a close relationship with these morphological and behavioral developments.     

Long-range tertiary interactions in single hammerhead ribozymes bias motional sampling toward catalytically active conformations

Enzymes generally are thought to derive their functional activity from conformational motions. The limited chemical variation in RNA suggests that such structural dynamics may play a particularly important role in RNA function. Minimal hammerhead ribozymes are known to cleave efficiently only in ～ 10-fold higher than physiologic concentrations of Mg(2+) ions. Extended versions containing native loop-loop interactions, however, show greatly enhanced catalytic activity at physiologically relevant Mg(2+) concentrations, for reasons that are still ill-understood. Here, we use Mg(2+) titrations, activity assays, ensemble, and single molecule fluorescence resonance energy transfer (FRET) approaches, combined with molecular dynamics (MD) simulations, to ask what influence the spatially distant tertiary loop-loop interactions of an extended hammerhead ribozyme have on its structural dynamics. By comparing hammerhead variants with wild-type, partially disrupted, and fully disrupted loop-loop interaction sequences we find that the tertiary interactions lead to a dynamic motional sampling that increasingly populates catalytically active conformations. At the global level the wild-type tertiary interactions lead to more frequent, if transient, encounters of the loop-carrying stems, whereas at the local level they lead to an enrichment in favorable in-line attack angles at the cleavage site. These results invoke a linkage between RNA structural dynamics and function and suggest that loop-loop interactions in extended hammerhead ribozymes-and Mg(2+) ions that bind to minimal ribozymes-may generally allow more frequent access to a catalytically relevant conformation(s), rather than simply locking the ribozyme into a single active state.     

Thrombin enhanced migration and MMPs expression of human chondrosarcoma cells involves PAR receptor signaling pathway

Thrombin is a multifunctional protease that can activate hemostasis and coagulation through the cleavage of fibrinogen to form fibrin clots. Thrombin also plays a crucial role in migration and metastasis of human cancer cells. However, the effect of thrombin on migration activity in human chondrosarcoma cells is mostly unknown. Here, we found that thrombin increased the migration and expression of matrix metalloproteinase (MMP)‐2 and MMP‐13 in human chondrosarcoma cells (JJ012 and SW1353 cells). By using pharmacological inhibitors or activators or genetic inhibition by the protease‐activated receptor (PAR), we found that the PAR1 and PAR4 receptor but not PAR3 receptor are involved in thrombin‐mediated cell migration and MMPs expression. Thrombin‐mediated migration and MMPs up‐regulation was attenuated by phospholipase C (PLC), protein kinase C, and c‐Src inhibitor. Activations of PLCβ, PKCα, c‐Src, and NF‐κB pathways after thrombin treatment was demonstrated, and thrombin‐induced MMPs expression and migration activity was inhibited by the specific inhibitors and mutants of PLC, PKC, c‐Src, and NF‐κB cascades. Taken together, our results indicated that thrombin enhances the migration of chondrosarcoma cells by increasing MMP‐2 and MMP‐13 expression through the PAR/PLC/PKCα/c‐Src/NF‐κB signal transduction pathway. J. Cell. Physiol. 223:737–745, 2010. © 2010 Wiley‐Liss, Inc.     

A Novel Type of E3 Ligase for the Ufm1 Conjugation System

The ubiquitin fold modifier 1 (Ufm1) is the most recently discovered ubiquitin-like modifier whose conjugation (ufmylation) system is conserved in multicellular organisms. Ufm1 is known to covalently attach with cellular protein(s) via a specific E1-activating enzyme (Uba5) and an E2-conjugating enzyme (Ufc1), but its E3-ligating enzyme(s) as well as the target protein(s) remain unknown. Herein, we report both a novel E3 ligase for Ufm1, designated Ufl1, and an Ufm1-specific substrate ligated by Ufl1, C20orf116. Ufm1 was covalently conjugated with C20orf116. Although Ufl1 has no obvious sequence homology to any other known E3s for ubiquitin and ubiquitin-like modifiers, the C20orf116·Ufm1 formation was greatly accelerated by Ufl1. The C20orf116·Ufm1 conjugate was cleaved by Ufm1-specific proteases, implying the reversibility of ufmylation. The conjugation was abundant in the liver and lungs of Ufm1-transgenic mice, fractionated into membrane fraction, and impaired in Uba5 knock-out cells. Intriguingly, immunological analysis revealed localizations of Ufl1 and C20orf116 mainly to the endoplasmic reticulum. Our results provide novel insights into the Ufm1 system involved in cellular regulation of multicellular organisms.