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Low temperature is a major factor limiting rice productivity and geographical distribution. Improved cold tolerance and expanded cultivation to high-altitude or high-latitude regions would help meet growing rice demand. Here we explored a QTL for cold tolerance and cloned the gene, CTB4a (cold tolerance at booting stage), encoding a conserved leucine-rich repeat receptor-like kinase. We show that different CTB4a alleles confer distinct levels of cold tolerance and selection for variation in the CTB4a promoter region has occurred on the basis of environmental temperature. The newly generated cold-tolerant haplotype Tej-Hap-KMXBG was retained by artificial selection during temperate japonica evolution in cold habitats for low-temperature acclimation. Moreover, CTB4a interacts with AtpB, a beta subunit of ATP synthase. Upregulation of CTB4a correlates with increased ATP synthase activity, ATP content, enhanced seed setting and improved yield under cold stress conditions. These findings suggest strategies to improve cold tolerance in crop plants.

We present the results for CAPRI Round 30, the first joint CASP-CAPRI experiment, which brought together experts from the protein structure prediction and protein-protein docking communities. The Round comprised 25 targets from amongst those submitted for the CASP11 prediction experiment of 2014. The targets included mostly homodimers, a few homotetramers, and two heterodimers, and comprised protein chains that could readily be modeled using templates from the Protein Data Bank. On average 24 CAPRI groups and 7 CASP groups submitted docking predictions for each target, and 12 CAPRI groups per target participated in the CAPRI scoring experiment. In total more than 9500 models were assessed against the 3D structures of the corresponding target complexes. Results show that the prediction of homodimer assemblies by homology modeling techniques and docking calculations is quite successful for targets featuring large enough subunit interfaces to represent stable associations. Targets with ambiguous or inaccurate oligomeric state assignments, often featuring crystal contact-sized interfaces, represented a confounding factor. For those, a much poorer prediction performance was achieved, while nonetheless often providing helpful clues on the correct oligomeric state of the protein. The prediction performance was very poor for genuine tetrameric targets, where the inaccuracy of the homology-built subunit models and the smaller pair-wise interfaces severely limited the ability to derive the correct assembly mode. Our analysis also shows that docking procedures tend to perform better than standard homology modeling techniques and that highly accurate models of the protein components are not always required to identify their association modes with acceptable accuracy.

Background & Aims MicroRNAs (miRNAs) have been shown to be involved in many biological processes by affecting their target gene expression. miR-122 has been extensively studied in hepatocarcinogenesis. However, the role of miR-122 in liver fibrosis remains unknown. Methods The mRNA expression levels of miR-122, prolyl 4-hydroxylase subunit alpha-1 (P4HA1), and CCAAT/enhancer binding protein alpha (C/EBPα) were assessed by real-time PCR. The protein expression levels of P4HA1, C/EBPα and collagen, type I, alpha 1 (COL1A1) were analyzed by Western blot and immunofluorescence. MTT assay was used to assess cell proliferation. Chromatin immunoprecipitation (ChIP) assay was used to examine the binding activity of C/EBPα to miR-122 promoter. Results miR-122 expression was significantly reduced in transactivated HSCs and in the livers of mice treated with CCl4. Overexpression of miR-122 inhibited the proliferation of LX2 cells. We also demonstrated that P4HA1 was a target gene of miR-122. The mRNA expression level of PAHA1 inversely correlated with that of miR-122 in HSCs and in the mouse liver. Overexpression of miR-122 markedly attenuated the expression of P4HA1 via targeting a binding site located at 3′-UTR of P4HA1 mRNA. We further showed that miR-122 overexpression led to decreased collagen maturation and ECM production. Finally, the binding activity of C/EBPα to miR-122 promoter was significantly decreased in activated HSCs. Conclusions Our study suggests that miR-122 may play an important role in negatively regulating collagen production in HSCs and that targeted expression of miR-122 in HSCs may represent a new strategy for the treatment of liver fibrosis.

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S-Nitrosylation is a redox-based protein post-translational modification in response to nitric oxide signaling and is involved in a wide range of biological processes. Detection and quantification of protein S-nitrosylation have been challenging tasks due to instability and low abundance of the modification. Many studies have used mass spectrometry (MS)-based methods with different thiol-reactive reagents to label and identify proteins with S-nitrosylated cysteine (SNO-Cys). In this study, we developed a novel iodoTMT switch assay (ISA) using an isobaric set of thiol-reactive iodoTMTsixplex reagents to specifically detect and quantify protein S-nitrosylation. Irreversible labeling of SNO-Cys with the iodoTMTsixplex reagents enables immune-affinity detection of S-nitrosylated proteins, enrichment of iodoTMT-labeled peptides by anti-TMT resin, and importantly, unambiguous modification site-mapping and multiplex quantification by liquid chromatography–tandem MS. Additionally, we significantly improved anti-TMT peptide enrichment efficiency by competitive elution. Using ISA, we identified a set of SNO-Cys sites responding to lipopolysaccharide (LPS) stimulation in murine BV-2 microglial cells and revealed effects of S-allyl cysteine from garlic on LPS-induced protein S-nitrosylation in antioxidative signaling and mitochondrial metabolic pathways. ISA proved to be an effective proteomic approach for quantitative analysis of S-nitrosylation in complex samples and will facilitate the elucidation of molecular mechanisms of nitrosative stress in disease.

A series of beta-formyl-BODIPYs 2 were synthesized in high yields from tetramethyl-BODIPYs 1 via the Vilsmeier-Haack reaction and were further functionalized using a Knoevenagel condensation to generate novel BODIPYs 3 and 4.

Dosage compensation, the equalized X chromosome gene expression between males and females in Drosophila, has also been found in triple X metafemales. Inverse dosage effects, produced by genomic imbalance, are believed to account for this modulated expression, but they have not been studied on a global level. Here, we show a global expression comparison of metafemales (XXX; AA) with normal females (XX; AA) with high-throughput RNAsequencing. We found that the majority of the X-linked genes in metafemales exhibit dosage compensation with an expression level similar to that of normal diploid females. In parallel, most of the autosomal genes were expressed at about two-thirds the level of normal females, the ratio of inverse dosage effects produced by the extra X chromosome. Both compensation and inverse effects were further confirmed by combination of X-linked and autosomally located miniwhite reporter genes in metafemales and relative quantitative PCR of selected genes. These data provide evidence for an inverse dosage component to X chromosome compensation.aneuploidy | epigenetics | transcription