Evaluating coverage of exons by HapMap SNPs

Genome-wide association (GWA) studies are currently one of the most powerful tools in identifying disease-associated genes or variants. In typical GWA studies, single-nucleotide polymorphisms (SNPs) are often used as genetic makers. Therefore, it is critical to estimate the percentage of genetic variations which can be covered by SNPs through linkage disequilibrium (LD). In this study, we use the concept of haplotype blocks to evaluate the coverage of five SNP sets including the HapMap and four commercial arrays, for every exon in the human genome. We show that although some Chips can reach similar coverage as the HapMap, only about 50% of exons are completely covered by haplotype blocks of HapMap SNPs. We suggest further high-resolution genotyping methods are required, to provide adequate genome-wide power for identifying variants.     

Amazonian Anthrosols Support Similar Microbial Communities that Differ Distinctly from Those Extant in Adjacent, Unmodified Soils of the Same Mineralogy

We compared the microbial community composition in soils from the Brazilian Amazon with two contrasting histories; anthrosols and their adjacent non-anthrosol soils of the same mineralogy. The anthrosols, also known as the Amazonian Dark Earths or terra preta, were managed by the indigenous pre-Colombian Indians between 500 and 8,700 years before present and are characterized by unusually high cation exchange capacity, phosphorus (P), and calcium (Ca) contents, and soil carbon pools that contain a high proportion of incompletely combusted biomass as biochar or black carbon (BC). We sampled paired anthrosol and unmodified soils from four locations in the Manaus, Brazil, region that differed in their current land use and soil type. Community DNA was extracted from sampled soils and characterized by use of denaturing gradient gel electrophoresis (DGGE) and terminal restriction fragment length polymorphism. DNA bands of interest from Bacteria and Archaea DGGE gels were cloned and sequenced. In cluster analyses of the DNA fingerprints, microbial communities from the anthrosols grouped together regardless of current land use or soil type and were distinct from those in their respective, paired adjacent soils. For the Archaea, the anthrosol communities diverged from the adjacent soils by over 90%. A greater overall richness was observed for Bacteria sequences as compared with those of the Archaea. Most of the sequences obtained were novel and matched those in databases at less than 98% similarity. Several sequences obtained only from the anthrosols grouped at 93% similarity with the Verrucomicrobia, a genus commonly found in rice paddies in the tropics. Sequences closely related to Proteobacteria and Cyanobacteria sp. were recovered only from adjacent soil samples. Sequences related to Pseudomonas, Acidobacteria, and Flexibacter sp. were recovered from both anthrosols and adjacent soils. The strong similarities among the microbial communities present in the anthrosols for both the Bacteria and Archaea suggests that the microbial community composition in these soils is controlled more strongly by their historical soil management than by soil type or current land use. The anthrosols had consistently higher concentrations of incompletely combusted organic black carbon material (BC), higher soil pH, and higher concentrations of P and Ca compared to their respective adjacent soils. Such characteristics may help to explain the longevity and distinctiveness of the anthrosols in the Amazonian landscape and guide us in recreating soils with sustained high fertility in otherwise nutrient-poor soils in modern times.     

酚酸类物质的抑草效应分析

运用正交旋转回归试验设计分析5种常见的化感物质替代物水饧酸、对羟基苯甲酸、肉桂酸、香草酸和阿魏酸对田间伴生杂草稗草的抑制效应．结果表明,肉桂酸对稗草根长抑制率的影响最显著。其关系函数的二次项系数为-6．18,达极显著水平,水杨酸、对羟基苯甲酸和阿魏酸对稗草根长的抑制效应趋势与肉桂酸相同,效应曲线均为“n”形抛物线;而香草酸的效应曲线则为“U”形抛物线．当水饧酸、对羟基苯甲酸、肉桂酸、香草酸和阿魏酸浓度水平分别为0．06、0．60、0．24、0．02和0．02mmol·L^-1时,混合物对稗草根长的抑制率最大,达到78．65％。     

Expression of the pfl gene and resulting metabolite flux distribution in nuo and ackA-pta E. coli mutant strains

Our laboratory previously studied the interaction between nuo and the acetate-producing pathway encoded by ackA-pta in Escherichia coli. We examined metabolic patterns, particularly the ethanol and acetate production rates, of several mutant strains grown under anaerobic growth conditions. Since the pyruvate formate-lyase (PFL) pathway is the major route for acetyl-CoA and formate production under anaerobic conditions, we examined the effects of nuo and ackA/pta mutations on the expression of pyruvate formate-lyase (pfl) under anaerobic conditions. The ackA-pta mutant has a pfl::lacZ expression level much higher than that of the wild-type strain, and cultures also exhibit the highest ethanol production. Real-time PCR demonstrated that the adhE gene expression in the ack-pta mutant strain was approximately 100 fold that of the same gene in the ackA-pta nuo mutant strain. This result correlates with the observed ethanol production rates in cultures of the strain. However, the lack of exact correlation between the ethanol production rates and the RT-PCR data suggests additional regulation actions at the posttranslation level. In addition, the activity of the pfl gene as indicated by mRNA levels was also considerably greater in theack-pta mutant. We can conclude that deletions of nuo and ack/pta can partially affect the expression of the genes encoding adhE and pfl under anaerobic conditions.     

L-精氨酸测定方法的研究

就放置时间、温度、盐类对精氨酸坂口试剂测定法的影响进行研究,得出结论：Ｔ＝２０．５℃,放置时间为４０ｍｉｎ及加入０．１ｍｇ／ｍＬ的盐溶液对标准曲线进行校正,使此测定方法准确度提高。     

水溶性红曲红色素的制备与表征

以碱解法制备水溶性红曲红色素,碱解过程可使红斑素和红曲红素分子中的内酯键找开,生成闳酸盐,提高其亲水性。当反应体系ＮａＯＨ与红曲色素用量比例为１：１３时,碱解过程可在１５ｍｉｎ内完成。在ＰＨ５～６范围同,生成的水溶性红色素扣及光值随ＰＨ增大面临略有提高。加热和光照都将影响其稳定性,绝氧则对提高其稳定性无明显影响。在中性条件下,Ｃａ＾２＋、Ｍｇ＾２＋导致色素溶液沉淀,Ｓｎ＾２＋、Ａｌ＾２＋、Ｆ３＾３     

In Situ OH Generation from O2 ? and H2O2 Plays a Critical Role in Plasma-Induced Cell Death

Reactive oxygen and nitrogen species produced by cold atmospheric plasma (CAP) are considered to be the most important species for biomedical applications, including cancer treatment. However, it is not known which species exert the greatest biological effects, and the nature of their interactions with tumor cells remains ill-defined. These questions were addressed in the present study by exposing human mesenchymal stromal and LP-1 cells to reactive oxygen and nitrogen species produced by CAP and evaluating cell viability. Superoxide anion (O₂ ⁻) and hydrogen peroxide (H₂O₂) were the two major species present in plasma, but their respective concentrations were not sufficient to cause cell death when used in isolation; however, in the presence of iron, both species enhanced the cell death-inducing effects of plasma. We propose that iron containing proteins in cells catalyze O₂ ⁻ and H₂O₂ into the highly reactive OH radical that can induce cell death. The results demonstrate how reactive species are transferred to liquid and converted into the OH radical to mediate cytotoxicity and provide mechanistic insight into the molecular mechanisms underlying tumor cell death by plasma treatment.     

应用差异蛋白质组学方法分析作物化感作用的分子机理

试验旨在分析运用分子标记技术(QTL)和差异蛋白组学技术研究作物化感作用分子机理的差异性。首先运用差异蛋白组学技术探讨在生物胁迫(稗草)下水稻化感作用潜力变化的内在分子机理。分别用稗草和水稻的根系分泌物培养切自一株5叶龄化感水稻P I312777植株并经恢复的2个分蘖。7d后,提取处理和对照相同叶位叶片的全蛋白质并进行双向电泳,每张电泳胶片上获得800多个电泳胶点,其中差异表达的蛋白质点有4个。采用M ALD I-TOF-M S对各差异蛋白质点进行肽质量指纹图谱分析,经过SW ISS-PROT数据库查询,结果表明化感水稻P I312777在稗草胁迫下的特异蛋白分别与苯丙氨酸氨解酶(PAL)、硫还原型蛋白(T rx-m)、3-羟基-3-甲基戊二酰辅酶A还原酶(HM GR)和过氧化物酶(POD)相匹配。根据编码以上4个差异蛋白质的DNA序列,发现编码以上4个差异蛋白的基因分别位于水稻染色体4、7、8和12上的特定克隆位点,这就是与化感作用相关基因。前人也运用QTL方法开展作物化感作用的分子机理研究,但由于所采用的供体材料、受体植物及对表型性状的评价方法等的不同,定位结果存在较大的差异。综合比较两种方法后认为,运用差异蛋白组学技术分析水稻化感作用的分子机理,比QTL技术更加直接和深入。因为比较胁迫处理和对照植物组织的2-DE图谱将能鉴定出由表达候选基因编码的胁迫蛋白质,氨基酸残基序列的测定将揭示那些功能与胁迫性状密切相关的蛋白质,这种编码的基因就是兼具功能与表达的候选基因。     

粉煤灰滤泥混合物对土壤性质、萝卜产量与品质的影响

粉煤灰和滤泥以1：1（w/w）比例混合并添加少量化肥配制成混合物,通过盆栽试验研究该混合物农用对土壤生物化学性质、萝卜产量和品质的影响以及重金属在土壤和萝卜中的富集状况。结果表明,该混合物中Dd、Pb、Cr、As和Hg含量均明显低于国家农用粉煤灰中污染物控制标准;施用一定数量的该混合物未见导致重金属在土壤和萝卜中的明显富集作用,重金属污染指数均＜1;土壤细菌数量显著增加;脲酶、磷酸酶和纤维素酶的活性增强;促进了萝卜的生长发育和代谢作用,萝卜的生物产量、经济产量、还原糖和维生素C的含量均明显提高,因此,适量施用该混合物未见导致重金属对土壤和萝卜的明显污染,且具有较明显的改土培肥、增产和提高萝卜品质的效果。