In plants, the known microRNAs (miRNAs) are produced as approximately 21 nucleotide (nt) duplexes from their precursors by Dicer-like 1 (DCL1). They are incorporated into Argonaute 1 (AGO1) protein to regulate target gene expression primarily through mRNA cleavage. We report here the discovery of a class of miRNAs in the model monocot rice (Oryza sativa). These are 24 nt in length and require another member of the Dicer family, DCL3, for their biogenesis. The 24 nt long miRNAs (lmiRNAs) are loaded into AGO4 clade proteins according to hierarchical rules, depending on the upstream biogenesis machinery and the 5'-terminal nucleotide. We demonstrated that lmiRNAs direct DNA methylation at loci from which they are produced as well as in trans at their target genes and play roles in gene regulation. Considered together, our findings define a miRNA pathway that mediates DNA methylation.

Misfolded proteins in the endoplasmic reticulum (ER) are destroyed by a pathway termed ER-associated protein degradation (ERAD). Glycans are often removed from glycosylated ERAD substrates in the cytosol before substrate degradation, which maintains the efficiency of the proteasome. Png1, a deglycosylating enzyme, has long been suspected, but not proven, to be crucial in this process. We demonstrate that the efficient degradation of glycosylated ricin A chain requires the Png1–Rad23 complex, suggesting that this complex couples protein deglycosylation and degradation. Rad23 is a ubiquitin (Ub) binding protein involved in the transfer of ubiquitylated substrates to the proteasome. How Rad23 achieves its substrate specificity is unknown. We show that Rad23 binds various regulators of proteolysis to facilitate the degradation of distinct substrates. We propose that the substrate specificity of Rad23 and other Ub binding proteins is determined by their interactions with various cofactors involved in specific degradation pathways.

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Highlights d Multiple infections reduce DHCR7 expression but increase AKT3 expression in macrophages d DHCR7 deficiency and 7-DHC treatment activate the PI3K-AKT3 pathway d AKT3 binds IRF3 to enhance IRF3 Ser385 phosphorylation needed for full IRF3 activation d Targeting DHCR7 protects mice from various viral infections

Ribosome production is an early event during skeletal muscle hypertrophy and precedes muscle protein accretion. Signaling via mTOR is crucial for ribosome production and hypertrophy; however, the mechanisms by which it regulates these processes remain to be identified. Herein, we investigated the activation of mTOR signaling in hypertrophying myotubes and determined that mTOR coordinates various aspects of gene expression important for ribosome production. First, inhibition of translation with cycloheximide had a more potent effect on protein synthesis than rapamycin indicating that mTOR function during hypertrophy is not on general, but rather on specific protein synthesis. Second, blocking Pol II transcription had a similar effect as Rapamycin and, unexpectedly, revealed the necessity of Pol II transcription for Pol I transcription, suggesting that mTOR may regulate ribosome production also by controlling Class II genes at the transcriptional level. Third, Pol I activity is essential for rDNA transcription and, surprisingly, for protein synthesis as selective Pol I inhibition blunted rDNA transcription, protein synthesis, and the hypertrophic response of myotubes. Finally, mTOR has nuclear localization in muscle, which is not sensitive to rapamycin. Inhibition of mTOR signaling by rapamycin disrupted mTOR-rDNA promoter interaction and resulted in altered histone marks indicative of repressed transcription and formation of higher-order chromatin structure. Thus mTOR signaling appears to regulate muscle hypertrophy by affecting protein synthesis, Class I and II gene expression, and chromatin remodeling.

Users engaged in information search often reformulate or modify their queries. This paper reports on an investigation of how task type and task situation influence users' query reformulation behavior. A controlled experiment was conducted with 48 participants, each working on six web search tasks classified into three types according to the task structure: Simple, Hierarchical and Parallel. We developed a taxonomy of query reformulation and used an automated method to detect the reformulations. Our results showed that Specialization was most frequently used in Simple tasks, and Word Substitution was most frequently used in Parallel tasks. After visiting and saving a useful web page, Generalization was less likely to be used while New query was more likely to be used. We also found that the effectiveness of each query reformulation type varied in different task types. The results of this study demonstrate the effect of task type on users' query reformulation behavior and have implications for the design of query suggestions that are offered to users during searching.

Lactobacillus plantarum is a lactic acid bacterium (LAB) species commonly used as a probiotic. We have sequenced the genome of Lactobacillus plantarum JDM1, which is a Chinese commercial LAB with several probiotic functions, using a GS 20 system. We recommend that each commercial probiotic strain should undergo complete genome sequencing to ensure safety and stability.Lactic acid bacteria (LAB) play a prominent role in the world food supply, performing the main bioconversions in fermented food, and are also used as probiotic supplements in dairy products and other foods. Lactobacillus plantarum is a LAB species commonly used as a probiotic. We have sequenced the genome of Lactobacillus plantarum JDM1, which is a widely used Chinese commercial LAB with several probiotic functions, using a GS 20 system (454 Life Science Corporation) (11). Two hundred thirty-six thousand, five hundred sixty-three high-quality reads were assembled with the 454 assembly tool, which had an average depth of 18.6-fold coverage of the genome and yielded 367 contigs. Among these, 225 large contigs represented 99.17% of the draft sequence. In the finishing process, the order of the selected large contigs was determined by BLAST analysis with the originally published genome sequence of strain WCFS1 (GenBank accession number AL935263) (8). Physical gaps were filled through sequencing of PCR products that spanned these regions using ABI 3730 xl DNA sequencers. Sequence assembly was accomplished by using the Phred/Phrap/Consed software package (4, 7). To ensure final accuracy, the errors in homopolymer sites that arose from the pyrosequencing method were solved via comparison with the corresponding sites on WCFS1 and then resequencing of the ambiguous bases using the ABI 3730 xl DNA sequencer.The complete genome of Lactobacillus plantarum JDM1 contains a single, circular chromosome of 3,197,759 bp and two plasmids (pLP2000 [2,062 bp] and pLP9000 [9,254 bp]). The two plasmids have been sequenced and published, with GenBank accession numbers AY096004 and AY096005 (3). The overall GC content of the chromosome is 44.66%, whereas the plasmids have a GC content slightly lower than that of the chromosome. The entire genome of JDM1 contains 2,948 protein-coding genes, 62 tRNA-encoding genes, and 16 rRNAencoding genes. Several repeated sequences, designated ISP2, were found in the chromosome which were almost the same as those in WCSF1, identified as a class of transposase-encoding regions representing mobile genetic elements. The other repeated sequence, ISP1 of WCSF1, was absent in JDM1.The entire genomic sequence of L. plantarum JDM1 was a little shorter than that of L. plantarum WCSF1 (3.3 Mb). The two genomes were highly similar (Ͼ90% by BLASTN analysis) with respect to genome structure and gene order. Intraspecies diversity may be required for successful adaptation in a complex ecological habitat (2). L. plantarum JDM1 has been grown as a probiotic in rich nutritional medium for so long that the genome may have gradually contracted. As supporting...

AIM: To elaborate the clinicopathologic features of colorectal cancer-related pyogenic liver abscess (PLA). METHODS: Reported cases of colorectal cancer-related PLAs were collected from the literature published up to October 2011 and evaluated for their clinicopathologic features. Data of collected cases included demographics, clinical presentation, microbial findings and treatment. Categorical variables were compared by χ2 analysis and continuous variables were evaluated using Student’s t test. RESULTS: A total 96 cases of colorectal cancer-related PLA were collected from the previous literature. Most patients (60%) were male and 40% cases occurred in the age group of 61-70 years. Apart from some special types of PLA, there were significant differences in the microbiological spectrum between Eastern Asia and non-Eastern Asian countries, which implied different risk factors and courses of the disease. Gram negative bacteria especially Klebsiella pneumoniae (K. pneumoniae) PLA was predominant in Eastern Asia (80.0%) in contrast to non-Eastern Asian countries (P < 0.01). Meanwhile, most of the Eastern Asian patients exhibited smaller size of liver abscess and atypical presentation. Sigmoid colon and rectum (72.73%) were the main sites of tumor in Eastern Asian patients, whereas tumor sites were uneven among most of the non-Easter Asian PLA patients. CONCLUSION: K. pneumoniae PLA was strongly associated with colorectal cancer, especially those occurring in sigmoid colon and rectum, in elderly Eastern Asian male patients