Identification and analysis of phosphorylation status of proteins in dormant terminal buds of poplar

<p>Abstract</p> <p>Background</p> <p>Although there has been considerable progress made towards understanding the molecular mechanisms of bud dormancy, the roles of protein phosphorylation in the process of dormancy regulation in woody plants remain unclear.</p> <p>Results</p> <p>We used mass spectrometry combined with TiO₂phosphopeptide-enrichment strategies to investigate the phosphoproteome of dormant terminal buds (DTBs) in poplar (<it>Populus simonii × P. nigra</it>). There were 161 unique phosphorylated sites in 161 phosphopeptides from 151 proteins; 141 proteins have orthologs in <it>Arabidopsis</it>, and 10 proteins are unique to poplar. Only 34 sites in proteins in poplar did not match well with the equivalent phosphorylation sites of their orthologs in <it>Arabidopsis</it>, indicating that regulatory mechanisms are well conserved between poplar and <it>Arabidopsis</it>. Further functional classifications showed that most of these phosphoproteins were involved in binding and catalytic activity. Extraction of the phosphorylation motif using Motif-X indicated that proline-directed kinases are a major kinase group involved in protein phosphorylation in dormant poplar tissues.</p> <p>Conclusions</p> <p>This study provides evidence about the significance of protein phosphorylation during dormancy, and will be useful for similar studies on other woody plants.</p

An Experimental Study on the Water-Induced Strength Reduction in Zigong Argillaceous Siltstone with Different Degree of Weathering

The water-softening property of soft rocks is a key problem in geotechnical engineering. A typical red-bed soft rock (the Zigong argillaceous siltstones) with different weathering degree is selected as an example to study the water-softening property and the influence of degree of weathering. A series of mechanical and microstructure tests are carried out to analyze the weathering characteristics and mechanism of the Zigong argillaceous siltstones. The results of mechanical experiments reveal that the water content and the weathering degree of rock specimens both have a weakening effect on the compressive and shear strengths. According to the results of present microstructure tests, the mechanical properties of the Zigong argillaceous siltstones are closely correlated with their physical properties, including internal microstructure and material composition for highly weathered rocks or moderately weathered rocks (in both natural and saturation conditions). Finally, experimental results indicate that the changes of microstructure and internal materials are two main factors that influence rock strength parameters after contacting with water and that these properties reflect the rock weathering degree. In a word, when red-bed soft rocks are encountered in geotechnical engineering, special attention should be paid to presence of water

Y Chromosomes of 40% Chinese Are Descendants of Three Neolithic Super-grandfathers

Demographic change of human populations is one of the central questions for delving into the past of human beings. To identify major population expansions related to male lineages, we sequenced 78 East Asian Y chromosomes at 3.9 Mbp of the non-recombining region (NRY), discovered >4,000 new SNPs, and identified many new clades. The relative divergence dates can be estimated much more precisely using molecular clock. We found that all the Paleolithic divergences were binary; however, three strong star-like Neolithic expansions at ~6 kya (thousand years ago) (assuming a constant substitution rate of 1e-9/bp/year) indicates that ~40% of modern Chinese are patrilineal descendants of only three super-grandfathers at that time. This observation suggests that the main patrilineal expansion in China occurred in the Neolithic Era and might be related to the development of agriculture.Comment: 29 pages of article text including 1 article figure, 9 pages of SI text, and 2 SI figures. 5 SI tables are in a separate ancillary fil

Clinical Study Replanning Criteria and Timing Definition for Parotid Protection-Based Adaptive Radiation Therapy in Nasopharyngeal Carcinoma

The goal of this study was to evaluate real-time volumetric and dosimetric changes of the parotid gland so as to determine replanning criteria and timing for parotid protection-based adaptive radiation therapy in nasopharyngeal carcinoma. Fifty NPC patients were treated with helical tomotherapy; volumetric and dosimetric ( mean , 1 , and 50 ) changes of the parotid gland at the 1st, 6th, 11th, 16th, 21st, 26th, 31st, and 33rd fractions were evaluated. The clinical parameters affecting these changes were studied by analyses of variance methods for repeated measures. Factors influencing the actual parotid dose were analyzed by a multivariate logistic regression model. The cut-off values predicting parotid overdose were developed from receiver operating characteristic curves and judged by combining them with a diagnostic test consistency check. The median absolute value and percentage of parotid volume reduction were 19.51 cm 3 and 35%, respectively. The interweekly parotid volume varied significantly ( &lt; 0.05). The parotid mean , 1 , and 50 increased by 22.13%, 39.42%, and 48.45%, respectively. The actual parotid dose increased by an average of 11.38% at the end of radiation therapy. Initial parotid volume, initial parotid mean , and weight loss rate are valuable indicators for parotid protection-based replanning

International consensus on natural orifice specimen extraction surgery (NOSES) for colorectal cancer

In recent years, natural orifice specimen extraction surgery (NOSES) in the treatment of colorectal cancer has attracted widespread attention. The potential benefits of NOSES including reduction in postoperative pain and wound complications, less use of postoperative analgesic, faster recovery of bowel function, shorter length of hospital stay, better cosmetic and psychological effect have been described in colorectal surgery. Despite significant decrease in surgical trauma of NOSES have been observed, the potential pitfalls of this technique have been demonstrated. Particularly, several issues including bacteriological concerns, oncological outcomes and patient selection are raised with this new technique. Therefore, it is urgent and necessary to reach a consensus as an industry guideline to standardize the implementation of NOSES in colorectal surgery. After three rounds of discussion by all members of the International Alliance of NOSES, the consensus is finally completed, which is also of great significance to the long-term progress of NOSES worldwide.info:eu-repo/semantics/publishedVersio

Wolfberry genomes and the evolution of Lycium (Solanaceae)

AbstractWolfberry Lycium, an economically important genus of the Solanaceae family, contains approximately 80 species and shows a fragmented distribution pattern among the Northern and Southern Hemispheres. Although several herbaceous species of Solanaceae have been subjected to genome sequencing, thus far, no genome sequences of woody representatives have been available. Here, we sequenced the genomes of 13 perennial woody species of Lycium, with a focus on Lycium barbarum. Integration with other genomes provides clear evidence supporting a whole-genome triplication (WGT) event shared by all hitherto sequenced solanaceous plants, which occurred shortly after the divergence of Solanaceae and Convolvulaceae. We identified new gene families and gene family expansions and contractions that first appeared in Solanaceae. Based on the identification of self-incompatibility related-gene families, we inferred that hybridization hotspots are enriched for genes that might be functioning in gametophytic self-incompatibility pathways in wolfberry. Extremely low expression of LOCULE NUBER (LC) and COLORLESS NON-RIPENING (CNR) orthologous genes during Lycium fruit development and ripening processes suggests functional diversification of these two genes between Lycium and tomato. The existence of additional flowering locus C-like MADS-box genes might correlate with the perennial flowering cycle of Lycium. Differential gene expression involved in the lignin biosynthetic pathway between Lycium and tomato likely illustrates woody and herbaceous differentiation. We also provide evidence that Lycium migrated from Africa into Asia, and subsequently from Asia into North America. Our results provide functional insights into Solanaceae origins, evolution and diversification.</jats:p

Finishing the euchromatic sequence of the human genome

The sequence of the human genome encodes the genetic instructions for human physiology, as well as rich information about human evolution. In 2001, the International Human Genome Sequencing Consortium reported a draft sequence of the euchromatic portion of the human genome. Since then, the international collaboration has worked to convert this draft into a genome sequence with high accuracy and nearly complete coverage. Here, we report the result of this finishing process. The current genome sequence (Build 35) contains 2.85 billion nucleotides interrupted by only 341 gaps. It covers ∼99% of the euchromatic genome and is accurate to an error rate of ∼1 event per 100,000 bases. Many of the remaining euchromatic gaps are associated with segmental duplications and will require focused work with new methods. The near-complete sequence, the first for a vertebrate, greatly improves the precision of biological analyses of the human genome including studies of gene number, birth and death. Notably, the human enome seems to encode only 20,000-25,000 protein-coding genes. The genome sequence reported here should serve as a firm foundation for biomedical research in the decades ahead