Genome‐wide analysis of Nilaparvata lugens nymphal responses to high‐density and low‐quality rice hosts

The brown planthopper (BPH) Nilaparvata lugens is an economically important pest on rice plants. In this study, the higher population density and yellow‐ripe stage of rice plants were used to construct adverse survival conditions (ASC) against BPH nymphs. Simultaneously, the low population density and tillering stage of rice plants were used to establish a suitable survival condition (SSC) as a control. Solexa/Illumina sequencing was used to identify genes of BPH nymphs responding to ASC. Significantly longer duration development of BPH nymphs and significantly lower brachypterous ratio of BPH adults were observed by ASC compared with SSC. A total of 2 544 differentially expressed genes (DEGs) were obtained and analyzed by BLASTx, Gene Ontology and KEGG Orthology. Gene ontology analysis revealed that the DEGs were mainly involved in categories of cell, cell part, cellular process, binding, catalytic, organelle and metabolic processes. 1 138 DEGs having enzyme commission numbers were assigned to different metabolic pathways. The largest clusters were neurodegenerative diseases (137, 12.0%), followed by carbohydrate metabolism (113, 9.9%), amino acid metabolism (94, 8.3%), nucleotide metabolism (76, 6.7%), energy metabolism (64, 5.6%), translation (60, 5.3%), lipid metabolism (58, 5.1%), and folding, sorting and degradation (52, 4.6%). Expressing profile of 11 DEGs during eight nymphal developmental stages of BPH were analyzed by quantitative real‐time polymerase chain reaction. The 11 genes exhibited differential expression between ASC and SSC during at least one developmental stage. The DEGs identified in this study provide molecular proof of how BPH reconfigures its gene expression profile to adapt to overcrowding and low‐quality hosts.     

Highly sensitive chemiluminescence immunoassay on chitosan membrane modified paper platform using TiO2 nanoparticles/multiwalled carbon nanotubes as label

A highly sensitive chemiluminescence (CL) immunoassay was incorporated into a low‐cost microfluidic paper‐based analytical device (μ‐PAD) to fabricate a facile paper‐based CL immunodevice (denoted as μ‐PCLI). This μ‐PCLI was constructed by covalently immobilizing capture antibody on a chitosan membrane modified μ‐PADs, which was developed by simple wax printing methodology. TiO₂ nanoparticles coated multiwalled carbon nanotubes (TiO₂/MWCNTs) were synthesized as an amplification catalyst tag to label signal antibody (Ab₂). After sandwich‐type immunoreactions, the TiO₂/MWCNTs were captured on the surface of μ‐PADs to catalyze the luminol‐p‐iodophenol‐H₂O₂ CL system, which produced an enhanced CL emission. Using prostate‐specific antigen as a model analyte, the approach provided a good linear response range from 0.001 to 20 ng/mL with a low detection limit of 0.8 pg/mL under optimal conditions. This μ‐PCLI showed good reproducibility, selectivity and stability. The assay results of prostate‐specific antigen in clinical serum samples were in good agreement with that obtained by commercially used electrochemiluminescence methods at the Cancer Research Center of Shandong Tumor Hospital (Jinan, Shandong Province, China). This μ‐PCLI could be very useful to realize highly sensitive, qualitative point‐of‐care testing in developing or developed countries. Copyright © 2013 John Wiley & Sons, Ltd.     

Analysis of genetic variability and relationships among Mentha L. using the limonene synthase gene, LS

The genus Mentha comprises a group of aromatic plants with worldwide distribution. Because of frequent interspecific hybridization, the genetic relationships within the genus are not clearly understood. Limonene synthase, which catalyses the first committed step in the essential oil monoterpene biosynthetic pathway, is considered to be a possible rate limiting enzyme. With the homology-based cloning method, primers were designed according to cDNA sequence to amplify full-length DNA sequences in 13 Mentha samples from five species, using Perilla as an outgroup. Analyses of gene structure, length variation, GC-content, Ts/Tv ratio and evolutionary diversity were carried out. Consensus phylogenetic trees were obtained using maximum likelihood, neighbor-joining, and maximum parsimony, respectively, based on the full-length genomic DNA sequences, complete ORF coding sequences and predicted amino acid sequences. The results presented here based on the sequence of MhLS provide the first credibly supported genetic relationships for Mentha, which enables a basis for further mint taxonomy, cultivation and breeding.     

基于CSCD的盐生植物研究文献计量评价

以中国科学引文数据库（CSCD,477篇）为主线,以维普、万方和CNKI数据库（3329篇）为基础数据,采用文献计量分析的方法,对盐生植物研究文献进行统计分析,分别从文献的年代、机构、作者、来源期刊、学科类别、高被引论文和文献的关键词这7个方面,对盐生植物研究文献的分布规律和研究现状进行总体回顾与评价。全面概括、总结和分析该研究领域研究热点、区域、内容、技术和方法,优秀人才、领先机构和主要团队,揭示中国盐生植物研究的进展情况。结果表明：1956年有盐生植物论文发表,2007年文献总量340篇为最高记录;在CSCD,1991年有盐生植物论文发表,至2011年62篇为最高,均呈逐年上升趋势。中国在盐生植物研究方面已经形成了引领该研究方向的4个主要科研团队,分别是山东师范大学、中国科学院新疆生态与地理研究所、中国农业大学和南京大学。盐生植物的研究呈现明显的地域相关性,热点地区包括新疆、山东、北京、南京、东北、内蒙古、宁夏、兰州等地。盐生植物研究热点是：耐盐性（耐盐机制）、盐胁迫、盐碱地、基因克隆、土壤盐分、植物生长、开发利用、渗透调节、生理指标、种子萌发、脯氨酸、基因工程（基因表达）和植物群落等。     

基于VAR模型的森林植被碳储量影响因素分析——以陕西省为例

森林作为陆地生态系统最大的碳库,对现在及未来的气候变化、碳平衡都具有重要影响。而对影响森林植被碳库的自然和非自然因素进行研究更是对增强森林的碳汇作用,继而改善生态环境状况意义重大。现有的森林动态模型虽然可以很好的模拟碳储量各影响因子之间的联系,但研究往往集中于小尺度从单一影响因素着手,且由于确定模型输入变量和参数的复杂性,使得这些模型在区域甚至更大尺度上的应用存在着一些困难。因此,运用VAR模型,以陕西省为例,构建森林植被碳储量与病虫害发生面积、木材产量、森林火灾面积、森林抚育面积、人工更新造林面积、降水和温度之间的动态关系,来验证该模型在省级尺度条件下的区域森林植被碳储量影响因素分析中的可行性。结果表明:各变量在5%的显著性水平下呈一阶单整序列并具有长期稳定的均衡关系,VAR模型也通过了平稳性检验满足运行的前提条件。通过脉冲响应和方差分解分析可知,森林病虫害、木材产量对陕西省森林植被碳储量呈现出很明显的负作用,并且贡献度很高,分别为5.61%和4.52%;森林抚育、人工更新造林对碳储量的影响存在一定的滞后期;火灾、温度和降水的冲击给碳储量带来的影响均不明显。模型较好的模拟了各影响因素对陕西省碳储量的影响,且具有一定的现实意义,因此,该模型可应用于省级尺度条件下的区域森林植被碳储量影响因素分析。     

Manipulation of the Rice L-Galactose Pathway: Evaluation of the Effects of Transgene Overexpression on Ascorbate Accumulation and Abiotic Stress Tolerance

Ascorbic acid (AsA) is the most abundant water-soluble antioxidant in plants, and it plays a crucial role in plant growth, development and abiotic stress tolerance. In the present study, six key Arabidopsis or rapeseed genes involved in AsA biosynthesis were constitutively overexpressed in an elite Japonica rice cultivar. These genes encoded the GDP-mannose pyrophosphorylase (GMP), GDP-mannose-3'',5''-epimerase (GME), GDP-L-galactose phosphorylase (GGP), L-galactose-1-phosphate phosphatase (GPP), L-galactose dehydrogenase (GDH), and L-galactono-1,4-lactone dehydrogenase (GalLDH). The effects of transgene expression on rice leaf AsA accumulation were carefully evaluated. In homozygous transgenic seedlings, AtGGP transgenic lines had the highest AsA contents (2.55-fold greater than the empty vector transgenic control), followed by the AtGME and AtGDH transgenic lines. Moreover, with the exception of the AtGPP lines, the increased AsA content also provoked an increase in the redox state (AsA/DHA ratio). To evaluate salt tolerance, AtGGP and AtGME transgenic seedlings were exposed to salt stress for one week. The relative plant height, root length and fresh weight growth rates were significantly higher for the transgenic lines compared with the control plants. Altogether, our results suggest that GGP may be a key rate-limiting step in rice AsA biosynthesis, and the plants with elevated AsA contents demonstrated enhanced tolerance for salt stress.     

Structural and Kinetic Analysis of Nucleoside Triphosphate Incorporation Opposite an Abasic Site by Human Translesion DNA Polymerase η

The most common lesion in DNA is an abasic site resulting from glycolytic cleavage of a base. In a number of cellular studies, abasic sites preferentially code for dATP insertion (the “A rule”). In some cases frameshifts are also common. X-ray structures with abasic sites in oligonucleotides have been reported for several microbial and human DNA polymerases (pols), e.g. Dpo4, RB69, KlenTaq, yeast pol ι, human (h) pol ι, and human pol β. We reported previously that hpol η is a major pol involved in abasic site bypass (Choi, J.-Y., Lim, S., Kim, E. J., Jo, A., and Guengerich, F. P. (2010 J. Mol. Biol. 404, 34–44). hpol η inserted all four dNTPs in steady-state and pre-steady-state assays, preferentially inserting A and G. In LC-MS analysis of primer-template pairs, A and G were inserted but little C or T was inserted. Frameshifts were observed when an appropriate pyrimidine was positioned 5′ to the abasic site in the template. In x-ray structures of hpol η with a non-hydrolyzable analog of dATP or dGTP opposite an abasic site, H-bonding was observed between the phosphate 5′ to the abasic site and water H-bonded to N1 and N6 of A and N1 and O6 of G nucleoside triphosphate analogs, offering an explanation for what appears to be a “purine rule.” A structure was also obtained for an A inserted and bonded in the primer opposite the abasic site, but it did not pair with a 5′ T in the template. We conclude that hpol η, a major copying enzyme with abasic sites, follows a purine rule, which can also lead to frameshifts. The phenomenon can be explained with H-bonds.     

Integrated genome sequence and linkage map of physic nut (Jatropha curcas L.), a biodiesel plant

The family Euphorbiaceae includes some of the most efficient biomass accumulators. Whole genome sequencing and the development of genetic maps of these species are important components in molecular breeding and genetic improvement. Here we report the draft genome of physic nut (Jatropha curcas L.), a biodiesel plant. The assembled genome has a total length of 320.5 Mbp and contains 27 172 putative protein‐coding genes. We established a linkage map containing 1208 markers and anchored the genome assembly (81.7%) to this map to produce 11 pseudochromosomes. After gene family clustering, 15 268 families were identified, of which 13 887 existed in the castor bean genome. Analysis of the genome highlighted specific expansion and contraction of a number of gene families during the evolution of this species, including the ribosome‐inactivating proteins and oil biosynthesis pathway enzymes. The genomic sequence and linkage map provide a valuable resource not only for fundamental and applied research on physic nut but also for evolutionary and comparative genomics analysis, particularly in the Euphorbiaceae.     

Archaeal biogeography and interactions with microbial community across complex subtropical coastal waters

Marine Archaea are crucial in biogeochemical cycles, but their horizontal spatial variability, assembly processes, and microbial associations across complex coastal waters still lack characterizations at high coverage. Using a dense sampling strategy, we investigated horizontal variability in total archaeal, Thaumarchaeota Marine Group (MG) I, and Euryarchaeota MGII communities and associations of MGI/MGII with other microbes in surface waters with contrasting environmental characteristics across ~200 km by 16S rRNA gene amplicon sequencing. Total archaeal communities were extremely dominated by MGI and/or MGII (98.9% in average relative abundance). Niche partitioning between MGI and MGII or within each group was found across multiple environmental gradients. “Selection” was more important than “dispersal limitation” in governing biogeographic patterns of total archaeal, MGI, and MGII communities, and basic abiotic parameters (such as salinity) and inorganic/organic resources as a whole could be the main driver of “selection”. While “homogenizing dispersal” also considerably governed their biogeography. MGI‐Nitrospira assemblages were speculatively responsible for complete nitrification. MGI taxa commonly had negative correlations with members of Synechococcus but positive correlations with members of eukaryotic phytoplankton, suggesting that competition or synergy between MGI and phytoplankton depends on specific MGI‐phytoplankton assemblages. MGII taxa showed common associations with presumed (photo)heterotrophs including members of SAR11, SAR86, SAR406, and Candidatus Actinomarina. This study sheds light on ecological processes and drivers shaping archaeal biogeography and many strong MGI/MGII‐bacterial associations across complex subtropical coastal waters. Future efforts should be made on seasonality of archaeal biogeography and biological, environmental, or ecological mechanisms underlying these statistical microbial associations.