iBench: A ground truth approach for advanced validation of mass spectrometry identification method

The discovery of many noncanonical peptides detectable with sensitive mass spectrometry inside, outside, and on cells shepherded the development of novel methods for their identification, often not supported by a systematic benchmarking with other methods. We here propose iBench, a bioinformatic tool that can construct ground truth proteomics datasets and cognate databases, thereby generating a training court wherein methods, search engines, and proteomics strategies can be tested, and their performances estimated by the same tool. iBench can be coupled to the main database search engines, allows the selection of customized features of mass spectrometry spectra and peptides, provides standard benchmarking outputs, and is open source. The proof-of-concept application to tryptic proteome digestions, immunopeptidomes, and synthetic peptide libraries dissected the impact that noncanonical peptides could have on the identification of canonical peptides by Mascot search with rescoring via Percolator (Mascot+Percolator).     

燕麦-绿豆间作效应及氮素转移特性

为探究燕麦(Avena sativa)-绿豆(Phaseolus radiatus)间作效应及氮素转移特性, 在不施氮肥的大田试验条件下, 设置3种种植模式(燕麦单作、绿豆单作和燕麦-绿豆间作), 采用传统挖根法和¹⁵N同位素标记法进行研究。结果表明, 间作系统中燕麦侵袭力强于绿豆, 绿豆生长受到抑制。整个生育期, 间作燕麦地上部干物质积累量比单作增加14.9%-33.1%, 2年成熟期间作燕麦的氮素积累量比单作分别提高53.1%和44.8%; 间作减少了开花结荚期绿豆氮素积累量和根瘤重量, 降低了绿豆的固氮效率, 绿豆的固氮效率2年平均降低23.7%, 生物固氮量平均减少11.66%。间作绿豆向燕麦的氮素转移率2年平均值达31.7%, 氮素转移量为212.16 kg∙hm^-2。燕麦-绿豆间作降低了开花结荚期绿豆的根瘤固氮酶活性和固氮效率, 但绿豆体内氮素转移增加了燕麦对氮素的吸收利用, 实现了地上部与地下部生长的相互调节和促进, 优化了农田生态系统的氮素管理。     

ACCUMULATION OF ASTAXANTHIN IN HAEMATOCOCCUS LACUSTRIS (CHLOROPHYTA)1

In N-limited continuous chemostat cultures of the green alga Haematococcus lacustris (Gir.) Rostaf. (UTEX 16), the steady-state astaxanthin content of the cells was determined by the specific growth rate of the cultures. The highest, pigment content was obtained at the lowest dilution rate. The specific rate of astaxanthin accumulation was, however, a function of the photon flux density measured at the illuminated culture surface. In nongrowing Haematococcus cultures, the specific rate of astaxanthin accumulation was determined by the growth rate of the culture during growth phase. The highest possible cellular astaxanthin content of all cultures was comparable and independent of the culture parameters.     

Genetic metabolic polymorphisms and the risk of cancer: a review of the literature

The purpose of this paper is to systematically analyse the design and results of epidemiological studies on the association between various types of cancer (lung, bladder, breast, colon, stomach) and four genetically-based metabolic polymorphisms, involved in the metabolism of several carcinogens (glutathione-S-transferase M1, debrisoquine hydroxylase, N acetyltransferase, aryl hydrocarbon hydroxylase). These inherited polymorphisms usually cause modifications in the quality or quantity of the relevant enzymes. Such enzymes are involved in the activation/inactivation of known carcinogens and seem to modify the extent to which carcinogens interact with DNA in target tissues. Two enzymes, debrisoquine hydroxylase and aryl hydrocarbon hydroxylase, activate procarcinogens to carcinogens (phase I enzymes). The other two, glutathione-S-transferase M1 and N-acetyltransferase, mainly detoxity carcinogenic substances (phase II enzymes). Because of their role as host factors (modulating the action of carcinogens), it has been hypothesized that subjects presenting a specific phenotype for such polymorphisms could be at a greater risk of developing various types of cancer. A number of epidemiological studies have investigated such associations, often with discordant results. We examine and discuss the design of the studies, and present a meta-analysis of the available data.     

蝮蛇毒碱性磷脂酶A_2基因的克隆

从蝮蛇毒腺中抽提总ＲＮＡ．利用人工合成寡核苷酸引物作逆转录,以ｃＤＮＡ为模板进行体外扩增,获得磷脂酶Ａ２（简称ＰＬＡ２）基因,克隆至ｐＢＳ－ｋｓ载体中。通过对３个碱性ＰＬＡ２（简称ＢＰＬＡ２）基因单独克隆分别作ＤＮＡ全序列分析,推导ｐｒｏ－ＢＰＬＡ２由１３８个氨基酸残基构成,与已测定的部分氨基酸序列比较,基本相符。该基因成功的克隆,不仅推导出ＢＰＬＡ２的蛋白质全序列,也为进一步开展蛇毒功能肽蛋白质工程的研究工作打下了良好的基础。     

西双版纳石灰岩森林的植物区系地理研究

西双版纳石灰岩森林植物区系经调查有维管束植物１５３科,６４０属,１３９４种及变种,其中,种子植物占１２９科５５８属１２６９种及变种。种子植物的分布区类型组成是热带和主产热带的科占总科数的７１．３％;热带分布属占总属数的９０．１％;热带分布种超过总种数的９０％。热带分布属中又以热带亚洲分布属最多,占总数的３５．３％;热带分布种中则以热带亚洲分布及其变型的种类占总种数的６４．５％为特点。这表明该石灰岩森林植物区系是热带性质的植物区系,属于热带亚洲区系的一部分。由于特殊的地理位置,西双版纳地区是许多典型热带植物的分布北界,同时又是几种地理成分的交汇地带,这又使该石灰岩区系带有明显热带边缘性质和多种地理成分交汇的特点。     

栝楼核糖核酸酶在RNA序列分析中的应用

栝楼核糖核酸酶（RNase TCS）对U碱基具有高度的专一性,在无脲、pH3.5、50℃时,它几乎都在-NP ↓ U-处裂解RNA.它与RNase T1,U₂和有限的碱水解一起,可用于直接的酶法RNA序列分析．     

稻茎毛眼水蝇幼虫田间分布型及抽样技术

根据14丘稻田稻茎毛眼水蝇幼虫调查资料．对其幼虫分布型进行了分析。结果表明;用I、CAm／m、Iσ四种聚集指标法测定,64．3％的田块呈随机分布．28．4%为均匀分布．7．3%为聚集分布。用Iwao平均拥挤度和Taylor幂法则测定．其田间分布型符合随机分布。用频次拟合法测验,50%的田块同时符合渡松、奈曼和负二项分布三种分布型;35．7%的田块同时符合2种分布型。根据该虫田间分布型的特点．制定了相应的序贯抽样技术。     

CaM BP－10对NAD激酶的抑制效应

ＮＡＤ激酶在光合作用等植物生理过程中起重要作用。ＮＡＤ激酶的激活依赖于钙离子和钙调素（ＣａｌｍＯｄｕｌｉｎ,ＣａＭ）．从植物中分离得到的一种新的ＣａＭ结合蛋白ＣａＭＢＰ－１０（ＢＰ－１０）明显抑制ＮＡＤ激酶的激活活性,抑制作用可被ＣａＭ所克服．动力学研究表明,抑制效应是ＢＰ－１０与ＣａＭ之间特异性相互作用的结果。实验证实ＢＰ－１０对ＮＡＤ激酶活性起着重要调节作用．