Hypoxic metabolism in wild rice (Zizania palustris): enzyme induction and metabolite production

Alcohol dehydrogenase (ADH, EC 1. 1. 1. 1), lactate dehydrogenase (LDH, EC 1. 1. 1. 27) and alanine aminotransferase (AlaAT, EC 2. 6. 1. 2) activity in wild rice ( Zizania palustris L.) root tissue increased after 4 days of exposure to hypoxic stress. The activities of ADH and AlaAT also increased in leaf tissue under these same conditions, whereas LDH activity did not. Isozyme banding patterns indicate that wild rice has at least two functional Adh genes, only one of which is hypoxically induced in root and leaf tissue. The isozyme profile of LDH also indicates the presence of two functional Ldh genes in wild rice. Two bands of AlaAT activity are visible on native electrophoretic gels of root and leaf tissue. Neither of these bands appears to increase in activity in hypoxic samples, even though spectrophotometric assays indicate an increase in AlaAT activity. Ethanol accumulation was the highest of all the metabolites measured. Alanine and malate also accumulated under hypoxic conditions but only to about one-fifth the level of ethanol. Succinate, aspartate and lactate showed no observable changes throughout the induction period. These results show that wild rice differs from domesticated rice ( Oryza sativa L.) in its metabolic responses to anaerobic stress. The possible role of these responses in conferring flood tolerance is discussed.     

Review of general algorithmic features for genome assemblers for next generation sequencers

In the realm of bioinformatics and computational biology,the most rudimentary data upon which all the analysis is built is the sequence data of genes,proteins and RNA.The sequence data of the entire genome is the solution to the genome assembly problem.The scope of this contribution is to provide an overview on the art of problem-solving applied within the domain of genome assembly in the nextgeneration sequencing(NGS) platforms.This article discusses the major genome assemblers that were proposed in the literature during the past decade by outlining their basic working principles.It is intended to act as a qualitative,not a quantitative,tutorial to all working on genome assemblers pertaining to the next generation of sequencers.We discuss the theoretical aspects of various genome assemblers,identifying their working schemes.We also discuss briefly the direction in which the area is headed towards along with discussing core issues on software simplicity.     

金针菇基因组测序与组装策略分析

采用二代和三代测序技术分别对金针菇单核体菌株“6-3”进行测序,应用4种组装策略进行基因组的de novo组装,对比组装效果。基因组组装的参数方面,仅使用二代测序组装的效果最差,长度大于10kb的Contig全长只有24.6Mb,Contig N50只有23kb,组装率只有59.27%。采用三代组装二代校正的组装策略效果最好,长度大于10kb的Contig全长为38.3Mb,Contig N50为2.8Mb,组装率高达92.16%。保守单拷贝基因拼接效果方面,4种组装策略获得基因组序列与BUSCO数据库里的担子菌的保守单拷贝基因比对,基因完整性均大于94%。在组装准确性方面,经过PCR扩增、Sanger测序验证,三代组装二代校正的基因组序列完整并且连续,同时序列上碱基的SNP、InDel数量最少。综上所述,三代组装二代校正得到的基因组序列具有Contig N50值大、组装率高、碱基准确性高的特点,是食用菌基因组测序较为理想的方案。     

Isolation and Characterization of a Cyclic Phosphate of Neopterin and Other 6-Alkylpterin Compounds Enzymatically Synthesized from GTP by Cell-free Extracts of Serratia indica

A cell-free system for the biosynthesis of l-threo-neopterin, a growth factor for protozoan, Crithidia fasciculata from guanosine-5′-triphosphate (GTP) was obtained from extracts of Serratia indica IFO 3759. This preparation catalyzed the production of a specific pteridine from GTP, which was isolated and characterized as a cyclic phosphate of neopterin (cNP). Among the other products, l-threo-neopterin, as the Crithidia factor, 6-hydroxymethylpterin, and erythro-neopterin were tentatively identified. Requirements for the synthesis of these products include GTP, Mg²⁺, and disodium phosphate. Fluorescence formation was inhibited by purine nucleotides.

When a disodium phosphate was included in the reaction system, cNP and erythro-neopterin were effectively synthesized from GTP. On the other hand, when the phosphate was omitted 6-hydroxymethylpterin was formed.

The possible biosynthetic process of l-threo-neopterin was discussed.     

四倍体野生稻快速驯化: 启动人类新农业文明

通过人工选择优良遗传变异,将野生植物驯化为栽培作物,以满足人类对食物的需求,是人类发展历史中的重要事件,推动了人类文明的持续发展。随着世界人口持续增加,耕地面积不断减少,灾害性天气频发,全球粮食安全问题日趋严峻。基于作物驯化的分子机理及重要农艺性状的遗传基础,结合高通量基因组测序和高效基因组编辑技术,从头驯化野生植物,...     

De novo assembly of the Pseudomonas syringae pv. syringae B728a genome using Illumina/Solexa short sequence reads

Illumina's Genome Analyzer generates ultra-short sequence reads, typically 36 nucleotides in length, and is primarily intended for resequencing. We tested the potential of this technology for de novo sequence assembly on the 6 Mbp genome of Pseudomonas syringae pv. syringae B728a with several freely available assembly software packages. Using an unpaired data set, velvet assembled >96% of the genome into contigs with an N50 length of 8289 nucleotides and an error rate of 0.33%. edena generated smaller contigs (N50 was 4192 nucleotides) and comparable error rates. ssake and vcake yielded shorter contigs with very high error rates. Assembly of paired-end sequence data carrying 400 bp inserts produced longer contigs (N50 up to 15 628 nucleotides), but with increased error rates (0.5%). Contig length and error rate were very sensitive to the choice of parameter values. Noncoding RNA genes were poorly resolved in de novo assemblies, while >90% of the protein-coding genes were assembled with 100% accuracy over their full length. This study demonstrates that, in practice, de novo assembly of 36-nucleotide reads can generate reasonably accurate assemblies from about 40 × deep sequence data sets. These draft assemblies are useful for exploring an organism's proteomic potential, at a very economic low cost.