药用资源植物山莨菪的转录组信息分析

为了增强对资源植物山莨菪的深入了解,本研究采用高通量测序技术对山莨菪进行转录组测序分析,经过处理得到71 463个Unigenes。通过与多个数据库进行比对,对基因进行分类和分析注释,最终成功获得注释的基因有47 624条。将Unigenes比对到KOG蛋白质库中,有13 110个基因被注释,共有26个子类;比对到NR库中后有39 621个Unigenes被注释;转录本与Swissprot、Tr EMBL的比对结果得到GO功能注释信息,注释得到的29 309个Unigenes可被分为分子功能、生物学过程和细胞组分3个大类,62个子类;以KEGG数据库为参考,3 679条基因被注释,参与的代谢通路可归为4个大类,分别是代谢相关的通路、遗传信息处理、细胞过程、环境信息处理,其中与代谢相关的通路最多,约占所有代谢通路的一半。对山莨菪的药用活性成分的代谢通路及相关Unigenes数量和类型的统计结果表明,与生物碱相关的代谢通路最多,萜类和苯丙素类所对应的Unigenes数量最多。另外,结果还检测到31 382个SNP位点,6种SSR重复类型,其中单碱基重复类型所占的比例最高,每百万碱基中出现的单碱基重复的SSR个数有56. 52个,占45. 30%。该结果丰富了山莨菪的转录组信息数据,为该物种分子生物学方面的研究奠定了基础,有助于进一步开展对山莨菪的合理保护及开发利用工作。     

N2-fixation can sustain wastewater treatment performance of photogranules under nitrogen-limiting conditions

Wastewater characteristics can vary significantly, and in some municipal wastewaters the N:P ratio is as low as 5 resulting in nitrogen-limiting conditions. In this study, the microbial community, function, and morphology of photogranules under nitrogen-replete (N+) and limiting (N−) conditions was assessed in sequencing batch reactors. Photogranules under N− condition were nitrogen deprived 2/3 of a batch cycle duration. Surprisingly, this nitrogen limitation had no adverse effect on biomass productivity. Moreover, phosphorus and chemical oxygen demand removal were similar to their removal under N+ conditions. Although performance was similar, the difference in granule morphology was obvious. While N+ photogranules were dense and structurally confined, N− photogranules showed loose structures with occasional voids. Microbial community analysis revealed high abundance of cyanobacteria capable of N₂-fixation. These were higher at N− (38%) than N+ (29%) treatments, showing that photogranules could adjust and maintain treatment performance and high biomass productivity by means of N₂-fixation.     

The At4g11330 (ATMPK5) locus of<Emphasis Type="Italic">Arabidopsis thaliana</Emphasis>: Updating the annotation

The completed sequence of theArabidopsis genome shows that a single base pair deletion exists in the gene encoding the MAP kinase ATMPK5 (locus At4g11330) when compared with the cDNA. This has led to the annotation of ATMPK5 in databases as a truncated protein kinase or with a deletion in kinase subdomain I. Both situations would lead to a mutated nonfunctional protein. We amplified and sequenced the relevant region from genomic DNA of theArabidopsis ecotypes Columbia and Wassilewskija, and we found that both contain sequences that are in accordance with the cDNA sequence. We propose, therefore, that the ATMPK5 locus can encode a functional MAP kinase protein. This finding is relevant to the further functional analysis of this locus.     

A timesaving, accurate method for locating and re-locating plants in ecological field studies

We present a method for increasing the accuracy and acquisition rate of the initial location data of plants within fixed areas. Using a personal digital assistant (PDA) to create a link between various electronic measurement devices (pantograph, micrometers etc.) and a database of the study individual's location information, has significantly increased measurement reliability and speed in a demographic field study. The method also provides a means to quickly and accurately re-identify the same individuals during subsequent visits to the study plot. Application of the same method can be used in all ecological field studies with sessile organisms in permanent plots, increasing speed and accuracy of coordinate measurement.     

A GIS-based tool for storage,selection and visualization of time series 4D marine datasets

We present an initial attempt for the development of a distributed and scalable GIS-like tool for the storage, selection and visualization of 4D marine datasets. The aim of this tool is to standardize the variety of data available for the water column and support non-technical marine biologists in manipulating 4D marine datasets. The tool is developed towards answering specific environmental and biological questions regarding ocean processes and essential fish habitat mapping in three dimensions. Guest editor: V. D. Valavanis Essential Fish Habitat Mapping in the Mediterranean     

闽楠转录组分析及基因功能注释

采用第二代Illumina HiSeq测序技术对闽楠的木质部、韧皮部、叶片进行转录组测序，分别获得Clean Reads片段41 383 707条、43 343 922条、44 191 586条，经转录本拼接后得到序列总长度达120 535 288 bp的383 331条Conting片段，进一步组装得到平均长度为542 bp的151 729条Unigenes。将闽楠转录组Unigenes进行基因功能注释，与NR数据库比对发现，其与葡萄的相似序列最多（34%），与黄瓜、野草莓、大豆的同源性较低（各占3%）；进行GO功能注释，可将其划分为生物过程、细胞成分、分子功能3大类共计52个分支，与eggNOG数据库比对可分为25类，通过KEGG功能注释可知转录组中涉及的基因共参与了176条代谢通路，其中核糖体和碳代谢获得的注释较多。另外通过MISA软件分析，共获得35 972个SSR位点。其中，单核苷酸、二核苷酸和三核苷酸为优势重复类型，SSR位点数分别为21 762（60.50%），8 931（24.83%），4 924（13.69%）。闽楠转录组分析及基因功能注释为深入开展闽楠遗传育种及分子生物学相关研究奠定基础。     

Essential molecular functions associated with the circular code evolution

A circular code is a set of trinucleotides allowing the reading frames in genes to be retrieved locally, i.e. anywhere in genes and in particular without start codons, and automatically with a window of few nucleotides. In 1996, a common circular code, called X, was identified in large populations of eukaryotic and prokaryotic genes. Hence, it is believed to be an ancestral structural property of genes. A new computational approach based on comparative genomics is developed to identify essential molecular functions associated with circular codes. It is based on a quantitative and sensitive statistical method (FPTF) to identify three permuted trinucleotide sets in the three frames of genes, a flower automaton algorithm to determine if a trinucleotide set is a circular code or not, and an integrated Gene Ontology and Taxonomy (iGOT) database. By carrying out automatic circular code analyses on a huge number of gene populations where each population is associated with a particular molecular function, it identifies 266 gene populations having circular codes close to X. Surprisingly, their molecular functions include 98% of those covered by the essential genes of the DEG database (Database of Essential Genes). Furthermore, three trinucleotides GTG, AAG and GCG, replacing three trinucleotides of the code X and called “evolutionary” trinucleotides, significantly occur in these 266 gene populations. Finally, a new method developed to analyse and quantify the stability of a set of trinucleotides demonstrates that these evolutionary trinucleotides are associated with a significant increase of the stability of the common circular code X. Indeed, its stability increases from the 1502th rank to the 16th rank after the replacement of the three evolutionary trinucleotides among 9920 possible trinucleotide replacement sets.     

Exploring the molecular mechanism of acute heat stress exposure in broiler chickens using gene expression profiling

The process of heat regulation is complex and its exact molecular mechanism is not fully understood. In this study, to investigate the global gene regulation response to acute heat exposure, gene microarrays were exploited to analyze the effects of heat stress on three tissues (brain, liver, leg muscle) of the yellow broiler chicken (Gallus gallus). We detected 166 differentially expressed genes (DEGs) in the brain, 219 in the leg muscle and 317 in the liver. Six of these genes were differentially expressed in all three tissues and were validated by qRT-PCR, and included heat shock protein genes (HSPH1, HSP25), apoptosis-related genes (RB1CC1, BAG3), a cell proliferation and differentiation-related gene (ID1) and the hunger and energy metabolism related gene (PDK). All these genes might be important factors in chickens suffering from heat stress. We constructed gene co-expression networks using the DEGs of the brain, leg muscle and liver and two, four and two gene co-expression modules were identified in these tissues, respectively. Functional enrichment of these gene modules revealed that various functional clusters were related to the effects of heat stress, including those for cytoskeleton, extracellular space, ion binding and energy metabolism. We concluded that these genes and functional clusters might be important factors in chickens under acute heat stress. Further in-depth research on the newly discovered heat-related genes and functional clusters is required to fully understand their molecular functions in thermoregulation.