A novel plant nuclear gene encoding chloroplast ribosomal protein S9 has a transit peptide related to that of rice chloroplast ribosomal protein L12

AbstractWe have cloned a novel nuclear gene for a ribosomal protein of rice and Arabidopsis that is like the bacterial ribosomal protein S9. To determine the subcellular localization of the gene product, we fused the N-terminal region and green fluorescent protein and expressed it transiently in rice seedlings. Localized fluorescence was detectable only in chloroplasts, indicating that this nuclear gene encodes chloroplast ribosomal protein S9. The N-terminal region of rice ribosomal protein S9 was found to have a high sequence similarity to the transit peptide region of the rice chloroplast ribosomal protein L12, suggesting that these transit peptides have a common lineage

Transfer of rice mitochondrial ribosomal protein L6 gene to the nucleus: acquisition of the 5'-untranslated region via a transposable element

<p>Abstract</p> <p>Background</p> <p>The mitochondria of contemporary organisms contain fewer genes than the ancestral bacteria are predicted to have contained. Because most of the mitochondrial proteins are encoded in the nucleus, the genes would have been transferred from the mitochondrion to the nucleus at some stage of evolution and they must have acquired cis-regulatory elements compatible with eukaryotic gene expression. However, most of such processes remain unknown.</p> <p>Results</p> <p>The ribosomal protein L6 gene (<it>rpl6</it>) has been lost in presently-known angiosperm mitochondrial genomes. We found that each of the two rice <it>rpl6 </it>genes (<it>OsRpl6-1 </it>and <it>OsRpl6-2</it>) has an intron in an identical position within the 5'-untranslated region (UTR), which suggests a duplication of the <it>rpl6 </it>gene after its transfer to the nucleus. Each of the predicted RPL6 proteins lacks an N-terminal extension as a mitochondrial targeting signal. Transient assays using green fluorescent protein indicated that their mature N-terminal coding regions contain the mitochondrial targeting information. Reverse transcription-PCR analysis showed that <it>OsRpl6-2 </it>expresses considerably fewer transcripts than <it>OsRpl6-1</it>. This might be the result of differences in promoter regions because the 5'-noncoding regions of the two <it>rpl6 </it>genes differ at a point close to the center of the intron. There are several sequences homologous to the region around the 5'-UTR of <it>OsRpl6-1 </it>in the rice genome. These sequences have characteristics similar to those of the transposable elements (TE) belonging to the <it>PIF</it>/Harbinger superfamily.</p> <p>Conclusion</p> <p>The above evidences suggest a novel mechanism in which the 5'-UTR of the transferred mitochondrial gene was acquired via a TE. Since the 5'-UTRs and introns within the 5'-UTRs often contain transcriptional and posttranscriptional cis-elements, the transferred rice mitochondrial <it>rpl6 </it>gene may have acquired its cis-element from a TE.</p

Association between plasma levels of pigment epithelium-derived factor and renal dysfunction in patients with coronary artery disease

Background: Although plasma pigment epithelium-derived factor (PEDF) levels have been shown to be significantly correlated with the levels of creatinine (Cr) in type 2 diabetes, little is known about the association between PEDF levels and renal dysfunction in patients with coronary artery disease (CAD). Methods: We enrolled 134 consecutive patients with diagnosed CAD and measured plasma levels of PEDF, serum Cr, uric acid (UA) and high-sensitive C-reactive protein (hsCRP). Results: Plasma PEDF levels were positively correlated with serum Cr (p < 0.0001) and UA (p < 0.0001) and negatively correlated with the estimated glomerular filtration rate (eGFR) (p < 0.0001), whereas there was no association between plasma PEDF and age or hsCRP. When the subjects were divided into five groups (0&#8211;4) according to the number of metabolic factors (obesity, diabetes, hypertension and dyslipidemia), PEDF levels in patients with four factors were significantly higher than those in patients without factors. Next, we divided the patients into quartiles according to their plasma PEDF levels (< 9.9 &#956;g/mL, 9.9&#8211;12.8, 12.9&#8211; &#8211;15.7, > 15.7). The eGFR in the first group was significantly higher than those in the third and fourth groups. Multivariate logistic analysis indicated that eGFR (p < 0.0001) and age (p = 0.030) were significant independent variables that correlated with the quartile classification according to PEDF levels. Conclusions: This study revealed that PEDF may play a role in renal dysfunction in CAD patients. (Cardiol J 2011; 18, 5: 515&#8211;520

Selective labeling of a single organelle by using two-photon conversion of a photoconvertible fluorescent protein

SPIE BiOS, 2008, San Jose, California, United StatesWataru Watanabe, Tomoko Shimada, Sachihiro Matsunaga, Daisuke Kurihara, Shin-ichi Arimura, Nobuhiro Tsutsumi, Kiichi Fukui, Kazuyoshi Itoh, "Selective labeling of a single organelle by using two-photon conversion of a photoconvertible fluorescent protein," Proc. SPIE 6860, Multiphoton Microscopy in the Biomedical Sciences VIII, 68601B (15 February 2008); https://doi.org/10.1117/12.768745

Frequent Closed Item Set Mining Based on Zero-suppressed BDDs

Frequent item set mining is one of the fundamental techniques for knowledge discovery and data mining. In the last decade, a number of efficient algorithms for frequent item set mining have been presented, but most of them focused on just enumerating the item set patterns which satisfy the given conditions, and it was a different matter how to store and index the result of patterns for efficient data analysis. Recently, we proposed a fast algorithm of extracting all frequent item set patterns from transaction databases and simultaneously indexing the result of huge patterns using Zero-suppressed BDDs (ZBDDs). That method, ZBDD-growth, is not only enumerating/listing the patterns efficiently, but also indexing the output data compactly on the memory to be analyzed with various algebraic operations. In this paper, we present a variation of ZBDD-growth algorithm to generate frequent closed item sets. This is a quite simple modification of ZBDD-growth, and additional computation cost is relatively small compared with the original algorithm for generating all patterns. Our method can conveniently be utilized in the environment of ZBDD-based pattern indexing.論文特集:データマイニングと統計数

Cold Treatment Induces Transient Mitochondrial Fragmentation in Arabidopsis thaliana in a Way that Requires DRP3A but not ELM1 or an ELM1-Like Homologue, ELM2

The number, size and shape of polymorphic plant mitochondria are determined at least partially by mitochondrial fission. Arabidopsis mitochondria divide through the actions of a dynamin-related protein, DRP3A. Another plant-specific factor, ELM1, was previously shown to localize DRP3A to mitochondrial fission sites. Here, we report that mitochondrial fission is not completely blocked in the Arabidopsis elm1 mutant and that it is strongly manifested in response to cold treatment. Arabidopsis has an ELM1 paralogue (ELM2) that seems to have only a limited role in mitochondrial fission in the elm1 mutant. Interestingly, cold-induced mitochondrial fragmentation was also observed in the wild-type, but not in a drp3a mutant, suggesting that cold-induced transient mitochondrial fragmentation requires DRP3A but not ELM1 or ELM2. DRP3A: GFP localized from the cytosol to mitochondrial fission sites without ELM1 after cold treatment. Together, these results suggest that Arabidopsis has a novel, cold-induced type of mitochondrial fission in which DRP3A localizes to mitochondrial fission sites without the involvement of ELM1 or ELM2