三个编码富含甘氨酸异构体的基因在棉花不同组织的差异表达

从棉花cDNA文库中分离了3个编码富含甘氨酸蛋白（glycine-rich proteins, GRPs）的基因,分别命名为GhGRP1、GhGRP2、GhGRP3.推断的编码蛋白质的氨基酸序列都富含甘氨酸,甘氨酸含量超过40%.而且GhGRP1和GhGRP2蛋白质序列同源性高达99%,仅在C末端有1个氨基酸残基（Arg/Pro）的差别.这3个蛋白在富含甘氨酸区相互显示较高的同源性,GhGRP1与GhGRP2达到100%,而GhGRP2与GhGRP3达到45.1%,但它们与基因数据库中其它蛋白质的同源性很低.根据结构域的组织特点,将GhGRP1和GhGRP2归为C端富含半胱氨酸结构域(C-cysteine-rich )类GRP,将GhGRP3归为N端有信号肽的GRP. GhGRP1和GhGRP2都含有12个GGX （此处X代表P/W/F）重复,GhGRP3含有22个GGX(此处X代表A/F/V/L/T/P)重复.此外,它们还含有不同数量GX, GGGX等的重复.实时RT-PCR分析表明,GhGRP1在花药中优势表达.GhGRP2在10 dpa(day post anthesis)胚珠中表达最强,10 dpa纤维和下胚轴次之,而在花药、根和花瓣中表达量相对较低.GhGRP3在花药,根和下胚轴中表达量较高,而在子叶,花瓣、纤维和胚珠中表达较低.上述结果表明, GhPRP基因家族的不同成员可能分别在棉花不同组织细胞的发育过程中发挥作用.     

Sequencing of high G+C microbial genomes using the ultrafast pyrosequencing technology

Next generation pyrosequencing of high G + C content genomes still poses problems to automated sequencing and assembly processes which necessitates cost and time intensive manual work in order to finish such genomes completely. The sequencing of the high G + C actinomycete Actinoplanes sp. SE50/110 was performed with standard pyrosequencing technology (454 Life Sciences) and revealed a high number of gaps. The reasons for the introduction of gaps were analyzed on a previously known 41 kb long DNA reference sequence from Actinoplanes sp. SE50/110, hosting the acarbose biosynthesis gene cluster. Mapping of the sequencing results on the reference gene cluster sequence revealed a fragmentation into 30 contiguous sequences of different lengths. The gaps between these sequences were characterized by extremely low read coverage which strongly correlated with the G + C content in the gap regions in a negative manner. Furthermore, the gap-sequences contained strong stem-loop structures which hindered the amplification of these sequences during the emulsion PCR. Being significantly underrepresented or absent in the subsequent sequencing process, these sequences lead to weakly or uncovered genomic regions which forces the assembly algorithm to output multiple contiguous sequences instead of one finished genome. However, by applying a different pyrosequencing protocol, it was possible to sequence the complete acarbose biosynthesis gene cluster. The changes to the protocol include longer read length and addition of chemicals to the amplification chemistry, which reduces the self-annealing of DNA fragments during the amplification process and enables the complete reconstruction of high G + C content genomes without manual intervention.     

Mn(II) coordination architectures with mixed ligands of 3-(2-pyridyl)pyrazole and carboxylic acids bearing different secondary coordination donors and pendant skeletons

In our efforts to investigate the factors that affect the formation of coordination architectures, such as secondary coordination donors and pendant skeletons of the carboxylic acid ligands, as well as H-bonding and other weak interactions, two kinds of ligands: (a) 3-(2-pyridyl)pyrazole (L¹) with a non-coordinated N atom as a H-bonding donor, a 2,2′-bipyridyl-like chelating ligand, and (b) four carboxylic ligands with different secondary coordination donors and/or pendant skeletons, 1,4-benzenedicarboxylic acid (H₂L²), 4-sulfobenzoic acid (H₂L³), quinoline-4-carboxylic acid (HL⁴) and fumaric acid (H₂L⁵), have been selected to react with Mn(II) salts, and five new complexes, [Mn(L¹)₂(SO₄)]₂ (1), [Mn(L¹)₂(L²)]_∞ (2), [Mn(L¹)(HL³)₂]_∞ (3), Mn(L¹)₂(L⁴)₂ (4), and [Mn(L¹)₂(L⁵)]_∞ (5), have been obtained and structurally characterized. The structural differences of 1-5 can be attributed to the introduction of the different carboxylic acid ligands (H₂L², H₂L³, HL⁴, and H₂L⁵) with different secondary coordination donors and pendant skeletons, respectively. This result also reveals that the typical H-bonding (i.e. N-H?O and O-H?O) and some other intra- or inter-molecular weak interactions, such as C-H?O weak H-bonding and π?π interactions, often play important roles in the formation of supramolecular aggregates, especially in the aspect of linking the multi-nuclear discrete subunits or low-dimensional entities into high-dimensional supramolecular networks.     

The nucleotide sequence of the tobacco chloroplast gene for the large subunit of ribulose-l,5-bisphosphate carboxylase/oxygenase

The gene for the large subunit (LS) of ribulose-l,5-bisphosphate carboxylase/oxygenase (RuBPCase/ Oase) from tobacco has been cloned in pBR322 and sequenced. The coding region contains 1431 bp (477 codons). The deduced arnino acid sequence of tobacco LS protein shows 90% homology with those of maize and spinach LS. The positions in the gene corresponding to the 5' and the 3' ends of tobacco LS mRNA have been located on the DNA sequence by the S1 nuclease mapping procedure. The LS gene promoter sequence has homology with Escherichia coli promoter sequences; its terminator sequence is capable of forming a stem-and-loop structure. A sequence GGAGG, which is complementary to a sequence near the 3' end of tobacco chloroplast 16S rRNA and a putative ribosome binding site, occurs 6–10 bp upstream from the initiation codon.     

Mannosylerythritol lipids: a review

Mannosylerythritol lipids (MELs) are surface active compounds that belong to the glycolipid class of biosurfactants (BSs). MELs are produced by Pseudozyma sp. as a major component while Ustilago sp. produces them as a minor component. Although MELs have been known for over five decades, they recently regained attention due to their environmental compatibility, mild production conditions, structural diversity, self-assembling properties and versatile biochemical functions. In this review, the MEL producing microorganisms, the production conditions, their applications, their diverse structures and self-assembling properties are discussed. The biosynthetic pathways and the regulatory mechanisms involved in the production of MEL are also explained here.     

基于结构信息的RNA多序列比对

多序列比对是生物信息学中重要的基础研究内容,对各种RNA序列分析方法而言,这也是非常重要的一步。不像DNA和蛋白质,许多功能RNA分子的序列保守性要远差于其结构的保守性,因此,对RNA的分析研究要求其多序列比对不仅要考虑序列信息,而且要充分考虑到其结构信息。本文提出了一种考虑了结构信息的同源RNA多序列比对算法,它先利用热力学方法计算出每条序列的配对概率矩阵,得到结构信息,由此构造各条序列的结构信息矢量,结合传统序列比对方法,提出优化目标函数,采用动态规划算法和渐进比对得到最后的多序列比对。试验证实该方法的有效性。     

海洛因成瘾模型建立及中脑腹侧被盖区Bax的表达

目的探索海洛因对中脑腹侧被盖区细胞Bax表达的影响。方法肌肉注射海洛因,建立成瘾大鼠模型,用免疫组化方法检测中脑腹侧被盖区细胞Bax的表达。结果连续给大鼠注射海洛因7d后,大鼠出现明显的戒断症状;中脑腹侧被盖区细胞Bax表达阳性细胞比对照组明显增多,与对照组相比差异有显著性（P〈0.01）。结论海洛因具有诱导Bax基因表达、损伤脑组织细胞的作用。     

Synthesis, structure and properties of TTF-carboxylate bridged paddlewheel dirhodium complexes, Rh2(BuCO2)3(TTFCO2) and Rh2(BuCO2)2(TTFCO2)2

Reaction of tetrathiafulvalene carboxylic acid (TTFCO₂H) with paddlewheel dirhodium complex Rh₂(Bu^tCO₂)₄ yielded TTFCO₂-bridged complexes Rh₂(Bu^tCO₂)₃(TTFCO₂) (1) and cis- and trans-Rh₂(Bu^tCO₂)₂(TTFCO₂)₂ (cis- and trans-2). Their triethylamine adducts [1(NEt₃)₂] and cis-[2(NEt₃)₂] were purified and isolated with chromatographic separation, and characterized with single crystal X-ray analysis. Trans-[2(NEt₃)₂] is not completely separated from a mixture of cis- and trans-[2(NEt₃)₂], but its single crystals were obtained from a solution of the mixture. A three-step quasi-reversible oxidation process was observed for 1 in MeCN. The first two steps correspond to the oxidation of the TTFCO₂ moiety and the last one is the oxidation of the Rh₂ core. The oxidation of cis-2 is observed as a two-step process with very similar E_1/2 values to those of the first two processes for 1. Both 1⁺ and cis-2²⁺ in MeCN at room temperature show isotropic ESR spectra with a g value of 2.008 and a_H = 0.135 mT for two equivalent H atoms and a_H = 0.068 mT for one H atom. The redox and ESR data of cis-2 suggest that the intramolecular interaction between the TTF moieties is very small.     

Shotgun Crystallization Strategy for Structural Genomics II: Crystallization Conditions that Produce High Resolution Structures for T. maritima Proteins

Currently, 119 high resolution structures of Thermotoga maritima proteins have been determined by the Joint Center for Structural Genomics (JCSG, www.jcsg.org). Sixty-seven of these were solved using the first implementation of the multi-tiered crystallization strategy at the JCSG for the efficient crystallization of large numbers of protein targets. Previously, we reported the analysis of all proteins crystallized using this multi-tiered strategy [Lesley, S.A. et al. (2002) Proc. Natl. Acad. Sci. USA 99, 11664–11669; Page, R. et al. (2003) Acta Crystallogr. D Biol. Crystallogr. 59, 1028–1037]. Here, we extend the analysis and describe the crystallization characteristics of those proteins that produced diffraction quality crystals, ultimately resulting in high resolution structures. First, we found that over 77% (52) of the crystals used for structure determination were produced directly from high-throughput coarse screens, indicating that less than one quarter of the crystals (15) required fine screening. In addition, as observed for the proteome screen [Page, R. et al. (2003) Acta Crystallogr. D Biol. Crystallogr. 59, 1028–1037], the majority of conditions that produced crystals for natively expressed proteins, whose structures have been determined, were distinct from those of their more extensively purified and selenomethionine-labeled counterparts. Finally, 99% of the proteins whose structures were solved crystallized in conditions contained in the JCSG Minimal Core Screen [Page, R. et al. (2003) Acta Crystallogr. D Biol. Crystallogr. 59, 1028–1037; Page, R. and Stevens, R.C. (2004) Methods 34, 373–389], a set of 67 conditions previously identified as those most likely to produce crystals of a diverse set of proteins, confirming its success for rapid identification of proteins with a natural propensity to crystallize.     

The effect of water level management on the soils and vegetation of two coastal Louisiana marshes

Wetland degradation and loss is the result of a combination of natural causes and anthropogenic activities and is a serious problem in coastal Louisiana, where approximately 80% of the total US coastal wetland loss since the 1930's has occurred. One method currently used to address this wetland loss problem is structural marsh management, which is the use of levees and water control structures to control hydroperiod. The effects of structural marsh management on two managed marshes in Southern Louisiana (Unit 4 of the Rockefeller Wildlife Refuge and the Fina LaTerre Mitigation Bank) were evaluated by comparing the soils and the dominant emergent marsh vegetation (Spartina patens) of the two managed marshes with those of two nearby unmanaged marshes. Soil redox potential, water depth, interstitial water sulfide concentration, salinity, NH₄-N and elemental concentrations of Na, K, Ca, Mg, P, Fe and Zn were measured four times during 1989 which was a drawdown year. Net and total CO₂ exchange rate, primary productivity, leaf area, stem density, and live, dead and total aboveground biomass were also measured. The managed marsh at Rockefeller had lower water levels, significantly less reduced surface and 15 cm deep soils and significantly lower interstitial sulfide concentrations and salinity levels. Na, K, Mg and Ca concentrations reflected the same pattern as salinity. Live aboveground biomass, primary productivity and leaf area were 3–4 times greater in the managed marsh. This indicates that marsh management improved soil conditions and provided an environment favorable to more vigorous plant growth. The management scheme at Fina LaTerre was also successful at maintaining lower water levels than in the adjacent unmanaged area. However, surface soils were more reduced and interstitial salinity higher, on average, in the managed marsh indicating generally poorer water circulation. Primary productivity was 50% less and stem density, leaf area, net CO₂ and total CO₂ exchange rates were significantly lower in the managed marsh, compared to the nearby reference marsh. Conditions in the managed marsh indicate that the management scheme was not successful at improving soil conditions when compared to those in the adjacent unmanaged marsh. This study indicates that structural marsh management is not the universal answer to problems faced by Louisiana's coastal wetlands, but may be of value in specific situations.