Micropropagation of Populus trichocarpa ‘Nisqually-1’: the genotype deriving the Populus reference genome

Populus serves as a model tree for biotechnology and molecular biology research due to the availability of the reference genome sequence of Populus trichocarpa (Torr. & Gray) genotype ‘Nisqually-1’. However, ‘Nisqually-1’ has been shown to be very recalcitrant to micropropagation, regeneration and transformation. In this study, a highly efficient micropropagation protocol from greenhouse-grown shoot tips of ‘Nisqually-1’ was established. The optimal micropropagation protocol involves growing in vitro shoots in plant growth regulator-free Murashige and Skoog (MS) basal medium supplemented with 3% sucrose, 0.3% Gelrite^? and 5–10 g L⁻¹ of activated charcoal. Plants grown on this medium were significantly longer, and contained significantly higher concentrations of chlorophyll. This highly effective protocol provides a consistent supply of quality leaf and stem materials throughout the year for transformation experiments and other in vitro manipulations, therefore eliminating inconsistency due to seasonal and greenhouse environmental variations and the need for repetitive tissue sterilization.     

急性心肌梗死患者冠脉搭桥术前中性粒细胞-淋巴细胞比率与围术期心肌损伤相关分析

目的：探讨急性心肌梗死患者冠脉搭桥（CABG）术前中性粒细胞．淋巴细胞比率（NLR）与围术期心肌损伤的关系,为,临床CABG围术期心肌保护提供参考依据。方法：选取2012年1月至2012年6月于首都医科大学附属北京安贞医院因急性心肌梗死接受冠脉搭桥手术（CABG）患者210例,收集术前血常规及术后肌钙蛋白I（cTnI）？Life酸激酶同工酶（CK-MB）,计算NLR;采用四分位法根据NLR水平将患者分为四组,比较各组cTnI及CK—MB峰值,多元逐步回归分析NLR与cTnI及CK-MB峰值的相关性。结果：随着NLR水平升高,高血压病史和射血分数〈50％患者比例逐渐增多;白细胞计数、术后CK-MB及cTnI峰值、术后血肌酐值均逐渐增加;多元逐步回归分析显示,NLR、WBC分别与cTnI峰值呈正相关（r=0．526,r=0．186,P〈0．05）。结论：术前NLR、WBC与cTnI峰值呈正相关,NLR可能是反应急性心肌梗死患者冠脉搭桥围术期心肌损伤的良好标志物。     

Genetic Modification of Short Rotation Popular Wood: Properties for Ethanol Fuel and Fiber Productions

Opportunities for matching wood chemical and physical properties to manufacturing and product requirements via genetic modification have long been recognized. Exploitation is now feasible due to advances in trait measurement, breeding, genetic mapping and marker, and genetic transformation technologies. With respect to classic selection and breeding of short-rotation poplars, genetic parameters are favorable for decreasing lignin content and increasing specific gravity, but less so for increasing cellulose content. Knowledge of functional genomics is expanding, as is that needed for eventual application of marker-aided breeding, trait dissection, candidate gene identification, and gene isolation. Research on gene transfer has yielded transgenic poplars with decreased lignin and increased cellulose contents, but otherwise normal growth and development. Until effective marker-aided breeding technologies become available, the most promising approach for enhancing ethanol fuel and fiber production and processing efficiencies centers on selecting and breeding poplars for high wood substance yields and genetically transforming them for decreased lignin and increased cellulose contents.     

MicroSyn: A user friendly tool for detection of microsynteny in a gene family

Background  

The traditional phylogeny analysis within gene family is mainly based on DNA or amino acid sequence homologies. However, these phylogenetic tree analyses are not suitable for those "non-traditional" gene families like microRNA with very short sequences. For the normal protein-coding gene families, low bootstrap values are frequently encountered in some nodes, suggesting low confidence or likely inappropriateness of placement of those members in those nodes.     

Differential detection of genetic Loci underlying stem and root lignin content in Populus

In this study, we established a comprehensive genetic map with a large number of progeny from a three-generation hybrid Populus intercross, and phenotyped the lignin content, S/G ratio and 28 cell wall subcomponents both in stems and roots for the mapping individuals. Phenotypic analysis revealed that lignin content and syringyl-to-guaiacyl (S/G) ratio using pyrolysis molecular beam mass spectroscopy (pyMBMS) varied among mapping individuals. Phenotypic analysis revealed that stem lignin content is significantly higher than that in root and the quantified traits can be classified into four distinct groups, with strong correlations observed among components within organs. Altogether, 179 coordinating QTLs were detected, and they were co-localized into 49 genetic loci, 27 of which appear to be pleiotropic. Many of the detected genetic loci were detected differentially in stem and root. This is the first report of separate genetic loci controlling cell wall phenotypes above and below ground. These results suggest that it may be possible to modify lignin content and composition via breed and/or engineer as a means of simultaneously improving Populus for cellulosic ethanol production and carbon sequestration.     

Characterization of Transposable Elements in the Ectomycorrhizal Fungus Laccaria bicolor

Background

The publicly available Laccaria bicolor genome sequence has provided a considerable genomic resource allowing systematic identification of transposable elements (TEs) in this symbiotic ectomycorrhizal fungus. Using a TE-specific annotation pipeline we have characterized and analyzed TEs in the L. bicolor S238N-H82 genome.

Methodology/Principal Findings

TEs occupy 24% of the 60 Mb L. bicolor genome and represent 25,787 full-length and partial copy elements distributed within 171 families. The most abundant elements were the Copia-like. TEs are not randomly distributed across the genome, but are tightly nested or clustered. The majority of TEs exhibits signs of ancient transposition except some intact copies of terminal inverted repeats (TIRS), long terminal repeats (LTRs) and a large retrotransposon derivative (LARD) element. There were three main periods of TE expansion in L. bicolor: the first from 57 to 10 Mya, the second from 5 to 1 Mya and the most recent from 0.5 Mya ago until now. LTR retrotransposons are closely related to retrotransposons found in another basidiomycete, Coprinopsis cinerea.

Conclusions

This analysis 1) represents an initial characterization of TEs in the L. bicolor genome, 2) contributes to improve genome annotation and a greater understanding of the role TEs played in genome organization and evolution and 3) provides a valuable resource for future research on the genome evolution within the Laccaria genus.